The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures

• Published in: PloS one Vol. 12; no. 5; p. e0177735
• Main Authors: Michl, Stéphanie Céline, Ratten, Jenni-Marie, Beyer, Matt, Hasler, Mario, LaRoche, Julie, Schulz, Carsten
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 12.05.2017; Public Library of Science (PLoS)
• Subjects: Alteromonadaceae - genetics; Alteromonadaceae - isolation & purification; Amino acid composition; Amylases; Analysis; Animal breeding; Animal Feed; Animal protein; Animal welfare; Animals; Aquaculture; Assembly; Bacillales - genetics; Bacillales - isolation & purification; Bacteria; Bacteroides - genetics; Bacteroides - isolation & purification; Biology; Biology and Life Sciences; Breeding; Breeding of animals; Carbohydrate metabolism; Carbohydrates; Carnivores; Cell culture; Cellulase; Cellulose; Chitin; Clostridiales - genetics; Clostridiales - isolation & purification; Colonization; Community structure; Diet; Digestive system; Digestive tract; DNA, Ribosomal - genetics; Documents; Earth Sciences; Eggs; Enzymes; Feeding; Fermentation; Fish; Fish diseases; Fusobacterium - genetics; Fusobacterium - isolation & purification; Gastrointestinal Microbiome - genetics; Gastrointestinal Microbiome - physiology; Gastrointestinal tract; Genetics; Health aspects; High resolution; Histology; Immunology; Inhibition; Intestinal microflora; Intestine; Juveniles; Liver; Local government; Medicine and Health Sciences; Metabolism; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Network analysis; Nutrition; Nutrition research; Oncorhynchus mykiss; Oncorhynchus mykiss - microbiology; Pathogens; Physiological aspects; Physiological factors; Physiology; Plant breeding; Plants; Polysaccharides; Proteins; Salmon; Species richness; Starvation; Studies; Trout; Utilization; Vertebrates; Zebrafish; United States; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0177735

Plant-derived protein sources are the most relevant substitutes for fishmeal in aquafeeds. Nevertheless, the effects of plant based diets on the intestinal microbiome especially of juvenile Rainbow trout (Oncorhynchus mykiss) are yet to be fully investigated. The present study demonstrates, based on 16S rDNA bacterial community profiling, that the intestinal microbiome of juvenile Rainbow trout is strongly affected by dietary plant protein inclusion levels. After first feeding of juveniles with either 0%, 50% or 97% of total dietary protein content derived from plants, statistically significant differences of the bacterial gut community for the three diet-types were detected, both at phylum and order level. The microbiome of juvenile fish consisted mainly of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria, and thus fits the salmonid core microbiome suggested in previous studies. Dietary plant proteins significantly enhanced the relative abundance of the orders Lactobacillales, Bacillales and Pseudomonadales. Animal proteins in contrast significantly promoted Bacteroidales, Clostridiales, Vibrionales, Fusobacteriales and Alteromonadales. The overall alpha diversity significantly decreased with increasing plant protein inclusion levels and with age of experimental animals. In order to investigate permanent effects of the first feeding diet-type on the early development of the microbiome, a diet change was included in the study after 54 days, but no such effects could be detected. Instead, the microbiome of juvenile trout fry was highly dependent on the actual diet fed at the time of sampling.