ArticleLiterature Review

The impact of nutrition on the human microbiome

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Abstract

Diet-derived carbohydrates that are not fully digested in the upper gut, known as nondigestible carbohydrates, provide a major source of energy for bacteria that colonize the human large intestine. It is well established that dietary intake of nondigestible carbohydrates influences microbial fermentation and total bacterial numbers in the colon. Recent evidence from molecular ecology has also shown that the amount and type of nondigestible carbohydrates (e.g., resistant starch, non-starch polysaccharides, and prebiotics) influences the species composition of the intestinal microbiota both in short-term dietary interventions and in response to habitual long-term dietary intake. Interindividual variation in gut microbiota may, in part, reflect differences in dietary intake, but the response of the gut microbiota to dietary change can also differ among individuals. As a better understanding is gained of the impact of different groups of bacteria on host metabolism, the ability to manipulate the microbiota through diet should provide a route for delivering health benefits.

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... The role of the gut microbiota in the onset and perpetuation of intestinal inflammation in IBD has been systematically studied over the last decades (Eckburg et al., 2005;Flint, 2012;Cao et al., 2014). It is assumed that the gut microbiome has high relevance in health. ...
... It is assumed that the gut microbiome has high relevance in health. Besides fundamental metabolic functions, it is clue to modulate the relative production of proinflammatory vs. anti-inflammatory signals received by the immune system (Flint, 2012). The gut microbiota has also been extensively linked to host immunity development and gut homeostasis maintenance (Sears, 2005). ...
... The gut microbiota has also been extensively linked to host immunity development and gut homeostasis maintenance (Sears, 2005). Moreover, it is well-established by studies performed both in fecal and mucosa-associated communities that CD patients have an altered microbiota, which differs from that found in patients with UC and both from healthy controls (Flint, 2012). ...
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Inflammatory bowel disease (IBD), including its two main categories (Crohn's disease and ulcerative colitis), has been linked both to gut microbiota and to diet. Bread is a daily food that has a potential capacity as a prebiotic. Our aim was to evaluate different bread-making processes and their effect on fecal colonic microbiota in IBD patients. The microbial composition of several sourdoughs and dough samples was analyzed by high-throughput sequencing of 16S and 18S rRNA genes. Three types of bread, which followed different bread-making processes, were in vitro digested and incubated with feces from IBD patients. Changes in gut microbiota were assessed by a quantitative polymerase chain reaction using specific bacterial sequence targets. Short-chain fatty acid production was also analyzed by gas chromatography. Lactobacillus sanfranciscensis was the dominant lactic acid bacteria species found in sourdough and bread doughs prepared using sourdough, whereas Saccharomyces cerevisiae was the most dominant yeast in all groups, especially in bread doughs before baking. Differences in microbial composition in raw bread doughs were more related to the type of dough and elaboration than to fermentation time lengths. The analysis of in vitro fecal incubations with bread conditions revealed an increase in most bacterial groups analyzed and short-chain fatty acid production, both in Crohn's disease and ulcerative colitis samples. Most remarkable increases in short-chain fatty acid production mirrored higher abundances of Roseburia species. The potential prebiotic properties observed were mainly obtained when using a high quantity of bread, regardless of bread type. Overall, this study highlights the bacterial dynamics within the bread-making process and the potential prebiotic effect in IBD patients.
... The role of the gut microbiota in the onset and perpetuation of intestinal inflammation in IBD has been systematically studied over the last decades (Eckburg et al., 2005;Flint, 2012;Cao et al., 2014). It is assumed that the gut microbiome has high relevance in health. ...
... It is assumed that the gut microbiome has high relevance in health. Besides fundamental metabolic functions, it is clue to modulate the relative production of proinflammatory vs. anti-inflammatory signals received by the immune system (Flint, 2012). The gut microbiota has also been extensively linked to host immunity development and gut homeostasis maintenance (Sears, 2005). ...
... The gut microbiota has also been extensively linked to host immunity development and gut homeostasis maintenance (Sears, 2005). Moreover, it is well-established by studies performed both in fecal and mucosa-associated communities that CD patients have an altered microbiota, which differs from that found in patients with UC and both from healthy controls (Flint, 2012). ...
Article
Full-text available
Inflammatory bowel disease (IBD), including its two main categories (Crohn’s disease and ulcerative colitis), has been linked both to gut microbiota and to diet. Bread is a daily food that has a potential capacity as a prebiotic. Our aim was to evaluate different bread-making processes and their effect on fecal colonic microbiota in IBD patients. The microbial composition of several sourdoughs and dough samples was analyzed by high-throughput sequencing of 16S and 18S rRNA genes. Three types of bread, which followed different bread-making processes, were in vitro digested and incubated with feces from IBD patients. Changes in gut microbiota were assessed by a quantitative polymerase chain reaction using specific bacterial sequence targets. Short-chain fatty acid production was also analyzed by gas chromatography. Lactobacillus sanfranciscensis was the dominant lactic acid bacteria species found in sourdough and bread doughs prepared using sourdough, whereas Saccharomyces cerevisiae was the most dominant yeast in all groups, especially in bread doughs before baking. Differences in microbial composition in raw bread doughs were more related to the type of dough and elaboration than to fermentation time lengths. The analysis of in vitro fecal incubations with bread conditions revealed an increase in most bacterial groups analyzed and short-chain fatty acid production, both in Crohn’s disease and ulcerative colitis samples. Most remarkable increases in short-chain fatty acid production mirrored higher abundances of Roseburia species. The potential prebiotic properties observed were mainly obtained when using a high quantity of bread, regardless of bread type. Overall, this study highlights the bacterial dynamics within the bread-making process and the potential prebiotic effect in IBD patients.
... The human gut harbours about 100 trillion microbes constituting the human gut microbiota (HGM) [1,2]. The HGM performs a wide variety of functions vital for normal physiology, including the development of the gastrointestinal tract [3], promoting maturation of the immune system [4], pathogen exclusion [5,6], and improving energy capture from dietary components through fermentation [7]. ...
... All results were analysed using the Bruker FlexAnalysis software. 1 H, 13 C, DEPT, and HSQC-NMR spectra were recorded on a Bruker Avance III 400 MHz spectrometer equipped with a broadband BBFO probe. Chemical shifts (δ) were accounted for in parts per million (ppm) using the residual solvent signal for referencing. ...
Article
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Xylan is one of the major structural components of the plant cell wall. Xylan present in the human diet reaches the large intestine undigested and becomes a substrate to species of the gut microbiota. Here, we characterised the capacity of Limosilactobacillus reuteri and Blautia producta strains to utilise xylan derivatives. We showed that L. reuteri ATCC 53608 and B. producta ATCC 27340 produced β-D-xylosidases, enabling growth on xylooligosaccharide (XOS). The recombinant enzymes were highly active on artificial (p-nitrophenyl β-D-xylopyranoside) and natural (xylobiose, xylotriose, and xylotetraose) substrates, and showed transxylosylation activity and tolerance to xy-lose inhibition. The enzymes belong to glycoside hydrolase family 120 with Asp as nucleophile and Glu as proton donor, as shown by homology modelling and confirmed by site-directed mutagene-sis. In silico analysis revealed that these enzymes were part of a gene cluster in L. reuteri but not in Blautia strains, and quantitative proteomics identified other enzymes and transporters involved in B. producta XOS utilisation. Based on these findings, we proposed a model for an XOS metabolism pathway in L. reuteri and B. producta strains. Together with phylogenetic analyses, the data also revealed the extended xylanolytic potential of the gut microbiota.
... In addition, soil microbes are an essential part of the forest ecosystem, playing vital roles in sustainable aquaculture [3,4]. Microorganisms also positively impact human health through nutrient cycles and microbiomes [5,6]. On the other hand, some microbes are considered life-threatening because of their ability to cause diseases and produce harmful toxins. ...
Article
Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.
... Dietary fibres in F&V are a series of complex polysaccharides, such as pectin, inulin, cellulose, hemicellulose and resistant starch (Davison & Temple, 2018). Fibres are indigestible by human intestines but can be broken down by gut bacterial fermentation (Flint, 2012). Metabolites produced from the fermentation, such as short-chain fatty acids, lactate and pyruvate , can be absorbed to the host and used as nutrients. ...
Article
The objective of the current review is to systematically investigate health‐promoting manipulating effects of fruits and vegetables (F&V) on the gut microbiota. The function of gut microbes was found to promote health effects in the host by scavenging free radicals, modulating immune system, alleviating obesity and diabetes. Masters that manipulate the gut microbiota are the phytochemicals within specific types of F&V, where polyphenols account for the largest proportion, along with alkaloids, terpenes, nitrogen‐containing compounds, polysaccharides, and natural pigments present in plants. These bioactive compounds exhibit the regulative influences on gut microorganisms characterized by rescuing dysbiosis of gut microbiota, increasing/decreasing microbial abundance, restructuring microbial composition, and rebalancing gut microbial homeostasis. This review indicated that F&V extracts targeting at gut microbiota could be a new scope of ingredient selection in the field of functional food especially for amelioration of dysfunction of intestinal ecosystem.
... Interventions have been shown to have a positive and significant effect on human health [144]. In addition, dietary supplements like fiber and probiotics have been shown to improve microbial derangements in health [145], but the precise mechanisms of how nutrition and dietary supplements modulate the gut microbiome remain to be determined. ...
Article
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The pandemic of Coronavirus Disease 2019 (COVID-19) has shocked world health authorities generating a global health crisis. The present study discusses the main finding in nutrition sciences associated with COVID-19 in the literature. We conducted a consensus critical review using primary sources, scientific articles, and secondary bibliographic indexes, databases, and web pages. The method was a narrative literature review of the available literature regarding nutrition interventions and nutrition-related factors during the COVID-19 pandemic. The main search engines used in the present research were PubMed, SciELO, and Google Scholar. We found how the COVID-19 lockdown promoted unhealthy dietary changes and increases in body weight of the population, showing obesity and low physical activity levels as increased risk factors of COVID-19 affection and physiopathology. In addition, hospitalized COVID-19 patients presented malnutrition and deficiencies in vitamin C, D, B12 selenium, iron, omega-3, and medium and long-chain fatty acids highlighting the potential health effect of vitamin C and D interventions. Further investigations are needed to show the complete role and implications of nutrition both in the prevention and in the treatment of patients with COVID-19.
... The metabolic effects, as well as the group of bacteria that are favored after the incorporation of starch, depending on the type of resistant starch that is consumed [264]. For example, type 4 resistant starches have been found to favor the growth of Bacteroides and Parabacteroides spp. in the intestine [256]. ...
Article
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Gut microbiota is a group of microorganisms that are deposited throughout the entire gastrointestinal tract. Currently, thanks to genomic tools, studies of gut microbiota have pointed towards the understanding of the metabolism of important bacteria that are not cultivable and their relationship with human homeostasis. Alterations in the composition of gut microbiota could explain, at least in part, some epidemics, such as diabetes and obesity. Likewise, dysbiosis has been associated with gastrointestinal disorders, neurodegenerative diseases, and even cancer. That is why several studies have recently been focused on the direct relationship that these types of conditions have with the specific composition of gut microbiota, as in the case of the microbiota–intestine–brain axis. In the same way, the control of microbiota is related to the diet. Therefore, this review highlights the importance of gut microbiota, from its composition to its relationship with the human health–disease condition, as well as emphasizes the effect of probiotic and prebiotic consumption on the balance of its composition.
