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mRNA expression of all 171 CAZymes during growth on pectins A–C, hemicelluloses D–E, glucans F–H, and raw corn stover I relative to expression on glucose. Expression was quantified as log2(RPKM) with significantly differentially expressed genes on a given polysaccharide shown as triangles and unchanged genes as circles. The 56 purified CAZymes are red and others are blue.
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Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequ...
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Polysaccharides are macromolecules of monosaccharides linked by glycosidic bonds. Non-starch polysaccharides (NSP) are principally non-α-glucan polysaccharides of the plant cell wall. They are a heterogeneous group of polysaccharides with varying degrees of water solubility, size, and structure. The water insoluble fiber fraction include cellulose,...
Citations
... Interestingly, strains lacking pectinregulatory genes can rely on synergisms between different enzymes to modify substrates, such as the polygalacturonase GH 28 enzyme, which further relies on pectin methyl lipase CE8-1 to modify substrates, and some enzymes such as rhamnogalacturonate hydrolase GH105-1 and rhamnogalacturonate acetylesterase CE12-1, which have a wide range of substrates (Benz et al. 2014). According to Boutard et al. (2014), CAZymes are carbohydrate-active enzymes that exhibit functional diversity in addition to specificity, allowing bacteria to completely ferment a variety of polysaccharides in the plant matrix. Figure 8 illustrates how the enzymes express themselves and work together when bacteria ferment and degrade polysaccharides. ...
Polysaccharides are natural chemical compounds that are extensively employed in the food and pharmaceutical industries. They exhibit a wide range of physical and biological properties. These properties are commonly improved by using chemical and physical methods. However, with the advancement of biotechnology and increased demand for green, clean, and safe products, polysaccharide modification via microbial fermentation has gained importance in improving their physicochemical and biological activities. The physicochemical and structural characteristics, biological activity, and modification mechanisms of microbially fermented polysaccharides were reviewed and summarized in this study. Polysaccharide modifications were categorized and discussed in terms of strains and fermentation techniques. The effects of microbial fermentation on the physicochemical characteristics of polysaccharides were highlighted. The impact of modification of polysaccharides on their antioxidant, immune, hypoglycemic, and other activities, as well as probiotic digestive enhancement, were also discussed. Finally, we investigated a potential enzyme-based process for polysaccharide modification via microbial fermentation. Modification of polysaccharides via microbial fermentation has significant value and application potential.
... Limited growth was observed in xylose containing medium and maximum growth was 4.63 ± 0.24log cell/mL. Boutard et al. [28] reported L. phytofermentans growth was supported by the faster growth when using mixed sugars. The cellular growth on the mixture of sugars shows diauxic growth with the rapid utilization of preferred sugar and followed by the next preferred sugar. ...
Contemporary studies suggest that macroalgal biomass is an attractive and alternate source for ethanol production to replace fossil fuel. Sargassum wightii, a brown macroalgae, rich in cellulose is suitable for bioethanol production. This investigation focused on the pretreatment, enzyme saccharification and fermentation for bio-ethanol production through consolidated bioprocessing (CBP) using Lachnoclostridium phytofermentans KSM 1203 isolate. The cellulose extraction from S. wightii biomass and essential medium components for L. phytofermentans KSM 1203 were optimized using Response Surface Methodology. The alkali pretreatment on S. wightii biomass removed lignin and hemicelluloses with the cellulose recovery of 82.35%. The sodium hyphochlorite treatment removes other contaminants, results the semi crystalline to amorphous cellulose structure. The optimized medium components for L. phytofermentans KSM 1203 was found to be pre-treated biomass 3.92 g/L, peptone 2.21 g/L, dipotassium hydrogen phosphate 1.84 g/L and sodium chloride 2.03 g/L and for the growth and co-production of cellulase activity and ethanol productivity. The maximum bioethanol yield was obtained under the optimal conditions to be 13.75 ± 0.687 g/L for L. phytofermentans KSM 1203 from pre-treated S. wightii biomass. Hence, this investigation suggests that wild type L. phytofermentans KSM 1203 strain could be exploited for the utilization of cellulose for production ethanol in a single-step CBP procedure.
