Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments

The ISME Journal
Maureen BergMichael Shapira

Abstract

It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut...Continue Reading

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Citations

May 11, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Katja DierkingHinrich Schulenburg
May 11, 2016·BMC Biology·Laura C Clark, Jonathan Hodgkin
Apr 4, 2016·Trends in Ecology & Evolution·Michael Shapira
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Methods Mentioned

BETA
electron microscopy
PCR

Software Mentioned

R package bipartite
Greengenes
QIIME
uclust
R package phyloseq
CoNet
R package indicspecies
PERMANOVA
Cytoscape

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