... For example, gut bacteria encode enzymes involved in the formation of beneficial vitamins and metabolites [55]. These bacteria possess many biochemical pathways that humans have not developed, such as the bioactivation, degradation and metabolism of exogenous compounds, including indigestible dietary compounds [58]. Lately, the impact of the gut microbiota on drugs and the mutual drug-microbiome interactions have been highlighted, and the fields of pharmacomicrobiomics and toxicomicrobiomics are rapidly developing to systematically study such interactions and catalogue their pharmacotherapeutic and clinical impacts [59][60][61][62][63]. ...
Article
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Tannins represent a heterogeneous group of high-molecular-weight polyphenols that are ubiquitous among plant families, especially in cereals, as well as in many fruits and vegetables. Hydrolysable and condensed tannins, in addition to phlorotannins from marine algae, are the main classes of these bioactive compounds. Despite their low bioavailability, tannins have many beneficial pharmacological effects, such as anti-inflammatory, antioxidant, antidiabetic, anticancer, and cardioprotective effects. Microbiota-mediated hydrolysis of tannins produces highly bioaccessible metabolites, which have been extensively studied and account for most of the health effects attributed to tannins. This review article summarises the effect of the human microbiota on the metabolism of different tannin groups and the expected health benefits that may be induced by such mutual interactions. Microbial metabolism of tannins yields highly bioaccessible microbial metab-olites that account for most of the systemic effects of tannins. This article also uses explainable artificial intelligence to define the molecular signatures of gut-biotransformed tannin metabolites that are correlated with chemical and biological activity. An understanding of microbiota-tannin interactions , tannin metabolism-related phenotypes (metabotypes) and chemical tannin-metabolites motifs is of great importance for harnessing the biological effects of tannins for drug discovery and other health benefits.
... The ingestion of digestible fibres associates with an increase in the proportion of Bacteroides species and butyrate-producing bacteria, such as Eubacterium rectale and Clostridium leptum [81,82]. Only a fraction of the diet remains undigested as complex carbohydrates when it reaches the colon, including plant cell wall polysaccharides, cellulose and resistant starches [83]. Using an anaerobic in vitro continuous flow system and faecal samples from human participants, Leitch and colleagues showed that the ingestion of non-digestible resistant starches was associated with an increased abundance of Ruminococcus species, Bifidobacterium adolescentis, Eubacterium rectale and Roseburia species [84]. ...
Article
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Over unimaginable expanses of evolutionary time, our gut microbiota have co-evolved with us, creating a symbiotic relationship in which each is utterly dependent upon the other. Far from confined to the recesses of the alimentary tract, our gut microbiota engage in complex and bi-directional communication with their host, which have far-reaching implications for overall health, wellbeing and normal physiological functioning. Amongst such communication streams, the microbiota–gut–brain axis predominates. Numerous complex mechanisms involve direct effects of the microbiota, or indirect effects through the release and absorption of the metabolic by-products of the gut microbiota. Proposed mechanisms implicate mitochondrial function, the hypothalamus–pituitary–adrenal axis, and autonomic, neuro-humeral, entero-endocrine and immunomodulatory pathways. Furthermore, dietary composition influences the relative abundance of gut microbiota species. Recent human-based data reveal that dietary effects on the gut microbiota can occur rapidly, and that our gut microbiota reflect our diet at any given time, although much inter-individual variation pertains. Although most studies on the effects of dietary macronutrients on the gut microbiota report on associations with relative changes in the abundance of particular species of bacteria, in broad terms, our modern-day animal-based Westernized diets are relatively high in fats and proteins and impoverished in fibres. This creates a perfect storm within the gut in which dysbiosis promotes localized inflammation, enhanced gut wall permeability, increased production of lipopolysaccharides, chronic endotoxemia and a resultant low-grade systemic inflammatory milieu, a harbinger of metabolic dysfunction and many modern-day chronic illnesses. Research should further focus on the colony effects of the gut microbiota on health and wellbeing, and dysbiotic effects on pathogenic pathways. Finally, we should revise our view of the gut microbiota from that of a seething mass of microbes to one of organ-status, on which our health and wellbeing utterly depends. Future guidelines on lifestyle strategies for wellbeing should integrate advice on the optimal establishment and maintenance of a healthy gut microbiota through dietary and other means. Although we are what we eat, perhaps more importantly, we are what our gut microbiota thrive on and they thrive on what we eat.
... On the other hand, the influence of diet on microbiota composition has been extensively investigated and documented (41)(42)(43). Gut microbiota is involved in essential functions for host physiology such as metabolism (through, for example, the fermentation of indigestible carbohydrates and the production of metabolites important for organism homeostasis maintenance) (44,45), immune system development and function (46), protection against pathogen colonization (47) or intestinal barrier shaping, been involved in their development, reparation and integrity and functionality maintenance (48)(49)(50)(51). Additionally, a large number of studies reported that host-derived miRNAs could shape gut microbiota composition through modulation of expression of genes that affect microbe growth (52,53). ...
Article
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MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules from 18 to 24 nucleotides that are produced by prokaryote and eukaryote organisms, which play a crucial role in regulating gene expression through binding to their mRNA targets. MiRNAs have acquired special attention for their potential in cross kingdom communication, notably food-derived microRNAs (xenomiRs), which could have an impact on microorganism and mammal physiology. In this review, we mainly aim to deal with new perspectives on: (1) The mechanism by which food-derived xenomiRs (mainly dietary plant xenomiRs) could be incorporated into humans through diet, in a free form, associated with proteins or encapsulated in exosome-like nanoparticles. (2) The impact of dietary plant-derived miRNAs in modulating gut microbiota composition, which in turn, could regulate intestinal barrier permeability and therefore, affect dietary metabolite, postbiotics or food-derived miRNAs uptake efficiency. Individual gut microbiota signature/composition could be also involved in xenomiR uptake efficiency through several mechanisms such us increasing the bioavailability of exosome-like nanoparticles miRNAs. (3) Gut microbiota dysbiosis has been proposed to contribute to disease development by affecting gut epithelial barrier permeability. For his reason, the availability and uptake of dietary plant xenomiRs might depend, among other factors, on this microbiota-related permeability of the intestine. We hypothesize and critically review that xenomiRs-microbiota interaction, which has been scarcely explored yet, could contribute to explain, at least in part, the current disparity of evidences found dealing with dietary miRNA uptake and function in humans. Furthermore, dietary plant xenomiRs could be involved in the establishment of the multiple gut microenvironments, in which microorganism would adapt in order to optimize the resources and thrive in them. Additionally, a particular xenomiR could preferentially accumulate in a specific region of the gastrointestinal tract and participate in the selection and functions of specific gut microbial communities.
... Further, microorganisms are generally considered to be critical for maintaining the metabolism and immune system development of the host in early life (Hooper et al. 2012;Cockburn et al. 2016). The establishment of intestinal microbiota in animals is a complex process affected by bacteria and host interactions, as well as external and internal factors, such as mode of birth, dietary intake and antibiotic exposure (Flint 2012;Chung et al. 2012;Stinson et al. 2017). Currently, little research has explored the colonization of intestinal microbiota and the dynamics of some physiological and immune parameters in mammalian young, which hampers the understanding of the physiology dynamics in host early life stage. ...
Article
Full-text available
Analysis of the intestinal microbiota and physiological parameters in mammalian infancy can reveal health status. In this study, we used a combination of molecular and immunochemical approaches to assess fecal microbiota as well as Cortisol (Cor), Triiodothyronine (T3) and immunoglobulin A (IgA) levels of young forest musk deer (FMD), from birth to one month after weaning (7 days of age ‐ 110 days of age). During development as the diet of FMD changes from consuming milk to eating plants, the richness and diversity of intestinal microbiota of young FMD increased significantly. Cor levels remained unchanged throughout early development while significantly increased after weaning, T3 and IgA initially were derived from milk during lactation, significantly decreased after weaning. Correlation network analysis showed that the community of food‐oriented microbes were highly structured and that many genera were correlated. Overall, this study provides scientific insights into effective management strategies for the protection of FMD population. This article is protected by copyright. All rights reserved
... In this Outlook, this microbial community is referred to as the microbiota, and the genes associated with the community are referred to as the microbiome. Although our microbiota constitutes a minor fraction of our total mass (∼2 kg), 4 it carries the brunt of our genetic diversity. Two individuals having >99.5% identity across their 46 chromosomes can have microbiomes that are >90% different. ...
Article
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Our gut harbors more microbes than any other body site, and accumulating evidence suggests that these organisms have a sizable impact on human health. Though efforts to classify the metabolic activities that define this microbial community have transformed the way we think about health and disease, our knowledge of gut microbially produced small molecules and their effects on host biology remains in its infancy. This Outlook surveys a range of approaches, hurdles, and advances in defining the chemical repertoire of the gut microbiota, drawing on examples with particularly strong links to human health. Progress toward understanding and manipulating this chemical language is being made with diverse chemical and biological expertise and could hold the key for combatting certain human diseases.
... One must also be aware that food consumption feeds and nurtures not only human cells but also the microbial populations that live in/on the human body, outnumbering our own cells 10:1 (Ercolini and Fogliano 2018;Flint 2012). Moreover, without normal microbial flora, many of the nutrients ingested would not be absorbed efficiently, adding another layer of complexity to food supply, human nutrition, and soil and food security issues (Yadav et al. 2018). ...
Chapter
Soils influence human health in many ways, both positive and negative. These include the supply of nutrients; exposure to heavy metals, organic chemicals, and pathogens; the supply of antibiotics and other medicines; and soils may even support mental health. Soils can impact all aspects of the human system, from the skin to the respiratory tract, digestive and nervous systems, and beyond. Human management of the soil system can have a major impact on these influences. In particular, any management that supports soil health also supports human health. Establishing the health of a soil involves the measurement of soil biological, chemical, and physical properties. Future needs in the area of soil and human health include well-designed scientific studies that investigate the links between soil abiotic and biotic properties and human health as well as soil science links to soils and human health.
... The gastrointestinal tract harbors diverse and dynamic microbial communities [68][69][70][71]. In general, the gut microbiota is dominated by the phyla Firmicutes and Bacteroidetes, with Proteobacteria, Actinobacteria, Fusobacteria and Verruomicrobia present in lower abundance [39,44,[72][73][74][75][76]. ...
Article
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The gut microbiota and the host are intimately connected. The host physiology dictates the intestinal environment through regulation of pH, ion concentration, mucus production, etc., all of which exerts a selective pressure on the gut microbiota [1]. Since different regions of the gastrointestinal tract are characterized by their own physicochemical conditions, distinct microbial communities are present in these locations. While it is widely accepted that the intestinal microbiome influences the host (tight junctions, cytokine/immune responses, diarrhea, etc.), the reciprocal interaction of the host on the microbiome is under-explored. This review aims to address these gaps in knowledge by focusing on how the host intestinal ion transport influences the luminal environment and thereby modulates the gut microbiota composition.
