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Verni M, Torreggiani A, Patriarca A, Brasili E, Sciubba F, Rizzello CG. Sourdough fermentation for the valorization of sorghum flour: Microbiota characterization and metabolome profiling. Int J Food Microbiol 2024; 421:110805. [PMID: 38917489 DOI: 10.1016/j.ijfoodmicro.2024.110805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
Due to a large adaptability to different cultivation conditions and limited input compared to other cereals, sorghum is considered an emerging crop. Its antioxidant properties, high fiber content and low glycemic index also make it a valuable addition to a healthy diet, nevertheless, the presence of antinutritional factors and the lack of gluten, hamper its use as food ingredient. This study investigated the impact of sourdough fermentation on sorghum nutritional quality. Lactic acid bacteria dominating sorghum flour and sourdough were identified by culture-dependent analysis revealing Lactiplantibacillus plantarum as the dominant species found in the mature sourdough, whereas Weissella cibaria and Weissella paramesenteroides were the species isolated the most after the first refreshment. Among yeasts, Saccharomyces cerevisiae was the most prevalent. Lactic acid bacteria pro-technological and functional performances as starter were evaluated in sorghum type-II sourdoughs through an integrated characterization combining chromatographic and NMR spectroscopic techniques. The metabolic profile of the strains mainly grouped together W. cibaria strains and W. paramesenteroides AI7 which distinguished for the intense proteolysis but also for the presence of compounds particularly interesting from a physiological perspective (allantoin, glutathione, γ-aminobutyric acid and 2-hydroxy-3-methylbutyric acid), whose concentration increased during fermentation in a species or strain specific matter.
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Affiliation(s)
- Michela Verni
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Andrea Torreggiani
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Adriano Patriarca
- Department of Chemistry, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Elisa Brasili
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; NMR-based Metabolomics Laboratory (NMLab), "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fabio Sciubba
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; NMR-based Metabolomics Laboratory (NMLab), "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carlo Giuseppe Rizzello
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Yoon KN, Lee HG, Yeom SJ, Kim SS, Park JH, Song BS, Yi SW, Do YJ, Oh B, Oh SI, Eun JB, Park SH, Lee JH, Kim HB, Lee JH, Hur TY, Kim JK. Lactiplantibacillus argentoratensis AGMB00912 alleviates salmonellosis and modulates gut microbiota in weaned piglets: a pilot study. Sci Rep 2024; 14:15466. [PMID: 38965336 PMCID: PMC11224356 DOI: 10.1038/s41598-024-66092-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
This study aimed to evaluate the efficacy of Lactiplantibacillus argentoratensis AGMB00912 (LA) in reducing Salmonella Typhimurium infection in weaned piglets. The investigation focused on the influence of LA on the gut microbiota composition, growth performance, and Salmonella fecal shedding. The results indicated that LA supplementation significantly improved average daily gain and reduced the prevalence and severity of diarrhea. Fecal analysis revealed reduced Salmonella shedding in the LA-supplemented group. Furthermore, LA notably altered the composition of the gut microbiota, increasing the levels of beneficial Bacillus and decreasing those of harmful Proteobacteria and Spirochaetes. Histopathological examination showed less intestinal damage in LA-treated piglets than in the controls. The study also observed that LA affected metabolic functions related to carbohydrate, amino acid, and fatty acid metabolism, thereby enhancing gut health and resilience against infection. Short-chain fatty acid concentrations in the feces were higher in the LA group, suggesting improved gut microbial activity. LA supplementation enriched the population of beneficial bacteria, including Streptococcus, Clostridium, and Bifidobacterium, while reducing the number of harmful bacteria, such as Escherichia and Campylobacter. These findings indicate the potential of LA as a probiotic alternative for swine nutrition, offering protective effects to the gut microbiota against Salmonella infection.
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Affiliation(s)
- Ki-Nam Yoon
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Han Gyu Lee
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Seo-Joon Yeom
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sang-Su Kim
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jong-Heum Park
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Beom-Seok Song
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung-Won Yi
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Yoon Jung Do
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Byungkwan Oh
- Biosafety Research Institute and College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Sang-Ik Oh
- Biosafety Research Institute and College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Jong-Bang Eun
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, 56212, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tai-Young Hur
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
| | - Jae-Kyung Kim
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.
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3
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Aljohani A, Rashwan N, Vasani S, Alkhawashki A, Wu TT, Lu X, Castillo DA, Xiao J. The Health Benefits of Probiotic Lactiplantibacillus plantarum: A Systematic Review and Meta-Analysis. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10287-3. [PMID: 38816672 DOI: 10.1007/s12602-024-10287-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2024] [Indexed: 06/01/2024]
Abstract
To ensure effective administration of probiotics in clinical practice, it is crucial to comprehend the specific strains and their association with human health. Therefore, we conducted a systematic review and meta-analysis to evaluate the scientific evidence on the impact of Lactiplantibacillus plantarum probiotic consumption on human health. Out of 11,831 records, 135 studies were assessed qualitatively, and 18 studies were included in the meta-analysis. This systematic review demonstrated that probiotic supplementation with L. plantarum, either alone or in combination, can significantly improve outcomes for patients with specific medical conditions. Meta-analysis revealed notable benefits in periodontal health, evidenced by reduced pocket depth and bleeding on probing (p < 0.001); in gastroenterological health, marked by significant reductions in abdominal pain (p < 0.001); and in infectious disease, through a reduction in C-reactive protein levels (p < 0.001). Cardiovascular benefits included lowered total cholesterol and low-density lipoprotein cholesterol in the L. plantarum intervention group (p < 0.05). Our study's clinical significance highlights the importance of considering probiotic strain and their application to specific diseases when planning future studies and clinical interventions, emphasizing the need for further research in this area.
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Affiliation(s)
- Amal Aljohani
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - Noha Rashwan
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - Shruti Vasani
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - Ahmed Alkhawashki
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
- Pediatrics, King Fahd Medical City, Riyadh, Saudi Arabia
| | - Tong Tong Wu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, USA
| | - Xingyi Lu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, USA
| | - Daniel A Castillo
- Miner Library, University of Rochester Medical Center, Rochester, NY, USA
| | - Jin Xiao
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA.
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Lan Z, Huang H, Liu C, Li J, Li X. Lactiplantibacillus sp. G6 isolated from goose intestine as starter culture for degrading nitrite and improving quality in Chinese pickle fermentation. Food Sci Biotechnol 2024; 33:1413-1423. [PMID: 38585556 PMCID: PMC10992155 DOI: 10.1007/s10068-023-01433-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/13/2023] [Accepted: 09/10/2023] [Indexed: 04/09/2024] Open
Abstract
Animal intestines is considered as a source of lactic acid bacteria (LAB) that have potential to decrease the nitrite level during fermentation of food such as pickles. It was hypothesized that optimized level of LAB has a high capacity to degrade nitrite during Chinese pickle fermentation and benefit a higher acceptability of the Chinese pickle product. This study aims to investigate the performance of a goose intestine-isolated LAB strain G6 under the species Lactiplantibacillus plantarum as a starter culture of Chinese pickles. The results showed that Lactiplantibacillus sp. G6 had a nitrite degradation rate close to 100% under the MRS broth condition of 25 °C, 2% inoculum volume and pH at 5. As a starter culture for Chinese pickle, this strain was able to achieve a higher LABs amount, lower nitrite residue after fermentation, compared with the group without the starter, which implicates its feasibility of applying on fermented food for reducing nitrite level. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01433-8.
