Preliminary assessment and metagenomic analysis of oral microbiota of the small Indian mongoose Herpestes auropunctatus through next-generation sequencing

  • R. Ajmal University of Veterinary and Animal Sciences
  • F. Imran University of Veterinary and Animal Sciences
  • A. Ayub University of Agriculture Faisalabad
  • A. Bilal University of Veterinary and Animal Sciences
  • M. Bilal University of Veterinary and Animal Sciences
  • K. Ali University of Education Lahore
  • S. Khan Quaid-i-Azam University
  • M. Hussain University of Veterinary and Animal Sciences
  • M. Masood University of Veterinary and Animal Sciences
DOI: https://doi.org/10.15421/0225010
Keywords: Escherichia coli, Stenotrophomonas, Fusobacterium, Bacillus.

Abstract

A total of 5 small Indian mongoose ( Herpestes auropunctatus (Hodgson, 1836)) specimens were captured to obtain oral swabs with all specimens being released after sampling. DNA extraction from oral swabs was done using the QIAamp DNA Microbiome and the 16S rRNA gene was amplified targeting variable region V1 to V8 (1350 bp). Next-generation sequen c ing (NGS) of PCR products was performed from Macrogen, Korea. A KORONA plot was constructed to visualize relative abundance of the top 10 bacterial taxa. The following bacterial phyla were identified; Proteobacteria (58.0%), Bacteroidetes (20.0%), Firmicutes (12.0%), Fusobacteria (7.0%), and Patescibacteria (2.0%). The dominant bacterial classes included Gammaproteobacteria (57.0%), Bacteroidia (20.0%), Bacilli (4.0%), and Alphaproteobacteria (0.8%). The prevalent bacter i al orders were Pseudomonadales (19.0%), Bacteroidales (10.0%), Flavobacteriales (9.0%), and Clostridiales (7.0%), with Fusobacteriales and Betaproteobacteriales each at 5.0%, and Lactobacillales, Absconditabacteriales, and Saccharimonadales at 4.0%, 1.0%, and 0.1%, respectively. The identified families and their relative abundances were Pasteurellaceae (29.0%), Weeksellaceae (5.0%), Neisseriaceae (4.0%), Peptostreptococcaceae (3.0%), with Erysipelotrichaceae, Leptotrichiaceae, and Enterobacteriaceae each at 2.0%, and Cardiobacteriaceae and Burkholderiaceae at 1.0% each. Other families included Xa n thomonadaceae (0.8%), Carnobacteriaceae (0.5%), and Streptococcaceae (0.2%). The genera identify ed were Pasteurella , Paracoccus , Escherichia , Shigella , Moraxella , Stenotrophomonas , Neisseria , Conchiformibius , Bergeyella , Capnocytoph a ga , Fusobacterium , Oceanivirga , Streptococcus , Bacillus , and Defluviitaleaceae. The identification of genera such as Pa s teurella , Neisseria , Eschrichia and Shigella warrants further investigation into their potential role as reservoirs of zoonotic pathogens especially given the mongoose's invasive nature, close contact with human and animal populations.

References

Bandeira, V., Virgós, E., Carvalho, J., Barros, T., Cunha, M. V., & Fonseca, C. (2018). Diet footprint of Egyptian mongoose along ecological gradients: Effects of primary productivity and life history traits. Mammalian Biology, 88(1), 16–25.

Barros, T., Carvalho, J., Pereira, M. J., Ferreira, J. P., & Fonseca, C. (2015). Following the trail: Factors underlying the sudden expansion of the Egyptian mongoose (Herpestes ichneumon) in Portugal. PLoS One, 10(8), e0133768.

Barun, A., Hanson, C. C., Campbell, K. J., & Simberloff, D. (2011). A review of small Indian mongoose management and eradications on islands. In: Veitch, C. R., Clout, M. N., & Towns, D. R. (Eds.). Island invasives: Eradication and management. IUCN, Gland. Pp. 17–25.

Berentsen, A. R., Pitt, W. C., & Sugihara, R. T. (2017). Ecology of the small Indian mongoose (Herpestes auropunctatus) in North America. In: Ecology and management of terrestrial vertebrate invasive species in the United States. CRC Press, Boca Raton. Pp. 251–268.