... PERMANOVA tests suggested significant differences (P = 0.004) in community structure between all pre-treatments and the CON group, though no significant differences were detected between the pre-treatments (Figure 3). Dietary fiber is known to have a considerable effect on gut microbiota composition (Flint, 2012;Yatsunenko et al., 2012;Cotillard et al., 2013). Glycome profiling of non-processed and processed RSM showed that polysaccharides structures were differentially shifted due to ALK, PECT1, PECT2, and CELL treatment in the current study, which were consistent with previous studies de Vries et al., 2014). ...
Article
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The aim of current study was to investigate in an in vitro study how enzymatic and chemical pretreated rapeseed meal (RSM) influences the fiber fermentation and microbial community in the swine large intestine. RSM was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. 16S rRNA gene sequencing data was performed to evaluate changes in the gut microbiota composition, whereas short-chain fatty acid (SCFA) production (ion-chromatography) and non-starch polysaccharides (NSP) composition (using monoclonal antibodies; mAbs) were used to assess fiber degradation. The results showed that ALK, CELL, PECT1, and PECT2 changed microbial community composition, increased the predicted abundance of microbial fiber-degrading enzymes and pathways, and increased acetic acid, propionic acid, butyric acid, and total SCFA production. The increased microbial genera positively correlated with SCFA production. Monoclonal antibody analyses showed that the cell wall polysaccharide structures of RSM shifted after ALK, CELL, PECT1, and PECT2 treatment. The degradation of NSP during the fermentation period was dynamic, and not continuous based on the epitope recognition by mAbs. This study provides the first detailed analysis of changes in the swine intestinal microbiota due to RSM modified by ALK, CELL, PECT1, and PECT2, which altered the microbial community structure, shifted the predicted functional metagenomic profile and subsequently increased total SCFA production. Our findings that ALK, CELL, PECT1, and PECT2 increased fiber degradability in RSM could help guide feed additive strategies to improve efficiency and productivity in swine industry. The current study gave insight into how enzymatic treatment of feed can alter microbial communities, which provides good opportunity to develop novel carbohydrase treatments, particularly in swine feed.
... For example, the microbiome is shaped by exposure to external factors, including antibiotics (1), diet (2), and social interactions (3)(4)(5). In turn, microbial communities influence host nutrition (6,7), play a vital role in proper immune system development in early life (8,9), and can influence mood and behavior (10). ...
Article
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This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).
... samples (Flint, 2012). Within topics, we identified roughly 11 clusters of interest that contained 468 ...
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Background Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest ( e.g., disease state). But elucidating key associations is often difficult since microbiome data are compositional, high dimensional, and sparse. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to, for example, host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. In addition, analyses that utilize both taxonomic and predicted functional abundances typically independently characterize the taxonomic and functional profiles before linking them to sample information. This prevents investigators from identifying the specific functional components associate with which subsets of co-occurring taxa. Results We provide an approach to explore co-occurring taxa using “topics” generated via a topic model and then link these topics to specific sample classes ( e.g., diseased versus healthy). Rather than inferring predicted functional content independently from taxonomic abundances, we instead focus on inference of functional content within topics, which we parse by estimating pathway-topic interactions through a multilevel, fully Bayesian regression model. We apply our methods to two large publically available 16S amplicon sequencing datasets: an inflammatory bowel disease (IBD) dataset from Gevers et al. and data from the American Gut (AG) project. When applied to the Gevers et al. IBD study, we demonstrate that a topic highly associated with Crohn’s disease (CD) diagnosis is (1) dominated by a cluster of bacteria known to be linked with CD and (2) uniquely enriched for a subset of lipopolysaccharide (LPS) synthesis genes. In the AG data, our approach found that individuals with plant-based diets were enriched with Lachnospiraceae, Roseburia , Blautia , and Ruminococcaceae , as well as fluorobenzoate degradation pathways, whereas pathways involved in LPS biosynthesis were depleted. Conclusions We introduce an approach for uncovering latent thematic structure in the context of sample features for 16S rRNA surveys. Using our topic-model approach, investigators can (1) capture groups of co-occurring taxa termed topics, (2) uncover within-topic functional potential, and (3) identify gene sets that may guide future inquiry. These methods have been implemented in a freely available R package https://github.com/EESI/themetagenomics .
... El "caso Helicobacter" es un ejemplo clarificador de la idea de que muchos desórdenes aparentemente complejos y heterogéneos pueden ser infecciosos en su origen y que, aun siendo multifactoriales, pueden resolverse eliminado de la compleja ecuación de la enfermedad, uno de los factores claves que la componen. Sin embargo, quizá la conclusión más importante que se puede extraer de esta historia es que la búsqueda de soluciones para muchas enfermedades crónicas ha de contemplar la interacción del microbioma humano con su hospedador 11 . ...
Article
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Resumen El componente microbiano del cuerpo humano apenas se ha podido comenzar a desentrañarse a partir del año 2001, con el abaratamiento y el mayor acceso a las tecno-logías de secuenciación de ADN. Constituye el área del microbioma humano. Por ahora, se trata de un campo de investigación muy joven, que se encuentra en una etapa más bien descriptiva. Esto es importante en las ciencias médicas, en particular, porque no podemos optimizar la salud hasta que no entendamos bien quiénes y cómo somos. Hasta ahora la placenta ha sido catalogada como un órgano multifuncional y aún se mantiene enigmática en muchas de sus funciones. Hay trabajos pioneros que evidencian presencia bacteriana que pudiera nominarse como microbiota, esto que debe ser estudiado. Todo esto es un campo apasionante en espera de grandes aportes en la medicina del futuro. Las Meditaciones del Quijote constituyen el primer libro del filósofo español José Or-tega y Gasset, publicado en 1914. En este libro expresó: "yo soy yo y mi circunstancias". Quizá hoy podríamos añadir: "…y mi microbioma". Palabras clave: Microbioma humano, Microbiota placentaria. Abstract The microbial component of the human body could ba
... El "caso Helicobacter" es un ejemplo clarificador de la idea de que muchos desórdenes aparentemente complejos y heterogéneos pueden ser infecciosos en su origen y que, aun siendo multifactoriales, pueden resolverse eliminado de la compleja ecuación de la enfermedad, uno de los factores claves que la componen. Sin embargo, quizá la conclusión más importante que se puede extraer de esta historia es que la búsqueda de soluciones para muchas enfermedades crónicas ha de contemplar la interacción del microbioma humano con su hospedador 11 . ...
Article
Full-text available
Resumen El componente microbiano del cuerpo humano apenas se ha podido comenzar a desentrañarse a partir del año 2001, con el abaratamiento y el mayor acceso a las tecnologías de secuenciación de ADN. Constituye el área del microbioma humano. Por ahora, se trata de un campo de investigación muy joven, que se encuentra en una etapa más bien descriptiva. Esto es importante en las ciencias médicas, en particular, porque no podemos optimizar la salud hasta que no entendamos bien quiénes y cómo somos. Hasta ahora la placenta ha sido catalogada como un órgano multifuncional y aún se mantiene enigmática en muchas de sus funciones. Hay trabajos pioneros que evidencian presencia bacteriana que pudiera nominarse como microbiota, esto que debe ser estudiado. Todo esto es un campo apasionante en espera de grandes aportes en la medicina del futuro. Las Meditaciones del Quijote constituyen el primer libro del filósofo español José Ortega y Gasset, publicado en 1914. En este libro expresó: “yo soy yo y mi circunstancias”. Quizá hoy podríamos añadir: “…y mi microbioma”.
... 11,12 High levels of microbial-derived SCFAs then promote a hyporesponsive immunological environment to commensal bacteria through the downregulation of those proinflammatory effectors, aiding homeostasis maintenance. 9,13 Dietary changes have been shown to alter the composition of the gut microbiome both short and long term, 14,15 supporting the role of diet as a powerful intervention target to prevent and treat these chronic disease conditions. Among adults, varying dietary patterns have been shown to predict microbiota profiles. ...
Article
Background Caribbean Latino adults have disproportionately high prevalence of chronic disease; however, underlying mechanisms are unknown. Unique gut microbiome profiles and relation to dietary quality may underlie health disparities. Objectives To examine the dietary quality of an underrepresented group of Caribbean Latino older adults with high prevalence of chronic disease; characterize gut microbiome profiles in this cohort; determine associations between dietary quality, gut microbiome composition, and short-chain fatty acid (SCFA) production; examine associations of clinical factors (body mass index, type 2 diabetes [T2D] status, and laxative use) with gut microbiome composition. Design The study design was cross-sectional. Participants/setting Recruitment and interviews occurred at the Senior Center in Lawrence, MA, from September 2016-September 2017. A total of 20 adults aged ≥50 years, self-identified of Caribbean Latino origin, without use of antibiotics in 6 months or intestinal surgery were included in the study. Exposure and outcome measures Diet was assessed by two, 24-hour recalls and dietary quality was calculated using the Healthy Eating Index 2015 and the Mediterranean Diet Score. The gut microbiome was assessed by 16S rRNA sequencing and fecal SCFA content. Anthropometrics (ie, weight and height) were measured by a trained interviewer, and self-reported laxative use, and other self-report health outcomes (ie, T2D status) were assessed by questionnaire. Statistical analyses Faith Phylogenetic Diversity (alpha diversity) and unique fraction metric, or UniFrac (beta diversity) and nonphylogenetic metrics, including Shannon diversity index (alpha diversity) were calculated. Spearman correlations and group comparisons using Kruskal-Wallis test between alpha diversity indexes and nutrient intakes were calculated. Patterns in the microbiome were estimated using a partitioning around medoids with estimation of number of clusters, with optimum average silhouette width. Log odds were calculated to compare predefined nutrients and diet score components between microbiome clusters using multivariable logistic regression, controlling for age and sex. Pearson correlation was used to relate SCFA fecal content to individual nutrients and diet indexes. Final models were additionally adjusted for laxative use. Differences in lifestyle factors by gut microbiome cluster were tested by Fisher's exact test. Results Generally, there was poor alignment of participant’s diets to either the Mediterranean Diet score or Healthy Eating Index 2015. Range in the Healthy Eating Index 2015 was 36 to 90, where only 5% (n=1) of the sample showed high adherence to the Dietary Guidelines for Americans. Mediterranean Diet scores suggested low conformance with a Mediterranean eating pattern (score range=2 to 8, where 45% scored ≤3 [poor adherence]). The gut microbiome separated into two clusters by difference in a single bacterial taxon: Prevotella copri (P copri) (permutational multivariate analysis of variance [PERMANOVA] R²=0.576, ADONIS function P=0.001). Significantly lower P copri abundance was observed in cluster 1 compared with cluster 2 (Mann-Whitney P<0.0001). Samples in the P copri dominated cluster 2 showed significantly lower alpha diversity compared with P copri depleted cluster 1 (Shannon diversity index P=0.01). Individuals in the P copri dominated cluster showed a trend toward higher 18:3 α-linolenic fatty acid intakes (P=0.09). Percentage of energy from total fat intake was significantly, positively correlated with fecal acetate (r=0.46; P=0.04), butyrate (r=0.50; P=0.03) and propionate (r=0.52; P=0.02). Associations between dietary intake and composition of the gut microbiome were attenuated by self-report recent laxative use. Individuals with T2D exhibited a significantly greater abundance of the Enterobacteriales (P=0.01) and a trend toward lower fecal content of butyric acid compared to subjects without T2D (P=0.08). Significant beta diversity differences were observed by weight (Mantel P<0.003) and body mass index (Mantel P<0.07). Conclusions Two unique microbiome profiles, identified by abundance of P copri, were identified among Caribbean Latino adults. Microbiome profiles and SCFA content were associated with diet, T2D, and lifestyle. Further research is needed to determine the role of P copri and SCFA production in the risk for chronic disease and associated lifestyle predictors.
