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Title: California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals

Abstract

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types ofmore » samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.« less

Authors:
 [1];  [1];  [2];  [1];  [1]; ORCiD logo [1];  [3]; ORCiD logo [1];  [4]; ORCiD logo [1]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. GenerisBio, Santa Fe, NM (United States)
  3. Viome, Los Alamos, NM (United States)
  4. The Peregrine Fund, Boise, ID (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1597331
Report Number(s):
[LA-UR-17-26676]
[Journal ID: ISSN 1932-6203]
Grant/Contract Number:  
[89233218CNA000001]
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
[ Journal Volume: 14; Journal Issue: 12]; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science; Microbiome

Citation Formats

Jacobs, Lindsey Lydia, McMahon, Benjamin H., Berendzen, Joel, Longmire, Jonathan Lee, Gleasner, Cheryl, Hengartner, Nicolas W., Vuyisich, Momchilo, Cohn, Judith D., Jenkins, Marti, Bartlow, Andrew William, and Fair, Jeanne Marie. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals. United States: N. p., 2019. Web. doi:10.1371/journal.pone.0225858.
Jacobs, Lindsey Lydia, McMahon, Benjamin H., Berendzen, Joel, Longmire, Jonathan Lee, Gleasner, Cheryl, Hengartner, Nicolas W., Vuyisich, Momchilo, Cohn, Judith D., Jenkins, Marti, Bartlow, Andrew William, & Fair, Jeanne Marie. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals. United States. doi:10.1371/journal.pone.0225858.
Jacobs, Lindsey Lydia, McMahon, Benjamin H., Berendzen, Joel, Longmire, Jonathan Lee, Gleasner, Cheryl, Hengartner, Nicolas W., Vuyisich, Momchilo, Cohn, Judith D., Jenkins, Marti, Bartlow, Andrew William, and Fair, Jeanne Marie. Wed . "California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals". United States. doi:10.1371/journal.pone.0225858. https://www.osti.gov/servlets/purl/1597331.
@article{osti_1597331,
title = {California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals},
author = {Jacobs, Lindsey Lydia and McMahon, Benjamin H. and Berendzen, Joel and Longmire, Jonathan Lee and Gleasner, Cheryl and Hengartner, Nicolas W. and Vuyisich, Momchilo and Cohn, Judith D. and Jenkins, Marti and Bartlow, Andrew William and Fair, Jeanne Marie},
abstractNote = {Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.},
doi = {10.1371/journal.pone.0225858},
journal = {PLoS ONE},
number = [12],
volume = [14],
place = {United States},
year = {2019},
month = {12}
}

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