Identification of chicken-specific fecal microbial sequences using a metagenomic approach.

Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Research Abstract Details 

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Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Abstract Text:

Jingrang Lu,Jorge Santo Domingo,Orin C Shanks,

In this study, we applied a genome fragment enrichment (GFE) method to select for genomic regions that differ among different fecal metagenomes. Competitive DNA hybridizations were performed between chicken fecal DNA and pig fecal DNA (CP) and between chicken fecal DNA and an avian DNA composite consisting of turkey, goose, and seagull fecal DNA extracts (CB) to enrich for chicken-specific DNA fragments. A total of 471 non-redundant chicken metagenomic sequences were retrieved and analyzed. All of the clone sequences were similar to prokaryotic genes, of which more than 60% could not be assigned to previously characterized functional roles. In general terms, sequences assigned characterized functional roles were associated with cellular processes (11.7%), metabolism (11.0%) and information storage and processing (13.4%). Approximately 53% of the non-redundant sequences are similar to genes present in intestinal bacteria belonging to Clostridia (20.9%), Bacteroidetes (15.0%), and Bacilli (17.3%). Twenty-five sequences from the CP and CB clone libraries were selected to develop chicken fecal-specific PCR assays. These assays were challenged against fecal DNA extracted from 21 different animal species, including mammals and birds. The results from the host-specificity studies showed that 12 of the assays had a high degree of specificity to chicken feces. In addition, three assays were specific to chicken and turkey while another four assays tested positive to more than two avian species, suggesting a broader distribution of some of the enriched gene fragments among different avian fecal microbial communities. Fecal pollution signals were detected using chicken-specific assays in contaminated water samples, although the PCR assays showed different detection limits. These results indicate the need for multiple assays to detect poultry fecal sources of pollution. The competitive DNA hybridization approach used in this study can rapidly select for numerous chicken fecal metagenomic regions that can be used as potential genetic markers for fecal source tracking.

Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Publishing Authors By Initials

J Lu,J Santo Domingo,OC Shanks,

For similar biological phenomena, cell phenomena, and immunity: immunity: antibody specificity: species specificity research abstracts see: biological phenomena, cell phenomena, and immunity: immunity: antibody specificity: species specificity research

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Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Water research

VOLUME: 41

Page Numbers: 3561-74

Journal Abbreviation: Water Res.

ISSN: 0043-1354

DAY: 24

MONTH: 05

YEAR: 2007

Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Information

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LANGUAGE: eng

NlmUniqueID: 105072

Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Keywords Mesh Terms:

KEYWORDS: Species Specificity

MESH TERMS: methods

Chemical & Substance for Abstract: Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Information

Substance Name: Genetic Markers

Registry Number: 0

Grant and Affiliation Information for Identification of chicken-specific fecal microbial sequences using a metagenomic approach.

AFFILIATION: US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, MS-387, Cincinnati, OH, USA.

Country: England

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MEDLINETA: Water Res

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