In silico, in vitro and in vivo characterization of host-associated Latilactobacillus curvatus strains for potential probiotic applications in farmed Atlantic salmon (Salmo salar)

Abstract

Salmon aquaculture is the fastest growing animal protein production system in the world; however, intensive farming leads to poor weight gain, stress, and disease outbreaks. Probiotics offer the potential to enhance growth performance and feed efficiency in Atlantic salmon, as well as immunostimulate fish against common pathogens, benefitting farmers and consumers with more efficient production. Here, we isolated and identified 900 native microbial isolates including 18 Lactobacilli from the farmed salmon intestines. Based on whole-genome sequencing and phylogenetic analysis, the Lactobacillus candidates belonged to Latilactobacillus curvatus (L. curvatus) species and formed two distinct phylogenetic groups. Using bioinformatics and in vitro analyses, we selected two candidates L. curvatus ATCC PTA-127116 and L. curvatus ATCC PTA-127117, which showed desirable safety and probiotic properties. The two L. curvatus candidates were evaluated for safety and efficacy (higher final weight) in Atlantic salmon alongside spore-forming Bacilli isolated from salmon, poultry, and swine. All the tested candidates were safe to salmon with no adverse effects. While we did not see efficacy in any Bacillus supplemented groups, compared to untreated group, the group administered with the two L. curvatus strains consortium in feed for seven weeks in freshwater showed indicators of improvement in final body weight by 4.2%. Similarly, the two L. curvatus candidates were also evaluated for safety and efficacy in Atlantic salmon in saltwater; the group administered with the two L. curvatus strains consortium in feed for 11 weeks showed indicators of improvement in final body weight by 4.7%. Comprehensive metabolomics analyses in the presence of different prebiotics and/or additives identified galactooligosaccharide as a potential prebiotic to enhance the efficacy of two L. curvatus candidates. All together, these data provide comprehensive genomic, phenotypic and metabolomic evidence of safety and desirable probiotic properties as well as indicators of in vivo efficacy of two novel endogenous L. curvatus candidates for potential probiotic applications in Atlantic salmon. The in vivo findings need to be confirmed in larger performance studies, including field trials.

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

“…In particular, the lactic acidproducing bacteria (LAB) Lactobacillus and Limosilactobacillus, which are renowned for their improvements to fish disease resistance via immunostimulation (16), were observed to express genes encoding xylosidases, glucosidases, and galactosidases related to xyloglucans and galactans utilization. These findings conform with their capabilities to metabolize commercially available galacto-oligosaccharides (GOS) previously identified to stimulate growth of similar LAB under in vitro culture conditions (17). However, our in vivo detection of GH42 β-galactosidases and GH43 arabinofuranosidases point to an improved capacity of using substrates with more complex structure, such as pectinderived galactans or (arabino)xyloligosaccharides from cereals, than many commercial undecorated GOS (synthesized from monomers obtained from animal products i.e., lactose from milk), and which could be extrapolated into sustainable feed supplements as a LAB-specific MDF (18).…”

The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping

“…Species novelty was additionally supported with established 16S rRNA gene sequence identity of 98.7-94.5% using available genomes in NCBI 21 . We further supplemented the resulting genome collection with 19 previously published genomes of gut-derived Latilactobacillus isolates from salmons farmed in Norway and North America 22 , amounting to a total of 131 genomes of isolated strains.…”