Bermingham, E. N., Young, W., Kittelmann, S., Kerr, K. R., Swanson, K. S., & Roy, N. C. (2013). Dietary format alters fecal bacterial populations in the domestic cat (Felis catus). Microbiology Open, 2, 173–181.

Bernal, R. C., Santín, M., Maloney, J. G., Martín-Perez, M., Habela, M. A., Fernandez-Garcia, J. L., Figueiredo, A., Najera, F., Palacios, M. J., Mateo, M., & Balseiro, A. (2020). Blastocystis sp. subtype diversity in wild carnivore species from Spain. Journal of Eukaryotic Microbiology, 67(2), 273–278.

Colston, T. J., & Jackson, C. R. (2016). Microbiome evolution along divergent branches of the vertebrate tree of life: What is known and unknown. Molecular Ecology, 25, 3776–3800.

Cunha, M. V., Albuquerque, T., Themudo, P., Fonseca, C., Bandeira, V., & Rosalino, L. M. (2020b). The gut microbiota of the Egyptian mongoose as an early warning indicator of ecosystem health in Portugal. International Journal of Environmental Research and Public Health, 17(9), 3104.

Cunha, M. V., Rosalino, L. M., Leão, C., Bandeira, V., Fonseca, C., Botelho, A., & Reis, A. C. (2020a). Ecological drivers of Mycobacterium avium subsp. paratuberculosis detection in mongoose (Herpestes ichneumon) using IS900 as proxy. Scientific Reports, 10(1), 860.

Deng, P., & Swanson, K. S. (2015). Gut microbiota of humans, dogs, and cats: Current knowledge and future opportunities and challenges. British Journal of Nutrition, 113(1), 6–17.

Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C., Yu, W. H., Lakshmanan, A., & Wade, W. G. (2010). The human oral microbiome. Journal of Bacteriology, 192(19), 5002–5017.

Dewhirst, F. E., Klein, E. A., Thompson, E. C., Blanton, J. M., Chen, T., Milella, L., Buckley, C. M., Davis, I. J., Bennett, M. L., & Marshall-Jones, Z. V. (2012). The canine oral microbiome. PLoS One, 7(4), e36067.

Dijk, V. E. L., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018). The third revolution in sequencing technology. Trends in Genetics, 34(9), 666–681.

Hussain, A., Khan, M. N., Iqbal, Z., & Sajid, M. S. (2008). An account of the botanical anthelmintics used in traditional veterinary practices in Sahiwal district of Punjab, Pakistan. Journal of Ethnopharmacology, 119(1), 185–190.

Hussain, M., Masood, M., Nawaz, L., Akhtar, N., Alam, H., Shaukat, M., Shabaan, M., Ullah, M., Sadique, A., & Ali, W. (2024). Characterization of oral microbiome from black rat (Rattus rattus) and assessment for pathogenicity. Journal of Wildlife and Biodiversity, 8(3), 449–462.

Liccioli, S., Giraudoux, P., Deplazes, P., & Massolo, A. (2015). Wilderness in the ‘city’ revisited: Different urbes shape transmission of Echinococcus multilocularis by altering predator and prey communities. Trends in Parasitology, 31(7), 297–305.

Maurice, C. F., Knowles, S. C. L., Ladau, J., Pollard, K. S., Fenton, A., Pedersen, A. B., & Turnbaugh, P. J. (2015). Marked seasonal variation in the wild mouse gut microbiota. ISME Journal, 9, 2423–2434.

McKenzie, V. J., Song, S. J., Delsuc, F., Prest, T. L., Oliverio, A. M., Korpita, T. M., Alexiev, A., Amato, K. R., Metcalf, J. L., Kowalewski, M., & Avenant, N. L. (2017). The effects of captivity on the mammalian gut microbiome. Integrative and Comparative Biology, 57(4), 690–704.

Medley, S., Ponder, M., & Alexander, K. A. (2020). Anthropogenic landscapes increase Campylobacter jejuni infections in urbanizing banded mongoose (Mungos mungo): A one health approach. PLoS Neglected Tropical Diseases, 14(3), e0007888.

