Metagenomic biomarker discovery and explanation

Genome biology, Journal Year: 2011, Volume and Issue: 12(6)

Published: June 24, 2011

Abstract This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests biological consistency effect size estimation. addresses the challenge finding organisms, genes, or pathways that consistently explain differences between two more microbial communities, which is central problem to metagenomics. We extensively validate our on several microbiomes convenient online interface provided at http://huttenhower.sph.harvard.edu/lefse/ .

Language: Английский

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The gut microbiota shapes intestinal immune responses during health and disease

Nature reviews. Immunology, Journal Year: 2009, Volume and Issue: 9(5), P. 313 - 323

Published: April 3, 2009

Language: Английский

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Evolution of Mammals and Their Gut Microbes

Science, Journal Year: 2008, Volume and Issue: 320(5883), P. 1647 - 1651

Published: May 23, 2008

Mammals are metagenomic in that they composed of not only their own gene complements but also those all associated microbes. To understand the coevolution mammals and indigenous microbial communities, we conducted a network-based analysis bacterial 16S ribosomal RNA sequences from fecal microbiota humans 59 other mammalian species living two zoos wild. The results indicate host diet phylogeny both influence diversity, which increases carnivory to omnivory herbivory; communities codiversified with hosts; gut modern life-style is typical omnivorous primates.

Language: Английский

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Bacterial Community Variation in Human Body Habitats Across Space and Time

Science, Journal Year: 2009, Volume and Issue: 326(5960), P. 1694 - 1697

Published: Nov. 6, 2009

Growing on You The human gut and skin harbor diverse microbial communities that are known to vary strikingly among individuals. Here, Costello et al. (p. 1694 , published online 5 November) analyzed diversity several distinct body habitats (including the gut, mouth, inside ears nose, skin) of same person at different times. They found habitat had more influence community composition than temporal differences variation people. Some locations, such as index finger, back knee, sole foot, occasion harbored higher or oral cavity.

Language: Английский

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Interaction between microbiota and immunity in health and disease

Cell Research, Journal Year: 2020, Volume and Issue: 30(6), P. 492 - 506

Published: May 20, 2020

Abstract The interplay between the commensal microbiota and mammalian immune system development function includes multifold interactions in homeostasis disease. microbiome plays critical roles training of major components host’s innate adaptive system, while orchestrates maintenance key features host-microbe symbiosis. In a genetically susceptible host, imbalances microbiota-immunity under defined environmental contexts are believed to contribute pathogenesis multitude immune-mediated disorders. Here, we review microbiome-immunity crosstalk their health disease, providing examples molecular mechanisms orchestrating these intestine extra-intestinal organs. We highlight aspects current knowledge, challenges limitations achieving causal understanding host immune-microbiome interactions, as well impact on diseases, discuss how insights may translate towards future microbiome-targeted therapeutic interventions.

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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The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

PLoS Biology, Journal Year: 2008, Volume and Issue: 6(11), P. e280 - e280

Published: Nov. 14, 2008

The human intestinal microbiota is essential to the health of host and plays a role in nutrition, development, metabolism, pathogen resistance, regulation immune responses. Antibiotics may disrupt these coevolved interactions, leading acute or chronic disease some individuals. Our understanding antibiotic-associated disturbance has been limited by poor sensitivity, inadequate resolution, significant cost current research methods. use pyrosequencing technology generate large numbers 16S rDNA sequence tags circumvents limitations shown reveal previously unexplored aspects "rare biosphere." We investigated distal gut bacterial communities three healthy humans before after treatment with ciprofloxacin, obtaining more than 7,000 full-length rRNA sequences over 900,000 reads from two hypervariable regions gene. A companion paper PLoS Genetics (see Huse et al., doi: 10.1371/journal.pgen.1000255) shows that taxonomic information obtained methods concordant. Pyrosequencing V6 V3 variable identified 3,300-5,700 taxa collectively accounted for 99% region could be samples. Ciprofloxacin influenced abundance about third gut, decreasing richness, diversity, evenness community. However, magnitude this effect varied among individuals, showed interindividual variation response ciprofloxacin. While differences community composition between individuals were largest source variability samples, we found unrelated shared surprising degree similarity. In all closely resembled its pretreatment state 4 weeks end treatment, but several failed recover within 6 months. These pervasive effects ciprofloxacin on contrast reports participants normal function prior assumptions only modest microbiota. observations support hypothesis functional redundancy rapid return indicative factors promoting resilience, nature which deserves future investigation.

Language: Английский

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A microbial symbiosis factor prevents intestinal inflammatory disease

Nature, Journal Year: 2008, Volume and Issue: 453(7195), P. 620 - 625

Published: May 1, 2008

Language: Английский

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Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

Proceedings of the National Academy of Sciences, Journal Year: 2010, Volume and Issue: 108(supplement_1), P. 4554 - 4561

Published: Sept. 16, 2010

The indigenous human microbiota is essential to the health of host. Although can be affected by many features modern life, we know little about its responses disturbance, especially repeated disturbances, and how these changes compare with baseline temporal variation. We examined distal gut three individuals over 10 mo that spanned two courses antibiotic ciprofloxacin, analyzing more than 1.7 million bacterial 16S rRNA hypervariable region sequences from 52 56 samples per subject. Interindividual variation was major source variability between samples. Day-to-day evident but constrained around an average community composition stable several months in absence deliberate perturbation. effect ciprofloxacin on profound rapid, a loss diversity shift occurring within 3–4 d drug initiation. By 1 wk after end each course, communities began return their initial state, often incomplete. broadly similar, varied among subjects subjects. In all subjects, stabilized experiment altered state. As other ecosystems, microbiome at dynamic regimen Antibiotic perturbation may cause alternative full consequences which remain unknown.

Language: Английский

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Metabonomics

Nature, Journal Year: 2008, Volume and Issue: 455(7216), P. 1054 - 1056

Published: Oct. 1, 2008

Language: Английский

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