... These effects may be due to the total phenolic in wild rice. Many studies have revealed the effects of proanthocyanidins from different sources against gut microbiota, including Prevotella [27,37]. Numerous reports revealed that Prevotellaceae and the included genera are associated with low-grade inflammation [38][39][40]. ...
Article
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Metabolic associated fatty liver disease (MAFLD) due to excess weight and obesity threatens public health worldwide. Gut microbiota dysbiosis contributes to obesity and related diseases. The cholesterol-lowering, anti-inflammatory, and antioxidant effects of wild rice have been reported in several studies; however, whether it has beneficial effects on the gut microbiota is unknown. Here, we show that wild rice reduces body weight, liver steatosis, and low-grade inflammation, and improves insulin resistance in high-fat diet (HFD)-fed mice. High-throughput 16S rRNA pyrosequencing demonstrated that wild rice treatment significantly changed the gut microbiota composition in mice fed an HFD. The richness and diversity of the gut microbiota were notably decreased upon wild rice consumption. Compared with a normal chow diet (NCD), HFD feeding altered 117 operational taxonomic units (OTUs), and wild rice supplementation reversed 90 OTUs to the configuration in the NCD group. Overall, our results suggest that wild rice may be used as a probiotic agent to reverse HFD-induced MAFLD through the modulation of the gut microbiota.
... Gut microbiota is a complex community of microorganisms residing in the gastrointestinal tract that can reach concentrations of almost a trillion cells per gram and may weight up to 2 kg in a normal weight human being [1,2]. Despite virus and fungi occurring in the intestine, gut microbiota is mainly composed of bacteria, being Bacteroidetes, Clostridium, Prevotella, Eubacterium, Ruminococcus, Fusobacterium, Peptococcus, and Bifidobacterium as the most abundant genera [3]. ...
Article
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Gut microbiota dysbiosis has been described in several metabolic disruptions, such as non-alcoholic fatty liver disease (NAFLD). Administration of resveratrol has been claimed to elicit benefits against NAFLD along with modulating gut microbiota composition. This investigation aims to study the putative mediating role of gut microbiota in the potential hepato-protective effects of resveratrol in a diet-induced NAFLD rat model. The involvement of bacteria from the Ruminococcaceae family in such effects was also addressed. Resveratrol administration resulted in lowered liver weight and serum total and non-HDL cholesterol concentrations, as well as in increased serum HDL cholesterol levels. The administration of this polyphenol also prevented obesogenic diet-induced serum transaminase increases. In addition, histopathological analysis revealed that resveratrol administration ameliorated the dietary-induced liver steatosis and hepatic inflammation. Gut microbiota sequencing showed an inverse relationship between some bacteria from the Ruminococcaceae family and the screened hepatic markers, whereas in other cases the opposite relationship was also found. Interestingly, an interaction was found between UBA-1819 abundance and resveratrol induced liver weight decrease, suggesting that for this marker resveratrol induced effects were greater when the abundance of this bacteria was high, while no actions were found when UBA-1819 abundance was low.
... The quality and quantity of food intake by the host, particularly non-digestible carbohydrates and fiber, may modify the population of bacteria residing in the gut. Moreover, colonic bacteria ferment these substrates and produce short-chain fatty acids (SCFA), which are active metabolites that regulate metabolic and immune functions [16][17][18]. Alterations in the composition and function of the microbiota, denominated dysbiosis, can affect intestinal permeability and alter mucosa integrity. This process can produce an increase of monosaccharides absorption, synthesis of fatty acids on the liver and alter hormonal production in entero-endocrine cells [9,10,12,19]. ...
Article
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Objective The objective of this study was to characterize the composition of the gut microbiota in type 2 Diabetes Mellitus (T2DM) patients with adequate and inadequate metabolic control, and its relationship with fiber consumption. Results A total of 26 patients with type 2 diabetes mellitus (T2DM) were enrolled, of which 7 (26.9%) cases had adequate metabolic control (HbA1c < 7%) and 19 (73.1%) inadequate metabolic control (HbA1c ≥ 7%). It was observed that among patients with controlled T2DM, 2 (28.6%) cases presented good intake of fiber and 5 (71.4%) cases a regular intake. In contrast, in patients with uncontrolled T2DM, 13 (68.4%) patients reported a regular intake and 6 (31.6%) a poor intake. In relation to the identification of the gut microbiota, both groups presented a similar characterization. There were differences in the population of bacteria identified in both groups, however, the results were not statistically significant. The most frequently identified bacteria in controlled and uncontrolled T2DM patients were Prevotella (71.4% vs 52.6%), followed by Firmicutes (71.4% vs 42.1%), Proteobacteria (71.4% vs 36.8%) and Bacteroidetes (57.1% vs 37.8%). On the other hand, Fusobacterium, Actinobacteria were not identified in either of the two groups of study.
... Nutrition is one of the main factors that influence the GM composition throughout the life course (74,75). In turn, microbiota mediate interplay between habitual diet and various processes of a host organism, including cognitive performance (6,10). ...
Article
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Nutrition is known to play an important role in the pathogenesis of Alzheimer's disease. Evidence is obtained that the gut microbiota is a key player in these processes. Dietary changes (both adverse and beneficial) may influence the microbiome composition, thereby affecting the gut-brain axis and the subsequent risk for Alzheimer's disease progression. In this review, the research findings that support the role of intestinal microbiota in connection between nutritional factors and the risk for Alzheimer's disease onset and progression are summarized. The mechanisms potentially involved in these processes as well as the potential of probiotics and prebiotics in therapeutic modulation of contributed pathways are discussed.
... In the present study, however, no effects of NBS supplementation were observed in fasting GLP-1 changes in comparison with DMS after four days of treatment. According to previous studies, only 1 to 3 days of supplementation are sufficient to induce a fermentation process in the colon [30][31][32]. ...
Article
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We previously observed beneficial effects of native banana starch (NBS) with a high resistant starch (RS) content on glycemic response in lean and obese participants. Here, we aimed to determine the effects of NBS and high-amylose maize starch (HMS) on glycemic control (GC) and glycemic variability (GV) in patients with type 2 diabetes (T2D) when treatments were matched for digestible starch content. In a randomized, crossover study, continuous glucose monitoring (CGM) was performed in 17 participants (aged 28–65 years, BMI ≥ 25 kg/m2, both genders) consuming HMS, NBS, or digestible maize starch (DMS) for 4 days. HMS and NBS induced an increase in 24 h mean blood glucose during days 2 to 4 (p < 0.05). CONGA, GRADE, and J-index values were higher in HMS compared with DMS only at day 4 (p < 0.05). Yet, NBS intake provoked a reduction in fasting glycemia changes from baseline compared with DMS (p = 0.0074). In conclusion, under the experimental conditions, RS from two sources did not improve GC or GV. Future longer studies are needed to determine whether these findings were affected by a different baseline microbiota or other environmental factors.
... The human microbiota is a broad category consisting of diverse bacteria, fungi, protists, archaea, and viruses that occur in and on the human body (1). The total number of these microbes is believed to be more than 100 trillion, which amounts to 2 kg in mass (2). Due to its important pathophysiological role in human health and disease, the microbiome has also been referred to as "the last human organ under active research" (3) and "the second brain" (4). ...
Article
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Accumulating recent evidence indicates that the human microbiome plays essential roles in pathophysiological states, including cancer. The tumor microbiome, an emerging concept that has not yet been clearly defined, has been proven to influence both cancer development and therapy through complex mechanisms. Small molecule metabolites produced by the tumor microbiome through unique biosynthetic pathways can easily diffuse into tissues and penetrate cell membranes through transporters or free diffusion, thus remodeling the signaling pathways of cancer and immune cells by interacting with biomacromolecules. Targeting tumor microbiome metabolism could offer a novel perspective for not only understanding cancer progression but also developing new strategies for the treatment of multiple cancer types. Here, we summarize recent advances regarding the role the tumor microbiome plays as a game changer in cancer biology. Specifically, the metabolites produced by the tumor microbiome and their potential effects on the cancer development therapy are discussed to understand the importance of the microbial metabolism in the tumor microenvironment. Finally, new anticancer therapeutic strategies that target tumor microbiome metabolism are reviewed and proposed to provide new insights in clinical applications.
... The gut microbiome seems to be very sensitive and does often change into several extrinsic and intrinsic factors such as genetics, dietary habits, age, geographic location, and ethnicity 26,28,29 . Amongst the above-mentioned factors, dietary habit seems to affect the gut microbiome with a huge impact that is substantially observed from the research studies [30][31][32][33][34][35][36] . ...
Article
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The COVID-19 had been emerged as a pandemic and resulted in more than 273 million reported cases and 5.3 million deaths worldwide. Concerns have been raised regarding this virus due to its unprecedented ability to move from human to human and cause infections, acute morbidity, and fatal outcome. Gut and lung microbiome profile substantially depends on dietary habits and plays a major role in modulating immunity thereby providing resistance to viral infections. The Gut-lung axis shows a correlation in microbial profile and the gastrointestinal microbiota can modulate lung microbiota majorly through the impact of microbial metabolites. Firmicutes and Actinobacteria specifically Bifidobacterium and Lactobacillus are responsible to modulate immunity and are widely used as probiotic species. In this review, we have concluded that different dietary habits affect microbial diversity and it can be a determining factor to fight SARS-CoV2 infections.
... The canine fecal microbiome has been the subject of a great deal of study, mostly centred around shifts in diet and resulting changes in fecal metabolites and microbes [13]. Dogs are ideal candidates for understanding shifts in the human microbiome in many respects: they are frequently companion animals and share human environments; their diet (in pet contexts) is consistent, the composition quantifiable by macronutrient, and they share an evolutionary history with humans, as through domestication, dogs underwent genetic, dietary and microbial shifts [14][15][16][17][18][19][20][21][22][23][24][25]. Recent canine microbiome studies have even recapitulated the results from human studies of microbiome responses to dietary shifts [26][27][28][29]. ...
Article
Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.
... In recent years, due to a development of DNA sequencing methods, with special emphasis on next generation sequencing techniques, more often a link has been reported between the host's health conditions and the bacterial composition in a gut. It has been proved that total microbiome weight in humans reaches up to 2 kg and the number of bacterial cells in intestines 10-fold exceeds the number of host cells in humans [60]. The microbiome is defined as all the bacteria, viruses, fungi, archaea and eukaryotes that inhabit the host's organism and the number of species is estimated at 5000 species [61]. ...