... The Weissela genus is associated with plants and fermented foods, with several strains being considered probiotics. Lachnospirales are fermenters of plant polysaccharides (Boutard et al., 2014). Oscillospirales are dependent on other bacteria or sugars generated from host mucins (Kohl et al., 2014). ...
The larvae of the Black Soldier Fly ( Hermetia illucens ) provide numerous ecological benefits, leading to significant commercial advancements. These benefits include the bioconversion of low-value waste into high-value feed and soil amendments. Understanding how the bacterial and eukaryotic microbiota communities affect host performance becomes vital for the optimization and specialization of industrial-scale rearing. This study investigates H. illucens -associated microbiota taxonomic composition and dynamics across the developmental cycle (eggs, neonates, larvae, prepupae, and imago X0 to second generation X1) when reared on two substrates: (i) plant-based (Housefly Gainesville diet) and (ii) animal-based (poultry hatchery waste). By using the 16S gene amplicon metataxonomic approach, we found that the results revealed that bacterial microbiota inherited from parents reared on a different substrate may have induced dysbiosis in the progeny. Specifically, the interaction networks of individuals reared on hatchery waste showed a high prevalence of negative interactions and low connectivity. Proteobacteria (39–92%), Firmicutes (4–39%), Bacteroidota (1–38%), and Actinobacteria (1–33%). In animal feed-reared individuals, Firmicutes reached the highest relative abundance (10–80%), followed by Proteobacteria (6–55%), Actinobacteria (1–31%), and Bacteroidota (0–22%). The rearing substrate was the main driver of microbiota composition, while the developmental stage influenced only the whole individual's bacterial microbiota composition. Gut regions were associated with distinct bacterial composition and richness, with diversity decreasing along the digestive tract. For the first time, microeukaryotes of the microbiota other than Fungi were investigated using 18S genetic marker amplicon sequencing with novel blocking primers specific to the Black Soldier Fly. Microeukaryotes are a neglected part of multitrophic microbiota communities that can have similar effects on their hosts as bacterial microbiota. Microeukaryotes from seven orders were identified in black soldier flies, including potential pathogens (e.g., Aplicomplexa group). Nucletmycea were the dominant class throughout development, followed by Holozoa and Stramenophiles. The eukaryote microbiota was structured by developmental stages but not by gut regions. Insights from this study are a stepping stone toward the microbiological optimization of black soldier flies for industrial rearing, highlighting how a synthetic microbiota assembly should be tailored to the rearing environment of the larvae at a targeted developmental stage.
... The relative abundances between members of the class Clostridia differed between KO and WT mice, which makes sense in relation to the observed changes in tissue metabolism. Lachnospiraceae is a family of anaerobic, spore-forming Clostridiales known for their ability to ferment plant polysaccharides into short-chain fatty acids, such as butyrate and acetate (66). Some well-defined Lachnospiraceae spp. ...
Inflammatory Bowel Disease (IBD) affects approximately 0.3% of the global population, with incidence rates rising dramatically worldwide. Emerging evidence points to an interplay between exposome factors such as diet and gut microbiota, host genetics, and the immune system as crucial elements in IBD development. ATP-binding cassette (ABC) transporters, including human p-glycoprotein encoded by the Abcb1 gene, influence intestinal inflammation, and their expression may interact with environmental factors such as diet and gut microbes. Our study aimed to examine the impact of protein sources on a genetic colitis mouse model.
Methods
Abcb1a-deficient colitis mice were fed either casein or red meat-supplemented diets to investigate potential colitis-aggravating components in red meat and their effects on host-microbiota interactions. We conducted deep label free quantitative proteomic inflammation profiling of gastrointestinal tissue (colon, ileum) and urine, and determined the overall microbiome in feces using 16S rRNA gene sequencing. Microbiota shifts by diet and protein transporter impairment were addressed by multivariate statistical analysis. Colon and systemic gut inflammation were validated through histology and immune assays, respectively.
