Gut microbiome in healthy dogs and cats

Dissertação de Mestrado Integrado em Medicina VeterináriaRecent studies show that the gut microbiome contributes to the vital physiologic and immunologic processes and is influenced by external factors such as diet, environment, medical interventions, and disease states. In this study, we describe the gut microbiome of healthy dogs and cats, from households and shelters, contributing for a better understanding of the effect that environment can have on it. The samples were collected between 2016 and 2017 and consisted of a household group (N=38, N=26 dogs and N=12 cats) and a shelter group (N=62, N=51 dogs and N=11 cats). DNA extraction was done directly from the faeces and the V4 region of the 16S rRNA gene was amplified, followed by sequencing using Illumina MiSeq. Raw sequences were treated using QIIME2 and Greengenes database was chosen for taxonomic classification alignment at 99% similarity. SAS statistical software was used, a p-value < 0.05 was considered. The Principal Coordinate Analysis plot demonstrated that the feline and canine microbiomes were well separated, as well as the household dog samples and the shelter dog samples, meaning that there is a difference in the gut microbiome between these groups. The same conclusion was not observed for the cat samples. The phyla Firmicutes and Bacteroidetes were the predominant ones in both species. For the dog samples, there was no difference between the two groups in Firmicutes and Bacteroidetes phyla (p>0.05), but the phyla Fusobacteria and Proteobacteria were in higher percentages in the shelter group (p<0.05). To our knowledge, this is the first study that describes and compares the gut microbiome composition of healthy household and shelter dogs and cats. This study demonstrates that the environment where animals are born and grow, as well as the amount of contact they have with humans, may have a great influence in their gut microbiome.RESUMO - Microbioma entérico em cães e gatos saudáveis - Estudos recentes demonstram que o microbioma gastrointestinal tem um papel essencial nos processos fisiológicos e imunológicos do hospedeiro e que é fortemente influenciado pela dieta, ambiente, intervenções médicas e estados de doenças. Neste estudo pretendemos descrever o microbioma entérico de cães e gatos saudáveis provenientes de canis e de casas, contribuindo para uma melhor compreensão do efeito que o ambiente pode ter neste. As amostras foram colhidas entre 2016 e 2017 e consistiam num grupo de casa (N=38, N=26 cães e N=12 gatos) e um grupo de canil (N=62, N=51 cães e N=11 gatos). Foi realizada extração de DNA diretamente a partir das fezes e amplificada a região V4 do gene 16S rRNA, seguindo-se de sequenciação com Illumina MiSeq. As sequências foram tratadas usando o QIIME2 e a biblioteca Greengenes foi escolhida para classificação taxonómica, com o alinhamento a 99% de semelhança. Foi usado o SAS e considerado um p-value<0.05. O Principal Coordinate Analysis plot demonstrou que os microbiomas felino e canino são diferentes, assim como o microbioma de cães de casa e canil. No entanto, não foi possível chegar à mesma conclusão nas amostras de gato. Os phyla Firmicutes e Bacteroidetes foram os predominantes em ambas as espécies sendo que, nas amostras de cão, não houve uma diferença estatisticamente significativa entre os dois grupos para estes phyla (p>0.05). Os phyla Fusobacteria e Proteobacteria foram identificados com maior frequência nas amostras de canil, tendo sido esta diferença estatisticamente significativa (p