Human Gut Microbiome

Created: August 2016, updated: September 2016. 

Research papers on Western populations

Age and gender affect the composition of fungal population of the human gastrointestinal tract – Francesco Strati – Frontiers in Microbiology – August 2016

We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals.

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome – June 2016

We sought to increase the concentration of butyrate in 20 healthy young adults through dietary supplementation with resistant starch (unmodified potato starch—resistant starch (RS) type 2).

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe – May 2016

Here we report a 16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs, a subset of which was previously reported.

Population-level analysis of gut microbiome variation – Gwen Falony – Science – April 2016

Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (N = 1106) and the Dutch LifeLines-DEEP study (N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science – April 2016

Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors.

The influence of non-steroidal anti-inflammatory drugs on the gut microbiome – M.A.M. Rogers – Clinical Microbiology and Infection – Feb 2016

Drug use within the past 30 days was ascertained in 155 adults, and stool specimens were submitted for analysis.

Host lifestyle affects human microbiota on daily timescales – LA David, AC Materna, J Friedman, I Baptista, MC Blackburn, A Perrotta, SE Erdman, EJ Alm. – Genome Biol, 15:R89 – 2014.

Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months.

A human gut microbial gene catalog established by metagenomic sequencing – Junjie Qin, Ruiqiang Li, Jeroen Raes, et al. – Nature – 2013

Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million nonredundant microbial genes, derived from 576.7 Gb sequence, from faecal samples of 124 European individuals.

Diet rapidly and reproducibly alters the gut microbiome – LA David, CF Maurice, RN Carmody, DB Gootenberg, JE Button, BE Wolfe, AV Ling, AS Devlin, Y Varma, MA Fischbach, SB Biddinger, RJ Dutton, PJ Turnbaugh – Nature – 2013

Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression.

Human gut microbiome viewed across age and geography – Tanya Yatsunenko,  Federico E. Rey, Mark J. Manary, et al. – Nature – 2012

…we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes.

Structure, function and diversity of the healthy human microbiome – The Human Microbiome Project Consortium – Nature – 2012

Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far.

Moving pictures of the human microbiome – J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon and Rob Knight – Genome Biology – 2011

Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.

Enterotypes of the human gut microbiome – Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier et al. – Nature – 2011

By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa – Carlotta De Filippo, Duccio Cavalieri, Monica Di Paola, Matteo Ramazzotti, Jean Baptiste Poullet, Sebastien Massart, Silvia Collini, Giuseppe Pieraccini, and Paolo Lionetti – PNAS – 2010

In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture.

Towards the human intestinal microbiota phylogenetic core – Julien Tap, Stanislas Mondot, Florence Levenez, et al. – Environmental Microbiology – 2009

A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected.

Microbial ecology: Human gut microbes associated with obesity – Ruth E. Ley, Peter J. Turnbaugh, Samuel Klein & Jeffrey I. Gordon – Nature – 2006

Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet.

Diversity of the Human Intestinal Microbial Flora – Paul B. Eckburg, Elisabeth M. Bik, Charles N. Bernstein, Elizabeth Purdom, Les Dethlefsen, Michael Sargent et al.- Science – 2005

We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity.

Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis  – Georgina L. Hold, Susan E. Pryde, Valerie J. Russell, Elizabeth Furrie, Harry J. Flint – FEMS Microbiology Ecology – 2002

The bacterial species diversity of three colonic tissue samples from elderly people was investigated by sequence analysis of randomly cloned eubacterial 16S rDNA.

Research papers on non-Western populations

Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns – Andres Gomez – Cell Reports – March 2016

Gut bacterial diversity of the tribes of India and comparison with the worldwide data – Madhusmita Dehingia – Scientific Reports – December 2015

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota – Simone Rampelli – Current Biology – June 2015

The microbiome of uncontacted Amerindians – Jose C. Clemente – Sci Advances – April 2015

Gut microbiome of the Hadza hunter-gatherers – Stephanie L. Schnorr – Nature Communications – April 2014

To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls.

Human gut microbiome viewed across age and geography – Tanya Yatsunenko – Nature – 2012

To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins.

Review papers

The gut microbiota: A treasure for human health – Daotong Li – Biotechnology Advances – August 2016

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism – Peter Spanogiannopoulos – Nature Reviews Microbiology – March 2016

Beyond the Venn diagram: the hunt for a core microbiome – Ashley Shade – Environmental Microbiology – January 2012

Gut flora in health and disease – Francisco Guarner, Juan-R Malagelada – The Lancet – 2003

Microbial Ecology of the Gastrointestinal Tract – Dwayne C. Savage – Annual Review of Microbiology – 1977

Popular press