The gut microbiota in IBD

Manichanh, Chaysavanh; Borruel, Natalia; Casellas, Francesc; Guarner, Francisco

doi:10.1038/nrgastro.2012.152

Cited by 1,027 publications

(792 citation statements)

References 76 publications

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“…6 and 7). Inflammation of the digestive tract can disrupt the intestinal cell barrier, thereby increasing the oxygen level in the normally anaerobic intestine 42 and reducing species variety in the gut microbiome 43 . A high-fiber diet might protect against the depletion of positive microbe-microbe interactions caused by the presence of oxygen.…”

Section: Pairwise Interactions Of Modelsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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1 r e s o u r c eChanges in the composition of the human gut microbiota have been associated with the development of chronic diseases including type 2 diabetes, obesity, and colorectal cancer 1 . Gut bacterial functions, such as synthesis of amino acids and vitamins 2 , breakdown of indigestible plant polysaccharides 3 , and production of metabolites involved in energy metabolism 4 , have been linked to human health. The use of 'omics approaches to study human microbiome communities has led to the generation of enormous data sets whose interpretations require systems biology tools to shed light on the functional capacity of gut microbiomes and their interactions with the human host 5 .In order to infer the metabolic repertoire of a gut metagenome data set, researchers usually map sequenced genes or organisms onto metabolic networks derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 6 , and functional annotations from KEGG ontologies 7 . However, this approach cannot identify the contribution of each bacterial species to the metabolic repertoire of the whole gut microbiome, nor can it infer the effects of different gut microbial communities on host metabolism.A technique that can bridge this gap is constraint-based reconstruction and analysis (COBRA) 8 using genome-scale metabolic reconstructions (GENREs) of individual human gut microbes. GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results. The models can be used to investigate genotype-phenotype relationships 10 , microbe-microbe interactions 11 , and host-microbe interactions 11 . Numerous tools can be used to automatically generate draft GENREs but such models contain errors 12 and are incomplete.Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .To provide an extensive resource of GENREs for human gut microbes, we developed a comparative metabolic reconstruction method that enables any refinement to one metabolic reconstruction to be propagated to others. This accelerates reconstruction and improves model quality. We generated AGORA, which includes 773 gut microbes, comprising 205 genera and 605 species. All reconstructions were based on literature-derived experimental data and comparative genomics. The metabolic predictions of two AGORA reconstructions and their derived metabolic models were validated against experimental data. RESULTS Metabolic reconstruction pipelineWe devised a comparative metabolic reconstruction method (Fig. 1a,c), which is analogous to the comparative microbial genome annotation approach 13 that has enabled accelerated annotation by propagation of refinements to one genome to others. First, we downloaded draft GENREs using Model SEED 14 and KBase (US Department of Energy Systems Biology Knowledgebase, http:/...

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Section: Pairwise Interactions Of Modelsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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“…[3][4][5] Most IBD studies have focused on luminal/fecal bacteria, instead of bacterial communities adherent to the intestinal mucosa, 6,7 although the mucosal microbiota are in closer proximity to immune cells. 8 Although the luminal microbiota may simply be a numerical transformation of the mucosal microbiome, 9 comparisons of mucosal and fecal samples have shown that these 2 intestinal compartments have significantly different microbial communities.…”

Section: Introductionmentioning

confidence: 99%

Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation

et al. 2015

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The mucosal microbiota lives in close proximity with the intestinal epithelium and may interact more directly with the host immune system than the luminal/fecal bacteria. The availability of nutrients in the mucus layer of the epithelium is also very different from the gut lumen environment. Inferred metagenomic analysis for microbial function of the mucosal microbiota is possible by PICRUSt. We recently found that by using this approach, actively inflamed tissue of ulcerative colitis (UC) patients have mucosal communities enriched for genes involved in lipid and amino acid metabolism, and reduced for carbohydrate and nucleotide metabolism. Here, we find that the same bacterial taxa (e.g. Acinetobacter) and predicted microbial pathways enriched in actively inflamed colitis tissue are also enriched in the mucosa of subjects undergoing routine screening colonoscopies, when compared with paired samples of luminal/fecal bacteria. These results suggest that the mucosa of healthy individuals may be a reservoir of aerotolerant microbial communities expanded during colitis.

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“…Children with IBD have been reported to have an altered gut microbiome compared with those without the disease, although it is not known for certain if the altered microbiome is causative of the disease [60]. The association of dysbiosis, including abnormal microbiota and, in particular, a reduced complexity of the gut microbial ecosystem, appears to be a hallmark of IBD [61]. Gut microbiota are not the only microbial factor.…”

Section: The Infant Microbiome In Immune Development and Diseasementioning

confidence: 99%

Natural Childbirth and Breastfeeding as Preventive Measures of Immune- Microbiome Dysbiosis and Misregulated Inflammation

Dietert¹

2013

J Anc Dis Prev Rem

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Much of the prior century was spent applying the latest emerging technologies toward managing pregnancy, childbirth, and infant development. The idea was that each change was significantly improving the health of our children across their lifetime. But it is now clear that with several of the adopted practices, there have been unintended consequences. We have run the risk of losing certain distinct advantages that were inherently embedded in ancient cultures and practices. Among these were the microbial-rich experiences of natural childbirth, breastfeeding, and agrarian living. These practices permitted children to acquire a complete microbiome thereby facilitating immune development and appropriate later-life immune responses. Perceived technology-associated benefits such as scheduled Caesarian births, urban sanitized living, and earlier and ever increasing vaccine burdens have helped to reduce the burden of some childhood illnesses. But recent studies suggest that they have also produced serious, unanticipated consequences for today's children: an increased likelihood for human-microbiome incompleteness, lifelong immune dysfunction, and inflammation-promoted chronic disease. This review will examine recent evidence suggesting that a more effective blending of ancient practices and remedies with modern technology and medical knowledge could help to restore the human-microbiome super organism to its historic status, improve pediatric immune homeostasis and reduce risk of later-life chronic diseases.historic birth and infant feeding practices. As discussed by Wolf [4], there is an irony that early in the 20 th century public health officials were advocating increased breastfeeding by mothers and early in the 21 st century the same exact message has been repeated albeit with a different mix of reasons [4]. In the case of the 20 th century call for increased breastfeeding, the primary health concerns were for acute illnesses such as diarrheal diseases, pneumonia, and necrotizing colitis [4]. But for the more recent call, the preventative focus is larger and includes the prevention of noncommunicable chronic diseases (NCDs) [5]. This review considers: 1) shifting historic views regarding the value of natural childbirth and breastfeeding as preventive measures, and 2) an emerging paradigm in which natural childbirth (NC) and prolonged infant breastfeeding combine to reduce the risk of inflammation-driven chronic diseases via immune-microbiome co-maturation as well as other possible developmentally-programmed routes. Additionally, NC and breastfeeding are discussed under the broader human ecological framework of a developmental model in which effective humanmicrobe super organism formation between the child's mammalian component and symbiotic microbes that form the child's microbiome, termed the "Completed Self " [6]. Timely, complete and individualized formation of this symbiotic human mammalian-microbial organism or "Completed Self " has been suggested as perhaps the single most important biological sign con...

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The gut microbiota in IBD

Cited by 1,027 publications

References 76 publications

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation

Natural Childbirth and Breastfeeding as Preventive Measures of Immune- Microbiome Dysbiosis and Misregulated Inflammation

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