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Affiliation(s)
- Ziya Lan
- South China Agricultural University, Guangzhou, 510000 China
| | - Huiling Huang
- South China Agricultural University, Guangzhou, 510000 China
| | - Chenyang Liu
- South China Agricultural University, Guangzhou, 510000 China
| | - Jincai Li
- South China Agricultural University, Guangzhou, 510000 China
| | - Xueling Li
- South China Agricultural University, Guangzhou, 510000 China
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Wang TY, Gu CT. Lactiplantibacillus paraxiangfangensis sp. nov., isolated from traditional Chinese pickle. Int J Syst Evol Microbiol 2024; 74. [PMID: 38427401 DOI: 10.1099/ijsem.0.006278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Three Gram-stain-positive bacterial strains (designated 231-9T, 142-6 and 463-4) were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strains 231-9T, 142-6 and 463-4 were phylogenetically related to the type strains of Lactiplantibacillus xiangfangensis, Lactiplantibacillus garii, Lactiplantibacillus carotarum, Lactiplantibacillus plajomi and Lactiplantibacillus modestisalitolerans, having 98.6-99.9 % 16S rRNA gene sequence similarities. Strains 231-9T, 142-6 and 463-4 were most closely related to the type strain of L. xiangfangensis, having 99.9 % 16S rRNA gene, 95.6 % pheS, 99.4 % rpoA and 98.2 % concatenated pheS and rpoA sequence similarities. Relatively low pheS (95.6 %) sequence similarity indicated that strain 231-9T should be further identified. Strain 231-9T shared 99.7-99.9 % average nucleotide identity (ANI) and 98.8-98.9 % digital DNA-DNA hybridization (dDDH) values with strains 142-6 and 463-4, indicating that they belonged to the same species. The ANI and dDDH values between strain 231-9T and L. xiangfangensis LMG 26013T were 92.4-92.9 and 49.6 %, respectively, less than the threshold for species demarcation (95-96% ANI and 70 % dDDH values, respectively), indicating that strains 231-9T, 142-6 and 463-4 represented a novel species within the genus Lactiplantibacillus. Acid production from d-ribose, d-adonitol, d-galactose and lactose, activity of β-galactosidase and β-glucosidase, Voges-Proskauer reaction, hydrolysis of hippurate, resistance to 5 µg ml-1 erythromycin, 100 µg ml-1 tetracycline hydrochloride, 50 µg ml-1 bacitracin, 300 µg ml-1 each of gentamicin sulphate, streptomycin sulphate and neomycin sulphate, tolerance to 6 % NaCl could distinguish strains 231-9T, 142-6 and 463-4 from L. xiangfangensis 3.1.1T. Based upon the data of polyphasic characterization obtained in the present study, a novel species, Lactiplantibacillus paraxiangfangensis sp. nov., is proposed and the type strain is 231-9T (=JCM 36258T=CCTCC AB 2023133T).
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Affiliation(s)
- Ting-Yu Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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6
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Kuri A, Iida H, Kawahara K. Comparative analysis of glyceroglycolipids from Lactiplantibacillus pentosus and other Lactiplantibacillus species. J GEN APPL MICROBIOL 2023; 69:135-141. [PMID: 36476588 DOI: 10.2323/jgam.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Cellular lipids of Lactiplantibacillus species were extracted and neutral glyceroglycolipids (GGLs) were purified, and analyzed by thin-layer chromatography (TLC). Four GGLs with known structures were detected in GGL preparation of L. plantarum, and the same GGL profiles of TLC were observed for all other strains of Lactiplantibacillus species examined, suggesting that the GGL profile could be one of the chemotaxonomic characters of the genus Lactiplantibacillus. On the other hand, the quantity of each GGL showed some variation among species, and L. pentosus was found to have higher proportion of disaccharide-type GGL, designated GGL-3 in this study, compared with other species including L. plantarum. The quantitative difference of GGL-3 found in this study could be regarded as the characteristics of L. pentosus. The carbohydrate structure of L. pentosus GGL-3 was precisely analyzed by 1H NMR and methylation analysis, and the structure was confirmed to be αGal-(1→2)-αGlc-diacylglycerol, with the carbohydrate structure identical to that of L. plantarum, although fatty acid composition of the two GGL-3 showed some difference.
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Affiliation(s)
- Ayako Kuri
- Graduate School of Engineering, Kanto Gakuin University
- Faculty of Food and Health Sciences, Showa Women's University
| | - Hirokazu Iida
- Graduate School of Engineering, Kanto Gakuin University
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University
| | - Kazuyoshi Kawahara
- Graduate School of Engineering, Kanto Gakuin University
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University
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Heng YC, Silvaraju S, Lee JKY, Kittelmann S. Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut. Int J Syst Evol Microbiol 2023; 73. [PMID: 38063497 DOI: 10.1099/ijsem.0.006194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030T, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030T was most closely related to the type strains Lactiplantibacillus nangangensis NCIMB 15186T, Lactiplantibacillus daoliensis LMG 31171T and Lactiplantibacillus pingfangensis LMG 31176T. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.6 to 84.9 % and from 24.1 to 24.7 %, respectively, and were below the 95.0 and 70.0% thresholds for species delineation. Substantiated by further physiological and biochemical analyses, strain WILCCON 0030T represents a novel species within the genus Lactiplantibacillus for which we propose the name Lactiplantibacillus brownii sp. nov. (type strain WILCCON 0030T=DSM 116485T=LMG 33211T).
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Affiliation(s)
- Yu Chyuan Heng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Shaktheeshwari Silvaraju
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Jolie Kar Yi Lee
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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Qiao N, Gaur G, Modesto M, Chinnici F, Scarafile D, Borruso L, Marin AC, Spiezio C, Valente D, Sandri C, Gänzle MG, Mattarelli P. Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar. J Appl Microbiol 2023; 134:lxad255. [PMID: 37934609 DOI: 10.1093/jambio/lxad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
AIMS Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris. METHODS AND RESULTS Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype. CONCLUSIONS Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.
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Affiliation(s)
- Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Gautam Gaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Fabio Chinnici
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano-Bozen, Bolzano 39100, Italy
| | - Antonio Castro Marin
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva, Bussolengo (Verona) 37012, Italy
| | - Daria Valente
- Department of Life Sciences and Systems Biology, University of Torino, Turin 10124, Italy
| | - Camillo Sandri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
- Department of Animal Health Care and Management, Parco Natura Viva, Bussolengo (Verona) 37012, Italy
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Escámez PSF, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 17: suitability of taxonomic units notified to EFSA until September 2022. EFSA J 2023; 21:e07746. [PMID: 36704192 PMCID: PMC9875162 DOI: 10.2903/j.efsa.2023.7746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, new information was found leading to the withdrawal of the qualification 'absence of aminoglycoside production ability' for Bacillus velezensis. The qualification for Bacillus paralicheniformis was changed to 'absence of bacitracin production ability'. For the other TUs, no new information was found that would change the status of previously recommended QPS TUs. Of 52 microorganisms notified to EFSA between April and September 2022 (inclusive), 48 were not evaluated because: 7 were filamentous fungi, 3 were Enterococcus faecium, 2 were Escherichia coli, 1 was Streptomyces spp., and 35 were taxonomic units (TUs) that already have a QPS status. The other four TUs notified within this period, and one notified previously as a different species, which was recently reclassified, were evaluated for the first time for a possible QPS status: Xanthobacter spp. could not be assessed because it was not identified to the species level; Geobacillus thermodenitrificans is recommended for QPS status with the qualification 'absence of toxigenic activity'. Streptoccus oralis is not recommended for QPS status. Ogataea polymorpha is proposed for QPS status with the qualification 'for production purposes only'. Lactiplantibacillus argentoratensis (new species) is included in the QPS list.
