Getting closer to the host-microbe evolutionary relationship
Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background
Recommendation: posted 17 August 2023, validated 17 August 2023
Kormas, K. (2023) Getting closer to the host-microbe evolutionary relationship. Peer Community in Microbiology, 100012. 10.24072/pci.microbiol.100012
The issue of whether there is a clear and detectable relationship -either deterministic or stochastic- of fish gut microbiota with evolutionary processes is far from being resolved. Studies on fish microbiota are more perplexed as this animal group includes species both from wild and farmed populations (for food production, ornamental fish and animal models), with variable life cycles and ecophysiologies, and all these features expand the type of interactions to be studied. Based on this biological features variability, multiple methodological limitations, especially for the species with wild populations, are perhaps among of the central reasons for this knowledge gap. Therefore, experimental approaches, which can eliminate some of this variability, seem to be the best approach.
The preprint by Evangelista et al. (2023) entitled "Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background" is an example of such a targeted study with a freshwater fish species. Due to the paper's finely detailed experimental design, the interdisciplinary skills of the participating co-authors and exhaustive data analysis, this paper manages to draw solid and reproducible results and conclusions. This renders it not only an insightful contribution towards the more general host-microbe interactions in an evolutionary framework, but also a perfect example on how current and future relevant research should be conducted. I feel confident that this paper will assist other scientits of the field to move forward with their current working hypotheses but also to generate novel ones.
Evangelista C, Kamenova S, Diaz Pauli B, Sandkjenn J, Vollestad A, Edeline E, Trosvik P, de Muinck E (2023) Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background. bioRxiv, 2023.02.17.528956, ver. 2 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.02.17.528956
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
This work was supported by The Research Council of Norway (projects 251307/F20 and 255601/E40) and its mobility program (projects 272354 to CE and 268218/MO to BDP). EE was supported by IDEX SUPER (project Convergences J14U257 MADREPOP) and by Rennes Métropole (AIS 18C0356). The experiments realized in the CEREEP Ecotron Ile-De-France benefited from the support received by an “Investissements d'Avenir” program from the Agence Nationale de la Recherche (ANR-10-EQPX-13-01 Planaqua and ANR-11-INBS-426 0001 AnaEE France).
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2023.02.17.528956
Version of the preprint: 1
Author's Reply, 16 Aug 2023
Decision by Konstantinos (Kostas) Kormas, posted 25 May 2023, validated 26 May 2023
This study investigated the gut microbiota of two medaka genetic lines to investigate wehther fishing pressure and/or environmental affect the development of the gut microbiota. Significant differences in the gut microbiota profiles were found between the two lines, and this effect seems to have been mediated by light intensity, but the host's fitness seemed unrelated to these microbiota changes. This part, host fitness in relation to the gut microbiota, could be explored in greater depth by the authors, with more targeted data analysis (no need for extra data or reanalysis of their raw sequencing data). Similar studies are not so common in the field, especially ones that paid extra attention to its experimental design and maticulate data analysis like this one. There are also several comments and suggestions provided by the three reviewers, which I also find accurate and righfully spotted, that could considerable increase the quality and the reading flow of the paper. Overall, I find this paper an important contribution in the field of fish-microbe interactions and co-evolutionary mechanisms which I believe it will be fully appreaciated by the scientists in the microbiome field when published.