Dataset Information

Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig.

ABSTRACT: Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180?bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome.

SUBMITTER: Zhou B

PROVIDER: S-EPMC7441245 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig.

Zhou Binghui B Albarracin Leonardo L Masumizu Yuki Y Indo Yuhki Y Islam M Aminul MA Garcia-Castillo Valeria V Ikeda-Ohtsubo Wakako W Suda Yoshihito Y Aso Hisashi H Villena Julio J Kitazawa Haruki H

Microbiology resource announcements 20200820 34

<i>Ligilactobacillus salivarius</i> FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome. ...[more]

PMID: 32816987

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Project description:In this article, Ligilactobacillus salivarius FFIG strains, isolated from the intestinal tract of wakame-fed pigs, are characterized according to their potential probiotic properties. Strains were evaluated by studying their interaction with porcine intestinal epithelial (PIE) cells in terms of their ability to regulate toll-like receptor (TLR)-3- or TLR4-mediated innate immune responses, as well as by assessing their adhesion capabilities to porcine epithelial cells and mucins. These functional studies were complemented with comparative genomic evaluations using the complete genome sequences of porcine L. salivarius strains selected from subgroups that demonstrated different "immune" and "adhesion" phenotypes. We found that their immunomodulatory and adhesion capabilities are a strain-dependent characteristic. Our analysis indicated that the differential immunomodulatory and adhesive activities of FFIG strains would be dependent on the combination of several surface structures acting simultaneously, which include peptidoglycan, exopolysaccharides, lipoteichoic acid, and adhesins. Of note, our results indicate that there is no correlation between the immunomodulatory capacity of the strains with their adhesion ability to mucins and epithelial cells. Therefore, in the selection of strains destined to colonize the intestinal mucosa and modulate the immunity of the host, both properties must be adequately evaluated. Interestingly, we showed that L. salivarius FFIG58 functionally modulated the innate immune responses triggered by TLR3 and TLR4 activation in PIE cells and efficiently adhered to these cells. Moreover, the FFIG58 strain was capable of reducing rotavirus replication in PIE cells. Therefore, L. salivarius FFIG58 is a good candidate for further in vivo studying the protective effect of lactobacilli against intestinal infections in the porcine host. We also reported and analyzed, for the first time, the complete genome of several L. salivarius strains that were isolated from the intestine of pigs after the selective pressure of feeding the animals with wakame. Further genomic analysis could be of value to reveal the metabolic characteristics and potential of the FFIG strains in general and of the FFIG58 strain, in particular, relating to wakame by-products assimilation.

Project description:Emerging threats of antimicrobial resistance necessitate the exploration of effective alternatives for healthy livestock growth strategies. 'Immunosynbiotics', a combination of immunoregulatory probiotics and prebiotics with synergistic effects when used together in feed, would be one of the most promising candidates. Lactobacilli are normal residents of the gastrointestinal tract of pigs, and many of them are able to exert beneficial immunoregulatory properties. On the other hand, wakame (Undaria pinnafida), an edible seaweed, has the potential to be used as an immunoregulatory prebiotic when added to livestock feed. Therefore, in order to develop a novel immunosynbiotic, we isolated and characterized immunoregulatory lactobacilli with the ability to utilize wakame. Following a month-long in vivo wakame feeding trial in 8-week-old Landrace pigs (n = 6), sections of intestinal mucous membrane were processed for bacteriological culture and followed by identification of pure colonies by 16S rRNA sequence. Each isolate was characterized in vitro in terms of their ability to assimilate to the wakame and to differentially modulate the expression of interleukin-6 (IL-6) and interferon beta (IFN-β) in the porcine intestinal epithelial (PIE) cells triggered by Toll-like receptor (TLR)-4 and TLR-3 activation, respectively. We demonstrated that feeding wakame to pigs significantly increased the lactobacilli population in the small intestine. We established a wakame-component adjusted culture media that allowed the isolation and characterization of a total of 128 Lactobacilli salivarius colonies from the gut of wakame-fed pigs. Interestingly, several L. salivarius isolates showed both high wakame assimilation ability and immunomodulatory capacities. Among the wakame assimilating isolates, L. salivarius FFIG71 showed a significantly higher capacity to upregulate the IL-6 expression, and L. salivarius FFIG131 showed significantly higher capacity to upregulate the IFN-β expression; these could be used as immunobiotic strains in combination with wakame for the development of novel immunologically active feeds for pigs.

Project description:BackgroundLigilactobacillus 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.ResultsIn 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.ConclusionsA 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.

Dataset Information

Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig.

Publications

Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig.

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