Michael L. Brown

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.

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

The seasonal dynamics of the northern largemouth bass (Micropterus salmoides salmoides) reproductive cycle was investigated in a Midwestern United States population. Mature largemouth bass (n = five males and five females) were collected each month over a one‐year period. Environmental cues (water temperature and photoperiod) were recorded in situ using data loggers. Temporal changes in plasma sex steroid hormones (testosterone [T], 11‐ketotestosterone [11‐KT], and estradiol‐17β [E₂]) and vitellogenin (Vtg), gamete development (histology), and organosomatic indices were highly associated with temporal water temperature and photoperiod dynamics. Female plasma concentrations of T and E₂ and organosomatic indices exhibited similar temporal patterns, with peaks occurring in early summer. Gamete development in females was associated with increases in gonadosomatic index (GSI) and Vtg. In males, plasma concentrations of T and organosomatic indices exhibited bimodal peaks; high peaks occurred in the spring for T and GSI and in the fall for viscerosomatic and hepatosomatic indices. Male gamete development and GSI closely tracked temporal patterns in plasma T, with GSI lagging behind the T cycle by approximately one sampling period. Plasma concentrations of 11‐KT were elevated in late winter and spring and were considerably higher than T throughout the reproductive cycle. Unlike the Florida largemouth bass (M. salmoides floridanus) advanced gamete development was observed in both sexes before winter, which may reduce the immediate energy required for gamete development in the spring. Results from this study also provide baseline information necessary for off‐season spawning procedures and endocrine‐disruption studies in northern largemouth bass.

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, USA), a strain genetically selected for disease resistance, and an Oceanic Institute (OI, Oahu, HI, USA) strain, selected for growth performance. BioWish 3P (BioWish Technologies, Cincinnati, OH, USA) was the selected probiotic. The study consisted of two separate trials, where all shrimp were raised under standard industry conditions and fed the same diet. Shrimp were stocked in 2920 L production tanks at a density of 200/m³ and acclimated for 14 days. After the acclimation period, triplicate tanks were supplemented daily for a duration of 28 days with probiotics, while three other tanks did not receive any treatment (controls). During the 28-day trial period, there was no statistically supported difference (p > 0.05) in either performance or health status as a result of genetic background or probiotic treatment. However, differences in gut bacterial composition, as assessed by high throughput sequencing of amplicons generated from the V1-V3 region of the bacterial 16S rRNA gene, were observed. The relative abundance of five major operational taxonomic units (OTUs) were found to vary significantly across experimental groups (p < 0.05). Notably, operational taxonomic unit (OTU) SD_Shr-00006 was at its highest abundance in d43 SIS samples, with levels greater than d71 samples of the same genetic line or any of the OI shrimp samples. OTUs for SD_Shr-00098 displayed a similar type of profile, but with highest abundance in the OI genetic line and lowest in the SIS shrimp. SD_Shr-00004 showed an opposite profile, with highest abundance in the SIS d71 samples and lowest in the SIS d43 samples. Together, these results suggest that host genetic background can be an important determinant of gut bacterial composition in aquaculture-raised whiteleg shrimp and indicate that development of strategies to manipulate the microbiome of this important seafood will likely need to be customized depending on the genetic line.

A 56‐day growth trial was conducted to determine the amount of fish meal (FM) in rainbow trout (Oncorhynchus mykiss) diets containing 200 g/kg FM as the sole animal protein source; that could be replaced with carinata (Brassica carinata) meal (CM) processed by aerobic conversion (AC, by fungi ssp.) followed by a single wash (ACCM). ACCM replaced 50, 100 and 150 g of FM. Replacement of ≥100 g of FM with ACCM, resulted in reduced (p < 0.01) growth, due to reduced dietary lysine and diet consumption (p < 0.01). Fulton's condition factor K decreased (p < 0.01) with increased FM replacement. FCR (p < 0.01) had an inverse relationship with diet consumption. The trend in FCR was similar to the trend in PER (p < 0.01). Apparent net protein utilization was lower (p < 0.01) for the highest FM replacement diet. There was no effect of FM replacement by ACCM on whole‐body composition or viscera, spleen and liver weights. However, visceral fat increased (p < 0.01) with increased feed consumption. There was no apparent effect of ACCM on hematocrit, haemoglobin or mean corpuscular haemoglobin contents. Results of this study indicate that replacement of ≥100 g of FM by ACCM in low FM/animal (200 g/kg) RBT diets may have been achieved if feed consumption and dietary lysine were similar.