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Gut Microbe Patterns Hold Clues For Studying Microbiome

NEW YORK (GenomeWeb News) – Looking at the variation in gut microbial communities within a larger ecological context has implications not only for understanding bugs in the gut but also for informing large-scale studies such as the Human Microbiome Project, a new analysis suggests.
By compiling published data on hundreds of microbial samples, a team of American researchers surveyed gut bacterial communities from a variety of animals and environments, comparing them with free-living communities. Their analysis, appearing online today in Nature Reviews Microbiology, suggests that diet, host morphology, and phylogeny all influence gut microbe community composition. Overall though, the work suggests gut bacterial communities, while variable, are distinct from free-living bacterial communities.
The analysis also illustrates the power of using broad and comparative studies to understand microbes within the biosphere — an approach that the authors say will benefit large-scale studies such as the Human Microbiome Project.
“We wanted to place the inter-personal variation in gut microbial ecology into a broader context,” senior author Jeffrey Gordon, director of Washington University School of Medicine’s Center for Genome Sciences, told GenomeWeb Daily News.
Microbial communities can influence, and are influenced by, their habitats and the biosphere as a whole. And as researchers struggle to get a handle on the microbial communities in diverse habitats — from bugs found in extreme natural environments to those in and on the human body — their focus is shifting from simply identifying organisms to understanding microbial patterns more broadly.
For this analysis, Gordon and his team amalgamated a large collection of published 16S rRNA sequence representing microbial communities from human, mammal, and other animal guts as well as free-living microbial communities.
“Comparing the human gut microbiota and microbiome ... with those of other primates and mammals could, in principle, reveal if there is a core set of gut microbial genes and organismal lineages that are shared by most, if not all, humans,” he and his colleagues wrote.
When they compared bacterial sequences from hundreds of samples, they found that bacterial communities could be compartmentalized many ways. For instance, despite inter-human variability, the bacterial communities in human fecal samples were more similar to each other than to other mammals. Similarly, communities in vertebrate guts were more similar than those in invertebrate guts. And, even more broadly, animal gut communities resembled each other more than they did free-living communities.
Even so, within the gut samples, factors such as diet, gut morphology, and host phylogeny all appear to affect microbial community composition to varying degrees.
This sort of analysis may continue proving useful as researchers gather more and more information about the microbial world. With the cost of sequencing dropping, the number of samples that can be processed increasing, and analytical tools improving, Gordon said, researchers have a unique opportunity to understand microbial ecology in all its diversity using deep sampling and metagenomics.
But that will require great sampling depth and breadth, he added, using broad sampling to look at many different habitats. The gut, for example, appears to be an environment containing many microhabitats, each their own microbial assemblies that may vary with time and between individuals.
And researchers working on the Human Microbiome Project and other microbial studies are coming up with newer and better ways to understand the spatial and temporal stability of these communities, the forces that shape them, and their place in a broader biosphere. By thinking of microbial communities broadly and from an ecological perspective, the authors noted, they will likely learn not only about microbes but also about the evolutionary history of the biosphere.
“This evolutionary ecology perspective helps put the recently initiated international Human Microbiome Project in the context of the biosphere within which humans and their microorganisms have evolved,” the authors wrote.
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