The meta-transcriptome of the rainbow trout gut microbiome in relation to stress and diet (MetaBac)

• Applicant: Professorin Dr. Stéphanie Céline Hornburg
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry
• Term: from 2018 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 401653591

• Final Report Year: 2023

Final Report Abstract

The MetaBac research project is investigating the interaction of genetic origin, stress and feed-ing on the structure and function of the intestinal microbiome of trout. Fish growth is based on optimal nutrient supply, which depends on a functional interaction with the microbiome. Chronic husbandry stress in aquaculture has a negative impact on fish growth and production success. The project therefore aimed to test the hypothesis of whether the microbiome can establish a link between nutrient supply and stress resistance. So far, a functional characterisation of the microbiota, i.e. a determination of the active microbial metabolic activities, has been lacking. The project attempts to close this research gap with a metatranscrip-tome analysis. By sequencing the mRNA from bacteria of the intestinal mucosa, the metabolic influence of the microbiome on its host can be analysed and specified. To this end, experimental studies were carried out in which trout from two different breeding lines were subjected to different feeding strategies (fishmeal-based vs. plant-based feeding) and a continuous stress load. In trout aquaculture, the feeding of plant-based proteins is standard and enables equivalent good growth performance to fishmeal-based feeds. However, it was previously un-clear how the associated modulation of the intestinal microbiome affects the metabolism and the immune system. No effects of feeding or stress on the growth parameters were found in the project experiments. However, the molecular biological analyses showed clear effects: Molecular immune markers were expressed significantly differently depending on the interaction between stress and feeding. The groups fed predominantly with fishmeal showed higher inflammatory activity, whereas stressed fish in the plant-based feeding group showed significantly lower expression of TNF α and immunoglobulins. The microbiota in the gut contents also changed significantly due to the interaction of stress and feeding: in stressed fish, there were significant changes between the fishmeal-based and plant-based diets. The microbiota of the intestinal mucosa was also influenced by feeding, but not by stress or a statistical interaction. However, a detailed analysis showed that the effects only occurred in stressed fish, indicating that the diet-induced changes are modulated by stress. Bacterial mRNA sequencing and dif-ferential gene expression analysis have so far identified 499 isoforms that are expressed significantly differently between the feeding strategies and stress situations and still need to be correlated with the 16S analyses. The results clearly support the initial hypotheses of the pro-ject and show that the intestinal microbiota occupies an important interface position between nutrition and stress physiology.

Publications

• Aquaculture Europe; 27.09.2022, Rimini, Italien; Poster: “The microbiota knows: handling-stress and diet transform the microbial landscape in the gut content of rainbow trout in RAS.”
  M. Suhr
  
• Interactions of plant‐based feeding and handling stress on the expression of selected immune markers in rainbow trout ( Oncorhynchus mykiss ). Aquaculture Research, 53(12), 4304-4315.
  Seibel, Henrike; Krassilnikova, Ksenia; Fichtner‐Grabowski, Finn‐Thorbjörn; Rebl, Alexander; Schulz, Carsten & Hornburg, Stéphanie Céline
  
• 21st international EAFP Conference, 11.09.2023, Aberdeen, GB; Poster: “Interaction of pre-dominantly plant-based feeding and handling stress on the expression of selected im-mune markers in rainbow trout (Oncorhynchus mykiss)”
  H. Seibel
  
• Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout. Scientific Reports, 13(1).
  Suhr, Marvin; Fichtner-Grabowski, Finn-Thorbjörn; Seibel, Henrike; Bang, Corinna; Franke, Andre; Schulz, Carsten & Hornburg, Stéphanie C.
  
• International Conference: Horizons in Metaorganism Research; 04.10.2023, Kiel; Vortrag: “Effects of plant-based proteins and handling stress on gut microbiota and meta-transcriptome in rainbow trout”
  M. Suhr
  
• The microbiota knows: handling-stress and diet transform the microbial landscape in the gut content of rainbow trout in RAS. Animal Microbiome, 5(1).
  Suhr, Marvin; Fichtner-Grabowski, Finn-Thorbjörn; Seibel, Henrike; Bang, Corinna; Franke, Andre; Schulz, Carsten & Hornburg, Stéphanie Céline