California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals
| Autor: | Jonathan L. Longmire, Andrew W. Bartlow, Jeanne M. Fair, Judith D. Cohn, Joel Berendzen, Benjamin H. McMahon, Marti Jenkins, Lindsey Jacobs, Momchilo Vuyisich, Cheryl D. Gleasner, Nicolas W. Hengartner |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Molecular biology
DNA cloning Animal Phylogenetics Bird Genomics Biochemistry Polymerases Data Management education.field_of_study Multidisciplinary biology Phylogenetic tree Shotgun sequencing food and beverages Eukaryota Phylogenetic Analysis Genomics Phylogenetics Medical Microbiology RNA polymerase Vertebrates Medicine Research Article Computer and Information Sciences Science Population Zoology Microbial Genomics Research and Analysis Methods Microbiology Birds Fusobacterium mortiferum DNA-binding proteins Genetics Animals Evolutionary Systematics education Molecular Biology Techniques Sequencing Techniques Feces Lactobacillus johnsonii Taxonomy Shotgun Sequencing Evolutionary Biology Biology and life sciences Organisms Proteins 16S ribosomal RNA biology.organism_classification Metagenomics Animal Genomics Amniotes Microbiome Cloning |
| Zdroj: | PLoS ONE PLoS ONE, Vol 14, Iss 12, p e0225858 (2019) |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
| Nepřihlášeným uživatelům se plný text nezobrazuje | K zobrazení výsledku je třeba se přihlásit. |