Structure, dynamics and predicted functional ecology of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico
- Published
- Accepted
- Subject Areas
- Bioinformatics, Microbiology, Molecular Biology
- Keywords
- Haliotis fulgens and H. corrugate microbiota composition, Bacterial interaction, Ecological function predictions., 454 Pyrosequencing
- Copyright
- © 2017 Cicala et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Structure, dynamics and predicted functional ecology of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico. PeerJ Preprints 5:e3233v1 https://doi.org/10.7287/peerj.preprints.3233v1
Abstract
The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intra-specific variation. This resulted from differences of the species with most reads in each GI metagenome, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found for the explored metabolic pathways between species despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a deep taxonomic and functional split between the microbiota of HF and HC abalone.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Exclusive bacterial species
OTUs showing differential abundances between yellow (HC) and blue (HF) abalone with statistical and biological significance obtained from LEfSe analyses. OTUs are ranked according to its effect size (LDA score).
Taxonomic comparison
Non-parametric multidimensional scaling (MDS) of Sorensen similarity index based on presence and absence of OTUs assembled at 97% similarity cut-off of the gut microbiota of Haliotis fulgens (HF) and H. corrugata (HC).
Genetic groups interactions
Regression of the average Jaccard distance based on phylogenetic groups of bacterial OTUs (10% similarity) as a function of their abundance –log scale – (HF: Haliotis fulgens, HC: Haliotis corrugata).
PICRUSt correction
Ranks of the KO genes according to their KO count number (log scale) obtained with the script categorize by function in PICRUSt.
Classified OTUs assignement
Reads number for each detected OTU.
PICRUSt identified KOs genes
Count number for each identified gene
PICRUSt identified metabolic functions
Count number for each identified metabolic function.
Bacterial species competitive pressures
Average value of Jaccard distance for each OTU detected in yellow (HC) and blue abalone (HF).