Moving pictures of the human microbiome

By J. Gregory Caporaso, C. Lauber, E. Costello, Donna berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer and 2 more. Genome Biology, 2011

1,133 citations recorded by the source corpus.

BackgroundUnderstanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.ResultsWe find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.ConclusionsDNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.

Subfields: Immunology, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/554f51f321757a69bd67607fac79076a054ef693

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Citations in the corpus

Host lifestyle affects human microbiota on daily timescales (2014, background): “We initially confirmed the general hypothesis that gut and saliva microbiota are usually stable [6,8,9,18].”
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Mathematical Modeling of Microbial Community Dynamics: A Methodological Review (2014, background): “Their complexity may range from dozens of “species” in extreme environments [8], to many hundreds (for example, on specific habitats on humans [9]) to tens of thousands per gram of soil [10].”
Conducting a Microbiome Study (2014, background): “However, within-subject diversity in one individual over time can approach the betweensubject diversity of many individuals at one time (Caporaso et al., 2011b).”
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Probiotics, gut microbiota, and their influence on host health and disease (2017, background): “However, its composition is highly variable between different individuals due to the strong influence that host and environmental factors exert on the gut microbial ecosystem, making it extremely difficult to establish a common “human core microbiome” [91].”
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome (2012, neutral): “, [6,20]), and sparse contingency tables are therefore becoming central data types in these studies.”