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

Liu, Yen-Yi; Hsu, Chu-Yi; Yang, Ya-Chu; Huang, Chien-Hsun; Chen, Chih-Chieh

doi:10.1093/bioadv/vbad153

Cited by 4 publications

(2 citation statements)

References 49 publications

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“…Putative biosynthetic gene clusters were predicted using AntiSMASH software (v. 6.0) [ 43 ]. Antimicrobial resistance genes were searched for in the genome of strain H164 T based on the Comprehensive Antibiotic Resistance Database (CARD) Variants v4.0.0 [ 44 ], ResFinder v4.0 [ 45 ], and AMRFinderPlus v3.10.42 [ 46 ] using ProbioMinServer [ 47 ].…”

Section: Methodsmentioning

confidence: 99%

Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

Wang,

Lin,

Hsieh

et al. 2024

Pathogens

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A novel coagulase-negative Staphylococcus strain (H164T) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164T strain is a member of the genus Staphylococcus. We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to Staphylococcus gallinarum, Staphylococcus nepalensis, Staphylococcus cohnii, and Staphylococcus urealyuticus. The average nucleotide identity and digital DNA-DNA hybridization values between H164T and its closest relatives were <95% and <70%, respectively. The H164T strain could also be distinguished from its closest relatives by the fermentation of fructose, maltose, maltose, trehalose, and mannitol; the activities of α-glucosidase; and alkaline phosphatase. The major cellular fatty acids and predominant menaquinones were C15:0 iso and C15:0 anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named Staphylococcus hsinchuensis sp. nov., with the type strain H164T (=BCRC 81404T = NBRC 116174T).

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Section: Methodsmentioning

confidence: 99%

Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

Wang,

Lin,

Hsieh

et al. 2024

Pathogens

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“…The primary metabolite gene clusters were predicted using gutSMASH (version 1.0) software [39]. The antimicrobial resistance, virulence factor and pathogenic genes were searched in the genomes of strains HLW78 T and CYL33 based on the Comprehensive Antibiotic Resistance Database Variants version 4.0.0 [40], ResFinder version 4.0 [41], AMRFinderPlus version 3.10.42 [42], the Virulence Factor Database (June 2022 release) [43], CGE VirulenceFinder 2.0.3 [44] and the Pathogen Host Interactions database version 4.14 [45] through the ProbioMinServer [46]. PlasmidFinder version 2.0.1 and PlasmidHunter version 1.0 were used for the detection of plasmids [47,48].…”

Section: Genome Featuresmentioning

confidence: 99%

Faecalibacterium taiwanense sp. nov., isolated from human faeces

Liou,

Zhang,

Hsu

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3–98.1 % and 79.0–79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8–97.9 % and 70.9–80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1–97.3 % and 80.3–80.5 %), Faecalibacterium longum CM04-06T(97.8–98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3–97.4 % and 82.7–82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA–DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6–85.1 %, 71.4–85.2 % and 28.3–30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).

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Probio-Ichnos: A Database of Microorganisms with In Vitro Probiotic Properties

Tsifintaris,

Kiousi,

Repanas

et al. 2024

Microorganisms

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Probiotics are live microorganisms that, when consumed in adequate amounts, exert health benefits on the host by regulating intestinal and extraintestinal homeostasis. Common probiotic microorganisms include lactic acid bacteria (LAB), yeasts, and Bacillus species. Here, we present Probio-ichnos, the first manually curated, literature-based database that collects and comprehensively presents information on the microbial strains exhibiting in vitro probiotic characteristics (i.e., resistance to acid and bile, attachment to host epithelia, as well as antimicrobial, immunomodulatory, antiproliferative, and antioxidant activity), derived from human, animal or plant microbiota, fermented dairy or non-dairy food products, and environmental sources. Employing a rigorous methodology, we conducted a systematic search of the PubMed database utilizing the keyword ‘probiotic’ within the abstracts or titles, resulting in a total of 27,715 studies. Upon further manual filtering, 2207 studies presenting in vitro experiments and elucidating strain-specific probiotic attributes were collected and used for data extraction. The Probio-ichnos database consists of 12,993 entries on the in vitro probiotic characteristics of 11,202 distinct strains belonging to 470 species and 143 genera. Data are presented using a binary categorization approach for the presence of probiotic attributes according to the authors’ conclusions. Additionally, information about the availability of the whole-genome sequence (WGS) of strains is included in the database. Overall, the Probio-ichnos database aims to streamline the navigation of the available literature to facilitate targeted validation and comparative investigation of the probiotic properties of the microbial strains.

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

Cited by 4 publications

References 49 publications

Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk

Faecalibacterium taiwanense sp. nov., isolated from human faeces

Probio-Ichnos: A Database of Microorganisms with In Vitro Probiotic Properties

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