Results
A quantitative discovery based proteomic analysis of intestinal tissue and urine revealed associations between ileum and urine proteomes in relation to Abcb1a deficiency. The absence of Abcb1a efflux pump function and diet-induced intestinal inflammation impacted multiple systemic immune processes, including extensive neutrophil extracellular trap (NET) components observed in relation to neutrophil degranulation throughout the gastrointestinal tract. The colitis model’s microbiome differed significantly from that of wild-type mice, indicating the substantial influence of efflux transporter deficiency on microbiota.
Conclusion
The proteomic and microbiota analyzes of a well-established murine model enabled the correlation of gastrointestinal interactions not readily identifiable in human cohorts. Insights into dysregulated biological pathways in this disease model might offer translational biomarkers based on NETs and improved understanding of IBD pathogenesis in human patients. Our findings demonstrate that drug transporter deficiency induces substantial changes in the microbiota, leading to increased levels of IBD-associated strains and resulting in intestinal inflammation.
GRAPHICAL ABSTRACT
... The above studies show that respiratory infections may lead to a decrease in SCFAs. Evidence suggests that RTI-induced changes in the gut microbiome can lead to the depletion of beneficial gut bacteria that produce SCFAs, such as Lachnospiraceae, which belongs to Firmicutes and can ferment pectin and fructose to produce acetate, propionate, and ethanol (Boutard et al., 2014). Reduced levels of SCFAs affect the immune system and aggravate asthma (Trompette et al., 2014;Cait et al., 2017). ...
... In general, respiratory virus infections lead to changes in the composition of intestinal flora, including an increase in Bacteroidetes, a decrease in short-chain fatty acid-producing bacteria such as Firmicutes and Pilospirillum, and an increase in opportunistic pathogens such as Enterococcus (Boutard et al., 2014;Groves et al., 2018;Woodall et al., 2022). These changes are similar to the changes observed in the gut microbiota of individuals with asthma, indicating that an imbalance in gut microbiota may contribute to the development and exacerbation of asthma following respiratory infections. ...
Asthma is one of the common chronic respiratory diseases in children, which poses a serious threat to children's quality of life. Respiratory infection is a risk factor for asthma. Compared with healthy children, children with early respiratory infections have a higher risk of asthma and an increased chance of developing severe asthma. Many clinical studies have confirmed the correlation between respiratory infections and the pathogenesis of asthma, but the underlying mechanism is still unclear. The gut microbiome is an important part of maintaining the body's immune homeostasis. The imbalance of the gut microbiome can affect the lung immune function, and then affect lung health and cause respiratory diseases. A large number of evidence supports that there is a bidirectional regulation between intestinal flora and respiratory tract infection, and both are significantly related to the development of asthma. The changes of intestinal microbial components and their metabolites in respiratory tract infection may affect the occurrence and development of asthma through the immune pathway. By summarizing the latest advancements in research, this review aims to elucidate the intricate connection between respiratory tract infections and the progression of asthma by highlighting its bridging role of the gut microbiome. Furthermore, it offers novel perspectives and ideas for future investigations into the mechanisms that underlie the relationship between respiratory tract infections and asthma.
... In addition, Ruminococcaceae and Oscillospiraceae, as short chain fatty acid (SCFA) producers, are also responsible for the degradation of diverse polysaccharides and are closely correlated with diseases linked to intestinal permeability, such as alcoholic cirrhotics, inflammatory bowel disease and non-alcoholic fatty liver disease [70][71][72][73][74][75][76]. Furthermore, Anaerovoracaceae is involved in the fermentation of plant polysaccharides in the gastrointestinal tract and is important for intestinal health [77,78], and Blautia has been reported to have antibacterial activity and be able to improve inflammatory and metabolic diseases [79,80]. Thus, rebalanced abundances of them in BNP-supplied mice represent the benefits of BNP on intestinal health. ...
