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 of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.

Highlights

  • The California condor (Gymnogyps californianus) is a species that dramatically declined during the 20th century from poaching, lead poisoning, and changes in habitat [1]

  • Twenty species of bacteria comprised 89% of the bacterial identifications in the captive healthy California condor microbiomes (Table 1). All of these bacteria had previously been associated with birds and/or gut microbiomes (For example, see Ballou 2016, Larsen 2015, Prabhakar 2012, Vela 2015, and Vital 2014)

  • Condor DNA contains a much smaller fraction of coding DNA than bacteria, and has a smaller fraction of reads that were recognized by the peptide signatures in Sequedex

Read more

Summary

Introduction

The California condor (Gymnogyps californianus) is a species that dramatically declined during the 20th century from poaching, lead poisoning, and changes in habitat [1]. In 1987, the last remaining individuals were captured from the wild to take part in a breeding program. This breeding program was successful, and in 1992 a small number of condors were. California condor microbiomes com/lanl/sequedex-core, while an executable release, complete with data modules, is available at https://github.com/Sequedex/Sequedex-build/ releases/tag/v2.r20181211. Documentation for the sequedex package is available at https://sequedex. Documentation for the sequedex package is available at https://sequedex. readthedocs.io/en/latest/

Objectives
Methods
Results
Discussion
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call