Microbial community profiling for human microbiome projects: Tools, techniques, and challenges DOI Creative Commons

Micah Hamady,

Rob Knight

Genome Research, Journal Year: 2009, Volume and Issue: 19(7), P. 1141 - 1152

Published: April 21, 2009

High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental computational methods can be daunting. In this review, we discuss some different approaches to profiling, highlighting strengths weaknesses various approaches, methodologies, analytical methods. We also address one key question emerging from Human Microbiome Projects: Is there a substantial core abundant organisms or lineages that all share? It appears in human body habitats, such as hand gut, diversity among individuals is so great rule out possibility any species at high abundance individuals: possible focus should instead on higher-level taxa functional genes instead.

Language: Английский

Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota DOI Creative Commons
Chih‐Jung Chang,

Chuan-Sheng Lin,

Chia‐Chen Lu

et al.

Nature Communications, Journal Year: 2015, Volume and Issue: 6(1)

Published: June 23, 2015

Abstract Obesity is associated with low-grade chronic inflammation and intestinal dysbiosis. Ganoderma lucidum a medicinal mushroom used in traditional Chinese medicine putative anti-diabetic effects. Here, we show that water extract of mycelium (WEGL) reduces body weight, insulin resistance mice fed high-fat diet (HFD). Our data indicate WEGL not only reverses HFD-induced gut dysbiosis—as indicated by the decreased Firmicutes-to-Bacteroidetes ratios endotoxin-bearing Proteobacteria levels—but also maintains barrier integrity metabolic endotoxemia. The anti-obesity microbiota-modulating effects are transmissible via horizontal faeces transfer from WEGL-treated to HFD-fed mice. We further high molecular weight polysaccharides (>300 kDa) isolated produce similar results G. its may be as prebiotic agents prevent dysbiosis obesity-related disorders obese individuals.

Language: Английский

Citations

1118

Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes DOI Open Access
Katherine R. Amato, Carl J. Yeoman, Angela D. Kent

et al.

The ISME Journal, Journal Year: 2013, Volume and Issue: 7(7), P. 1344 - 1353

Published: March 14, 2013

Language: Английский

Citations

1117

The influence of sex, handedness, and washing on the diversity of hand surface bacteria DOI Open Access
Noah Fierer,

Micah Hamady,

Christian L. Lauber

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2008, Volume and Issue: 105(46), P. 17994 - 17999

Published: Nov. 13, 2008

Bacteria thrive on and within the human body. One of largest human-associated microbial habitats is skin surface, which harbors large numbers bacteria that can have important effects health. We examined palmar surfaces dominant nondominant hands 51 healthy young adult volunteers to characterize bacterial diversity assess its variability between individuals. used a novel pyrosequencing-based method allowed us survey hand surface communities at an unprecedented level detail. The skin-associated was surprisingly high; typical harbored >150 unique species-level phylotypes, we identified total 4,742 phylotypes across all examined. Although there core set taxa commonly found palm observed pronounced intra- interpersonal variation in community composition: from same individual shared only 17% their with different individuals sharing 13%. Women had significantly higher than men, composition affected by handedness, time since last washing, individual's sex. ecology illustrated this study emphasizes challenges inherent defining what constitutes "healthy" community; addressing these will be critical for International Human Microbiome Project.

Language: Английский

Citations

1081

Temporal and spatial variation of the human microbiota during pregnancy DOI Open Access

Daniel B. DiGiulio,

Benjamin J. Callahan, Paul J. McMurdie

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(35), P. 11060 - 11065

Published: Aug. 17, 2015

Significance The human indigenous microbial communities (microbiota) play critical roles in health and may be especially important for mother fetus during pregnancy. Using a case-control cohort of 40 women, we characterized weekly variation the vaginal, gut, oral microbiota after Microbiota membership remained relatively stable at each body site An altered vaginal community was associated with preterm birth; this finding corroborated by an analysis samples from additional nine women. We also discovered abrupt change delivery that persisted some cases least 1 y. Our findings suggest pregnancy outcomes might predicted features early gestation.

Language: Английский

Citations

1012

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges DOI Creative Commons

Micah Hamady,

Rob Knight

Genome Research, Journal Year: 2009, Volume and Issue: 19(7), P. 1141 - 1152

Published: April 21, 2009

High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental computational methods can be daunting. In this review, we discuss some different approaches to profiling, highlighting strengths weaknesses various approaches, methodologies, analytical methods. We also address one key question emerging from Human Microbiome Projects: Is there a substantial core abundant organisms or lineages that all share? It appears in human body habitats, such as hand gut, diversity among individuals is so great rule out possibility any species at high abundance individuals: possible focus should instead on higher-level taxa functional genes instead.

Language: Английский

Citations

955