Article
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Inflammatory bowel diseases (IBD) are commonly considered as Crohn’s disease and ulcerative colitis, but the possibility that the alterations in gut microbiota and oxidative stress may affect the course of experimental colitis in obese physically exercising mice treated with the intestinal alkaline phosphatase (IAP) has been little elucidated. Mice fed a high-fat-diet (HFD) or normal diet (ND) for 14 weeks were randomly assigned to exercise on spinning wheels (SW) for 7 weeks and treated with IAP followed by intrarectal administration of TNBS. The disease activity index (DAI), grip muscle strength test, oxidative stress biomarkers (MDA, SOD, GSH), DNA damage (8-OHdG), the plasma levels of cytokines IL-2, IL-6, IL-10, IL-12p70, IL-17a, TNF-α, MCP-1 and leptin were assessed, and the stool composition of the intestinal microbiota was determined by next generation sequencing (NGS). The TNBS-induced colitis was worsened in obese sedentary mice as manifested by severe colonic damage, an increase in DAI, oxidative stress biomarkers, DNA damage and decreased muscle strength. The longer running distance and weight loss was observed in mice given IAP or subjected to IAP + SW compared to sedentary ones. Less heterogeneous microbial composition was noticed in sedentary obese colitis mice and this effect disappeared in IAP + SW mice. Absence of Alistipes, lower proportion of Turicibacter, Proteobacteria and Faecalibacterium, an increase in Firmicutes and Clostridium, a decrease in oxidative stress biomarkers, 8-OHdG content and proinflammatory cytokines were observed in IAP + SW mice. IAP supplementation in combination with moderate physical activity attenuates the severity of murine colitis complicated by obesity through a mechanism involving the downregulation of the intestinal cytokine/chemokine network and oxidative stress, the modulation of the gut microbiota and an improvement of muscle strength.
... Diet-derived carbohydrates that are not fully digested in the upper gut are metabolized by bacteria in the human large intestine. These non-digestible carbohydrates influence microbial fermentation and total bacterial number in the colon [43]. High growth rates of Clostridium histolyticum, Clostridium perfringens, and Sutterella; a high ratio of Escherichia/Shigella; and a low ratio of Bacteroidetes/Firmicutes were generally related to GI problems [44][45][46], while the relative abundance of Desulfovibrio, Clostridium spp., and Bacteroides vulgatus were associated with behavior disorders [47][48][49]. ...
Article
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The purpose of this review is to summarize the current acquiredknowledge of Candida overgrowth in the intestine as a possible etiology of autism spectrum disorder (ASD). The influence of Candida sp. on the immune system, brain, and behavior of children with ASD isdescribed. The benefits of interventions such as a carbohydrates-exclusion diet, probiotic supplementation, antifungal agents, fecal microbiota transplantation (FMT), and microbiota transfer therapy (MTT) will be also discussed. Our literature query showed that the results of most studies do not fully support the hypothesis that Candida overgrowth is correlated with gastrointestinal (GI) problems and contributes to autism behavioral symptoms occurrence. On the one hand, it was reported that the modulation of microbiota composition in the gut may decrease Candida overgrowth, help reduce GI problems and autism symptoms. On the other hand, studies on humans suggesting the beneficial effects of a sugar-free diet, probiotic supplementation, FMT and MTT treatment in ASD are limited and inconclusive. Due to the increasing prevalence of ASD, studies on the etiology of this disorder are extremely needed and valuable. However, to elucidate the possible involvement of Candida in the pathophysiology of ASD, more reliable and well-designed research is certainly required.
... The most widely studied and European Union approved prebiotics are fructo-oligosaccharides; galacto oligosaccharides and lactulose. DFs and prebiotics are resistant to human digestion and are fermented to acetate; propionate and butyrate, short chain fatty acids, due to synergistic action of colonic microflora (Flint, 2012). Propionate stimulates expression of leptin andreduces the pro-inflammatory factor resist in human adiposetissues (Al-Lahham, Roelofsen, Priebe, Weening, Dijkstra, Hoek, Rezaee, Venema, & Vonk, 2010). ...
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Obesity is a medical condition caused by the accumulation of excess fat in the body. The main causes of obesity are lifestyle, less physical activity, and increased health problems. Overweight and obesity have increased over the past 20 years in many regions of the world, particularly the prevalence of obesity in childhood. It is not only a problem of developed countries but also becoming a growing burden for the developing countries. Functional foods might play important role in prevention or treatment of overweight. Functional foods for obesity influences the energy balance equation regulated by the control of energy intake or of energy dissipated as heat (thermogenesis).
... In turn, there is a close, bi-directional interaction between sex hormones and gut microbiota, as they influence each other, thereby leading to sex-biased disease susceptibility and severity, ultimately leading to the observed sex differences in cardiovascular disease. geography, hygiene, nutrition and social behaviors (15,16). The gut microbes have an important role in human health and disease, affecting body weight and digestion, the protection against infection, the risk of autoimmune diseases, as well as the body's response to drugs (17)(18)(19)(20)(21). ...
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There has been a recent, unprecedented interest in the role of gut microbiota in host health and disease. Technological advances have dramatically expanded our knowledge of the gut microbiome. Increasing evidence has indicated a strong link between gut microbiota and the development of cardiovascular diseases (CVD). In the present article, we discuss the contribution of gut microbiota in the development and progression of CVD. We further discuss how the gut microbiome may differ between the sexes and how it may be influenced by sex hormones. We put forward that regulation of microbial composition and function by sex might lead to sex-biased disease susceptibility, thereby offering a mechanistic insight into sex differences in CVD. A better understanding of this could identify novel targets, ultimately contributing to the development of innovative preventive, diagnostic and therapeutic strategies for men and women.
... Large inter-individual variability in SCFA production was observed in both groups. High inter-individual variability in gut microbiota responses to dietary interventions has been reported [31][32][33] . Studies suggest that dietary habits and baseline gut microbiome compositions influence inter-individual variability 32 . ...
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Animal models indicate that butyrate might reduce motor symptoms in Parkinson’s disease. Some dietary fibers are butyrogenic, but in Parkinson’s disease patients their butyrate stimulating capacity is unknown. Therefore, we investigated different fiber supplements’ effects on short-chain fatty acid production, along with potential underlying mechanisms, in Parkinson’s patients and age-matched healthy controls. Finally, it was investigated if this butyrate production could be confirmed by using fiber-rich vegetables. Different fibers ( n = 40) were evaluated by in vitro fermentation experiments with fecal samples of Parkinson’s patients ( n = 24) and age-matched healthy volunteers ( n = 39). Short-chain fatty acid production was analyzed by headspace solid-phase micro-extraction gas chromatography-mass spectrometry. Clostridium coccoides and C. leptum were quantified through 16S-rRNA gene-targeted group-specific qPCR. Factors influencing short-chain fatty acid production were investigated using linear mixed models. After fiber fermentation, butyrate concentration varied between 25.6 ± 16.5 µmol/g and 203.8 ± 91.9 µmol/g for Parkinson’s patients and between 52.7 ± 13.0 µmol/g and 229.5 ± 42.8 µmol/g for controls. Inulin had the largest effect, while xanthan gum had the lowest production. Similar to fiber supplements, inulin-rich vegetables, but also fungal β-glucans, stimulated butyrate production most of all vegetable fibers. Parkinson’s disease diagnosis limited short-chain fatty acid production and was negatively associated with butyrate producers. Butyrate kinetics during 48 h fermentation demonstrated a time lag effect in Parkinson’s patients, especially in fructo-oligosaccharide fermentation. Butyrate production can be stimulated in Parkinson’s patients, however, remains reduced compared to healthy controls. This is a first step in investigating dietary fiber’s potential to increase short-chain fatty acids in Parkinson’s disease.
... The gut microbiota is the trillions of microorganisms inhabiting the digestive tract and make up the vast majority of the whole-body microbiota (Flint 2012). They make a rich and diverse community of microbes that are personalized as they are shaped from the very early stages of life (Gilbert 2015), and are influenced by several factors including host genetics (Goodrich et al. 2014), mode of birth (Nagpal et al. 2017), diet (Odamaki et al. 2016), antibiotic exposures (Willing, Russell, and Finlay 2011), environment and lifestyle (Rampelli et al. 2016). ...
Article
There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual's lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really "new," or "old wine in new bottles."
... Colonic butyrate levels can be modified by the diet (Flint, 2012), with fibre the preferred substrate for butyrate-producing bacteria. In indirect evidence for butyrate's role in muscle health, fibre supplementation has increased muscle mass in mice (Cani et al., 2009), and increased glucose metabolism in human muscle tissue (Robertson et al., 2012). ...
Article
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This study aimed to investigate the relationships between diet quality, the relative abundance of butyrate-producing bacteria of the gut microbiome and muscle mass, strength and function. In this cross-sectional study, n = 490 men (64.4 ± 13.5 years) from the Geelong Osteoporosis Study provided food frequency questionnaire data, from which the Australian Recommended Food Score (ARFS) and Dietary Inflammatory Index (DII) score were calculated. Muscle mass (skeletal muscle index from DXA-derived lean mass), muscle strength (handgrip strength) and muscle function (Timed Up-and-Go test) were measured. Participants provided stool samples for 16S rRNA gene sequencing. There was no evidence of associations between alpha or beta diversity and muscle health measures. A healthier ARFS score was positively associated with the relative abundance of butyrate-producing bacteria ( β 0.09, 95%CI 0.03, 0.15) and a higher (pro-inflammatory) DII score was associated with lower relative abundance of butyrate-producing bacteria ( β −0.60, 95%CI −1.06, −0.15). The relative abundance of butyrate-producing bacteria was positively associated with healthier muscle mass, strength and function; however, these relationships were attenuated in multivariable models. These findings support the role of diet quality in achieving a healthier gut microbiome, however, further evidence is required for a gut-muscle axis in humans.
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The gut microbiome has attracted increasing attention from researchers in recent years. The microbiota can have a specific and complex cross-talk with the host, particularly with the central nervous system (CNS), creating the so-called “gut–brain axis”. Communication between the gut, intestinal microbiota, and the brain involves the secretion of various metabolites such as short-chain fatty acids (SCFAs), structural components of bacteria, and signaling molecules. Moreover, an imbalance in the gut microbiota composition modulates the immune system and function of tissue barriers such as the blood–brain barrier (BBB). Therefore, the aim of this literature review is to describe how the gut–brain interplay may contribute to the development of various neurological disorders, combining the fields of gastroenterology and neuroscience. We present recent findings concerning the effect of the altered microbiota on neurodegeneration and neuroinflammation, including Alzheimer’s and Parkinson’s diseases, as well as multiple sclerosis. Moreover, the impact of the pathological shift in the microbiome on selected neuropsychological disorders, i.e., major depressive disorders (MDD) and autism spectrum disorder (ASD), is also discussed. Future research on the effect of balanced gut microbiota composition on the gut–brain axis would help to identify new potential opportunities for therapeutic interventions in the presented diseases.