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10
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Choi CH, Kim E, Yang SM, Kim DS, Suh SM, Lee GY, Kim HY. Comparison of Real-Time PCR and Droplet Digital PCR for the Quantitative Detection of Lactiplantibacillus plantarum subsp. plantarum. Foods 2022; 11:foods11091331. [PMID: 35564054 PMCID: PMC9105557 DOI: 10.3390/foods11091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 12/04/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is one of the newest and most promising tools providing absolute quantification of target DNA molecules. Despite its emerging applications in microorganisms, few studies reported its use for detecting lactic acid bacteria. This study evaluated the applicability of a ddPCR assay targeting molecular genes obtained from in silico analysis for detecting Lactiplantibacillus plantarum subsp. plantarum, a bacterium mainly used as a starter or responsible for fermentation in food. The performance characteristics of a ddPCR were compared to those of a quantitative real-time PCR (qPCR). To compare the linearity and sensitivity of a qPCR and ddPCR, the calibration curve for a qPCR and the regression curve for a ddPCR were obtained using genomic DNA [102−108 colony-forming units (CFU)/mL] extracted from a pure culture and spiked food sample. Both the qPCR and ddPCR assays exhibited good linearity with a high coefficient of determination in the pure culture and spiked food sample (R2 ≥ 0.996). The ddPCR showed a 10-fold lower limit of detection, suggesting that a ddPCR is more sensitive than a qPCR. However, a ddPCR has limitations in the absolute quantitation of high bacterial concentrations (>106 CFU/mL). In conclusion, a ddPCR can be a reliable method for detecting and quantifying lactic acid bacteria in food.
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Affiliation(s)
| | | | | | | | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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11
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Wang L, Yu T, Zhu Y, Luo Y, Dong F, Lin X, Zhao W, He Z, Hu S, Dong Z. Amplicon-based sequencing and co-occurence network analysis reveals notable differences of microbial community structure in healthy and dandruff scalps. BMC Genomics 2022; 23:312. [PMID: 35439925 PMCID: PMC9017024 DOI: 10.1186/s12864-022-08534-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/30/2022] [Indexed: 12/27/2022] Open
Abstract
Background Dandruff is a chronic, recurring, and common scalp problem that is caused by several etiopathogeneses with complex mechanisms. Management of this condition is typically achieved via antifungal therapies. However, the precise roles played by microbiota in the development of the condition have not been elucidated. Despite their omnipresence on human scalp little is known about the co-occurrence/co-exclusion network of cutaneous microbiota. Results We characterized the scalp and hair surface bacterial and fungal communities of 95 dandruff-afflicted and healthy individuals residing in China. The degree distributions of co-occurrence/co-exclusion network in fungi-bacteria and bacteria-bacteria were higher in the healthy group (P < 0.0001), whereas the betweenness values are higher in the dandruff group (P < 0.01). Meanwhile, the co-occurrence/co-exclusion network among fungi-fungi and fungi-bacteria showed that compared to the healthy group, the dandruff group had more positive links (P < 0.0001). In addition, we observed that Malassezia slooffiae, Malassezia japonica and Malassezia furfur, were more abundant in the dandruff group than in the healthy group. These microbiota were co-exclusion by either multiple bacterial genera or Malassezia sp. in healthy group. The lactic acid bacteria on the scalp and hair surface, especially the genera Lactobacillus and Lactococcus, exhibit a negative correlation with multiple bacterial genera on the scalp and hair surface. Lactobacillus plantarum and Pediococcus lactis isolated on the healthy human scalp can inhibit the growth of Staphylococcus epidermidis in vitro. Conclusions We showed that microbial networks on scalp and hair surface with dandruff were less integrated than their healthy counterparts, with lower node degree and more positive and stronger links which were deemed to be unstable and may be more susceptible to environmental fluctuations. Lactobacillus bacteria have extensive interactions with other bacteria or fungi in the scalp and hair surface micro-ecological network and can be used as targets for improving scalp health. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08534-4.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Department of Microbiology, College of Life Science, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, 36 Lushan Rd., Yuelu District, Changsha, Hunan, 410081, China
| | - Tao Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Fan Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xuemei Lin
- Lafang China Co.. Ltd., LAF Building, Wanji Industrial Park, Shantou, Guangdong, 515041, China
| | - Wenzhong Zhao
- Lafang China Co.. Ltd., LAF Building, Wanji Industrial Park, Shantou, Guangdong, 515041, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University , No. 37 Xueyuan Road, Haidian District, Beijing, 100191, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
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12
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Shukla I, Hill JE. cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae. Can J Microbiol 2022; 68:457-464. [PMID: 35230911 DOI: 10.1139/cjm-2021-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
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Affiliation(s)
- Ishika Shukla
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
| | - Janet E Hill
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
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13
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Effects of two-species probiotic combinations on production performance at peak lay, sulfur compounds in manure, and selected serum profile. J APPL POULTRY RES 2022. [DOI: 10.1016/j.japr.2022.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Gallus M, Vogel RF, Ehrmann MA. Optimization of a cultivation procedure to selectively isolate lactic acid bacteria from insects. J Appl Microbiol 2021; 132:3001-3016. [PMID: 34957661 DOI: 10.1111/jam.15427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/26/2022]
Abstract
AIMS Natural niches and transmission routes of lactic acid bacteria (LAB) are highly versatile. Proposed routes of transmission to food fermentations are from plant material via insects or vice versa. This study aimed to establish a method for the selective isolation of LAB from insects. METHODS AND RESULTS Varied parameters that influence growth and selectivity are temperature, type of carbohydrate and atmosphere. Additionally, effects of antibiotics to suppress non-LAB species were evaluated. A model consortium consisting of 12 species representing different lifestyles was inoculated in growth medium to identify conditions for highest diversity and recovery rate. The method was applied to isolate LAB from Drosophila melanogaster, Sitotroga cerealella, Tribolium castaneum and Tenebrio molitor. Isolated species were Leuconostoc mesenteroides, Paucilactobacillus vaccinostercus and Lactiplantibacillus plantarum from D. melanogaster and L. mesenteroides, Pediococcus pentosaceus and Latilactobacillus curvatus from T. molitor. No LAB could be isolated from T. castaneum and S. cerealella. 16S rDNA amplicon sequencing of DNA obtained from insects corroborated part of our results. CONCLUSION A combination of different enrichment conditions ensures a high probability to isolate LAB species from insects and can be helpful above already known non-cultivation methods. SIGNIFICANCE AND IMPACT OF THE STUDY The novel method allows to selectively isolate LAB from insects and the strategy of the method is of interest to study other niches.
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Affiliation(s)
- Marion Gallus
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
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15
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Nishioka H, Ohno T, Iwahashi H, Horie M. Diversity of Lactic Acid Bacteria Involved in the Fermentation of Awa-bancha. Microbes Environ 2021; 36. [PMID: 34840198 PMCID: PMC8674441 DOI: 10.1264/jsme2.me21029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The lactic acid bacteria involved in fermentation and components in the tea leaves of Awa-bancha, a post-fermented tea produced in Naka, Kamikatsu, and Miyoshi, Tokushima, were investigated in the present study. Lactic acid bacteria were isolated from tea leaves after anaerobic fermentation and identified by multiplex PCR targeting of the recA gene and 16S ribosomal RNA gene homology. Lactiplantibacillus pentosus was the most frequently isolated species in Naka and Kamikatsu and Lactiplantibacillus plantarum in Miyoshi. In the phylogenetic tree based on the dnaK gene, L. pentosus isolated from Awa-bancha was roughly grouped by the production area and producer. The bacterial flora after anaerobic fermentation was dominated by Lactiplantibacillus spp. for most producers, and the compositions of samples from each producer varied. Organic acids, free amino acids, and catechins were analyzed as components related to the flavor of Awa-bancha. These components were unique to each producer. The present results revealed diversity in the lactic acid bacteria and flavor of Awa-bancha that depended on the producer.
