Here is the coda to proceed to the bioinformatic tools and statistical analyses for study of the enteric microbiome of reef fishes in the Seychelles islands.
What's the study context?
Mahe and Praslin are two of the biggest inner island of Seychelles in Ocean Indien. This archipelago is under lot of climatic pressure by this location in the north western of the Indien Ocean. El niño phenomenon and the indian oscillation dipole bring positive temperature anomalies with big heat wave with a >30°C seawater temperature (Mishal et al., 2019). More than climatic pressure, Seychelles are under anthropic pressure with mass tourism and a population pool of more than 92 430 inhabitants living of fisheries (Hoegh-Gouldberg et al., 2007 ; Briggs et al.,2018 ; Graham et al., 2015). Few farms exist but nno study has been made about the potentiel input of nutrient in seawater. Nevertheless, all this context has put the coral reef under high stress with two dramatic episodes of bleaching in 1992 and in 2016 with more than 90% mortality. These bleaching events empowered the invasion of the red macroalgae Hypnea sp. which worries the environmental authority and scientist. This is not the only case of invaded reef by macroalgae. In Carribean sea, and in Australien lot of coral reef suffer of this invasion described as 'coral-macroalgal shift' and are in previsions for future coral reefs by all environmental scientists. This shift has dramatic consequences on population dynamics and thus, on trophic structure (Graham et al., 2015, 2016 ; Nyström et al., 2008) endegering the ecosystem services provided by the coral reef system as tourism and artisanal fisheries (Bellwood et al., 2019, Hugues et al., 2017, Broke et Carpenter, 2006). Lot of studies have demonstrate the efficiancy role of herbivory on the control top down on these algae. Many functional traits are taken into account but an invisible part is often forgotten : the microbiome. Not only in nutritional functions but also playing a key role for the fish by moderating stress and improving immunitary system, microorganisms living inside the enteric part of the fish has never been described in this case and is poorly known for reef fish.
Here, we propose a coda to access the diversity and description of the enteric microbiome of reef fish.
A first bioinformatics part is available in order to obtain microbial tables from raw data (paired- ends reads).
A second part is dedicated in statistical analyses for microbial taxa tables.
Enjoy !
Cheers, MC