Dataset Information

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains.

ABSTRACT:

Motivation

ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g. antimicrobial resistance, virulence, pathogenic, plasmid, and prophage genes) and functionality (e.g. functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucial methodology for investigating the safety and functionality of probiotics in food and feed. This shift is primarily attributed to the growing affordability of next-generation sequencing technologies. However, no integrated platform is available for simultaneously evaluating probiotic strain safety, investigating probiotic functionality, and identifying known phylogenetically related strains.

Results

Thus, we constructed a new platform, ProbioMinServer, which incorporates these functions. ProbioMinServer accepts whole-genome sequence files in the FASTA format. If the query genome belongs to the 25 common probiotic species collected in our database, the server performs a database search and analyzes the core-genome multilocus sequence typing. Front-end applications were implemented in JavaScript with a bootstrap framework, and back-end programs were implemented using PHP, Perl, and Python. ProbioMinServer can help researchers quickly and easily retrieve information on the safety and functionality of various probiotics.

Availability and implementation

The platform is available at https://probiomindb.imst.nsysu.edu.tw.

SUBMITTER: Liu YY

PROVIDER: S-EPMC10625473 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains.

Liu Yen-Yi YY Hsu Chu-Yi CY Yang Ya-Chu YC Huang Chien-Hsun CH Chen Chih-Chieh CC

Bioinformatics advances 20231018 1

<h4>Motivation</h4>ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g. antimicrobial resistance, virulence, pathogenic, plasmid, and prophage genes) and functionality (e.g. functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucia ...[more]

PMID: 37928343

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Project description:Roseburia intestinalis is an anaerobic bacterium that produces butyric acid and belongs to the phylum Firmicutes. There is increasing evidence that this bacterium has positive effects on several diseases, including inflammatory bowel disease, atherosclerosis, alcoholic fatty liver, colorectal cancer, and metabolic syndrome, making it a potential "Next Generation Probiotic." We investigated the genomic characteristics, probiotic properties, cytotoxicity, oral toxicity, colonization characteristics of the bacterium, and its effect on the gut microbiota. The genome contains few genes encoding virulence factors, three clustered regularly interspaced short palindromic repeat (CRISPR) sequences, two Cas genes, no toxic biogenic amine synthesis genes, and several essential amino acid and vitamin synthesis genes. Seven prophages and 41 genomic islands were predicted. In addition to a bacteriocin (Zoocin A), the bacterium encodes four metabolic gene clusters that synthesize short-chain fatty acids and 222 carbohydrate-active enzyme modules. This bacterium is sensitive to antibiotics specified by the European Food Safety Authority, does not exhibit hemolytic or gelatinase activity, and exhibits some acid resistance. R. intestinalis adheres to intestinal epithelial cells and inhibits the invasion of certain pathogens. In vitro experiments showed that the bacterium was not cytotoxic. R. intestinalis did not affect the diversity or abundance of the gut flora. Using the fluorescent labelling method, we discovered that R. intestinalis colonizes the cecum and mucus of the colon. An oral toxicity study did not reveal any obvious adverse effects. The lethal dose (LD)50 of R. intestinalis exceeded 1.9 × 109 colony forming units (CFU)/kg, whereas the no observed adverse effect level (NOAEL) derived from this study was 1.32 × 109 CFU/kg/day for 28 days. The current research shows that, R. intestinalis is a suitable next-generation probiotic considering its probiotic properties and safety.

Project description:BackgroundProbiotics are defined as adequate amount of live microorganisms able to confer health benefits on the host. Currently, most commercially available probiotic products in the market belong to genera Lactobacillus. Traditional dairy products are usually rich source of Lactobacillus strains with significant health benefits. In order to evaluate the probiotic potential of these bacteria, it is essential to assess their health benefits, efficacy, and safety.ObjectivesThe probiotic efficacy of two Lactobacillus strains namely Lactobacillus pentosus LP05 and L. brevis LB32 was evaluated. They were previously isolated from ewes' milk in a rural area in East Azerbaijan, Iran.Materials and methodsThe selected isolates were tested for certain phenotypic characters and identified to genus and species level by 16S rRNA gene sequencing and species specific primers. Further analysis included acid and bile resistance, antagonistic activity, cholesterol removing ability, survival in simulated gastric and upper intestine contents, aggregation and coaggregation properties. Finally, the adhering ability of the selected Lactobacillus strains to epithelial cells was tested using Caco-2 cell lines.ResultsThe selected isolates tolerated bile salt concentrations ranging from 0.5% to 3%, however their coefficient of inhibition were varied. Both isolates hydrolyzed bile and grew at pH values of 3, 4, and 5, while isolate LP05 was not able to hydrolyze arginine. Based on 16s rRNA gene sequencing and species-specific primers, the isolates were identified as L. brevis LB32 and L. pentosus LP05. In contrast to simulated gastric conditions, the growth rate of the isolates in alkaline conditions of upper intestine increased significantly with the passage of time reaching its maximum in 24 hours. These 2 isolates inhibited the growth of Listeria monocytogenes, Salmonella enteritidis, Shigella dysenteriae, Staphylococcus aureus, and Streptococcus pneumonia. Furthermore, L. brevis LB32 was able to reduce approximately 86% of cholesterol compared to L. pentosus LP05, which showed only 69% of reduction. Higher aggregation and coaggregation percentage and adherence to Caco-2 cell line was observed in L. pentosus LP05 compared to L. brevis LB32.ConclusionsThis research study proved the presence of viable probiotic LAB microflora in the ewe milk with enhanced health benefits. The 2 selected Lactobacillus strains could be exploited in dairy or pharmaceutical industry in future.

Dataset Information

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains.

Motivation

Results

Availability and implementation

Publications

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains.

Similar Datasets

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