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Affiliation(s)
- Hiroki Nishioka
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center.,United Graduate School of Agricultural Science, Gifu University
| | - Tomoki Ohno
- The Graduate School of Natural Science and Technology, Gifu University
| | | | - Masanori Horie
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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16
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Sangiorgio D, Cellini A, Spinelli F, Farneti B, Khomenko I, Muzzi E, Savioli S, Pastore C, Rodriguez-Estrada MT, Donati I. Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity? Microorganisms 2021; 9:microorganisms9081617. [PMID: 34442697 PMCID: PMC8400319 DOI: 10.3390/microorganisms9081617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022] Open
Abstract
Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry (Rubus idaeus L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of Gluconobacter, Sphingomonas, Rosenbergiella, Brevibacillus and Methylobacterium on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits.
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Affiliation(s)
- Daniela Sangiorgio
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Antonio Cellini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
- Correspondence: ; Tel.: +39-051-2096443
| | - Brian Farneti
- Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (B.F.); (I.K.)
| | - Iuliia Khomenko
- Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (B.F.); (I.K.)
| | - Enrico Muzzi
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Stefano Savioli
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Chiara Pastore
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - María Teresa Rodriguez-Estrada
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Irene Donati
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
- Zespri Fresh Produce, 40132 Bologna, Italy
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17
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Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa. Microorganisms 2021; 9:microorganisms9081570. [PMID: 34442649 PMCID: PMC8399863 DOI: 10.3390/microorganisms9081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
- Correspondence:
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Chun-Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
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Phuengjayaem S, Kuncharoen N, Booncharoen A, Ongpipattanakul B, Tanasupawat S. Genome analysis and optimization of γ-aminobutyric acid (GABA) production by lactic acid bacteria from plant materials. J GEN APPL MICROBIOL 2021; 67:150-161. [PMID: 34092710 DOI: 10.2323/jgam.2020.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Gamma-aminobutyric acid (GABA) plays a key role as an inhibitory neurotransmitter in the mammalian sympathetic nervous system and has other health benefits. Molecular characterization, genome analysis, and optimization were investigated to improve GABA production of a selected strain of lactic acid bacteria. Eleven isolates from plant materials were screened for GABA productivity and were identified based on phenotypic and genotypic characteristics. The most potent strain was chosen for genome analysis and GABA production optimization using the response surface methodology (RSM). Each of the two strains was closely related to Lactobacillus plantarum, Lactobacillus brevis, Weissella cibaria, Leuconostoc pseudomesenteroides while each strain was similar to Lactobacillus pentosus, Enterococcus, and Leuconostoc mesenteroides. They produced GABA ranging from 0.036 ± 0.000 to 17.315 ± 0.171 g/L at 72 h-cultivation. Among them, the most potent strain, SL9-6, showed the highest GABA production (17.315 g/L) when cultivated with 10% (v/v) inoculum for 48 h. The draft genome sequence of strain SL9-6 exhibited 96.90% average nucleotide identity value and 74.50% digital DNA-DNA hybridization to Lactobacillus brevis NCTC 13768T. This strain contained a glutamate decarboxylase gene system (gadA, gadB and gadC). Optimal culture conditions were determined as 40.00 g/L glucose, 49.90 g/L monosodium glutamate, pH 5.94, and 31.10°C by RSM, giving maximum GABA production of 32.48 g/L. Results from RSM also indicated that monosodium glutamate concentration, pH, and temperature were significant variables. GABA production significantly improved here could promise further application of strain SL9-6.
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Affiliation(s)
- Sukanya Phuengjayaem
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
| | - Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
| | - Auttaporn Booncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
| | - Boonsri Ongpipattanakul
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
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Liang T, Xie X, Zhang J, Ding Y, Wu Q. Bacterial community and composition of different traditional fermented dairy products in China, South Africa, and Sri Lanka by high-throughput sequencing of 16S rRNA genes. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111209] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Battistelli N, Perpetuini G, Piva A, Pepe A, Sidari R, Wache Y, Tofalo R. Cultivable microbial ecology and aromatic profile of "mothers" for Vino cotto wine production. Food Res Int 2021; 143:110311. [PMID: 33992330 DOI: 10.1016/j.foodres.2021.110311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/06/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022]
Abstract
The aim of the present study was to assess the cultivable microbiota of "mothers" of Vino cotto collected from production of different years 1890, 1895, 1920, 1975, 2008. A total of 73 yeasts and 81 bacteria were isolated. Starmerella lactis-condensi, Starmerella bacillaris, Hanseniaspora uvarum, Saccharomyces cerevisiae, Hanseniaspora guillermondi and Metschnikowia pulcherrima were identified. Bacteria isolates belonged to lactic acid bacteria (Lactiplantibacillus plantarum and Pediococcus pentosaceus) and acetic acid bacteria (Gluconobacter oxydans). Remarkable biodiversity was observed for Starm. bacillaris, as well as L. plantarum and G. oxydans. Organic acids and volatile compounds were also determined. Malic and succinic acids were the main ones with values ranging from 8.49 g/L to 11.76 g/L and from 4.15 g/L to 7.73 g/L respectively, while citric acid was present at low concentrations (<0.2 g/L) in all samples. Esters and higher alcohols were the main volatile compounds detected followed by alkanes. This study permits to better understand the microbial communities associated to this product and could be considered a starting point for the definition of tailored starter cultures to improve the quality of Vino cotto preserving its typical traits.
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Affiliation(s)
- Noemi Battistelli
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy
| | - Giorgia Perpetuini
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy
| | - Andrea Piva
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy
| | - Alessia Pepe
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy
| | - Rossana Sidari
- Department of Agraria, Mediterranean University of Reggio Calabria, Loc. Feo di Vito, I-89122 Reggio Calabria, Italy
| | - Yves Wache
- Tropical Fermentation Network, France; International Joint Laboratory, Tropical Bioresources & Biotechnology, Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102 and School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Dijon, France; School of Food Science and Technology, Faculty of Science and Technology, Thammasat University, 12120, Thailand
| | - Rosanna Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini, 1, 64100 Teramo, Italy.
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21
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Characterization and comparative genomic analysis of gamma-aminobutyric acid (GABA)-producing lactic acid bacteria from Thai fermented foods. Biotechnol Lett 2021; 43:1637-1648. [PMID: 33999363 DOI: 10.1007/s10529-021-03140-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/23/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to screen, characterize, and annotate the genome along with the comparison of GABA synthesis genes presented in lactic acid bacteria (LAB). RESULTS Thirty-five LAB isolates from fermented foods were screened for GABA production using thin-layer chromatography (TLC). Fifteen isolates produced GABA ranging from 0.07 to 22.94 g/L. Based on their GTG5 profiles, phenotypic, and genotypic characteristics, isolates LSI1-1, LSI1-5, LSI2-1, LSI2-2, LSI2-3, LSI2-5, and LSM3-1-4 were identified as Lactobacillus plantarum subsp. plantarum; isolate LSM1-4 was Lactobacillus argentoratensis; isolates CAB1-2, CAB1-5, CAB1-7, and LSI1-4 were Lactobacillus pentosus; and CAB1-1, LSM3-1-1 and LSM3-2-3 were Lactobacillus fermentum. Strains LSI2-1 and CAB1-7 from pickled vegetables were selected for genome analysis. The gadA gene (1410 bp, 470aa) was encountered in GABA production of both strains and no other glutamate decarboxylase (GAD) genes were found in the genomes when compared with other LAB strains. The presence of gadA is evidence for GABA production. Strains LSI2-1 and CAB1-7 produced 22.94 g/L and 11.59 g/L of GABA in GYP broth supplemented with 3% (w/v) MSG at 30 °C for 72 h, respectively. CONCLUSIONS Our report highlights the characterization of LAB and GABA production of L. plantarum LSI2-1 strain with its GABA synthesis gene. GABA production of strains LSI2-1 and CAB1-7 in GYP broth with 3% (w/v) MSG and comparative GAD genes.
