Full-length ITS1 Genes Amplicon Analysis of Gut Mycobiome Using Nanopore Flongle Sequencing Reveals Unique Fungal Communities between Indoor and Outdoor Felines in Malaysia

Abstract

The gut mycobiome exhibits major influence on the feline gastrointestinal health and disease but received less attention due to low microbial abundance. This study aims to characterise the fungal community and compare the microbial diversity between indoor and outdoor cats that devoured to different diets. The fecal samples used in this study were obtained from five indoor and five outdoor cats. Genomic DNA was extracted and sequenced by targeting the full-length internal transcribed spacer 1 (ITS1) region using Flongle flow cell on MinION™ sequencing platform. We discovered that the Ascomycota phylum and Peniophorella genus were numerous in indoor cats, whereas the Basidiomycota phyla and Pichia genus were abundant in outdoor cats. The genus Peniophorella formed the core mycobiome in both indoor and outdoor feline populations. Furthermore, alpha diversity (p-value = 0.0207) revealed that the fungal composition of outdoor cats had greater variety within the sample than that of indoor cats. The mycobiome composition differed significantly between the two groups, as demonstrated by beta diversity (p-value = 0.009) using the Bray-Curtis index distance technique. Overall, indoor cats have greater amounts of Peniophorella, whereas outdoor cats have higher Trichosporon and unclassified Sordariaceae. The study also suggests that keeping a cat indoors or left as a stray will affect their respective gut mycobiome.