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Background: Gestational diabetes mellitus (GDM) is carbohydrate intolerance first recognised during pregnancy and associated with complications for mothers and babies. Probiotics are naturally occurring micro-organisms, which when ingested in adequate amounts, may confer health benefits. Evidence of the role of probiotics as treatment for GDM is limited. Objectives: To evaluate the safety and effectiveness of probiotics in treating women with GDM on maternal and infant outcomes. Search methods: We searched the Cochrane Pregnancy and Childbirth's Trials Register ClinicalTrials.gov, WHO International Clinical Trials Registry Platform (ICTRP) (24 July 2019), and reference lists of retrieved studies. Selection criteria: Randomised controlled trials (RCTs) comparing the use of probiotics versus placebo/standard care for the treatment of GDM. Data collection and analysis: Two review authors independently assessed study eligibility, extracted data, checked data accuracy, and assessed risk of bias of included trials. The certainty of evidence for selected maternal and infant/child outcomes was assessed using GRADE. Main results: Nine RCTs (695 pregnant women with GDM) comparing probiotics versus placebo were identified. The overall risk of bias in the nine RCTs was low to unclear and the evidence was downgraded for imprecision due to the small numbers of women participating in the trials. The trials were carried out in hospitals and universities in Iran (seven trials), Thailand (one trial) and Ireland (one trial). All trials compared probiotics with placebo. Maternal outcomes We are uncertain if probiotics have any effect compared with placebo on hypertensive disorders of pregnancy, (risk ratio (RR) 1.50, 95% confidence interval (CI) 0.64 to 3.53; participants = 256; studies = 3; low-certainty evidence) and mode of birth as caesareans (average RR 0.64, 95% CI 0.30 to 1.35; participants = 267; studies = 3; low-certainty evidence) because the certainty of evidence is low and the 95% CIs span possible benefit and possible harm. No trials reported primary outcomes of: mode of birth as vaginal/assisted and subsequent development of type 2 diabetes. We are uncertain if probiotics have any effect compared with placebo on induction of labour (RR 1.33, 95% CI 0.74 to 2.37; participants = 127; studies = 1; very low-certainty evidence). For other secondary maternal outcomes, we are uncertain if there are differences between probiotics and placebo for: postpartum haemorrhage; weight gain during pregnancy intervention and total gestational weight gain; fasting plasma glucose and need for extra pharmacotherapy (insulin). Probiotics may be associated with a slight reduction in triglycerides and total cholesterol. In probiotics compared with placebo, there was evidence of reduction in markers for insulin resistance (HOMA-IR) and HOMA-B; and insulin secretion. There was also an increase in quantitative insulin sensitivity check index (QUICKI). Probiotics were associated with minor benefits in relevant bio-markers with evidence of a reduction in inflammatory markers high-sensitivity C-reactive protein (hs-CRP), interleukin 6 (IL-6), and marker of oxidative stress malondialdehyde; and an increase in antioxidant total glutathione, but we are uncertain if there is any difference in total antioxidant capacity. No trials reported secondary outcomes: perineal trauma, postnatal weight retention or return to pre-pregnancy weight and postnatal depression. Infant/child/adult outcomes We are uncertain if probiotics have any effect, compared with placebo, on the risk of large-for-gestational-age babies (RR 0.73, 95% CI 0.35 to 1.52; participants = 174; studies = 2; low-certainty evidence) or infant hypoglycaemia (RR 0.85, 95% CI 0.39 to 1.84; participants = 177; studies = 3; low-certainty evidence) because the certainty of evidence is low and the 95% CIs span possible benefit and possible harm. No trials reported primary outcomes of: perinatal (fetal/neonatal) mortality; or neurosensory disability. For other secondary outcomes, we are uncertain if there is any difference between probiotics and placebo in gestational age at birth, preterm birth, macrosomia, birthweight, head circumference, length, infant hypoglycaemia, and neonatal intensive care unit (NICU) admissions. There was evidence of a reduction in infant hyperbilirubinaemia with probiotics compared with placebo. No trials reported secondary outcomes: infant adiposity, and later childhood adiposity. There were no adverse events reported by any of the trials. Authors' conclusions: Low-certainty evidence means we are not certain if there is any difference between probiotic and placebo groups in maternal hypertensive disorders of pregnancy, caesareans; and large-for-gestational-age babies. There were no adverse events reported by the trials. Due to the variability of probiotics used and small sample sizes of trials, evidence from this review has limited ability to inform practice. Well-designed adequately-powered trials are needed to identify whether probiotics may improve maternal blood glucose levels and/or infant/child/adult outcomes; and whether they can be used to treat GDM.
Article
The human gut microbiome is composed of communities of bacteria, viruses and fungi. Bacteria live in each part of digestive tract, increasing their density and changing composition in distal parts. The composition of gut microbiome mainly depends on method of childbirth, age, gender, diet, stress, infections, alcohol intake, diurnal variation, smoking, drugs (antibiotics), physical activity. Dysbiosis is defined as an imbalance or maladaptation in the gut microbial community. This imbalance favors many pathological states and it could be due to some diseases. Non-alcoholic fatty liver disease (NAFLD) has become increasingly common in parallel with the increasing prevalence of obesity and other components of the metabolic syndrome. In year 2020, a more comprehensive new definition of NAFLD was proposed – fatty liver disease associated with metabolic dysfunction (MAFLD). NAFLD/MALFD will become the major form of chronic liver disease in adults and children and could become the leading indication for liver transplantation within a decade. An increased level of Bacteroidetes and decreased level of Firmicutes is observed in fatty liver disease. This imbalance favors the collection of energy and insulin resistance. The prevention and treatment of dysbiosis in NAFLD/MAFLD is essential. The purpose of this review is an understanding related to the dysbiosis and non-alcoholic fatty liver disease in order to help physicians of different specialties in their clinical practice because of growing in population patients with metabolic syndrome and liver steatosis.
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The intestinal epithelial layer serves as a physical and functional barrier between the microbe-rich lumen and immunologically active submucosa; it prevents systemic translocation of microbial pyrogenic products (e.g. endotoxin) that elicits immune activation upon translocation to the systemic circulation. Loss of barrier function has been associated with chronic ‘low-grade’ systemic inflammation which underlies pathogenesis of numerous no-communicable chronic inflammatory disease. Thus, targeting gut barrier dysfunction is an effective strategy for the prevention and/or treatment of chronic disease. This review intends to emphasize on the beneficial effects of herbal formulations, phytochemicals and traditional phytomedicines in attenuating intestinal barrier dysfunction. It also aims to provide a comprehensive understanding of intestinal-level events leading to a ‘leaky-gut’ and systemic complications mediated by endotoxemia. Additionally, a variety of detectable markers and diagnostic criteria utilized to evaluate barrier improving capacities of experimental therapeutics has been discussed. Collectively, this review provides rationale for targeting gut barrier dysfunction by phytotherapies for treating chronic diseases that are associated with endotoxemia-induced systemic inflammation.
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This study focused on constructing a high-solid reaction system to prepare type 3 resistant starch (RS3) with high-amylose maize starch as raw material by mechanical activation (MA) pretreatment combined with thermal and freeze-thaw treatments. MA pretreatment effectively destroyed the crystal structure and molecular structure of native starch. MA damaged starch with a certain viscosity could form dough with a small amount of water to construct a starch continuous phase system. RS content increased with the damage levels of starch as the formation of double helix structure, attributed to that the molecules of MA damaged starch could be easy to move and form recrystallization structure. Thermal and freeze-thaw treatments contributed to strong interaction of starch-water and the re-formation of internal crystal structure of MA damaged starch to form RS3. This study provides insight into the development of a highly effective approach for large scale production of resistant starch.
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Barley is a fiber and starch rich crop. Historically, barley was used as a human nourishment supply. More recently, barley has mainly been used for animal feed formulation, one-third for malting and only a 2% has been used as food ingredient directly. Beneficial effects associated with barley inclusion in diet have been described. It can decrease the glycemic index (GI) and can be used for body weight and cardiac diseases control. Whole barley has also a positive effect in modulating of gut microbiota. Beer spent grain (BSG), representing a solid by-product of beer production, is a high value raw material with good nutritional quality and bioactive carbohydrate composition. Currently, BSG are underutilized materials with the great potential of having a second life as excellent source of isolated ingredients, particularly high fiber and protein for human consumption. Despite being challenging, the recovery of food industry by-products is necessary for reliving the environmental impact of the food production chain and reduce pollution. The positive effect on human health associated with the consumption of barley, alongside the potential recovery of barley waste-streams, make barley a value ingredient in sustainable formulated products and food supplements. Two developmental pathways can be identified in the use of barley as a sustainable food ingredient. The development of approaches for sustainable recovery of barley based by products and the selection of barley able to grow as perennial crops.
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The scientific community currently defines the human microbiome as all the bacteria, viruses, fungi, archaea, and eukaryotes that occupy the human body. When considering the variable locations, composition, diversity, and abundance of our microbial symbionts, the sheer volume of microorganisms reaches hundreds of trillions. With the onset of next generation sequencing (NGS), also known as high-throughput sequencing (HTS) technologies, the barriers to studying the human microbiome lowered significantly, making in-depth microbiome research accessible. Certain locations on the human body, such as the gastrointestinal, oral, nasal, and skin microbiomes have been heavily studied through community-focused projects like the Human Microbiome Project (HMP). In particular, the gastrointestinal microbiome (GM) has received significant attention due to links to neurological, immunological, and metabolic diseases, as well as cancer. Though HTS technologies allow deeper exploration of the GM, data informing the functional characteristics of microbiota and resulting effects on human function or disease are still sparse. This void is compounded by microbiome variability observed among humans through factors like genetics, environment, diet, metabolic activity, and even exercise; making GM research inherently difficult to study. This chapter describes an interdisciplinary approach to GM research with the goal of mitigating the hindrances of translating findings into a clinical setting. By applying tools and knowledge from microbiology, metagenomics, bioinformatics, machine learning, predictive modeling, and clinical study data from children with treatment-resistant epilepsy, we describe a proof-of-concept approach to clinical translation and precision application of GM research.
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In recent years, the potential of antiaging interventions that are effective against age-related diseases is gaining increased scientific interest. In this chapter, contribution of wholegrain-based foods can be considered as part of antiaging dietary interventions that are effective against age-related diseases is discussed. Naturally occurring compounds in wholegrain cereals comprised several categories, namely, nondigestible carbohydrates (fiber), phenolic acids, flavonoids, avenanthramides, lignans, alkylresorcinols, carotenoids, phytosterols, and tocols. This chapter highlights the influence of cereal bioactive compounds in preventing aging disorders and augmenting lifespan based on their influence on oxidative stress, inflammation, cellular senescence, and gut microbiota. Moreover, information presented herein encourages research on wholegrain-based strategies and clinical trials to develop a holistic nutrition-oriented antiaging therapy.
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Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing fifty-four individuals and causing approximately 4 000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonisers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 136 since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Mass mortality events due to disease outbreaks have recently affected almost every healthy population of fan mussel, Pinna nobilis in Mediterranean Sea. The devastating mortality of the species has turned the interest of the research towards the causes of these events. After the haplosporidan infestation and the infection by Mycobacterium sp., new emerging pathogens have arisen based on the latest research. In the present study, a metagenomic approach of 16S rRNA next generation sequencing (NGS) was applied in order to assess the bacterial diversity within the digestive gland of diseased individuals as well as to carry out geographical correlations among the biodiversity of microbiome in the endangered species Pinna nobilis. The specimens originated from the mortalities occurred in 2019 in the region of Greece. Together with other bacterial genera, the results confirmed the presence of Vibrio spp., assuming synergistic effects in the mortality events of the species. Alongside with the presence of Vibrio spp., numerous bacterial genera were detected as well, including Aliivibrio spp., Photobacterium spp., Pseudoalteromonas spp., Psychrilyobacter spp. and Mycoplasma spp. Bacteria of the genus Mycoplasma were in high abundance particularly in the sample originated from Limnos island representing the first time recorded in Pinna nobilis. In conclusion, apart from exclusively the Haplosporidan and the Mycobacterium parasites, the presence of potentially pathogenic bacterial taxa detected, such as Vibrio spp., Photobactrium spp. and Alivibrio spp. lead us to assume that mortality events in the endangered Fan mussel, Pinna nobilis, may be attributed to synergistic effects of more pathogens.
