Abstract
In the aquaculture industry, plant-based protein sources have emerged as an economically and environmentally sustainable replacement for traditional animal protein sources. Yet, due to decreased digestibility, the presence of anti-nutritional factors, and an increased risk of inflammation of the digestive system, the inclusions of plant-based protein ingredients must be limited in the diets of carnivorous fishes. To gain further insight on the adaptation of the fish digestive tract to plant-based protein ingredients, slurry from cultured Atlantic Salmon (Salmo salar) was used as a proxy in an in vitro model system to identify candidate gut bacterial species from fish that can metabolize bioprocessed soybean meal. Triplicate slurry cultures were supplemented with one of each of the following ingredients: fishmeal (FM – control#1), soybean meal (SBM-control#2), MEPro (bioprocessed soybean meal product), as well as three ingredients derived from bioprocessed soybean meal (SPC1 - soy protein isolate #1; SPC2 - soy protein isolate #2; SPC3 - soy protein isolate #3). Data were generated by Illumina MiSeq 2X300 sequencing of PCR-generated amplicons targeting the V1-V3 regions of the 16S rRNA gene. A comparative analysis of the most highly represented Operational Taxonomic Units (OTU) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified candidate bacterial species that were enriched in cultures supplemented with specific bioprocessed soybean meal-derived ingredients compared with non-supplemented cultures (negative control). These results indicate that certain species may utilize these ingredients. Notably, OTUs Ss_1-37437 and Ss_1-13316 were found in the greatest abundance in cultures supplemented with SPC1 (31.4 - 49.7%) and SPC2 (7.2 - 17.4%), respectively. Interestingly, both OTUs were likely to represent novel bacterial species, based on their limited nucleotide sequence identity to their corresponding valid relative: Ss_1-37437: Prevotella paludivivens (96.58%); Ss_1-13316: Acetoanaerobium sticklandii (86.51%). In contrast, the most abundant OTUs enriched in SBM- and MePro-supplemented cultures were likely strains of known bacterial species. Indeed, OTU Ss_1-00386 was most abundant in SBM-supplemented cultures (16.4 - 32.5%), and it was found to be closely related to Leuconostoc mesenteroides (98.69%), a bacterial species with reported probiotic properties, while OTU SS_1-10030, a close relative of Bacteroides graminisolvens (99.24%), was most highly represented in MePro-supplemented cultures (21.9 - 32.7%). Together, these results suggest that ingredients derived from bioprocessed soybean meal have the potential to be developed as prebiotics to modulate the gut microbiome of aquaculture fish species.