California Condor Microbiomes

Abstract

We present a metagenomic analysis of California condor (Gymnogyps californianus) microbiomes with a goal of developing indicators of condor and ecosystem health. 16S ribosomal DNA (rDNA) and shotgun metagenomic DNA sequences were acquired from fecal and cloacal samples of captive birds. Detailed classification of shotgun DNA sequence data with the Sequedex analysis package provided both phylogenetic and functional profiles of all samples. We observed numerous 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, probiotics 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, but more specific than, analysis based on 16S data. Classification of samples based on functional profiles of genomic fragments differentiated three distinct types of samples: fecal, mature cloacal, and immature cloacal. Statistical analysis of the determinants of sample classification indicated that fecal samples were enriched in metabolism-related genes involved in glycolysis, methionine degradation, maltose utilization, and butyrate production, while cloacal samples were enriched in aromatic metabolism, virulence genes, and membrane transporters. Our analysis was further supported by the recovery of protein sequences for phylogenetic analysis, such as the RNA polymerase of Delftia, a Shigella toxin, a nitrate reductase of Delftia, and beta lactamases from several species. Our work identifies several strategies by which metagenomic sequencing of condor microbiomes may inform us about condor diet, infections, intoxication, and other types of stress.