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22
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Kim E, Kim HB, Yang SM, Kim D, Kim HY. Real-time PCR assay for detecting Lactobacillus plantarum group using species/subspecies-specific genes identified by comparative genomics. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Kim E, Yang SM, Kim HB, Kim HY. Novel specific peaks for differentiating the Lactobacillus plantarum group using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2020; 178:106064. [PMID: 32961241 DOI: 10.1016/j.mimet.2020.106064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022]
Abstract
Identifying the Lactobacillus plantarum group using conventional taxonomic methods such as biochemical analysis and 16S rRNA gene sequencing is inaccurate, expensive, and time-consuming. In this study, for the first time, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to identify the L. plantarum group and develop a classification method for species level differentiation with specific peaks based on mass spectra. Furthermore, from the mass spectra of 131 isolates aligned with the biotyper database, 131 isolates (100%) were correctly identified at the species level with a mean score of 2.316. However, commercial databases could not accurately differentiate some isolates of L. plantarum group species because the same colony was identified as different species with similar score values. Moreover, these two species showed a similar mass pattern in the main spectrum profiles-dendrogram and Principal component analysis clustering generated by the mass peak of the reference strains and isolates. Specific peaks to each species were investigated from the analyzed mass peak, and they clearly showed that three species could be differentiated. These peaks were verified by re-identifying 131 isolates, and it demonstrated 100% specificity and accuracy. Also, using a specific peak, isolates that were undifferentiated from the biotyper database were clearly identified as one species, similar to species-specific polymerase chain reaction. Our data demonstrate that the specific peaks accurately differentiate the L. plantarum group and enable high-resolution identification at the species level; this methodology can be used to rapidly and easily identify them and determine their nomenclature.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeon-Be Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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Li TT, Liu DD, Fu ML, Gu CT. Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee ( Apis mellifera). Int J Syst Evol Microbiol 2020; 70:3123-3133. [PMID: 32250238 DOI: 10.1099/ijsem.0.004141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lactobacillus kosoi Chiou et al. 2018 and Lactobacillus micheneri McFrederick et al. 2018 are closely related, and they share 100 % 16S rRNA gene sequence similarity, 99.6 % pheS gene sequence similarity, 100 % rpoA gene sequence similarity, 97.3 % average nucleotide identity (ANI) value and 76.6 % in silico DNA-DNA hybridization (isDDH) value, indicating that they represent the same species. Fatty acid methyl esters (FAME) analysis and phenotypic characterization also indicated that L. kosoi and L. micheneri are very similar. We propose L. kosoi Chiou et al. 2018 as a later heterotypic synonym of L. micheneri McFrederick et al. 2018. The taxonomic position of Lactobacillus plantarum subsp. argentoratensis in the L. plantarum group was re-examined using a polyphasic approach, including sequence analyses of 16S rRNA, pheS, rpoA and recA genes, average nucleotide identity analysis, in silico DNA-DNA hybridization, fatty acid methyl ester analysis and phenotypic characterization. Results of 16S rRNA gene sequence analysis indicated that L. plantarum subsp. argentoratensis was closely related to L. plantarum subsp. plantarum, L. pentosus and L. paraplantarum in the L. plantarum group, sharing 99.6-99.7 % 16S rRNA gene sequence similarities. Results of pheS, rpoA and recA gene sequence analyses indicated that L. plantarum subsp. argentoratensis was most closely related to L. plantarum subsp. plantarum, having 91.8 % pheS gene sequence similarity, 98.9 % rpoA gene sequence similarity and 93.1 % recA gene sequence similarity. L. plantarum subsp. argentoratensis DSM 16365T shared 95.6 % ANI value and 62.9 % isDDH value with L. plantarum subsp. plantarum ATCC 14917T. The low isDDH value confirmed that L. plantarum subsp. argentoratensis and L. plantarum subsp. plantarum represent two different species, rather than two different subspecies in the L. plantarum group. On the basis of the data from polyphasic characterization obtained in the present study and in previous studies, L. plantarum subsp. argentoratensis is elevated to the species level and represents a novel species of the genus Lactobacillus, for which the name Lactobacillus argentoratensis sp. nov. is proposed and the type strain is DKO 22T (=CIP 108320T=DSM 16365T=JCM 16169T). Two novel Gram-stain-positive bacterial strains, designated 1206-1T and F027-1-2, were isolated from traditional pickle in Heilongjiang Province, PR China, and from the intestinal tract of a honey bee (Apis mellifera) in Hubei Province, PR China, respectively. The two bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, average nucleotide identity analysis, in silico DNA-DNA hybridization analysis and an analysis of phenotypic features. The results of 16S rRNA gene sequence analysis indicated that strains 1206-1T and F027-1-2 were distantly related to Lactobacillus sharpeae, Lactobacillus hulanensis, Lactobacillus songhuajiangensis, Lactobacillus pantheris, Lactobacillus thailandensis, Lactobacillus camelliae, Lactobacillus jixianensis, Lactobacillus nasuensis, Lactobacillus baoqingensis, Lactobacillus manihotivorans and Lactobacillus porcinae. Strain 1206-1T exhibited 94.2-96.4 % 16S rRNA gene sequence similarities, 69.5-83.3 % pheS gene sequence similarities and 73.1-90.3 % rpoA gene sequence similarities to type strains of phylogenetically related species. ANI and isDDH values between strain 1206-1T and the type strains of phylogenetically related species were 52.7-73.7 % and 21.1-30.1 %, respectively. On the basis of the data obtained in the present study, a novel species, Lactobacillus zhaodongensis sp. nov. is proposed and the type strain is 1206-1T (=CCM 8981T=CCTCC AB 2019200T=LMG 31620T).
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Affiliation(s)
- Ting Ting Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Dan Dan Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Mei Ling Fu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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25
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1493] [Impact Index Per Article: 373.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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26
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Characterization of natural Oenococcus oeni strains for Montepulciano d’Abruzzo organic wine production. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03466-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Li YQ, Tian WL, Gu CT. Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt. Int J Syst Evol Microbiol 2020; 70:2485-2492. [PMID: 32100692 DOI: 10.1099/ijsem.0.004062] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive bacterial strains, designated X0750T, X0278 and X0401, isolated from traditional yogurt in Tibet Autonomous Region, PR China, were characterized by a polyphasic approach, including sequence analyses of the 16S rRNA gene and three housekeeping genes (pheS, rpoA and recA), determination of average nucleotide identity (ANI) and average amino acid identity (AAI), in silico DNA-DNA hybridization (isDDH), fatty acid methyl ester (FAME) analysis and phenotypic characterization. Strain X0750T was phylogenetically related to the type strains of Weissella hellenica, Weissella bombi, Weissella paramesenteroides, Weissella jogaejeotgali, Weissella thailandensis, Weissella oryzae, Weissella cibaria and Weissella confusa, having 94.4-100 % 16S rRNA gene sequence similarities, 76.7-90.0 % pheS gene sequence similarities, 88.9-99.4 % rpoA gene sequence similarities and 77.6-92.8 % recA gene sequence similarities, respectively. ANI, isDDH and AAI values between strain X0750T and type strains of phylogenetically related species were less than 90.4, 40.9 and 92.8 % respectively, confirming that strain X0750T represents a novel species within the genus Weissella. Based upon the data obtained in the present study, a novel species, Weissella sagaensis sp. nov., is proposed and the type strain is X0750T(=NCIMB 15192T=CCM 8924T=LMG 31184T=CCTCC AB 2018403T).
