A comprehensive look at Xenopus gut microbiota: effects of feed, developmental stages and parental transmission
Gut microbial ecology of Xenopus tadpoles across life stages
Recommendation: posted 09 March 2021, validated 11 March 2021
It is well established that the gut microbiota play an important role in the overall health of their hosts (Jandhyala et al. 2015). To date, there are still a limited number of studies on the complex microbial communites inhabiting vertebrate digestive systems, especially the ones that also explored the functional diversity of the microbial community (Bletz et al. 2016).
This preprint by Scalvenzi et al. (2021) reports a comprehensive study on the phylogenetic and metabolic profiles of the Xenopus gut microbiota. The author describes significant changes in the gut microbiome communities at different developmental stages and demonstrates different microbial community composition across organs. In addition, the study also investigates the impact of diet on the Xenopus tadpole gut microbiome communities as well as how the bacterial communities are transmitted from parents to the next generation.
This is one of the first studies that addresses the interactions between gut bacteria and tadpoles during the development. The authors observe the dynamics of gut microbiome communities during tadpole growth and metamorphosis. They also explore host-gut microbial community metabolic interactions and demostrate the capacity of the microbiome to complement the metabolic pathways of the Xenopus genome. Although this study is limited by the use of Xenopus tadpoles in a laboratory, which are probably different from those in nature, I believe it still provides important and valuable information for the research community working on vertebrate’s microbiota and their interaction with the host.
Bletz et al. (2016). Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nature Communications, 7(1), 1-12. doi: https://doi.org/10.1038/ncomms13699
Jandhyala, S. M., Talukdar, R., Subramanyam, C., Vuyyuru, H., Sasikala, M., & Reddy, D. N. (2015). Role of the normal gut microbiota. World journal of gastroenterology: WJG, 21(29), 8787. doi: https://dx.doi.org/10.3748%2Fwjg.v21.i29.8787
Scalvenzi, T., Clavereau, I., Bourge, M. & Pollet, N. (2021) Gut microbial ecology of Xenopus tadpoles across life stages. bioRxiv, 2020.05.25.110734, ver. 4 peer-reviewed and recommended by Peer community in Geonmics. https://doi.org/10.1101/2020.05.25.110734
Wirulda Pootakham (2021) A comprehensive look at Xenopus gut microbiota: effects of feed, developmental stages and parental transmission. Peer Community in Genomics, 100005. 10.24072/pci.genomics.100005
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.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/2020.05.25.110734
Version of the preprint: version 2
Author's Reply, 04 Mar 2021
Decision by Wirulda Pootakham, posted 27 Feb 2021
Thank you for revising the manuscript. Both reviewers are happy with the revision. I've attached their comments below. Once these comments are addressed, I would be happy to recommend this preprint.
Thank you very much.
========================================================================== Comments from Reviewer #1: Here are only a few suggestions of modifications:
L. 692, 701: Since you have all the details, maybe could you provide info in Mat&Meth about the amount of DNA and RNA material obtained before sequencing/amplification?
Fig S7_C => please provide in legend the meaning for the abbreviations “TGA” and “SL”, or mention they are the strains’ names?
There were still some typos, the manuscript should be scrutinized for these.
Comments from Reviewer #2: One minor comment: L403: "Metagenomic and metatranscriptomic sequencing gave similar taxonomic profiles for bacteria in concordance with the 16S rRNA gene metabarcoding approach, while giving a finer taxonomic resolution (Figure 7A)." The figure however does not show a comparison with the 16S rDNA data, it also does not show a better taxonomic resolution (reported at phylum level). If a formal comparison between methods has been done, please indicate where to find the results. Otherwise I suggest deleting "in concordance with the …" Please also indicate (e.g. in the legend) whether the taxonomic profiles in Figure 7A were based on reads or MAGs.
Reviewed by anonymous reviewer, 11 Feb 2021
Reviewed by Vanessa Marcelino, 28 Jan 2021
Evaluation round #1
DOI or URL of the preprint: https://www.biorxiv.org/content/10.1101/2020.05.25.110734v1
Author's Reply, 08 Jan 2021
Decision by Wirulda Pootakham, posted 09 Aug 2020
This study provides an important resource to the field. The authors did a thorough study on the vertebrate microbiota; however, there are issues raised by reviewers that need to be addressed before I can recommend this preprint. I would like to ask the authors to carefully go through each reviewer's comments and try to address them.