Development of the Human Gastrointestinal Microbiota and Insights From High-Throughput Sequencing

Department of Biology, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico.
Gastroenterology (Impact Factor: 16.72). 05/2011; 140(6):1713-9. DOI: 10.1053/j.gastro.2011.02.011
Source: PubMed


Little was known about the development of the gastrointestinal (GI) tract microbiota, until recently, because of difficulties in obtaining sufficient sequence information from enough people or time points. Now, with decreased costs of DNA sequencing and improved bioinformatic tools, we can compare GI tract bacterial communities among individuals, of all ages from infancy to adulthood. Some key recent findings are that the initial bacterial community, even in the GI tract, depends strongly on delivery mode; that the process of early development of the microbiota is highly unstable and idiosyncratic; that the microbiota differs considerably among children from different countries; and that older adults have substantially different GI tract communities than younger adults, indicating that the GI tract microbiota can change throughout life. We relate these observations to different models of evolution including the evolution of senescence and suggest that probiotics be selected based on patient age. Studies of the microbiota in older people might tell us which probiotics could increase longevity. Drug metabolism varies among individuals with different microbial communities, so age- and region-specific clinical trials are required to ensure safety and efficacy.

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    • "In the gastrointestinal tract, there are greater densities of bacterial species, which are also known as intestinal flora, and the common bacterial divisions are Firmicutes, Bacteroidetes, Actinobacteria , Proteobacteria, and Verrucomicrobia [23] [24]. To date, increasing data have reported massive diversity of bacterial species and Bacteroidetes and Firmicutes are referred to be the dominant bacterial groups in the gut [25]. Recently, evidence has demonstrated that gut microbiota are involved in the pathogenesis and etiology of IBD, reinforcing the view that interactions between intestinal microbes and the mucosal immune system promote the progression of IBD [26] [27]. "
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    ABSTRACT: Objectives: Interactions between the host and gut microbial community contribute to the pathogenesis of Crohn's disease (CD). In this study, we aimed to detect lipopolysaccharide (LPS) and 1,3-β-D-glucan (BG) in the sera of CD patients and clarify the potential role in the diagnosis and therapeutic approaches. Materials and methods: Serum samples were collected from 46 patients with active CD (A-CD), 22 CD patients at remission stage (R-CD), and 20 healthy controls, and the levels of LPS, BG, and TNF in sera were determined by ELISA. Moreover, sixteen patients with A-CD received anti-TNF monoclonal antibody therapy (infliximab, IFX) at a dose of 5 mg/kg body weight at weeks 0, 2, and 6, and the levels of LPS and BG were also tested at week 12 after the first intravenous infusion. Results: Serum levels of LPS and BG were found to be markedly increased in A-CD patients compared with R-CD patients and healthy controls (P < 0.05). They were also observed to be positively correlated with CDAI, ESR, and SES-CD, respectively (P < 0.05). Furthermore, the levels of TNF in sera had a significant correlation with LPS and BG, respectively. The concentrations of LPS and BG were demonstrated to be significantly downregulated in the sera of A-CD patients 12 weeks after IFX treatment (P < 0.05), suggesting that blockade of TNF could inhibit bacterial endotoxin absorption, partially through improving intestinal mucosal barrier. Conclusions: Serum levels of LPS and BG are significantly increased in A-CD patients and positively correlated with the severity of the disease. Blockade of intestinal mucosal inflammation with IFX could reduce the levels of LPS and BG in sera. Therefore, this study has shed some light on measurement of serum LPS and BG in the diagnosis and treatment of CD patients.
    Mediators of Inflammation 06/2015; 2015:1-9. DOI:10.1155/2015/843089 · 3.24 Impact Factor
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    • "It is known that colonization initiates from maternally acquired bacteria during birth [6] and breastfeeding and continues throughout our life [7] [8] [9]. Over the lifetime of the individual, or at least until stabilization of colonizing microbiota in adulthood, there is a change in the profile of the predominant phyla in the gastrointestinal tract, migrating from a community dominated by Actinobacteria and Proteobacteria to one dominated by Firmicutes and Bacteroidetes [10]. The metagenome of an infant gut is characterized by an enrichment of genes required for the breakdown of simple sugars, such as lactose and galactose, while the weaned infant microbiota is enriched in genes for polysaccharide breakdown and vitamin production [11] [12]. "
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    ABSTRACT: The commensal microbiota is in constant interaction with the immune system, teaching immune cells to respond to antigens. Studies in mice have demonstrated that manipulation of the intestinal microbiota alters host immune cell homeostasis. Additionally, metagenomic-sequencing analysis has revealed alterations in intestinal microbiota in patients suffering from inflammatory bowel disease, asthma, and obesity. Perturbations in the microbiota composition result in a deficient immune response and impaired tolerance to commensal microorganisms. Due to altered microbiota composition which is associated to some inflammatory diseases, several strategies, such as the administration of probiotics, diet, and antibiotic usage, have been utilized to prevent or ameliorate chronic inflammatory diseases. The purpose of this review is to present and discuss recent evidence showing that the gut microbiota controls immune system function and onset, development, and resolution of some common inflammatory diseases.
    Research Journal of Immunology 09/2014; 2014:689492. DOI:10.1155/2014/689492
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    • "Advances in molecular techniques have enabled detailed studies of microbial communities and the roles of " microbiomes " in human and animal health [Dominguez‐Bello et al., 2011; Shendure & Ji, 2008; Turnbaugh et al., 2007]. The microbiome concept considers the community of fungi, bacteria, bacteriophages , viruses, and protozoa that inhabit a host and play important roles in digestion, development [McFall‐Ngai, 2002], metabolic disorders [Turnbaugh et al., 2009], behavior [Ezenwa et al., 2012], and immune function [Round & Mazmanian, 2009]. "
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    ABSTRACT: Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate "microbiomes" remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance. Am. J. Primatol. © 2013 Wiley Periodicals, Inc.
    American Journal of Primatology 04/2014; 76(4). DOI:10.1002/ajp.22238 · 2.44 Impact Factor
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