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The development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii , was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity ( p  < 0.05) in shrimp, Litopenaeus vannamei . The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.

Probiotics are live, non-pathogenic microorganisms that help to improve the host's gut health when administrated in sufficient proportions and are now serving as effective alternatives to antibiotics for managing animal infections and enhancing production. The objective of this study was to isolate, identify and characterize lactic acid bacteria (LAB) strains with excellent probiotic properties from the gastrointestinal tract (GIT) of retail broiler chickens. Samples were enriched in MRS broth at 37°C and plated on MRS agar to isolate distinct colonies of potential probiotic candidates. The isolates underwent a series of standard morphological and biochemical analysis to fulfill the criteria for presumptive identification of LAB and probiotic characteristics. These analyses included Gram staining, catalase testing, hemolytic activity assays, tolerance assays to NaCl, simulated gastric juice and bile salts, antagonistic activity assays, antibiotic susceptibility testing, cell adhesion assay and genotypic identification through 16S rRNA gene sequencing. A total of 40 microbial strains were isolated from the GIT of 20 retail broiler chickens. Among these, 4 LAB strains showed the best probiotic results and were genotypically identified as Enterococcus faecium MCI7, Pedicoccus pentosaceus MCI10, Pediococcus pentosaceus MCC6 and Pediococcus pentosaceus MCC12. The selected strains exhibited non-hemolytic activity and were able to survive in simulated gastric juice at pH 3. Furthermore, the strains displayed bile salt tolerance in the presence of 0.3% bile salt for 4 hours, ranging from 21.91 to 32.77% and a wide range of antimicrobial activities against various pathogenic bacterial strains with inhibition zones ranging from 10 to 16.5 mm. Moreover, three P. pentosaceus strains (MCI10, MCC6, MCC12) were sensitive to most of the tested antibiotics and demonstrated good adherence abilities. Our study identified four LAB strains as promising probiotic candidates for poultry feed additives to effectively establish intestinal microflora, enhance meat quality and growth, and control pathogens.

Background Compelling evidences demonstrated that gut microbiota dysbiosis plays a critical role in the pathogenesis of inflammatory bowel diseases (IBD). Therapies for targeting the microbiota may provide alternative options for the treatment of IBD, such as probiotics. Here, we aimed to investigate the protective effect of a probiotic strain, Pediococcus pentosaceus ( P. pentosaceus ) CECT 8330, on dextran sulfate sodium (DSS)-induced colitis in mice. Methods C57BL/6 mice were administered phosphate-buffered saline (PBS) or P. pentosaceus CECT 8330 (5 × 10 8  CFU/day) once daily by gavage for 5 days prior to or 2 days after colitis induction by DSS. Weight, fecal conditions, colon length and histopathological changes were examined. ELISA and flow cytometry were applied to determine the cytokines and regulatory T cells (Treg) ratio. Western blot was used to examine the tight junction proteins (TJP) in colonic tissues. Fecal short-chain fatty acids (SCFAs) levels and microbiota composition were analyzed by targeted metabolomics and 16S rRNA gene sequencing, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of orthologous groups of proteins (COG) pathway analysis were used to predict the microbial functional profiles. Results P. pentosaceus CECT 8330 treatment protected DSS-induced colitis in mice as evidenced by reducing the weight loss, disease activity index (DAI) score, histological damage, and colon length shortening. P. pentosaceus CECT 8330 decreased the serum levels of proinflammatory cytokines (TNF-α, IL-1β, and IL-6), and increased level of IL-10 in DSS treated mice. P. pentosaceus CECT 8330 upregulated the expression of ZO-1, Occludin and the ratio of Treg cells in colon tissue. P. pentosaceus CECT 8330 increased the fecal SCFAs level and relative abundances of several protective bacteria genera, including norank_f_Muribaculaceae , Lactobacillus , Bifidobacterium , and Dubosiella . Furthermore, the increased abundances of bacteria genera were positively correlated with IL-10 and SCFAs levels, and negatively associated with IL-6, IL-1β, and TNF-α, respectively. The KEGG and COG pathway analysis revealed that P. pentosaceus CECT 8330 could partially recover the metabolic pathways altered by DSS. Conclusions P. pentosaceus CECT 8330 administration protects the DSS-induced colitis and modulates the gut microbial composition and function, immunological profiles, and the gut barrier function. Therefore, P. pentosaceus CECT 8330 may serve as a promising probiotic to ameliorate intestinal inflammation.

