Meta-analyses of studies of the human microbiota
Top Cited Papers
Open Access
- 16 July 2013
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 23 (10), 1704-1714
- https://doi.org/10.1101/gr.151803.112
Abstract
Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.Keywords
This publication has 50 references indexed in Scilit:
- Cohabiting family members share microbiota with one another and with their dogseLife, 2013
- Diversity, stability and resilience of the human gut microbiotaNature, 2012
- Host Remodeling of the Gut Microbiome and Metabolic Changes during PregnancyCell, 2012
- Structure, function and diversity of the healthy human microbiomeNature, 2012
- Human gut microbiome viewed across age and geographyNature, 2012
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaThe ISME Journal, 2011
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specificationsNature Biotechnology, 2011
- Gut flora metabolism of phosphatidylcholine promotes cardiovascular diseaseNature, 2011
- UniFrac: an effective distance metric for microbial community comparisonThe ISME Journal, 2010
- A core gut microbiome in obese and lean twinsNature, 2008