Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes

Abstract

Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.

Characterization of the oral and faecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony

“…To investigate the microbiota, confounding factors should be considered in advance (Wang and LeCao 2020;Kurilshikov et al 2021). Various factors, including food and living environments, affect the gut microbiota (Wernimont et al 2020;Yarlagadda et al 2022). The dog breed also has an impact on the gut microbiota (Reddy et al 2019).…”

“…2020; Yarlagadda et al . 2022). The dog breed also has an impact on the gut microbiota (Reddy et al .…”

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

“…Fecal sample collection used DNA preservation cards, which have also been used previously for conservation genomic ( Régnier et al, 2011 ; Ward et al, 2019 ; Morrison et al, 2020 ) and microbiome research ( Song et al, 2016 ; Yarlagadda et al, 2022 ). We used Ahlstrom GenSaver 2.00™ cards, which are paper cards that have been treated with a chemical to minimize environmentally induced DNA degradation and the growth of microorganisms, allowing for collection, transport, and long-term preservation of DNA from biological samples at ambient temperature (Ahlstrom Corporation, Helsinki, Finland).…”

Non-invasive fecal DNA yields whole genome and metagenomic data for species conservation

“…The molecular pipeline used DNA preservation cards, which have also been used previously for conservation genomic (Régnier et al, 2011; Ward et al, 2019; Morrison et al, 2020) and microbiome research (Song et al, 2016; Yarlagadda et al, 2022). Preliminary testing compared two types of DNA preservation cards, the Whatman Flinders Technology Associates (FTA) card (Whatman plc, Maidstone, United Kingdom) and the Ahlstrom GenSaver 2.00™ card (GenTegra, Pleasanton, USA).…”

“…Genomic libraries were constructed using a tagmentation library building approach as part of the Illumina DNA Prep Kit (ThermoFisher Scientific, Waltham, USA) and using the protocol described by (Yarlagadda et al, 2022). Repeats two and three of one of the zoo individuals did not show evidence of successful DNA extraction based on Qubit quantitation and amplification of the shorter 500bp mitochondrial sequence.…”