Gymnogyps californianus microbiome raw sequence reads

Detrimental impacts of human activity on biodiversity and ecosystem health have been measured in a variety of ways, yet we are still in dire need of more directly informative signatures which can be used not only to follow broad trends, but to rapidly inform return on investments in mitigative efforts.We present data evaluating the suitability of genomic sequencing of California condor microbiomes to provide indicators of both condor and ecosystem health. Both 16S ribosomal DNA (rDNA) and shotgun metagenomic DNA sequences were acquired. Numerous species have been previously observed to be associated with birds and microbiomes. These species include opportunistic pathogens and their near-neighbors, probiotics, and environmental microbes. Detailed classification of shotgun DNA sequence data with the Sequedex analysis package provided both phylogenetic and functional profiles of all samples. Phylogenetic classification using reads from phylogenetic marker genes was consistent with (but more specific than) analysis based on 16S data. Classification of samples based on the profile of SEED subsystems indicated three distinct types of samples: fecal, mature cloacal, and immature cloacal. Statistical analysis of the determinants of sample classification indicated niche determinants in metabolism, short-chain fatty acid production, virulence, and stress response pathways. This analysis was further supported by the recovery of protein sequence of niche-specific proteins. Our work provides strong support of the hypothesis that metagenomic sequencing of condor microbiomes can inform us on diet, infections, toxicity, and several types of stress.