Polygonati Rhizoma is a widely used traditional Chinese medicine (TCM) with complex pre-processing steps. Fermentation is a common method for processing TCM to reduce herb toxicity and enhance their properties and/or produce new effects. Here, in this study, using Bacillus subtilis and Saccharomyces cerevisiae, we aimed to evaluate the potential application of solid fermentation in isolating different functional polysaccharides from Polygonatum cyrtonema Hua. With hot water extraction, ethanol precipitation, DEAE anion exchange chromatography and gel filtration, multiple neutral and acidic polysaccharides were obtained, showing different yields, content, compositions and functional groups after fermentation. Combining in vitro experiments and in vivo aging and immunosuppressed mouse models, we further compared the antioxidant and immunomodulating bioactivities of these polysaccharides and found a prominent role of a natural polysaccharide (BNP) from fermented P. cyrtonema via Bacillus subtilis in regulating intestinal antioxidant defense and immune function, which may be a consequence of the ability of BNP to modulate the homeostasis of gut microbiota. Thus, this work provides evidence for the further development and utilization of P. cyrtonema with fermentation, and reveals the potential values of BNP in the treatment of intestinal disorders.
... The ASVs that grouped into UMGS1375 were a close match (97 %-99 % identity) to Hominisplanchenecus faecis, a genus that was only very recently isolated using an automated high-throughput approach 37 but not yet characterized. The characteristic genera for RD, Acutalibacter and Eisenbergiella, have been observed in gut microbiomes 38,39 though their role has remained unclear so far, and Clostridium_A (e.g. C. leptum/Cluster IV) has been a group of interest for over a decade 32,40 . The NicheMap™ thus offers an approach to phenotypically attribute function to these ubiquitous yet elusive gut bacteria. ...
Microbiomes are an essential contributor to the metabolic activity in the human gastrointestinal tract. The fermentation of otherwise indigestible nutritional components like dietary fibers relies on a complex interplay of metabolic pathways that are distributed across the individual bacteria. Yet, which of the bacteria are responsible for which parts of the distributed metabolism and how they should be grouped together is insufficiently understood. Here, we present the NicheMap(TM), an approach to map the different bacterial taxa that make up the gut microbiome onto the different functional niches of microbial carbohydrate fermentation. Our approach uses in vitro measurements of bacterial growth and metabolic activity to identify which bacterial taxa are responsible for which metabolic function in the relevant complex context of whole human fecal microbiomes. We identified 'characteristic taxa' selected for by a panel growth substrates representative of dietary components that are resistant to digestion by host enzymes. These characteristic taxa offer predictions of which bacteria are stimulated by the various components of human diet. We validated these predictions using microbiome data from a human nutritional supplementation study. We suggest a template of how bacterial taxonomic diversity is organized along the trophic cascade of intestinal carbohydrate fermentation. We anticipate that our results and our approach will provide a key contribution towards building a structure-function map for gut microbiomes. Having such a map on hand is an important step in moving the microbiome from a descriptive science to an interventional one.
... In this study, mainly strong negative correlations were identified between fecal bacterial ASV and Neff and in general these ASV belonged to the class Clostridia. Microbes within the Clostridia taxon are obligate anaerobes that commonly reside within the gastrointestinal tract of farm animals and can ferment plant polysaccharides 40 . However, multiple species can produce toxins causing enteric diseases 41 . ...
Abstract Nitrogen efficiency (Neff; milk N/N intake) in dairy cows is limited and most of the consumed N is excreted in manure. Despite the crucial role of the gastrointestinal microbiome on N metabolism, associations between bacterial communities at different sections and Neff are not fully elucidated. Enhanced understanding of host-microbiome interactions can provide insights to improve Neff in dairy cows. Twenty-three Holstein cows were selected, and their Neff were determined using a N balance approach. From the cohort of cows, six cows were classified as low Neff and five cows as high Neff and their rumen and fecal bacterial communities were profiled using amplicon sequence variants (ASV) based on 16S rRNA gene sequencing. Then, relationships between differentially abundant bacterial features and Neff were evaluated. Neff in low and high cows averaged 22.8 and 30.3%, respectively. With similar N intake, high Neff cows wasted less N in manure compared to low Neff cows (P
... Bacteroides are beneficial bacteria that constitute a significant proportion of the mammalian gastrointestinal microbiome, are associated with diets with a considerable content of protein and animal fat, and have been suggested to halt the progression of obesity-related metabolic phenotypes [33], whereas the genera Lactobacillus and Lactococcus include well-studied probiotic bacteria found in a variety of mammals [34]. Lachnospiraceae occupy a substantial portion of the gastrointestinal microbiota of ruminants, as they metabolize a number of plant polysaccharides [35]. Therefore, they are expected to be more abundant in the lean-diet group than in those fed an HFD supplemented with protein hydrolysates of animal origin ( Figure 5B). ...
