Structure, function and diversity of the healthy human microbiome

Nature, Journal Year: 2012, Volume and Issue: 486(7402), P. 207 - 214

Published: June 1, 2012

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in microbes occupy habitats such as gut, skin and vagina. Much this diversity remains unexplained, although diet, environment, host genetics early microbial exposure all been implicated. Accordingly, to characterize ecology human-associated communities, Human Microbiome Project has analysed largest cohort set distinct, clinically relevant body so far. We found abundance each habitat's signature vary widely among subjects, with strong niche specialization both within individuals. The project encountered an estimated 81–99% genera, enzyme families community configurations occupied by Western microbiome. Metagenomic carriage metabolic pathways was stable despite variation structure, ethnic/racial background proved be one strongest associations clinical metadata. These results thus delineate range structural functional normal communities a population, enabling future characterization epidemiology, translational applications Consortium reports first their analysis from cohort; insights into population lay foundations for exploration (HMP), supported National Institutes Health Common Fund, goal characterizing inhabit interact sickness health. In two Articles issue Nature, HMP presents population-scale details organismal composition microbiota across five areas body. An associated News & Views discusses initial — which, along those series co-publications, already constitute most extensive catalogue organisms genes related yet published highlights some major questions will tackle next few years.

Language: Английский

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CD-HIT: accelerated for clustering the next-generation sequencing data

Bioinformatics, Journal Year: 2012, Volume and Issue: 28(23), P. 3150 - 3152

Published: Oct. 11, 2012

CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other analyses. In response rapid increase in amount sequencing data produced by next-generation technologies, we have developed new accelerated with novel parallelization strategy some techniques allow efficient such datasets. Our tests demonstrated very good speedup derived from up ∼24 cores quasi-linear ∼8 cores. The enhanced capable handling large datasets much shorter time than previous versions.http://[email protected] are available at Bioinformatics online.

Language: Английский

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The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2014, Volume and Issue: 11(8), P. 506 - 514

Published: June 10, 2014

Probiotics are widely regarded as live microorganisms that, when administered in sufficient amounts, confer a health benefit, but guidance is needed on the most appropriate use of term. This Consensus Statement outlines recommendations for scope and definition term 'probiotic' determined by an expert panel convened International Scientific Association Prebiotics October 2013. An was 2013 (ISAPP) to discuss field probiotics. It now 13 years since probiotics 12 after guidelines were published regulators, scientists industry Food Agriculture Organization United Nations WHO (FAO/WHO). The FAO/WHO probiotic—"live which adequate amounts benefit host"—was reinforced relevant sufficiently accommodating current anticipated applications. However, inconsistencies between Expert Consultation Report Guidelines clarified take into account advances science A more precise will be useful guide clinicians consumers differentiating diverse products market. document represents conclusions ISAPP consensus meeting probiotic.

Language: Английский

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Human gut microbiome viewed across age and geography

Nature, Journal Year: 2012, Volume and Issue: 486(7402), P. 222 - 227

Published: May 8, 2012

Language: Английский

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Enterotypes of the human gut microbiome

Nature, Journal Year: 2011, Volume and Issue: 473(7346), P. 174 - 180

Published: April 19, 2011

Language: Английский

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Bioinformatics, Journal Year: 2015, Volume and Issue: 31(10), P. 1674 - 1676

Published: Jan. 20, 2015

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in time- cost-efficient manner. It finished soil dataset with 252 Gbps 44.1 99.6 h on single computing node without graphics processing unit, respectively. assembles the as whole, i.e. no pre-processing like partitioning normalization was needed. When compared previous methods data, generated three-time larger assembly, longer contig N50 average length; furthermore, 55.8% of reads were aligned to giving fourfold improvement.

Language: Английский

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A metagenome-wide association study of gut microbiota in type 2 diabetes

Nature, Journal Year: 2012, Volume and Issue: 490(7418), P. 55 - 60

Published: Sept. 25, 2012

Language: Английский

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Origins and Evolution of Antibiotic Resistance

Microbiology and Molecular Biology Reviews, Journal Year: 2010, Volume and Issue: 74(3), P. 417 - 433

Published: Aug. 30, 2010

SUMMARY Antibiotics have always been considered one of the wonder discoveries 20th century. This is true, but real rise antibiotic resistance in hospitals, communities, and environment concomitant with their use. The extraordinary genetic capacities microbes benefitted from man's overuse antibiotics to exploit every source genes means horizontal gene transmission develop multiple mechanisms for each introduced into practice clinically, agriculturally, or otherwise. review presents salient aspects development over past half-century, oft-restated conclusion that it time act. To achieve complete restitution therapeutic applications antibiotics, there a need more information on role environmental microbiomes resistance. In particular, creative approaches discovery novel expedited controlled introduction therapy are obligatory.

Language: Английский

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Proceedings of the National Academy of Sciences, Journal Year: 2010, Volume and Issue: 107(33), P. 14691 - 14696

Published: Aug. 2, 2010

Gut microbial composition depends on different dietary habits just as health metabolism, but the association of microbiota with diets in human populations has not yet been shown. In this work, we compared fecal European children (EU) and that from a rural African village Burkina Faso (BF), where diet, high fiber content, is similar to early settlements at time birth agriculture. By using high-throughput 16S rDNA sequencing biochemical analyses, found significant differences gut between two groups. BF showed enrichment Bacteroidetes depletion Firmicutes ( P < 0.001), unique abundance bacteria genus Prevotella Xylanibacter , known contain set bacterial genes for cellulose xylan hydrolysis, completely lacking EU children. addition, significantly more short-chain fatty acids 0.001) than Also, Enterobacteriaceae Shigella Escherichia) were underrepresented 0.05). We hypothesize coevolved polysaccharide-rich diet individuals, allowing them maximize energy intake fibers while also protecting inflammations noninfectious colonic diseases. This study investigates compares intestinal characterized by modern western indicating importance preserving treasure diversity ancient communities worldwide.

Language: Английский

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Diversity, stability and resilience of the human gut microbiota

Nature, Journal Year: 2012, Volume and Issue: 489(7415), P. 220 - 230

Published: Sept. 1, 2012

Language: Английский

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