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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF GENOMIC TOOLS TO STUDY RUMINANT RESISTANCE TO GASTROINTESTINAL NEMATODES

Location: Animal Genomics and Improvement Laboratory

Title: Sequences from the hypervariable V3-V5 regions of the 16S rRNA gene amplified from the porcine proximal colon

Authors
item LI, ROBERT
item Wu, Sitao -
item Li, Weizhong -
item Hill, Dustin
item URBAN, JOSEPH

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: June 15, 2012
Publication Date: June 21, 2012
Citation: Li, R.W., Wu, S., Li, W., Hill, D.C., Urban Jr, J.F. 2012. Sequences from the hypervariable V3-V5 regions of the 16S rRNA gene amplified from the porcine proximal colon . National Center for Biotechnology Information (NCBI). SRX065852.

Technical Abstract: Helminths, including GI nematodes, colonize > 1/3 of the world’s population and have evolved with humans and their microbiome. Parasites inherently regulate the host immune response to ensure their survival through mechanisms that dampen host inflammation. These unique properties of nematodes have been exploited therapeutically to treat several human diseases, including Crohn's and multiple sclerosis, in multi-center clinical trials. In order to understand the complex relations between the host, its microbiota, and parasite, we characterized the colon microbiota in response to parasite infection using whole genome shortgun (WGS) and the 16S rRNA gene approaches. 32 to 55K sequences per sample from 16S rDNA hypervariable V3-V5 regions were generated. Compared to uninfected controls, a 21-day T. suis infection in pigs induced a significant change in the colon microbiota composition. The abundance of Protobacteria and Spirochaetes were significantly reduced in infected pigs. Notably, reduced Succinivibrio abundance implied that T. suis altered the metabolic potential of the carbohydrates in the colon microbial ecosystem. Conversely, Mucispirillum, a bacterium colonizing the GI mucus, was significantly increased in infected pigs but absent from the microbiota of uninfected pigs suggesting that mucosal disruption induced by invading parasites altered the local ecological niche. However, the biodiversity in the microbiota, judged by indexes such as ACE and Chao1, was seemingly unchanged by infection. To gain insight into the functional shift associated with these alterations, we generated ~ 3.8 million WGS reads. ORFs were annotated against Pfam and KEGG databases, and the metabolic pathways affected were identified. Parasite-induced alterations in the gut micriobiota may have important physiological and pathological consequences.

Last Modified: 8/19/2014
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