Obesity and type 2 diabetes are characterized by low-grade systemic inflammation and glucose intolerance, which can be partially controlled with nutritional interventions. Protein-containing nutritional supplements possess health-promoting benefits. Herein, we examined the effect of dietary supplementation with protein hydrolysates derived from fish sidestreams on obesity and diabetes, utilizing a mouse model of High-Fat Diet-induced obesity and type 2 diabetes. We examined the effect of protein hydrolysates from salmon and mackerel backbone (HSB and HMB, respectively), salmon and mackerel heads (HSH and HMH, respectively), and fish collagen. The results showed that none of the dietary supplements affected weight gain, but HSH partially suppressed glucose intolerance, while HMB and HMH suppressed leptin increase in the adipose tissue. We further analyzed the gut microbiome, which contributes to the metabolic disease implicated in the development of type 2 diabetes, and found that supplementation with selected protein hydrolysates resulted in distinct changes in gut microbiome composition. The most prominent changes occurred when the diet was supplemented with fish collagen since it increased the abundance of beneficial bacteria and restricted the presence of harmful ones. Overall, the results suggest that protein hydrolysates derived from fish sidestreams can be utilized as dietary supplements with significant health benefits in the context of type 2 diabetes and diet-induced changes in the gut microbiome.
... The relative abundance of Verrucomicrobia displayed a unimodal pattern with soil depth, which might be due to their preference for microaerobic rather than fully aerobic or anaerobic environments [39]. SB-34, an anaerobic class [43] belonging to Chloroflexi, peaked in subsoils, which is consistent with other reports [44,45]. ...
... Sedimentibacter and Tissierellaceae, belonging to Firmicutes which are the predominant C cyclers in the deep soil rhizosphere [46], were abundant in the 30~50 cm soil depth. They are classified as Clostridia, which use fermentative metabolism [43]. Crenarchaeota were the most abundant (14%) bacteria in the deepest soil depth, which is consistent with previous studies [8,47,48]. ...
Soil bacterial and fungal communities play different roles in maintaining the ecosystem structure and functions. However, these differences, which are related to soil depths, remain unclear and are the subject of this study. We selected six sample plots (20 m × 50 m) in a natural Picea crassifolia forest in an alpine meadow to determine the vertical patterns (0~10 cm, 10~20 cm, 20~30 cm, and 30~50 cm) of soil bacterial and fungal communities, and to predict their potential functions. The phyla Verrucomicrobia, Acidobacteria, and Proteobacteria dominated the soil bacteria, with more than 50% of the relative abundance, while the fungi Basidiomycota and Ascomycota dominated the soil fungi. The potential functions of bacteria, including metabolism and transcription, increased with soil depth, and corresponded to specific bacterial taxa. The functional guilds of fungi, including endophytes, arbuscular mycorrhiza, and ectomycorrhiza, did not change with soil depth. The structural equation modeling analysis revealed that soil organic carbon (SOC) and pH were the key drivers shaping the soil bacterial communities and potential functions in the 0–50 cm soil layer. SOC was also a key driver of soil fungal α diversity. The sample plot, namely, its geographic locations, was another key driver shaping soil fungal β diversity and potential functions, but soil depth was not. Our results differentiate the importance of SOC and geographic location in shaping soil bacterial and fungal communities, respectively, and indicate that examining soil microbial composition and corresponding functions concomitantly is important for the maintenance and management of forest ecosystem functions.