Pediococcus pentosaceus is well known for its probiotic properties, including roles in improving health, antimicrobial production, and enhancing fermented food quality. This study aimed to comprehensively analyze the whole genome of P . pentosaceus MBBL6, isolated from healthy cow milk, to assess its probiotic and antimicrobial potentials. P . pentosaceus MBBL6, isolated from a healthy cow milk at BSMRAU dairy farm, Gazipur, Bangladesh, underwent comprehensive genomic analysis, including whole genome sequencing, assembly, annotation, phylogenetic comparison, and assessment of metabolic pathways and secondary metabolites. Antimicrobial efficacy was evaluated through in-vitro and in-vivo studies, alongside in-silico exploration for potential mastitis therapy. We predicted 1,906 genes and 204 SEED sub-systems involved in carbohydrate metabolism and vitamin B complex biosynthesis, with a focus on lactose metabolism in MMBL6. Notably, 43 putative carbohydrate-active enzyme genes, including lysozymes, suggest the ability of MBBL6 for carbohydrate biotransformation and antimicrobial activity. The genome also revealed primary metabolic pathways for arginine and gallic acid metabolism and secondary metabolite gene clusters, including T3PKS and RiPP-like regions. Importantly, two bacteriocin biosynthesis gene clusters namely bovicin_255 _variant and penocin_A , were identified in MBBL6. The safety assessment of MBBL6 genome revealed no virulence genes and a low pathogenicity score (0.196 out of 1.0). Several genes related to survival in gastrointestinal tract and colonization were also identified. Furthermore, MBBL6 exhibited susceptibility to a wide range of antibiotics in-vitro , and effectively suppressed mastitis pathogens in an in-vivo mouse mastitis model trial. The observed bacteriocin, particularly bovicin, demonstrated the ability to disrupt the function of an essential protein, Rho factor of mastitis pathogens by blocking transcription termination process. Taken together, our in-depth genomic analysis underscores the metabolic versatility, safety profile, and antimicrobial potential of P . pentosaceus MBBL6, suggesting its promise for applications in therapeutics, bioremediation, and biopreservation.

Background The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. Results The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. Conclusion This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.

Currently, there is an increasing use of whole‐genome sequencing (WGS) studies to investigate the molecular taxonomy, metabolic properties, enzyme capabilities, and bioactive substances of lactic acid bacteria (LAB) species. In this study, the genome of strain Pediococcus pentosaceus BBS1 was sequenced using the Illumina HiSeq. 2500 platform to determine its classification, annotate its main features, and evaluate its safety characteristics. Results showed an average nucleotide identity (ANI) value of 99.60% for Pediococcus pentosaceus BBS1. P. pentosaceus BBS1 genome was composed of a 1,840,613 bp circular chromosome with a GC content of 37.23%, which contained 1778 predicted protein‐coding sequences (CDSs). Rapid Annotation using Subsystems Technology (RAST) linked to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that strain BBS1 possesses l‐acetate dehydrogenase (l‐LDH; EC 1.1.1.27) and d‐lactate dehydrogenase (d‐LDH; EC 1.1.1.28), which are the genes responsible for lactic acid production. Additionally, it was found to contain linamarase, or β‐glucosidases (EC 3.2.1.21), a gene that functions for cyanide degradation. Significantly, the safety studies carried out using WGS confirmed the absence of virulence factors, biogenic amines, and antibiotic‐resistance genes in BBS1. Our previous research conducted in this study have shown that BBS1 possesses probiotic features, including tolerance to the simulated artificial gastrointestinal tract, bacterial adhesion, antibacterial activity, and antioxidant function. The findings provided herein significantly enhanced the known information on BBS1, supporting its potential application in promoting health through food products. Pediococcus pentosaceus BBS1 was analyzed by whole genome sequencing for its classification, annotated its main features for significant genes, and safety characteristics. The strain has the potential to be used as a beneficial probiotic starter culture, improving the quality of the fermented bamboo and related products.

Pediococcus pentosaceus Li05, a strain of lactic acid bacteria isolated from the faeces of healthy volunteers, exhibited potential protective effects against various diseases. This study performed third‐generation sequencing and detailed characterisation of its genome. The Li05 chromosome harboured conserved genes associated with acid resistance (atp), bile salt resistance (bsh), oxidative stress resistance (hsl, dltA, and et al.), and adhesion (nrd, gap, and et al.), whereas the plasmid did not contain antibiotic resistance or virulence genes. Following intervention with Li05 in loperamide‐induced constipated mice, constipation symptoms improved. Meanwhile, alterations in gut microbiota, increased BSH activity in faeces, and modifications to the faecal bile acid profile were observed. Additionally, expression levels of TGR5 and TPH1 in the colon of the mice increased, leading to elevated 5‐HT levels. When the TGR5 gene was knocked out or the TPH1 inhibitor LX1606 was administered to suppress 5‐HT synthesis in constipated mice, the beneficial effects of Li05 on gastrointestinal motility and mucus secretion were reversed. Culturing intestinal organoids demonstrated that increased bile acids such as DCA, Iso‐LCA, and EALCA could enhance 5‐HT levels through the TGR5/TPH1 axis. Therefore, we concluded that Li05 regulated bile acid metabolism, subsequently increasing 5‐HT levels through the TGR5/TPH1 axis, thus alleviating constipation. The mechanism of Li05 in alleviating constipation. Li05 intervention regulated gut microbiota and bile acid metabolism, increasing 5‐HT levels through the TGR5/TPH1 activation to ameliorate constipation.

