Zoo elephant metagenomic Kraken2 reports

Non-invasive biological samples benefit studies that investigate rare,
elusive, endangered, and/or dangerous species. Integrating genomic
techniques that use non-invasive biological sampling with advances in
computational approaches can benefit and inform wildlife conservation and
management. We use non-invasive fecal DNA samples to generate low- to
medium-coverage genomes (e.g., >90% of the complete nuclear genome
at 6 X-fold coverage) and metagenomic sequences, combining widely
available and accessible DNA collection cards with commonly used DNA
extraction and library-building approaches. DNA preservation cards are
easy to transport and can be stored non-refrigerated, avoiding cumbersome
and/or costly sample methods. The genomic library construction and shotgun
sequencing approach did not require enrichment or targeted DNA
amplification. The utility and potential of the generated data generated
were demonstrated through genome-scale analysis and metagenomics of zoo
and free-ranging African savanna elephants (Loxodonta africana). Fecal
samples collected from free-ranging individuals contained an average of
12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these
elephants with others from the same geographic region was demonstrated by
principal component analysis of genetic variation using nuclear
genome-wide SNPs. Metagenomic analyses generated compositional taxon
classifications that included Loxodonta, green plants, fungi, arthropods,
bacteria, viruses, and archaea, showcasing the utility of this approach
for addressing complementary questions based on host-associated DNA, e.g.,
pathogen and parasite identification. The molecular and bioinformatic
analyses presented here contribute towards the expansion and application
of genomic techniques to conservation science and practice.