Gut microbiome community profiling of Bornean bats with different feeding guilds

Muhd Amsyari, Morni and Julius, William-Dee and Emy Ritta, Jinggong and Nor Al-Shuhada, Sabaruddin and Nur Afiqah Aqilah, Azhar and Muhammad Amin Iman, Azmi and Peter A., Larsen, and Jaya Seelan, Sathiya Seelan and Lesley Maurice, Bilung and Faisal Ali, Anwarali Khan (2025) Gut microbiome community profiling of Bornean bats with different feeding guilds. Animal Microbiome, 7 (21). pp. 1-12. ISSN 2524-4671

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Abstract

Bats are extraordinary mammals. They have evolved to consume various dietary sources, such as insects, fruits, nectar, blood, and meat. This diversity has generated considerable interest in the scientific community, resulting in efforts to leverage bats as model organisms to study the correlation between diet and gut microbiome community. Although such studies now commonly use Next Generation Sequencing (NGS), similar studies are early in their development in Southeast Asia, especially in Malaysia, which harbours an incredibly diverse bat fauna. This study provides pioneering NGS metabarcoding information on Bornean bats. By using a high-throughput Nanopore-based 16S rRNA gene sequencing method, Bacillota, Pseudomonadota, and Campylobacterota were found in insectivorous bats and phytophagous bats. Both nsectivorous and phytophagous groups harboured no dominant taxon (D=0.076; D=0.085). A comparative analysis of gut bacteria functional groups identified eight major groups in both phytophagous and insectivorous bats, with fermentation being the predominant group. The correlation network analysis revealed a negative correlation between the ‘good bacteria’ Lactobacillus and various pathogenic bacteria genera, such as Salmonella (-0.4124) and Yersinia (-0.4654), demonstrating its prebiotic characteristics. This study broadens our understanding of the bat gut microbiome from various diets, with emphasis on new data from Borneo

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