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This study investigates the evolution of the distributions of whole molecular size and of chain length of granular wheat starches (37∼93% amylose content), subjected to in vitro fermentation with a porcine faecal inoculum or digestion with pancreatic enzymes. The results showed that the molecular structures of high-amylose starch (HAS) unfermented residues largely remained unchanged during the fermentation process, while wild-type starch (37% amylose content) showed a preferential degradation of the amylopectin fraction. In contrast, under simulated digestion conditions, the undigested residues of HAS showed structural changes, including a decrease in amylose content, a shift of amylose peak position towards lower degrees of polymerisation, and an enzyme-resistant fraction. These changes of starch structure are likely to be dependent on the different starch-degrading enzyme activities present in pancreatic vs microbial systems. Molecular changes in response to fermentation metabolism revealed by size-exclusion chromatography can help understand the microbial utilization of resistant starch.
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Resistant starch (RS) in the diet reaches the large intestine and is fermented by the gut microbiota, providing beneficial effects on human health. The human gut bacterium FMB-CY1 was isolated and identified as a new species closest to Ruminococcus bromii. Ruminococcus sp. FMB-CY1 completely degraded RS including commercial RS types 2, 3, and 4, and generated glucose and maltose; however, it did not assimilate glucose. Genome analysis revealed 15 amylolytic enzymes (Amy) present in FMB-CY1. The evolutionary trees revealed that the Amys were well divided each other. All Amys (4, 9, 10, 12, and 16) containing cohesin and/or dockerin and scaffolding proteins known to be involved in constituting the amylosome, were identified. A new species of Ruminococcus, strain FMB-CY1, was considered to have the ability to form amylosomes for the degradation of RS. This new RS-degrading Ruminococcus species provides insights into the mechanism(s) underlying RS degradation in the human gut. Supplementary information: The online version contains supplementary material available at 10.1007/s10068-021-01027-2.
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Diet is a key modulator of fecal microbiota composition and function. However, the influence of diet on the microbiota from toddlerhood to adolescence and young adulthood is less well studied than for infancy and adulthood. We aimed to complete a qualitative systematic review of the impacts of diet on the fecal microbiota of healthy humans 1-20 y of age. English-language articles, published after 2008, indexed in the PubMed/MEDLINE, Cochrane, Web of Science, and Scopus databases were searched using keywords and Medical Subject Headings terms. Quality assessment of included studies was conducted using the Quality Criteria Checklist derived from the Nutrition Evidence Library of the Academy of Nutrition and Dietetics. A total of 973 articles were identified through database searching and 3 additional articles were included via cross-reference. Subsequent to de-duplication, 723 articles were screened by title and abstract, of which 709 were excluded based on inclusion criteria established a priori. The remaining 14 studies were independently screened by 2 reviewers for final inclusion. Included studies were published between 2010 and 2019 and included 8 comparative cross-sectional studies, 4 cross-sectional studies, 1 randomized crossover study, and 1 substudy of a randomized 2-period crossover trial. Associations of a diet rich in indigestible plant polysaccharides with Prevotella, or with an enterotype dominated by this genus, often comprised of the species Prevotella copri, were observed. In addition, associations of a high-fat and -sugar diet with Bacteroides, or with an enterotype dominated by this genus, were observed predominantly in comparative cross-sectional and cross-sectional studies spanning the ages of 1-15 y. This review identified a gap in the literature for ages 16-20 y. In addition, randomized controlled trials for dietary intervention are needed to move from association-based observations to causal relations between diet and microbiota composition and function. This systematic review was registered at www.crd.york.ac.uk/prospero as CRD42020129824.
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Background: The aim of current study was to investigate whether degradation of rapeseed meal (RSM) which was modified by a cellulase, two pectinase, or alkaline treatment was improved by the swine gut microbiota compared to untreated RSM, and whether the microbiota composition was changed. Methods: An in vitro study was performed to assess how enzymatic and chemical pretreated rapeseed meal (RSM) influences the fibre fermentation and microbial community in the swine large intestine. RSM was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. 16S rRNA gene sequencing data was performedto evaluate changes in the gut microbiota composition, whereas short chain fatty acid production (ion-chromatography) and non-starch polysaccharides (NSP) composition(using monoclonal antibodies; mAbs) were used to assess fibre degradation. Results: The results showed that ALK, CELL, PECT1, and PECT2changed microbial community composition, increased the abundance of microbial fibre-degrading enzymes and pathways,andincreased acetic acid, propionic acid, butyric acid, and total SCFA production. The increased genera also positively correlated with SCFA production. The cell wall polysaccharide structuresof RSM shiftedafter ALK, CELL, PECT1, and PECT2 treatment. The degradation of NSPduring the fermentation period was dynamic, and not continuous based on the epitope recognition by mAbs. Conclusion: This study provides the first detailed analysis of changes in the swine intestinal microbiota due to RSM modified by ALK, CELL, PECT1 and PECT2. ALK, CELL, PECT1 and PECT2 altered microbial community structure, shifted the predicted functional metagenomic profile and subsequently increased total SCFA production. Our findings that ALK, CELL, PECT1 and PECT2increased fiber degradability in RSM could help guide feed additive strategies to improve efficiency and productivity in swine industry. The current study gave insight into how feed enzyme modulate microbial status, which provides good opportunity to develop novel carbohydrase, particularly in swine feed.
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The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacter-oidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium, Ruminococcus, Eubac-terium, Dorea, Bacteroides, Alistipes and Bifidobac-terium. Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly , 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.
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Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
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Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.
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Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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To systematically develop dietary strategies based on resistant starch (RS) that modulate the human gut microbiome, detailed in vivo studies that evaluate the effects of different forms of RS on the community structure and population dynamics of the gut microbiota are necessary. The aim of the present study was to gain a community wide perspective of the effects of RS types 2 (RS2) and 4 (RS4) on the fecal microbiota in human individuals. Ten human subjects consumed crackers for three weeks each containing either RS2, RS4, or native starch in a double-blind, crossover design. Multiplex sequencing of 16S rRNA tags revealed that both types of RS induced several significant compositional alterations in the fecal microbial populations, with differential effects on community structure. RS4 but not RS2 induced phylum-level changes, significantly increasing Actinobacteria and Bacteroidetes while decreasing Firmicutes. At the species level, the changes evoked by RS4 were increases in Bifidobacterium adolescentis and Parabacteroides distasonis, while RS2 significantly raised the proportions of Ruminococcus bromii and Eubacterium rectale when compared to RS4. The population shifts caused by RS4 were numerically substantial for several taxa, leading for example, to a ten-fold increase in bifidobacteria in three of the subjects, enriching them to 18-30% of the fecal microbial community. The responses to RS and their magnitudes varied between individuals, and they were reversible and tightly associated with the consumption of RS. Our results demonstrate that RS2 and RS4 show functional differences in their effect on human fecal microbiota composition, indicating that the chemical structure of RS determines its accessibility by groups of colonic bacteria. The findings imply that specific bacterial populations could be selectively targeted by well designed functional carbohydrates, but the inter-subject variations in the response to RS indicates that such strategies might benefit from more personalized approaches.
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The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that 'blooms' in specific bacterial groups occurred rapidly after a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of RS remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual's gut microbiota.
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Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide.
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The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium, Ruminococcus, Eubacterium, Dorea, Bacteroides, Alistipes and Bifidobacterium. Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.
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Very low-carbohydrate diets are often used to promote weight loss, but their effects on bowel health and function are largely unknown. We compared the effects of a very low-carbohydrate, high-fat (LC) diet with a high-carbohydrate, high-fibre, low-fat (HC) diet on indices of bowel health and function. In a parallel study design, ninety-one overweight and obese participants (age 50.6 (sd 7.5) years; BMI 33.7 (sd 4.2) kg/m(2)) were randomly assigned to either an energy-restricted (about 6-7 MJ, 30 % deficit) planned isoenergetic LC or HC diet for 8 weeks. At baseline and week 8, 24 h urine and faecal collections were obtained and a bowel function questionnaire was completed. Compared with the HC group, there were significant reductions in the LC group for faecal output (21 (sd 145) v. - 61 (sd 147) g), defecation frequency, faecal excretion and concentrations of butyrate ( - 0.5 (sd 10.4) v. - 3.9 (sd 9.7) mmol/l) and total SCFA (1.4 (sd 40.5) v. - 15.8 (sd 43.6) mmol/l) and counts of bifidobacteria (P < 0.05 time x diet interaction, for all). Urinary phenols and p-cresol excretion decreased (P < or = 0.003 for time) with no difference between diets (P > or = 0.25). Faecal form, pH, ammonia concentration and numbers of coliforms and Escherichia coli did not change with either diet. No differences between the diets were evident for incidences of adverse gastrointestinal symptoms, which suggests that both diets were well tolerated. Under energy-restricted conditions, a short-term LC diet lowered stool weight and had detrimental effects on the concentration and excretion of faecal SCFA compared with an HC diet. This suggests that the long-term consumption of an LC diet may increase the risk of development of gastrointestinal disorders.
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An investigation was made of the effect of changing mean transit time (MTT) by administration of drugs which affect colonic motility on faecal microbial mass in man. Senokot was used to accelerate and codeine and/or loperamide to prolong transit in subjects maintained on a constant high fibre diet. Doses of Senokot or codeine/loperamide were adjusted to halve or double transit time measured during a three week control period on diet alone. Stools were collected throughout and analysed for bacterial mass by a gravimetric procedure. Transit was measured by a continuous marker method. Senokot decreased mean transit time from 63.9 to 25.0 hours (n = 6), with increased stool weight from 148 to 285 g/day. Bacterial mass increased in all subjects from a mean of 16.5 to 20.3 g/day (dry weight) (p less than 0.025). Codeine/loperamide increased mean transit time from 47.1 to 87.6 hours (n = 5), with decreased stool weight from 182 to 119 g/day. Bacterial mass decreased in all but one subject from a mean of 18.9 to 16.1 g/day (NS). There was a significant correlation between transit time and bacterial mass in all three periods (r = 0.77, p less than 0.001). Changes in transit time are shown to alter microbial growth in the human colon and result in altered stool output, on a constant diet. Factors which affect transit may be as important as diet in determining large bowel function and hence susceptibility to disease.