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Affiliation(s)
- Yu Qin Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Wen Li Tian
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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28
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Liu DD, Gu CT. Lactobacillus pingfangensis sp. nov., Lactobacillus daoliensis sp. nov., Lactobacillus nangangensis sp. nov., Lactobacillus daowaiensis sp. nov., Lactobacillus dongliensis sp. nov., Lactobacillus songbeiensis sp. nov. and Lactobacillus kaifaensis sp. nov., isolated from traditional Chinese pickle. Int J Syst Evol Microbiol 2019; 69:3237-3247. [DOI: 10.1099/ijsem.0.003619] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dan Dan Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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30
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Administration of Lactobacillus plantarum Lp62 to dam rats at the end of delivery and during lactation affects TGF-β1 level and nutritional milk composition, and body weight of pups. Eur J Nutr 2018; 58:1137-1146. [DOI: 10.1007/s00394-018-1628-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/29/2018] [Indexed: 12/23/2022]
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31
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Tomita S, Tanaka N, Okada S. A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum. FEMS Microbiol Lett 2017; 364:2975577. [PMID: 28175288 DOI: 10.1093/femsle/fnx034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 02/06/2017] [Indexed: 01/12/2023] Open
Abstract
The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate).
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Affiliation(s)
- Satoru Tomita
- Food Research Institute, National Agricultural and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Naoto Tanaka
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Sanae Okada
- Department of Applied Biology and Chemistry, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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32
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Lactobacillus plantarum and Its Probiotic and Food Potentialities. Probiotics Antimicrob Proteins 2017; 9:111-122. [DOI: 10.1007/s12602-017-9264-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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33
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Chen YS, Liao YJ, Lan YS, Wu HC, Yanagida F. Diversity of Lactic Acid Bacteria Associated with Banana Fruits in Taiwan. Curr Microbiol 2017; 74:484-490. [PMID: 28229214 DOI: 10.1007/s00284-017-1213-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/07/2017] [Indexed: 01/16/2023]
Abstract
Banana is a popular fruit worldwide. The lactic acid bacteria (LAB) microflora in banana fruits has not been studied in detail. A total of 164 LAB were isolated from banana fruits in Taiwan. These isolates were initially divided into nine groups (r1 to r9) using restriction fragment length polymorphism analysis and 16S ribosomal DNA sequencing. Isolates belonging to Lactobacillus plantarum group were further divided into three additional groups using multiplex PCR assay targeting the recA gene. The most common bacterial genera found in banana fruits were Lactobacillus and Weissella. The distribution of LAB indicated that, in most cases, neighboring regions shared common strains, but there were still some differences between regions. On the basis of phylogenetic analysis of 16S rRNA, rpoA, and pheS gene sequences, two strains included in the genera Lactobacillus were identified as potential novel species or subspecies. In addition, a total 36 isolates were found to have bacteriocin-producing abilities. These results suggest that various LAB are associated with banana fruits in Taiwan. This is the first report describing the distribution and varieties of LAB associated with banana fruits. In addition, one potential novel LAB species was also found in this study.
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Affiliation(s)
- Yi-Sheng Chen
- Department of Biotechnology, Ming Chuan University, No.5, Deming Rd., Guishan Dist., Taoyuan City, Taiwan, Republic of China.
| | - Yu-Jou Liao
- Department of Biotechnology, Ming Chuan University, No.5, Deming Rd., Guishan Dist., Taoyuan City, Taiwan, Republic of China
| | - Yi-Shan Lan
- Department of Biotechnology, Ming Chuan University, No.5, Deming Rd., Guishan Dist., Taoyuan City, Taiwan, Republic of China
| | - Hui-Chung Wu
- Department of Biotechnology, Ming Chuan University, No.5, Deming Rd., Guishan Dist., Taoyuan City, Taiwan, Republic of China
| | - Fujitoshi Yanagida
- The Institute of Enology and Viticulture, University of Yamanashi, 1-13-1 Kitashin, Kofu, Yamanashi, 400-0005, Japan
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34
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Suryavanshi MV, Paul D, Doijad SP, Bhute SS, Hingamire TB, Gune RP, Shouche YS. Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture. Stand Genomic Sci 2017; 12:15. [PMID: 28163824 PMCID: PMC5282701 DOI: 10.1186/s40793-017-0222-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022] Open
Abstract
Probiotic Lactobacillus species offer various health benefits, thus have been employed in treatment and prevention of various diseases. Due to the differences in the isolation source and the site of action, most of the lactobacilli tested in-vitro for probiotics properties fail to extend similar effects in-vivo. Consequently, the search of autochthonous, efficacious and probably population specific probiotics is a high priority in the probiotics research. In this regards, whole genome sequencing of as many Lactobacillus as possible will help to deepen our understanding of biology and their health effects. Here, we provide the genomic insights of two coherent oxalic acid tolerant Lactobacillus species (E2C2 and E2C5) isolated from two different healthy human gut flora. These two isolates were found to have higher tolerance towards oxalic acid (300 mM sodium oxalate). The draft genome of strain E2C2 consists of 3,603,563 bp with 3289 protein-coding genes, 94 RNA genes, and 43.99% GC content, while E2C5 contained 3,615,168 bp, 3293 coding genes (93.4% of the total genes), 95 RNA genes and 43.97% GC content. Based on 16S rRNA gene sequence analysis followed by in silico DNA-DNA hybridization studies, both the strains were identified as Lactobacillus plantarum belonging to family Lactobacillaceae within the phylum Firmicutes. Both the strains were genomically identical, sharing 99.99% CDS that showed 112 SNPs. Both the strains also exhibited deconjugation activity for the bile salts while genome analysis revealed that the L. plantarum strains E2C2 and E2C5 also have the ability to produce vitamins, biotin, alpha- and beta- glucosidase suggesting potential probiotic activities of the isolates. The description presented here is based on the draft genomes of strains E2C2 and E2C5 which are submitted to GenBank under the accession numbers LSST00000000.1 and LTCD00000000.1, respectively.
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Affiliation(s)
- Mangesh V Suryavanshi
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
| | - Dhiraj Paul
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
| | - Swapnil P Doijad
- Institute of Medical Microbiology, Biomedizinisches Forschungszentrum Seltersberg, Schubertstr. 81, Giessen, 35392 Germany
| | - Shrikant S Bhute
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 India
| | - Tejashri B Hingamire
- Biochemical Science Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune, 411008 India
| | - Rahul P Gune
- Department of Urology, RCSM Govt. Medical College, CPR Hospital Compound, Bhausingji Rd, Kolhapur, 416002 India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
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35
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Moraes Filho M, Busanello M, Garcia S. Optimization of the fermentation parameters for the growth of Lactobacillus in soymilk with okara flour. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2016; 35:173-184. [PMID: 27867804 PMCID: PMC5107635 DOI: 10.12938/bmfh.16-003] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/27/2016] [Indexed: 12/15/2022]
Abstract
Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.