Nelson, K. E. (2015). An update on the status of current research on the mammalian microbiome. ILAR Journal, 56(2), 163–168.

Nikaido, M., Kondo, S., Zhang, Z., Wu, J., Nishihara, H., Niimura, Y., & Minakuchi, Y. (2020). Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera. DNA Research, 27(4), dsaa021.

Pereira, A. C., & Cunha, M. V. (2020). An effective culturomics approach to study the gut microbiota of mammals. Research in Microbiology, 171(8), 290–300.

Pieter, A. P., Powers, K. E., & Hyzy, B. A. (2016). Initial explorations into the feeding ecology of the invasive small Indian mongoose in the Caribbean using stable isotope analyses. Bios, 87, 155–162.

Roberts, T. J. (1977). The mammals of Pakistan. Ernest Benn. Oxford University Press, London.

Rosalino, L. M., Santos, M. J., Pereira, I., & Santos-Reis, M. (2009). Sex-driven differences in Egyptian mongoose’s (Herpestes ichneumon) diet in its Northwestern European range. European Journal of Wildlife Research, 55, 293–299.

Ruparell, A., Inui, T., Staunton, R., Wallis, C., Deusch, O., & Holcombe, L. J. (2020). The canine oral microbiome: Variation in bacterial populations across different niches. BMC Microbiology, 20(1), 42.

Schneider, T. C., & Kappeler, P. M. (2016). Gregarious sexual segregation: The unusual social organization of the Malagasy narrow-striped mongoose (Mungotictis decemlineata). Behavioral Ecology and Sociobiology, 70(6), 913–926.

Shriner, D. (2012). Moving toward system genetics through multiple trait analysis in genome-wide association studies. Frontiers in Genetics, 3, 1.

Suzuki, T. A. (2017). Links between natural variation in the microbiome and host fitness in wild mammals. Integrative and Comparative Biology, 57(4), 756–769.

Trevelline, B. K., Fontaine, S. S., Hartup, B. K., & Kohl, K. D. (2019). Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proceedings of the Royal Society B: Biological Sciences, 286, 20182448.

Trick, F. E. C., Getz, L. J., Slaine, P. D., Thornbury, M., Lamoureux, E., Cook, J., Langille, M. G., Murray, L. E., McCormick, C., Rohde, J. R., & Cheng, Z. (2017). Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals. PLoS One, 12(12), e0189404.

Ulloa, P. C., van der Veen, M. H., & Krom, B. P. (2019). Modulation of the oral microbiome by the host to promote ecological balance. Odontology. 107, 437–448.

Veron, G., Patou, M. L., Pothet, G., Simberloff, D., & Jennings, A. P. (2007). Systematic status and biogeography of the Javan and small Indian mongooses (Herpestidae, Carnivora). Zoologica Scripta, 36(1), 1–10.

Weldon, L., Abolins, S., Lenzi, L., Bourne, C., Riley, E. M., & Viney, M. (2015). The gut microbiota of wild mice. PLoS One, 10, e0134643.

West, A. G., Waite, D. W., Deines, P., Bourne, D. G., Digby, A., McKenzie, V. J., & Taylor, M. W. (2019). The microbiome in threatened species conservation. Biological Conservation, 229, 85–98.

Whyte, A., Gracia, A., Bonastre, C., Tejedor, M. T., Whyte, J., Monteagudo, L. V., & Simon, C. (2017). Oral disease and microbiota in free-roaming cats. Topics in Companion Animal Medicine, 32(3), 91–95.

Zhu, Y., Jiang, W., Holyoak, R., Liu, B., & Li, J. (2020). Investigation of oral microbiome in donkeys and the effect of dental care on oral microbial composition. Animals, 10(12), 2245.

Published
2025-02-12
How to Cite
Ajmal, R., Imran, F., Ayub, A., Bilal, A., Bilal, M., Ali, K., Khan, S., Hussain, M., & Masood, M. (2025). Preliminary assessment and metagenomic analysis of oral microbiota of the small Indian mongoose Herpestes auropunctatus through next-generation sequencing. Regulatory Mechanisms in Biosystems, 16(1), e25010. https://doi.org/10.15421/0225010
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Vol 16 No 1 (2025): Regulatory Mechanisms in Biosystems
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