Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers

Abstract

Background Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a “generalist” species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. Results In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. Conclusions A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers’ gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.

Characterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine

“…In this study, CAZymes were annotated from L. johnsonii N5 and N7 genomes using dbCAN2, and an identical number of CAZymes were identified in N5 and N7 genomes, including three carbohydrate esterase (CE) families, 13 carbohydrate-binding modules (CBM) families, 57 glycosyl transferases (GT) families, and 62 glycoside hydrolases (GH) families (Figure 4). Genes belonging to GHs and GTs exhibited the highest number in L. johnsonii N5 and N7, which is consistent with that identified in other Lactobacillus species including L. salivarius [17]. The GHs play a crucial role in the degradation of glycosidic bonds between the chain residues of the carbohydrate compounds, with GH13 being the predominant subgroup in L. johnsonii N5 and N7.…”

“…With the recent advancements in high-throughput sequencing technologies, notably longread sequencing technologies, it has become feasible to acquire complete genome sequences of bacterial strains [16]. This capability enhances the precise and confident identification of genes associated with probiotic properties and other traits through genome mining, as well as genes linked to evolution, including those related to host adaptation [17,18]. L. johnsonii was suggested to be positively associated with the ability to resist chronic heat stress-induced diarrhea in weaned piglets, as revealed by comparative microbiome profiling analysis in our previous study [19].…”

Comparative genomics and fermentation flavor characterization of five selected lactic acid bacteria provide predictions for flavor biosynthesis metabolic pathways in fermented muskmelon puree

“…The number of predicted CRISPR sequences ranged from 4 (Pp4) to 15 (Lp8). The current study suggests that the CRISPR regions, together with some Cas-related proteins, form an immune system that can block external DNA invasion (Wang, Xu, et al, 2023).…”

“…There were no predicted prophage sequences in Pp4; 2 to 11 gene islands were predicted in six LAB genomes (Table 2). Prophages and gene islands may enable bacteria to enhance adaptation to the environment, improve adhesion, or make bacteria pathogenic, and may also be used to assess genomic diversity during bacterial evolution (Wang, Xu, et al, 2023). The number of predicted CRISPR sequences ranged from 4 (Pp4) to 15 (Lp8).…”

Ligilactobacillus Salivarius improve body growth and anti-oxidation capacity of broiler chickens via regulation of the microbiota-gut-brain axis

“…Numerous studies have suggested that probiotic bacteria can promote livestock animals production. However, some studies have reported contrasting results [ 29 , 30 ]. Therefore, the benefits of candidate probiotic bacteria as a supplement for chicks should be further evaluated.…”