Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism?

Abstract

The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens.

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories

“…In flow-through water systems, there may be cross contamination between the bacterial communities in fish intestine, fish skin, and those adhering to tank wall. Microbiota associated with cutaneous mucus was influenced by the diet in Atlantic salmon [27], and by genetic background in brook charr [28]. The interactions between fish individuals and bacterial communities within each tank may therefore cause partly the dissimilarity that was observed between intestinal microbiota collected from different tanks.…”

“…Such relationship should be carefully interpreted, as the correlation network is likely intricate. However it seems possible to associate physiological traits such as growth potential and hypoxia resistance to some characteristics of gut microbiota in fish, as already attempted between quantitative trait loci and specific bacterial strains associated with the skin of brook charr [28]. Using DGGE, Forberg et al [3] noted higher band richness in large killifish larvae compared to small individuals, but Shannon index and evenness were not significantly different, whereas the reverse observations were done with Atlantic cod larvae.…”

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

“…We pooled, in equimolar proportions (measured spectrophotometrically), DNA elutes of gut microflora of different individuals captured from the same habitat (i.e., same species) of each location. This step assured that the gut microflora for each location was represented as a community for that location, rather than as the characteristic of an individual, minimizing noise in the data, which is most often caused by interindividual variation (Boutin, Sauvage, Bernatchez, Audet, & Derome, 2014; Hildebrand et al., 2013). Thus, there were ten pooled samples from each location for each species.…”

Current Advances in Functional Genomics in Aquaculture

“…Boutin et al [71] combined 16S RNA metagenomics and QTL analyses to show that host genotype can regulate the microbiota composition on the skin surface of brook charr (Salvelinus fontinalis). They found a strong negative correlation between Flavobacterium and Methylobacterium, pointing to a mutually competitive relationship between pathogenic and non-pathogenic bacteria on the skin mucosa of brook charr.…”