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Affiliation(s)
- Yasuhiro Tanizawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan; Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Eli Kaminuma
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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37
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Mao Y, Chen M, Horvath P. Lactobacillus herbarum sp. nov., a species related to Lactobacillus plantarum. Int J Syst Evol Microbiol 2015; 65:4682-4688. [DOI: 10.1099/ijsem.0.000636] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain TCF032-E4 was isolated from a traditional Chinese fermented radish. It shares >99% 16S rRNA sequence identity with L. plantarum, L. pentosus and L. paraplantarum. This strain can ferment ribose, galactose, glucose, fructose, mannose, mannitol, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, maltose, lactose, melibiose, trehalose and gentiobiose. It cannot ferment sucrose, which can be used by L. pentosus, L. paraplantarum, L. fabifermentans, L. xiangfangensis and L. mudanjiangensis, as well as most of the L. plantarum strains (88.7%). TCF032-E4 cannot grow at temperature above 32 °C. This strain shares 78.2–83.6% pheS (phenylalanyl-tRNA synthetase alpha subunit) and 89.5–94.9% rpoA (RNA polymerase alpha subunit) sequence identity with L. plantarum, L. pentosus, L. paraplantarum, L. fabifermentans, L. xiangfangensis and L. mudanjiangensis. These results indicate that TCF032-E4 represents a distinct species. This hypothesis was further confirmed by whole-genome sequencing and comparison with available genomes of related species. The draft genome size of TCF032-E4 is approximately 2.9 Mb, with a DNA G+C content of 43.5 mol%. The average nucleotide identity (ANI) between TCF032-E4 and related species ranges from 79.0 to 81.1%, the highest ANI value being observed with L. plantarum subsp. plantarum ATCC 14917T. A novel species, Lactobacillus herbarum sp. nov., is proposed with TCF032-E4T ( = CCTCC AB2015090T = DSM 100358T) as the type strain.
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Affiliation(s)
- Yuejian Mao
- DuPont Nutrition & Health, Shanghai, PR China
| | - Meng Chen
- DuPont Nutrition & Health, Shanghai, PR China
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38
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Amadoro C, Rossi F, Piccirilli M, Colavita G. Tetragenococcus koreensis is part of the microbiota in a traditional Italian raw fermented sausage. Food Microbiol 2015; 50:78-82. [DOI: 10.1016/j.fm.2015.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/25/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
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Amadoro C, Rossi F, Piccirilli M, Colavita G. Features of Lactobacillus Sakei Isolated from Italian Sausages: Focus on Strains from Ventricina del Vastese. Ital J Food Saf 2015; 4:5449. [PMID: 27802352 PMCID: PMC5076685 DOI: 10.4081/ijfs.2015.5449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 01/24/2023] Open
Abstract
In this study bacterial isolates from Ventricina del Vastese sausage, previously identified as Lactobacillus (L.) sakei, were characterised genotypically, physiologically and on the basis of some technologically relevant traits. A total of 70 L. sakei isolates from sausages manufactured with spontaneous fermentation in the same producing plant were taken into account. Six genotypic groups were distinguished on the basis of Rep-polymerase chain reaction with the GTG5 primer, some of which were found only in the sausages ripened at temperatures lower than 10°C for the first two months and lower than 16°C for the remaining three months, according to the traditional ripening process. Six strains were selected as representative of the genotypic profiles and further characterised. A high diversity in their fermentation profiles was observed, and different groups were separated on the basis of growth and acidifying capacity in meat extract. None of the strains produced histamine or tyramine in vitro. One strain was able to slightly inhibit Listeria (L.) monocytogenes and L. innocua and all six strains were able to slightly inhibit Enterobacteriaceae isolated from Ventricina del Vastese sausages in vitro. Results showed that most L. sakei strains can have a role in improving the safety of low acidity fermented sausages, even though a limited acidifying capacity was observed in a meat-like substrate, and that L. sakei strains able to produce biogenic amines are unlikely to occur in spontaneously fermented meat products.
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Affiliation(s)
- Carmela Amadoro
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Franca Rossi
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Michele Piccirilli
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Giampaolo Colavita
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
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Huang CH, Chang MT, Huang L, Chu WS. The dnaJ gene as a molecular discriminator to differentiate among species and strain within the Lactobacillus casei group. Mol Cell Probes 2015; 29:479-484. [PMID: 26050941 DOI: 10.1016/j.mcp.2015.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/11/2015] [Accepted: 05/31/2015] [Indexed: 11/20/2022]
Abstract
Identifying Lactobacillus casei and its closely related taxa at the species and strain level using only phenotypic and genotypic (16S rDNA sequence homology analysis) techniques often yields inaccurate results. In this study, the dnaJ chaperone gene was investigated as a molecular target for inter- and intraspecies discrimination within the Lb. casei group as well as for the development of specific primers for species identification. The results showed that most of the examined strains could be clearly distinguished from closely related species based on the sequenced fragments. At the interspecies level, the dnaJ sequence similarities were 81.7%-85.5%. However, at the intraspecies level, the dnaJ sequence similarities were 96.2-100% and could be assigned to different haplotypes in Lactobacillus paracasei and Lactobacillus rhamnosus, respectively. Compared to the 16S rRNA gene, the dnaJ sequence showed greater variation at both the species and strain level. Thus, the dnaJ gene can be proposed as an alternative marker for the Lb. casei group that provides higher discriminatory power than the 16S rRNA gene. In addition, species-specific primers were developed and subsequently employed in two-plex minisequencing analysis and shown to be specific for Lb. paracasei and Lb. rhamnosus. Our data indicate that phylogenetic relationships in the Lb. casei group can be resolved using comparative sequence analysis of the dnaJ gene and that the Lb. paracasei and Lb. rhamnosus species can be simultaneously identified using a novel species-specific minisequencing assay.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Mu-Tzu Chang
- National Health Research Institutes, Institute of Biotechnology and Pharmaceutical Research, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Wen-Shen Chu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan.