Lactic acid bacteria (LAB) are important in food fermentation and may enhance overall host health. Previous studies to explore LAB metabolism mainly focused on the genera Lacticaseibacillus and Lactococcus. Pediococcus pentosaceus, historically recognized as an important food fermentation bacterial strain, can produce bacteriocins and occasionally demonstrated probiotic functionalities. This study thoroughly surveyed the growth kinetic of three P. pentosaceus isolates in various culture formulations, especially in fructooligosaccharide (FOS), xylooligosaccharide (XOS), or konjac mannooligosaccharide (KMOS) conditions. Results showed that P. pentosaceus effectively metabolized KMOS, the culture of which led to 23.6-fold population increase. However, FOS and XOS were less metabolized by P. pentosaceus. On functional oligosaccharide cultures, P. pentosaceus could result in higher population proliferation, more acidified fermentation environment, and higher glycoside hydrolysis activities in the culture. RNA-Seq analysis classified 1572 out of 1708 putative genes as mRNA-coding genes. The dataset also revealed that the three functional oligosaccharides led to extensive global functional gene regulations. Phosphate conservation and utilization efficiency enhancement may serve as a leading transcriptional regulation direction in functional oligosaccharide metabolisms. In summary, these discovered metabolic characteristics could be employed to support future studies.Key points• Konjac mannooligosaccharides effectively promoted P. pentosaceus proliferation.• Functional genes were highly regulated in functional oligosaccharide utilization.• Phosphate conservation was an important transcriptional regulation direction.

A total of 187 lactic acid bacteria were isolated from four types of grains collected in South Korea. The bacterial strains were assigned as members of Levilactobacillus brevis, Latilactobacillus curvatus, Lactiplantibacillus plantarum , Lactococcus taiwanensis , Pediococcus pentosaceus , and Weissella paramesenteroides based on the closest similarity using 16S rRNA gene sequence analysis. The strains belonging to the same species were analyzed using RAPD-PCR, and one or two among strains showing the same band pattern were selected. Finally, 25 representative strains were selected for further functional study. Inhibitory effects of lipid accumulation were observed in the strains tested. Pediococcus pentosaceus K28, Levilactobacillus brevis RP21 and Lactiplantibacillus plantarum RP12 significantly reduced lipid accumulation and did not show cytotoxicity in C3H10T1/2 cells at treatment of 1–200 μg/mL. The three LAB strains decreased significantly expression of six adipogenic marker genes, PPARγ , C/EBPα , CD36 , LPL , FAS and ACC , in C3H10T1/2 adipocytes. The three strains survived under strong acidity and bile salt conditions. The three strains showed adhesion to Caco-2 cells similar to a reference strain LGG. The resistance of the three strains to several antibiotics was also assessed. Strains RP12 and K28 were confirmed not to produce harmful enzymes based on API ZYM kit results. Based on these results, strains K28, RP21 and RP12 isolated from grains had the ability to inhibit adipogenesis in adipocytes and potentially be useful as probiotics.

Lactic acid bacteria (LAB) exopolysaccharides (EPS) are highly valuable due to their unique structure and functional properties. Pediococcus pentosaceus E3 is a promising marine probiotic strain. An investigation of the E3 genome identified a gene cluster responsible for EPS production, comprising 13 genes organized into four regions: the regulatory region for EPS expression, the chain length determination region, genes that catalyze the biosynthesis of EPS repeat units, and genes for polymerization and EPS transportation. Furthermore, a total of 16 key enzymes involved in the nucleotide sugar biosynthesis pathway were predicted according to the KEGG metabolic pathways in the E3 genome sequence. Therefore, the current study investigates the characteristics and bioactivities of E3-EPS. E3 strain was grown in MRS broth supplied with 1.0% sucrose for EPS production, and E3 produced a significant quantity of EPS (400 mg/L). Structural characteristics of E3-EPS were investigated through carbohydrate content determination, FTIR, SEM, EDX, TGA, HPLC, and NMR. HPLC analysis revealed that E3-EPS is a heteropolysaccharide composed of four sugar moieties: galactose, glucose, mannose, and fucose. Moreover, E3-EPS demonstrated promising bioactivities, as its anticancer activity was evaluated against colon cancer cell lines, and the IC 50 value was determined to be 77.05 ± 0.24 µg/mL. E3-EPS inhibited α-amylase activity by 58.3% and 82.8% at 10 and 100 µg/mL concentrations, respectively. Additionally, E3-EPS successfully decreases the expression levels of inflammatory cytokines (TNF-α and IL-6). The findings of this study suggest that the safe marine probiotic P. pentosaceus E3 is a source of unique EPS suitable for pharmacological applications.