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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Biology of Human Pathogens Associated with Food

Location: Produce Safety and Microbiology Research

Title: The microbiome structure and Campylobacter jejuni transcriptome in naturally-raised chickens

Authors
item Taveirne, Michael -
item Miller, William
item Parker, Craig
item Huynh, Steven
item Dirita, Victor -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 21, 2014
Publication Date: N/A

Interpretive Summary: The food-borne pathogen Campylobacter is a natural contaminant of most birds and livestock. Campylobacter jejuni, the leading cause of human, Campylobacter-related food-borne illness, is often isolated from chickens and chicken meat. Although this organism can cause sometimes severe illness in humans, it does not cause illness in chickens, even though it colonizes the chicken gut at very high levels. Very little is known of the changes in C. jejuni gene regulation that occur during colonization of poultry flocks as the organism moves from the environment into the chicken gut. Also, most experiments to date have used ‘pathogen-free’ birds as hosts, birds that do not have the other intestinal microorganisms that would be present within chickens raised on conventional poultry farms. These other microorganisms would be expected to influence the C. jejuni colonization process. This study analyzes gene expression of Campylobacters isolated from naturally-raised birds. While the majority of birds were infected with C. jejuni solely, some were infected both with C. jejuni and the related organism Campylobacter coli. As expected, the organisms present within naturally-raised birds were more diverse than the populations isolated from lab animals. The chromosomal sequences of a C. jejuni strain and a C. coli strain, isolated during this study, were solved and analyzed for the presence of unique genes.

Technical Abstract: Campylobacter jejuni is a leading cause of bacterially derived gastroenteritis in humans worldwide. C. jejuni regulates gene expression under various environmental conditions and stresses, indicative of its ability to survive in diverse niches. Few transcription factors have been identified, and the genome sequence does not predict many canonical regulators, thus the mechanisms underlying conditional gene expression are not well understood. Experiments using high throughput deep sequencing of mRNA transcripts (RNAseq), to identify differential transcript abundances from C. jejuni grown in vitro and in vivo, have relied on experimental colonization of specific pathogen free (SPF), laboratory-reared chickens. In contrast, little has been done to identify mechanisms of colonization in naturally-colonized chickens. To address this, we harvested cecal contents from Campylobacter positive farm-raised chickens and analyzed colonization load, Campylobacter speciation, structure of the microbiota, and transcriptome profile. Of 20 birds sampled, 13 were mono-colonized with C. jejuni while seven were co-colonized with C. jejuni and C. coli. With Illumina-based 16S sequencing, we determined the structure of the microbiome, showing it to be vastly richer than SPF, lab animals. Genome sequences of C. jejuni and C. coli isolates were determined to identify unique genes present in these animal isolates and to use for mapping transcripts for RNAseq transcriptome profiling.

Last Modified: 9/22/2014
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