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To investigate whether transit time could influence H2 consuming flora and certain indices of colonic bacterial fermentation. Eight healthy volunteers (four methane excretors and four non-methane excretors) were studied for three, three week periods during which they received a controlled diet alone (control period), and then the same diet with cisapride or loperamide. At the end of each period, mean transit time (MTT) was estimated, an H2 lactulose breath test was performed, and stools were analysed. In the control period, transit time was inversely related to faecal weight, sulphate reducing bacteria counts, concentrations of total short chain fatty acids (SCFAs), propionic and butyric acids, and H2 excreted in breath after lactulose ingestion. Conversely, transit time was positively related to faecal pH and tended to be related to methanogen counts. Methanogenic bacteria counts were inversely related to those of sulphate reducing bacteria and methane excretors had slower MTT and lower sulphate reducing bacteria counts than non-methane excretors. Compared with the control period, MTT was significantly shortened (p < 0.05) by cisapride and prolonged (p < 0.05) by loperamide (73 (11) hours, 47 (5) hours and 147 (12) hours for control, cisapride, and loperamide, respectively, mean (SD)). Cisapride reduced transit time was associated with (a) a significant rise in faecal weight, sulphate reducing bacteria, concentrations of total SCFAs, and propionic and butyric acids and breath H2 as well as (b) a significant fall in faecal pH and breath CH4 excretion, and (c) a non-significant decrease in the counts of methanogenic bacteria. Reverse relations were roughly the same during the loperamide period including a significant rise in the counts of methanogenic bacteria and a significant fall in those of sulphate reducing bacteria. Transit time differences between healthy volunteers are associated with differences in H2 consuming flora and certain indices of colonic fermentation. Considering the effects of some fermentation products on intestinal morphology and function, these variations may be relevant to the pathogenesis of colorectal diseases.
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Nondigestible carbohydrates (NDCHs) are fermented in the colon, where they can selectively promote the growth of bifidobacteria. Our aim was to determine the bifidogenic potential of different NDCHs used in human diets. Two hundred healthy volunteers participated in this double-blind study. During phase 1 (screening), 64 volunteers were randomly assigned to 8 groups of 8 subjects each; for 7 d, they ingested 10 g/d of 1 of the 7 NDCHs tested or of the placebo. During phase 2 (dose-response study), 136 volunteers were randomly assigned to 4 groups of 32 subjects who received 2.5, 5.0, 7.5, or 10 g/d, respectively (8 subjects/dose), of one of the NDCHs that were proven to be bifidogenic during phase 1 and a fifth group of 8 subjects (control subjects) who received the placebo. Stools were recovered before and after NDCH consumption. In phase 1, 4 NDCHs were found to be bifidogenic: short-chain fructooligosaccharides (P=0.008), soybean oligosaccharides (P=0.006), galactooligosaccharides (P <0.0001), and type III resistant starch (P=0.02); lactulose, long-chain inulin, and isomaltooligosaccharides were not bifidogenic. In phase 2, the effects of 7-d treatment on bifidobacteria concentrations were found to differ significantly among the 4 NDCHs (P=0.009 for time x treatment interaction). However, no significant differences were found among doses, and there was no significant dose x time interaction. A low baseline bifidobacteria count was significantly associated with the bifidogenic response to treatment (P <0.001). This study showed the different bifidogenic properties among the substrates and underlined the importance of taking into account the baseline bifidobacteria counts when evaluating the effect of the treatment.
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Germ-free mice were maintained on polysaccharide-rich or simple-sugar diets and colonized for 10 days with an organism also found in human guts, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling of bacteria and mass spectrometry of cecal glycans. We found that these bacteria assembled on food particles and mucus, selectively induced outer-membrane polysaccharide-binding proteins and glycoside hydrolases, prioritized the consumption of liberated hexose sugars, and revealed a capacity to turn to host mucus glycans when polysaccharides were absent from the diet. This flexible foraging behavior should contribute to ecosystem stability and functional diversity.
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In vitro coculture fermentations of Bifidobacterium longum BB536 and two acetate-converting, butyrate-producing colon bacteria, Anaerostipes caccae DSM 14662 and Roseburia intestinalis DSM 14610, with oligofructose as the sole energy source, were performed to study interspecies interactions. Two clearly distinct types of cross-feeding were identified. A. caccae DSM 14662 was not able to degrade oligofructose but could grow on the fructose released by B. longum BB536 during oligofructose breakdown. R. intestinalis DSM 14610 could degrade oligofructose, but only after acetate was added to the medium. Detailed kinetic analyses of oligofructose breakdown by the last strain revealed simultaneous degradation of the different chain length fractions, in contrast with the preferential degradation of shorter fractions by B. longum BB536. In a coculture of both strains, initial oligofructose degradation and acetate production by B. longum BB536 took place, which in turn also allowed oligofructose breakdown by R. intestinalis DSM 14610. These and similar cross-feeding mechanisms could play a role in the colon ecosystem and contribute to the combined bifidogenic/butyrogenic effect observed after addition of inulin-type fructans to the diet.
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Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.
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Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species of Bifidobacterium are stimulated in vivo and whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive species Faecalibacterium prausnitzii exhibited a significant increase (10.3% for control period v. 14.5% during inulin intake, P=0.019). The composition of the genus Bifidobacterium was studied in four of the volunteers by clone library analysis. Between three and five Bifidobacterium spp. were found in each volunteer. Bifidobacterium adolescentis and Bifidobacterium longum were present in all volunteers, and Bifidobacterium pseudocatenulatum, Bifidobacterium animalis, Bifidobacterium bifidum and Bifidobacterium dentium were also detected. Real-time PCR was employed to quantify the four most prevalent Bifidobacterium spp., B. adolescentis, B. longum, B. pseudocatenulatum and B. bifidum, in ten volunteers carrying detectable levels of bifidobacteria. B. adolescentis showed the strongest response to inulin consumption, increasing from 0.89 to 3.9% of the total microbiota (P=0.001). B. bifidum was increased from 0.22 to 0.63% (P<0.001) for the five volunteers for whom this species was present.
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Because the human gut microbiota can play a major role in host health, there is currently some interest in the manipulation of the composition of the gut flora towards a potentially more remedial community. Attempts have been made to increase bacterial groups such as Bifidobacterium and Lactobacillus that are perceived as exerting health-promoting properties. Probiotics, defined as microbial food supplements that beneficially affect the host by improving its intestinal microbial balance, have been used to change the composition of colonic microbiota. However, such changes may be transient, and the implantation of exogenous bacteria therefore becomes limited. In contrast, prebiotics are nondigestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of one or a limited number of bacterial species already resident in the colon, and thus attempt to improve host health. Intake of prebiotics can significantly modulate the colonic microbiota by increasing the number of specific bacteria and thus changing the composition of the microbiota. Nondigestible oligosaccharides in general, and fructooligosaccharides in particular, are prebiotics. They have been shown to stimulate the growth of endogenous bifidobacteria, which, after a short feeding period, become predominant in human feces. Moreover, these prebiotics modulate lipid metabolism, most likely via fermentation products. By combining the rationale of pro- and prebiotics, the concept of synbiotics is proposed to characterize some colonic foods with interesting nutritional properties that make these compounds candidates for classification as health-enhancing functional food ingredients.
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Populations at low risk of colonic cancer consume large amounts of fibre and starch and pass acid, bulky stools. One short chain fatty acid (SCFA), butyrate, is the colon's main energy source and inhibits malignant transformation in vitro. To test the hypothesis that altering colonic transit rate alters colonic pH and the SCFA content of the stools. Thirteen healthy adults recruited by advertisement. Volunteers consumed, in turn, wheat bran, senna and loperamide, each for nine days with a two week washout period between study periods, dietary intake being unchanged. Before, and in the last four days of each intervention, whole gut transit time (WGTT), defaecation frequency, stool form, stool beta-glucuronidase activity, stool pH, stool SCFA concentrations and intracolonic pH (using a radiotelemetry capsule for continuous monitoring) were assessed. WGTT decreased, stool, output and frequency increased with wheat bran and senna, vice versa with loperamide. The pH was similar in the distal colon and stool. Distal colonic pH fell with wheat bran and senna and tended to increase with loperamide. Faecal SCFA concentrations, including butyrate, increased with senna and fell with loperamide. With wheat bran the changes were non-significant, possibly because of the short duration of the study. Baseline WGTT correlated with faecal SCFA concentration (r = -0.511, p = 0.001), with faecal butyrate (r = -0.577, p < 0.001) and with distal colonic pH (r = 0.359, p = 0.029). Bowel transit rate is a determinant of stool SCFA concentration including butyrate and distal colonic pH. This may explain the inter-relations between colonic cancer, dietary fibre intake, stool output, and stool pH.
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Starches are important as energy sources for humans and also for their interactions with the gut microflora throughout the digestive tact. Largely, those interactions promote human health. In the mouth, less gelatinised starches may lower risk of cariogensis. In the large bowel, starches which have escaped small intestinal digestion (resistant starch), together with proteins, other undigested carbohydrates and endogenous secretions are fermented by the resident microflora. The resulting short chain fatty acids contribute substantially to the normal physiological functions of the viscera. Specific types of resistant starch (e.g. the chemically modified starches used in the food industry) may be used to manipulate the gut bacteria and their products (including short chain fatty acids) so as to optimise health. In the upper gut, these starches may assist in the transport of probiotic organisms thus promoting the immune response and suppressing potential pathogens. However, it appears unlikely that current probiotic organisms can be used to modulate large bowel short chain fatty acids in adults although resistant starch and other prebiotics can do so. Suggestions that starch may exacerbate certain conditions (such as ulcerative colitis) through stimulating the growth of certain pathogenic organisms appear to be unfounded. Short chain fatty acids may modulate tissue levels and effects of growth factors in the gut and so modify gut development and risk of serious disease, including colo-rectal cancer. However, information on the relationship between starches and the microflora is relatively sparse and substantial opportunities exist both for basic research and food product development.
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The microbiota of the human intestinal tract play an important role in health, in particular by mediating many of the effects of diet upon gut health. Surveys of 16S rRNA sequence diversity in the human colon have emphasized the low proportion of sequences that match cultured bacterial species. This may reflect limited recent effort on cultivation rather than inherent unculturability, however, as anaerobic isolation methods can apparently recover a wide range of the diversity found. A combination of information from representative cultures, molecular tools for enumeration and tracking of bacterial metabolites offers the most powerful route to understanding the roles played by different groups of bacteria in the gut ecosystem. Progress is being made for example in defining key functional groups including primary colonizers of insoluble dietary substrates, and major contributors to metabolites such as butyrate that influence the health of the gut mucosa. There is increasing evidence that bacterial populations in the large intestine respond to changes in diet, in particular to the type and quantity of dietary carbohydrate. A general consequence of increased carbohydrate consumption is to reduce the pH of the gut lumen, which is likely to play a major role in determining bacterial metabolism and competition. Oligosaccharides used as dietary prebiotics must inevitably have complex effects upon the bacterial community that include non-target organisms and the consequences of metabolic cross-feeding and changes in the gut environment.
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To further understand how diets containing high levels of fibre protect against colorectal cancer, we examined the effects of diets high in nonstarch polysaccharides (NSP) or high in NSP plus resistant starch (RS) on the composition of the faecal microbial community in 46 healthy adults in a randomized crossover intervention study. Changes in bacterial populations were examined using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Bacterial profiles demonstrated changes in response to the consumption of both RS and NSP diets [analysis of similarities (ANOSIM): R=0.341-0.507, P<0.01]. A number of different DGGE bands with increased intensity in response to dietary intervention were attributed to as-yet uncultivated bacteria closely related to Ruminococcus bromii. A real-time PCR assay specific to the R. bromii group was applied to faecal samples from the dietary study and this group was found to comprise a significant proportion of the total community when individuals consumed their normal diets (4.4+/-2.6% of total 16S rRNA gene abundance) and numbers increased significantly (+/-67%, P<0.05) with the RS, but not the NSP, dietary intervention. This study indicates that R. bromii-related bacteria are abundant in humans and may be significant in the fermentation of complex carbohydrates in the large bowel.
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