A human gut microbial gene catalogue established by metagenomic sequencing

Nature, Journal Year: 2010, Volume and Issue: 464(7285), P. 59 - 65

Published: March 1, 2010

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe Illumina-based metagenomic sequencing, assembly characterization 3.3 million non-redundant microbial genes, derived from 576.7 gigabases sequence, faecal samples 124 European individuals. The gene set, ∼150 times larger than complement, contains an overwhelming majority prevalent (more frequent) genes cohort probably includes a large proportion intestinal genes. are largely shared among individuals cohort. Over 99% bacterial, indicating that entire harbours between 1,000 1,150 bacterial species each individual at least 160 such species, which also shared. We define minimal metagenome genome in terms functions present all most bacteria, respectively. body plays host estimated 100 trillion cells, them where they have profound influence physiology nutrition — now regarded as for life. Gut contribute energy harvest food, changes microbiome may be associated with bowel diseases or obesity. Now international MetaHIT (Metagenomics Human Intestinal Tract) project has published catalogue healthy, overweight obese adults, well inflammatory disease patients, Denmark Spain. resulting data provide first insights into this set over 150 complement show Based variety encoded by possible both genome. Deep sequencing healthy individuals, those suffering disease, how much described.

Language: Английский

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Changes of Intestinal Functions in Liver Cirrhosis

Inflammatory Intestinal Diseases, Journal Year: 2016, Volume and Issue: 1(1), P. 24 - 40

Published: Jan. 1, 2016

<b><i>Background:</i></b> Understanding of the gut-liver axis is important for up-to-date management liver cirrhosis, and changes intestinal functions form core this interesting research field. <b><i>Summary:</i></b> Most investigators noted small dysmotility in their patients with cirrhosis. Marked contraction pattern were observed early manometric studies. The orocecal transit time, particularly transit, has generally been reported to be prolonged, which demonstrated multiple investigations related severity disease (e.g., Child-Pugh class), presence bacterial overgrowth (SIBO) hepatic encephalopathy (HE) as well a history spontaneous peritonitis. Bacteriologically proven SIBO proximal jejunal aspiration present up 59% cirrhotic associated systemic endotoxemia. Clinical experimental studies suggest that delayed bowel cirrhosis may lead SIBO, could contribute symptoms abdominal pain diarrhea. In addition autonomic neuropathy, metabolic derangements diabetic state, itself delay patients. Several studies, both from West East, have shown gut microbiota altered those HE. Further, quantitative change <i>Bacteroides/Firmicutes</i> ratio, prevalence potentially pathogenic bacteria <i>Enterobacteriaceae</i>) reduction specific commensals <i>Lachnospiraceae</i>), described. Structural functional mucosa increases permeability products considered an pathogenetic factor several complications. mechanism barrier dysfunction multifactorial, including alcohol, portal hypertension (vascular congestion dysregulation), endotoxemia, local inflammation and, most likely, immunological factors medications. <b><i>Key Messages:</i></b> This review summarizes major achievements regarding future gastroenterology research. question whether accompanied and/or at least partly caused by structural epithelial tight junction proteins yet unsolved. Development new strategies modulate interaction urgently needed.

Language: Английский

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Obesity alters gut microbial ecology

Proceedings of the National Academy of Sciences, Journal Year: 2005, Volume and Issue: 102(31), P. 11070 - 11075

Published: July 20, 2005

We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob / mice, lean /+ and wild-type siblings, their mothers, all fed same polysaccharide-rich diet. Although majority mouse gut species are unique, human microbiota(s) similar at division (superkingdom) level, with Firmicutes Bacteroidetes dominating. Microbial-community composition is inherited mothers. However, compared mice regardless kinship, animals a 50% reduction in abundance proportional increase Firmicutes. These changes, which division-wide, indicate that, this model, obesity affects diversity suggest that intentional manipulation community structure may be useful for regulating energy balance individuals.

Language: Английский

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Metagenomic Analysis of the Human Distal Gut Microbiome

Science, Journal Year: 2006, Volume and Issue: 312(5778), P. 1355 - 1359

Published: June 2, 2006

The human intestinal microbiota is composed of 10 13 to 14 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes our own genome. We analyzed ∼78 million base pairs unique DNA sequence and 2062 polymerase chain reaction–amplified 16 S ribosomal sequences obtained from the fecal DNAs two healthy adults. Using metabolic function analyses identified genes, we compared with average content previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism glycans, amino acids, xenobiotics; methanogenesis; 2-methyl- d -erythritol 4-phosphate pathway–mediated biosynthesis vitamins isoprenoids. Thus, humans are superorganisms represents an amalgamation attributes.

