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Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes
Article

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome

1
National Institute for Agrarian and Veterinary Research (INIAV, IP), Wildlife, Hunting and Biodiversity R&D Unit, 2780-157 Oeiras, Portugal
2
Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
3
Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
4
Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(6), 808; https://doi.org/10.3390/microorganisms8060808
Received: 10 April 2020 / Revised: 10 May 2020 / Accepted: 26 May 2020 / Published: 27 May 2020
(This article belongs to the Special Issue Wildlife Microbiology 2.0)
Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose’ gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics. View Full-Text
Keywords: Egyptian mongoose; gut microbiota; culturomics; microbial profiling Egyptian mongoose; gut microbiota; culturomics; microbial profiling
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MDPI and ACS Style

Pereira, A.C.; Bandeira, V.; Fonseca, C.; Cunha, M.V. Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome. Microorganisms 2020, 8, 808. https://doi.org/10.3390/microorganisms8060808

AMA Style

Pereira AC, Bandeira V, Fonseca C, Cunha MV. Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome. Microorganisms. 2020; 8(6):808. https://doi.org/10.3390/microorganisms8060808

Chicago/Turabian Style

Pereira, André C., Victor Bandeira, Carlos Fonseca, and Mónica V. Cunha 2020. "Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome" Microorganisms 8, no. 6: 808. https://doi.org/10.3390/microorganisms8060808

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