Human and canine interactions shape the skin and fecal microbiome in an environment dependant manner

The present study observed the alterations in the skin and fecal microbiota of humans, dogs and wolves sharing the same environment. Skin swab samples and fecal samples of 16 wolves, 15 dogs, 12 human care takers and 12 pet dogs of the human care takers where collected and total genomic DNA was isolated using the DNeasy PowerSoil Kit (Quiagen, Hilden, Germany). Illumina MiSeq sequencing of the 16S rRNA gene variable region V4 was applied and bioinformatics processing was done with QIIME. Skin microbiota results: Humans have the least diverse skin microbiomes and pet dogs have the most diverse. Outdoor dogs and wolves have very similar levels of diversity. Pet dog skin is likely exposed to more varying environmental microbiomes. Humans and pet dogs cluster separately, while outdoor dogs and wolves cluster together. This is consistent with the levels of alpha diversity. This suggests that the environmental exposure is more important than group in terms of shaping the dog and wolf microbiome. Further, there are three humans that were originally classified as have close interactions with the animals that cluster more closely with the dogs and wolves. Wolf, Dog and Humans with close contact to the animals have microbiome that show higher proportions of Proteobacteria, Acidobacteria, Verrucomicrobioa, Cyanobacteria and Bacteroidetes. The proportions of Firmicutes and Actinobacteria are lower in these groups. This suggested that animal contact increases the ratio of gram negative to gram positive microorganisms on the skin, and the phylum level diversity. The relatively abundant ASVs that seemed to be shared between Humans with close animal contact and pet dogs are mostly from the Proteobacteria, Acidobacteria, Verrucomicrobioa and Cyanobacteria.Fecal microbiota results: Canine microbiota cluster together and human fecal microbiota cluster separately. Diet seems to have a stronger effect on shaping the microbial community compared with environment and contact to other species.