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


Autoři: Lindsey Jacobs aff001;  Benjamin H. McMahon aff001;  Joel Berendzen aff002;  Jonathan Longmire aff001;  Cheryl Gleasner aff001;  Nicolas W. Hengartner aff001;  Momchilo Vuyisich aff003;  Judith R. Cohn aff001;  Marti Jenkins aff004;  Andrew W. Bartlow aff001;  Jeanne M. Fair aff001
Působiště autorů: Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America aff001;  GenerisBio, Santa Fe, New Mexico, United States of America aff002;  Viome, Los Alamos, New Mexico, United States of America aff003;  The Peregrine Fund, Boise, Idaho, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225858

Souhrn

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.

Klíčová slova:

Animal phylogenetics – Bird genomics – Birds – Metagenomics – Microbiome – Phylogenetic analysis – RNA polymerase – Shotgun sequencing


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Článek vyšel v časopise

PLOS One


2019 Číslo 12