Language: Английский

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Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Proceedings of the National Academy of Sciences, Journal Year: 2007, Volume and Issue: 104(34), P. 13780 - 13785

Published: Aug. 16, 2007

The two primary human inflammatory bowel diseases, Crohn's disease (CD) and ulcerative colitis (UC), are idiopathic relapsing disorders characterized by chronic inflammation of the intestinal tract. Although several lines reasoning suggest that gastrointestinal (GI) microbes influence (IBD) pathogenesis, types involved have not been adequately described. Here we report results a culture-independent rRNA sequence analysis GI tissue samples obtained from CD UC patients, as well non-IBD controls. Specimens were through surgery variety sites included both pathologically normal abnormal states. Our provide comprehensive molecular-based microbiota small intestine. Comparison clone libraries reveals statistically significant differences between microbiotas patients those Significantly, our indicate subset contained microbiotas, depletion commensal bacteria, notably members phyla Firmicutes Bacteroidetes . Patient stratification provides further evidence represents spectrum states suggests treatment some forms IBD may be facilitated redress detected microbiological imbalances.

Language: Английский

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Cell, Journal Year: 2009, Volume and Issue: 139(3), P. 485 - 498

Published: Oct. 1, 2009

Language: Английский

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Introduction to the human gut microbiota

Biochemical Journal, Journal Year: 2017, Volume and Issue: 474(11), P. 1823 - 1836

Published: May 16, 2017

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert marked influence on host during homeostasis disease. Multiple factors contribute to establishment microbiota infancy. Diet is considered as one main drivers in shaping across life time. Intestinal bacteria play crucial role maintaining immune metabolic protecting against pathogens. Altered bacterial composition (dysbiosis) has been associated with pathogenesis many inflammatory diseases infections. interpretation these studies relies better understanding inter-individual variations, heterogeneity communities along GI tract, functional redundancy need distinguish cause from effect states dysbiosis. This review summarises our current development its impact integrity health, underlying for mechanistic focusing host–microbe interactions.

Language: Английский

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Role of the normal gut microbiota

World Journal of Gastroenterology, Journal Year: 2015, Volume and Issue: 21(29), P. 8787 - 8787

Published: Jan. 1, 2015

Relation between the gut microbiota and human health is being increasingly recognised.It now well established that a healthy flora largely responsible for overall of host.The normal comprises two major phyla, namely Bacteroidetes Firmicutes.Though in an infant appears haphazard, it starts resembling adult by age 3 years.Nevertheless, there exist temporal spatial variations microbial distribution from esophagus to rectum all along individual's life span.Developments genome sequencing technologies bioinformatics have enabled scientists study these microorganisms their function microbehost interactions elaborate manner both disease.The imparts specific host nutrient metabolism, xenobiotic drug maintenance structural integrity mucosal barrier, immunomodulation, protection against pathogens.Several factors play role shaping microbiota.They include (1) mode delivery (vaginal or caesarean); (2) diet during infancy (breast milk formula feeds) adulthood (vegan based meat based); (3) use antibiotics antibiotic like molecules are derived environment commensal community.A concern long-term alteration horizontal transfer resistance genes could result reservoir organisms with multidrug resistant gene pool.

Language: Английский

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Mechanisms underlying the resistance to diet-induced obesity in germ-free mice

Proceedings of the National Academy of Sciences, Journal Year: 2007, Volume and Issue: 104(3), P. 979 - 984

Published: Jan. 9, 2007

The trillions of microbes that colonize our adult intestines function collectively as a metabolic organ communicates with, and complements, own human apparatus. Given the worldwide epidemic in obesity, there is interest how interactions between microbial metabolomes may affect energy balance. Here we report that, contrast to mice with gut microbiota, germ-free (GF) animals are protected against obesity develops after consuming Western-style, high-fat, sugar-rich diet. Their persistently lean phenotype associated increased skeletal muscle liver levels phosphorylated AMP-activated protein kinase (AMPK) its downstream targets involved fatty acid oxidation (acetylCoA carboxylase; carnitine-palmitoyltransferase). Moreover, GF knockout lacking fasting-induced adipose factor (Fiaf), circulating lipoprotein lipase inhibitor whose expression normally selectively suppressed epithelium by not from diet-induced obesity. Although Fiaf-/- exhibit similar AMPK their wild-type littermates gastrocnemius muscle, they have reduced genes encoding peroxisomal proliferator-activated receptor coactivator (Pgc-1alpha) enzymes oxidation. Thus, two complementary but independent mechanisms result metabolism: (i) elevated Fiaf, which induces Pgc-1alpha; (ii) activity. Together, these findings support notion microbiota can influence both sides balance equation, underscore importance considering metabolome supraorganismal context.

Language: Английский

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The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Microbiology and Molecular Biology Reviews, Journal Year: 2015, Volume and Issue: 79(3), P. 293 - 320

Published: July 2, 2015

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, diversification. The increasing awareness of information on endophytes provide insight into the complexity microbiome. nature plant-endophyte interactions ranges from mutualism to pathogenicity. This depends a set abiotic biotic factors, including genotypes microbes, environmental conditions, dynamic network within biome. In this review, we address concept endophytism, considering latest insights evolution, ecosystem functioning, multipartite interactions.

Language: Английский

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