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“Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?”

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Abstract

The use of museum preserved specimens to know microbiome in extinct and threatened species has been explored recently. The fishes of the genus Herichthys are distributed mainly in the Pánuco-Tamesí system in Northeastern Mexico, one of the most polluted basins in the country leading to near half of the species be considering as threatened. In this paper we used the hypervariable V4 region of the 16S rRNA gene from the 11 species of the genus Herichthys obtained from museum collections to evaluate the potential use of fixed preserved vouchers in the knowledge of gut microbiota diversity and the potential role of sympatric and allopatric speciation of the hosts in the gut microbiome evolution. The 100% of the samples were successfully amplified where the number of amplicons ranged from 4500 from a formaldehyde fixed specimen up to 55,000 in ethanol preserved specimens. Differences in gut microbiota were found between sympatric species and among the comparison of some trophic guilds. A non-random association between the gut host and their microbiome was found allow to suggest a potential phylosymbiosis relationship. In conclusion, the most abundant phyla recovered from the gut microbiota in this study were similar to those previously reported in other cichlids supporting the idea that a gut microbial core is conserved in this group of fishes despite millions of years of evolution and leading to support the potential use of museum specimens in microbiome studies.

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Data Availability

All sequences obtained were uploaded to the NCBI database under the Bioproject number PRJNA715246.

Code Availability

Scripts used in the analysis of the above data can be found at https://github.com/HOmarMejiaG/Herichthys-microbiome.

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Acknowledgements

Technical assistance is acknowledged to O Gaona (IE, UNAM) and J Ortiz (FC, UNAM). We also like to thank Eduardo Soto Galera for provide access to the museum collections and to four anonymous reviewers for their useful comments that allow to improve the manuscript.

Funding

This study was funded by Instituto de Ecología, UNAM (LIF). ASQ received a graduate studies scholarship from CONACyT. ESGA received a postdoctoral scholarship from DGAPA-UNAM.

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Authors and Affiliations

  1. Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico

    Omar Mejía & Fabian Pérez-Miranda

  2. Laboratorio de Ecología Bacteriana, Instituto de Ecología, UNAM, 04510, Mexico City, Mexico

    Andrés Sánchez-Quinto, Elizabeth S. Gómez-Acata & Luisa I. Falcón

  3. Instituto de Ecología, Campus Yucatán, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, Mexico

    Andrés Sánchez-Quinto, Elizabeth S. Gómez-Acata & Luisa I. Falcón

  4. Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Chiapas, Mexico

    Fabian Pérez-Miranda

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  1. Omar Mejía
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Contributions

OM, LIF: Developed the idea. FPM, ESGA: Carried out the molecular work. OM, ASQ, FPM: Carried out the data analyses. OM, LIF, ASQ, FPM, ESGA: Wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Omar Mejía.

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No approval of research ethics committees was required due that all samples used proceed from museum specimens.

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Mejía, O., Sánchez-Quinto, A., Gómez-Acata, E.S. et al. “Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?”. Curr Microbiol 79, 346 (2022). https://doi.org/10.1007/s00284-022-03047-5

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