Aquaculture Europe 2021

October 4 - 7, 2021

Funchal, Madeira

Add To Calendar 07/10/2021 14:30:0007/10/2021 14:50:00Europe/LisbonAquaculture Europe 2021A MULTI OMIC APPROACH REVEALS ESSENTIAL HOST-MICROBIOTA INTERACTIONS IN THE INTESTINAL ENVIRONMENT OF RAINBOW TROUT Oncorhynchus mykissSidney-HotelThe European Aquaculture Societywebmaster@aquaeas.orgfalseDD/MM/YYYYaaVZHLXMfzTRLzDrHmAi181982

A MULTI OMIC APPROACH REVEALS ESSENTIAL HOST-MICROBIOTA INTERACTIONS IN THE INTESTINAL ENVIRONMENT OF RAINBOW TROUT Oncorhynchus mykiss

 

Jacob Agerbo Rasmussen*1,2, Kasper Rømer Villumsen3, Madeleine Ernst,4 Martin Hansen5, Torunn Forberg6 , Shyam Gopalakrishnan2, M. Thomas P. Gilbert2,7, Anders Miki Bojesen3, Karsten Kristiansen1,8, Morten Tønsberg Limborg1,2

 

1 Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark

2 Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences,

 3 Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Denmark

 4  Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark

 5 Department of Environmental Science, Aarhus University, Aarhus, Denmark

6 BioMar Group, Trondheim, Norway

 7 University Museum NTNU, Trondheim, Norway

 8 Institute of Metagenomics, BGI- Shenzhen, Shenzhen, China

 Email: jacob.rasmussen@bio.ku.dk

 



Introduction

The microbial communities that inhabit the vertebrate gastrointestinal tract are tightly connected to many traits displayed by its host

 .  Applying a multi omic framework to investigate host-microbe interactions could be used in aquaculture related to improve growth, health, and sustainable production

. Here, we investigate the functional effects of pro- and synbiotic feed additives on microbiome associated functions in the commercially important rainbow trout (Oncorhynchus mykiss ). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, genome resolving metagenomes, and untargeted metabolomics, to investigate bacterial metagenomic assembled genomes (MAGs) and their molecular interactions with host metabolism.

Methods

An experimental feeding trial was carried out over an eight-week period. Three experimental, proprietary feed formulations were selected: I) a control feed without any pre- or probiotic additives (CTRL), II) control feed plus the commercial probiotic with commercially available Pediococcus acidilactici MA18/5M (PRO) , and III) control feed with a synbiotic additive, consisting of same probiotic and galactooligosaccharides (SYN ). Bacterial profiling using the V3-V4 region of the bacterial 16S rRNA gene, were applied to investigate microbial profiles related to usage of  supplemented feed in two gut sections of 120 individuals (40 individuals per feed group) of rainbow trout. A subset of these samples  was whole-genome sequenced to investigate bacterial functionality of MAGs . Furthermore, A combination of two untargeted metabolomics approaches, including UHPLC-MS/MS and IC HR-MS/MS, were applied to 30 individuals (10 individuals per feed group) in order to decipher the metabolic landscape in the intestinal environment.

Results

 Our findings reveal, that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related species Candidatus Mycoplasma salmoninae in both the mid and distal gut content (Figure 1a) , (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated  with presence of the native gut bacteria Candidatus Mycoplasma salmoninae (Figure 1a) , (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites (Figure 1b-d).

Conclusions

Our results demonstrate how use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments.

References

1.                       Huang, Q. et al. Diversity of gut microbiomes in marine fishes is shaped by host-related factors. Mol. Ecol. (2020) doi:10.1111/mec.15699.

2.                       Perry, W. B., Lindsay, E., Payne, C. J., Brodie, C. & Kazlauskaite, R. The role of the gut microbiome in sustainable teleost aquaculture. Proc. Biol. Sci. 287, 20200184 (2020).

3.                       Limborg, M. T. et al. Applied Hologenomics: Feasibility and Potential in Aquaculture. Trends Biotechnol. 36, 252–264 (2018).