Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome
Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (<i>Herpestes ichneumon</i>) 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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/6/808 |
| _version_ | 1797566911290015744 |
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| author | André C. Pereira Victor Bandeira Carlos Fonseca Mónica V. Cunha |
| author_facet | André C. Pereira Victor Bandeira Carlos Fonseca Mónica V. Cunha |
| author_sort | André C. Pereira |
| collection | DOAJ |
| description | Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (<i>Herpestes ichneumon</i>) 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 <i>Firmicutes</i> 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. |
| first_indexed | 2024-03-10T19:34:07Z |
| format | Article |
| id | doaj.art-d55356314ce24cb1aad396a0fe11bafb |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T19:34:07Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-d55356314ce24cb1aad396a0fe11bafb2023-11-20T01:55:35ZengMDPI AGMicroorganisms2076-26072020-05-018680810.3390/microorganisms8060808Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut MicrobiomeAndré C. Pereira0Victor Bandeira1Carlos Fonseca2Mónica V. Cunha3National Institute for Agrarian and Veterinary Research (INIAV, IP), Wildlife, Hunting and Biodiversity R&D Unit, 2780-157 Oeiras, PortugalDepartamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, PortugalDepartamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, PortugalNational Institute for Agrarian and Veterinary Research (INIAV, IP), Wildlife, Hunting and Biodiversity R&D Unit, 2780-157 Oeiras, PortugalRecently, we unveiled taxonomical and functional differences in Egyptian mongoose (<i>Herpestes ichneumon</i>) 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 <i>Firmicutes</i> 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.https://www.mdpi.com/2076-2607/8/6/808Egyptian mongoosegut microbiotaculturomicsmicrobial profiling |
| spellingShingle | André C. Pereira Victor Bandeira Carlos Fonseca Mónica V. Cunha Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome Microorganisms Egyptian mongoose gut microbiota culturomics microbial profiling |
| title | Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome |
| title_full | Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome |
| title_fullStr | Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome |
| title_full_unstemmed | Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome |
| title_short | Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (<i>Herpestes ichneumon</i>) Gut Microbiome |
| title_sort | crosstalk between culturomics and microbial profiling of egyptian mongoose i herpestes ichneumon i gut microbiome |
| topic | Egyptian mongoose gut microbiota culturomics microbial profiling |
| url | https://www.mdpi.com/2076-2607/8/6/808 |
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