Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae

Abstract

The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.

Gastrointestinal tract microbial community of Babylonia areolata and its diversity are closely correlated with the outbreak of disease

“…For example, the intestinal microbiota dysbiosis contributes to shrimp white faeces syndrome (Huang et al, 2020). Vibrio anguillarum infection would modify the function of microbiome of zebrafish larvae and its influences include amino acid metabolism, membrane transport, cellular community‐prokaryotes, metabolism of cofactor and vitamins (Vargas et al, 2021). To further explore relationship between the decline of GI microbiota diversity and occurrence of disease, metabolic functions of GI microbiota in B. areolata were analysed.…”

Application of zebrafish in the study of the gut microbiome

“…It has been demonstrated that gut bacteria themselves (endogenous bacteria) or exogenous addition of protective bacteria in larvae could prevent or decrease the chance of pathogenic infection and improve the survival rate of fish. Vargas et al showed that V. anguillarum changed the gut microbial β‐diversity, and probiotic yeasts could inhibit the enrichment of Vogesella and Ensifer , which were identified as a negative predictive factor of survival rate in larvae 134 . Besides, probiotics of selected bacteria with high surface glycotope Galα1‐3Galβ1‐(3)4GlcNAc‐R (α‐Gal) content were effective and safe for Mycobacterium marinum .…”

“…Vargas et al showed that V. anguillarum changed the gut microbial β‐diversity, and probiotic yeasts could inhibit the enrichment of Vogesella and Ensifer , which were identified as a negative predictive factor of survival rate in larvae. 134 Besides, probiotics of selected bacteria with high surface glycotope Galα1‐3Galβ1‐(3)4GlcNAc‐R (α‐Gal) content were effective and safe for Mycobacterium marinum . It was found that probiotics with high α‐Gal content activated gut microbial structure modification, B‐cell maturation, and anti‐α‐Gal antibody‐mediated control of Mycobacteria .…”

Multispecies biofilm architecture determines bacterial exposure to phages

“…Beyond the experimental tractability that makes E. coli and V. cholerae excellent for controlled experiments, these species can be found in natural environments together: for example, residing in brackish water 32,33 and within surface-fouling biofilms in coastal waters near human populations 34 . Members of the Escherichia and Vibrio genera are also common components of zebrafish microbiota 35,36 . The cellular arrangement and secreted matrix architectures of V. cholerae have been explored in great detail in the last decade [37][38][39][40][41][42][43][44][45][46][47] .…”

“…Beyond the experimental tractability that makes E. coli and V. cholerae excellent for controlled experiments, these species can be found in natural environments together: for example, residing in brackish water (32,33) and within surface-fouling biofilms in coastal waters near human populations (34). Members of the Escherichia and Vibrio genera are also common components of zebrafish microbiota (35,36). Their tractability make E. coli and V. cholerae together a superb platform for exploring principles of how multispecies biofilm structure could influence bacteria-phage interactions in fine detail.…”