A diet-change modulates the previously established bacterial gut community in juvenile brown trout (Salmo trutta)

The aim of the present study was to investigate the impact of dietary plant proteins on the gut microbiome of first feeding brown trout (Salmo trutta) reproduced from wild stocks and to evaluate whether the initial microbiome of brown trout fry can be permanently manipulated by the first feeding diet. Therefore, brown trout fry was fed diets based on either 0%, 50% or 90% plant-derived proteins from first feeding onwards and via 16S rRNA gene sequencing a strong dietary influence on the bacterial gut community on phylum and order level was detected. Proteobacteria and Fusobacteria were significantly enhanced when fishmeal was integrated into the experimental diet, whereas plant-derived proteins significantly promoted Firmicutes and Bacteroidetes. In order to evaluate whether the first feeding diet had a permanent effect on the initially established microbial gut community of juvenile brown trout, a cross-over diet-change was applied 61 days post first feeding. 48 days after the diet-change, the gut microbiome of all dietary groups was significantly different from the one initially established after first feeding. Moreover, the first feeding diet had no statistically significant influence on the gut microbiome after the diet-change, demonstrating no permanent effect on the gut microbiome formation

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

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

Composition of experimental diets.

<p>Composition of experimental diets.</p

Scheme of the experimental design used in this study.

<p>The fishmeal diet A, the intermediate diet B and the plant-based diet C were fed as first feeding diet until day 54 post first feeding, which was the first sampling day for microbiome analysis. Afterwards fish of each dietary group were divided into three subgroups and the same three diets were fed as second feeding diet in a cross-over design until day 93 post first feeding, which was the second sampling day. The treatments reveal the nine resulting combinations of first and second feeding diet.</p

Mean relative abundance in percent of the top five phyla found in GI tract samples of fish for each treatment at two different sampling days.

<p>Mean relative abundance in percent of the top five phyla found in GI tract samples of fish for each treatment at two different sampling days.</p

Sources of iron and phosphate affect the distribution of diazotrophs in the North Atlantic

International audienceBiological nitrogen fixation (BNF) supplies nutrient-depleted oceanic surface waters with new biologically available fixed nitrogen. Diazotrophs are the only organisms that can fix dinitrogen, but the factors controlling their distribution patterns in the ocean are not well understood. In this study, the relative abundances of eight diazotrophic phylotypes in the subtropical North Atlantic Ocean were determined by quantitative PCR (qPCR) of the nifH gene using TaqMan probes. A total of 152 samples were collected at 27 stations during two GEOTRACES cruises; Lisbon, Portugal to Mindelo, Cape Verde Islands (USGT10) and Woods Hole, MA, USA via the Bermuda Time Series (BATS) to Praia, Cape Verde Islands (USGT11). Seven of the eight diazotrophic phylotypes tested were detected. These included free-living and symbiotic cyanobacteria (unicellular groups (UCYN) A, B and C, Trichodesmium, the diatom-associated cyanobacteria Rhizoselinia-Richelia and Hemiaulus-Richelia) and a γ-proteobacterium (Gamma A, AY896371). The nifH gene abundances were analyzed in the context of a large set of hydrographic parameters, macronutrient and trace metal concentrations measured in parallel with DNA samples using the PRIMER-E software. The environmental variables that most influenced the abundances and distribution of the diazotrophic phylotypes were determined. We observed a geographic segregation of diazotrophic phylotypes between east and west, with UCYN A, UCYN B and UCYN C and the Rhizosolenia-Richelia symbiont associated with the eastern North Atlantic (east of 40°W), and Trichodesmium and Gamma A detected across the basin. Hemiaulus-Richelia symbionts were primarily found in temperate waters near the North American coast. The highest diazotrophic phylotype abundance and diversity were associated with temperatures greater than 22. °C in the surface mixed layer, a high supply of iron from North African aeolian mineral dust deposition and from remineralized nutrients upwelled at the edge of the oxygen minimum zone off the northwestern coast of Afric

Venn diagram presenting the shared OTUs of fish fed the experimental diets.

<p>Presented are the numbers of OTUs present in at least 80% of all samples from one of the experimental groups fed one of the three experimental diets A, B or C. The numbers in the overlapping circles indicate OTUs shared by either two or three experimental groups. Plot (a) visualizes the core microbiota at the end of the first feeding period (54 dpff). Plot (b) visualizes the core microbiota at the end of the second feeding period (93 dpff). All samples were pooled for their respective first feeding diet and analyzed only for the second feeding diet.</p

Alpha diversity indices in relation to the dietary treatment and sampling day.

<p>The number of observed OTUs (Fig 3a), Chao1 richness estimator (Fig 3b), Simpson’s evenness measure (Fig 3c) and Shannon diversity index (Fig 3d) are presented. Statistically significant differences between treatments or between sampling days for continuously fed diets are indicated with asterisks: p<0.05 (*), p<0.01 (**), p<0.001 (***).</p

Graphical visualisation of the Principal Component Analysis (PCA) in relation to the second feeding diet and the individual bodymass.

<p>The first two principal components PC1 and PC2 (together representing 63% of the variance explained) are presented as axes of the ordination space. Each point represents the intestinal microbiome of one individual fish. Data were pooled for the first feeding diet according to the results of the multivariate model. Different gray shades and shapes of points indicate the three second feeding diets A, B and C. The size of the points indicates the final bodymass of each fish categorized as 0 (i.e. between 0.0g and 2.0g), 2 (i.e. between 2.1g and 4.0g), 4 (i.e. between 2.1g and 4.0g) and 6 (i.e. >6.0g).</p