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United States Department of Agriculture

Agricultural Research Service

Research Project: ANIMAL INTESTINAL MICROBIOMES, FOODBORNE PATHOGENS, AND ANTIMICROBIALS Title: Dynamic phages in the swine gut ecosystem

Authors
item Allen, Heather
item Looft, Torey
item Bayles, Darrell
item Alt, David
item Stanton, Thaddeus

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: July 12, 2013
Publication Date: July 22, 2013
Citation: Allen, H.K., Looft, T.P., Bayles, D.O., Alt, D.P., Stanton, T.B. 2013. Dynamic phages in the swine gut ecosystem [abstract]. Molecular Genetics of Bacteria and Phage Meeting. p. 94.

Technical Abstract: Phages are important drivers of ecosystem functions, yet they are often overlooked in gut microbiome studies. Inclusion of phages in gut microbiome analyses is essential to deciphering complex gut ecology under both normal and disturbed conditions. To assess the effect of antibiotics on phage activity, we have defined the lumenal and mucosal microbial communities from the swine small intestine (ileum) and large intestine (cecum and colon, plus feces) and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine, and penicillin [ASP250]). 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between the small and large intestines, including enrichment of Firmicutes and phage-encoding genes in the ileum. Assembly of the ileal metagenomes from non-medicated pigs was attempted. The high abundance of phage sequences yielded two partial phage genomes that were greater than 10 kilobases long with more than 10x coverage. One genome contains a putative DNA polymerase gene with 54 percent amino acid identity to that of a Lactobacillus phage, while the other genome encodes weak homologues of phage tail proteins from an unknown host. Ileal metagenomes from multiple pigs contributed proportionate numbers of sequences to the contigs, indicating that the phages were significant contributors to the swine ileal environment. Additionally, that these phages were assembled from whole-cell metagenomes suggests that they were actively being produced in the small intestine. To investigate the stability of the phages over time, phage metagenomes prepared from fecal samples collected up to three months prior to the ileal metagenomes were mapped onto the partial phage genomes. Over 200 reads mapped to each genome, suggesting the consistent production of these phages over time. The effect of in-feed antibiotics on fecal phages was also examined. Analysis of fecal phage metagenomes over time suggested that prophages were induced by antibiotic treatment. However, the two ileal phage genomes nearly disappeared from the ileal metagenomes after two weeks of antibiotic treatment, indicating that the bacterial hosts of these particular phages were likely inhibited by ASP250. The results emphasize the diversity and active role of phages in the gut ecosystem. Isolating phages from the intestinal tract will further define the functions and impact of phages on ecosystem functions.

Last Modified: 10/22/2014
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