Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

Qu, Ani, Brulc, Jennifer M., Wilson, Melissa K., Law, Bibiana F., Theoret, James R., Joens, Lynn A., Konkel, Michael E., Angly, Florent, Dinsdale, Elizabeth A., Edwards, Robert A., Nelson, Karen E. and White, Bryan A. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One, 3 8: e2945 - 1-e2945 - 19. doi:10.1371/journal.pone.0002945

Author Qu, Ani
Brulc, Jennifer M.
Wilson, Melissa K.
Law, Bibiana F.
Theoret, James R.
Joens, Lynn A.
Konkel, Michael E.
Angly, Florent
Dinsdale, Elizabeth A.
Edwards, Robert A.
Nelson, Karen E.
White, Bryan A.
Title Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2008-08
Sub-type Article (original research)
DOI 10.1371/journal.pone.0002945
Open Access Status DOI
Volume 3
Issue 8
Start page e2945 - 1
End page e2945 - 19
Total pages 19
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
Abstract Background The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni. Methodology/Principal Findings Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families. Conclusion/Significance This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 100 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 105 times in Scopus Article | Citations
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Created: Mon, 21 Feb 2011, 14:31:02 EST