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Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, Guo Z, Hou Q, Menhe B, Zhang H. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia. BMC Microbiol 2015; 15:45. [PMID: 25887414 PMCID: PMC4345014 DOI: 10.1186/s12866-015-0385-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Traditional fermented dairy products are major components of the typical Mongolian diet since ancient times. However, almost all the previous studies on the microbial composition of traditional Mongolian fermented dairy products analyzed food samples from the Chinese Mongolian region and Mongolia but not the Russian Mongolian region. In this study, the bacterial and fungal community diversity of nineteen naturally fermented cow’s milk (NFCM) samples from local Mongolian families residing in Kalmykia and Chita of Russia was investigated with pyrosequencing. Results Firmicutes and Ascomycota were the predominant phyla respectively for bacteria and fungi. The abundance of the bacterial phylum Acidobacteria was considerably different between the samples from the two regions. At genus level, Lactobacillus and Pichia were the predominating bacterial and fungal genera, respectively, while six bacterial genera significantly differed between the Kalmykia (enrichment of Aeromonas, Bacillus, Clostridium, Streptococcus, Vogesella) and Chita (enrichment of Lactococcus) samples. The results of principal coordinate analysis (PCoA) based on the bacterial or fungal composition of the Kalmykia and Chita samples revealed a different microbiota structure between the samples collected in these two locations. The redundancy analysis (RDA) identified 60 bacterial and 21 fungal OTUs as the key variables responsible for such microbiota structural difference. Conclusions Our results suggest that structural differences existed in the microbiota of NFCM between Kalmykia and Chita. The difference in geographic environment may be an important factor influencing the microbial diversity of NFCM made by the Mongolians in Russia. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0385-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Jiachao Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhuang Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Bilige Menhe
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
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Soro-Yao AA, Schumann P, Thonart P, Djè KM, Pukall R. The Use of MALDI-TOF Mass Spectrometry, Ribotyping and Phenotypic Tests to Identify Lactic Acid Bacteria from Fermented Cereal Foods in Abidjan (Côte d'Ivoire). Open Microbiol J 2014; 8:78-86. [PMID: 25279017 PMCID: PMC4181171 DOI: 10.2174/1874285801408010078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein analysis, automated ribotyping, and phenotypic tests (e.g., cell morphology, gas production from glucose, growth and acid production on homofermemtative-heterofermentative differential (HHD) agar medium, sugar fermentation patterns) were used to identify 23 lactic acid bacteria (LAB) isolated from fermented cereal foods available in Abidjan, Côte d'Ivoire. Pediococcus acidilactici (56.5%), Lactobacillus fermentum (30.4%), L. salivarius (4.3%), P. pentosaceus (4.3%) and L. plantarum subsp. plantarum (4.3%) were the species and subspecies identified. Protein based identification was confirmed by automated ribotyping for selected isolates and was similar to that provided by the phenotypic characterization. MALDI-TOF MS protein analysis provided a high level of discrimination among the isolates and could be used for the rapid screening of LAB starter cultures.
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Affiliation(s)
- Amenan A Soro-Yao
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Philippe Thonart
- Wallon Center for Industrial Microbiology (CWBI), University of Liège, Bld du Rectorat 29-B40, B 4000 Liège, Belgium
- Wallon Center of Industrial Biology, Bio-industry Unit, Gembloux Agro-BioTech, 5030 Gembloux, Belgium
| | - Koffi M Djè
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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43
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Use of highly variable gene (yycH) as DNA marker to resolve interspecific relationships within the Lactobacillus casei group and a target for developing novel species-specific PCR primers. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2278-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Tofalo R, Perpetuini G, Schirone M, Ciarrocchi A, Fasoli G, Suzzi G, Corsetti A. Lactobacillus pentosus dominates spontaneous fermentation of Italian table olives. Lebensm Wiss Technol 2014. [DOI: 10.1016/j.lwt.2014.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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Huang CH, Chang MT, Huang L. Cloning of a novel specific SCAR marker for species identification in Lactobacillus pentosus. Mol Cell Probes 2014; 28:192-4. [PMID: 24675147 DOI: 10.1016/j.mcp.2014.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/10/2014] [Accepted: 03/13/2014] [Indexed: 11/30/2022]
Abstract
Identifying Lactobacillus species using only phenotypic and genotypic (16S rDNA sequence analysis) techniques yields inaccurate results. The objective of this study was to develop species-specific primers based on randomly amplified polymorphic DNA (RAPD) fingerprinting to distinguish species within the closely related Lactobacillus plantarum group. One of these primers, OPD-3, produced a species-specific band that was found only in the tested Lactobacillus pentosus. This specific fragment was isolated from agarose gel and ligated into a vector for DNA sequencing. A pair of primers, SpOPD3Lpen-F1/R1, that were highly specific sequence-characterized-amplified-regions (SCARs) were designed according to the nucleotide sequences of the specific RAPD marker. These primers were used for PCR analysis of the template DNA of the Lactobacillus strains, and a single 542 bp species-specific band was found only in L. pentosus. Using PCR, a novel species-specific primer pair is shown to rapidly, accurately and effectively distinguish L. pentosus from other species in the L. plantarum group of probiotic bacteria.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Mu-Tzu Chang
- National Health Research Institutes, Institute of Biotechnology and Pharmaceutical Research, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan.
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan
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46
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Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. Int J Syst Evol Microbiol 2013; 63:4698-4706. [DOI: 10.1099/ijs.0.054296-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive bacterial strains, 11050T, 7-19T and 11102T, were isolated from traditional pickle and sourdough in Heilongjiang Province, China. These bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11050T belonged to the
Lactobacillus plantarum
species group and shared 98.0–98.4 % 16S rRNA gene sequence similarities and 84.7–88.9 % dnaK gene sequence similarities with type strains of
Lactobacillus plantarum subsp. plantarum
,
Lactobacillus plantarum subsp. argentoratensis
,
Lactobacillus pentosus
,
Lactobacillus paraplantarum
,
Lactobacillus fabifermentans
and
Lactobacillus xiangfangensis
and had 75.9–80.7 % pheS gene sequence similarities and 90.7–92.5 % rpoA gene sequence similarities with
Lactobacillus plantarum subsp. plantarum
LMG 6907T,
Lactobacillus plantarum subsp. argentoratensis
LMG 9205,
Lactobacillus pentosus
LMG 10755T,
Lactobacillus paraplantarum
LMG 16673T,
Lactobacillus fabifermentans
LMG 24284T and
Lactobacillus xiangfangensis
3.1.1T, respectively. Strain 7-19T was phylogenetically related to
Lactobacillus thailandensis
,
Lactobacillus pantheris
and
Lactobacillus sharpeae
, having 94.1–96.7 % 16S rRNA gene sequence similarities, 71.5–82.3 % pheS gene sequence similarities and 71.2–83.4 % rpoA gene sequence similarities with type strains of
Lactobacillus thailandensis
,
Lactobacillus pantheris
and
Lactobacillus sharpeae
, respectively. Strain 11102T was phylogenetically related to
Lactobacillus oligofermentans
,
Lactobacillus suebicus
,
Lactobacillus vaccinostercus
and
Lactobacillus hokkaidonensis
. Strain 11102T had 99.2 % 16S rRNA gene sequence similarity, 81.3 % pheS gene sequence similarity and 96.1 % rpoA gene sequence similarity with
Lactobacillus oligofermentans
LMG 22743T, respectively. Strain 11102T shared 96.0–96.8 % 16S rRNA gene sequence similarities, 73.3–81.0 % pheS gene sequence similarities and 74.6–76.9 % rpoA gene sequence similarities with type strains of
Lactobacillus suebicus
,
Lactobacillus vaccinostercus
and
Lactobacillus hokkaidonensis
, respectively. Based upon the data from polyphasic characterization obtained in the present study, three novel species, Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., are proposed and the type strains are 11050T ( = LMG 27194T = CCUG 62991T), 7-19T ( = LMG 27191T = NCIMB 14832T = CCUG 62990T) and 11102T ( = LMG 27192T = NCIMB 14833T), respectively.
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Affiliation(s)
- Chun Tao Gu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Jie Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Gui Cheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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47
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Hamon E, Horvatovich P, Marchioni E, Aoudé-Werner D, Ennahar S. Investigation of potential markers of acid resistance in Lactobacillus plantarum
by comparative proteomics. J Appl Microbiol 2013; 116:134-44. [DOI: 10.1111/jam.12339] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/03/2013] [Accepted: 09/03/2013] [Indexed: 11/28/2022]
Affiliation(s)
- E. Hamon
- Equipe de Chimie Analytique des Molécules Bio-Actives; IPHC-DSA; Université de Strasbourg; CNRS; Illkirch-Graffenstaden France
- Aérial Parc d'Innovation; Illkirch-Graffenstaden France
| | - P. Horvatovich
- Department of Analytical Biochemistry; Centre for Pharmacy; University of Groningen; Groningen the Netherlands
| | - E. Marchioni
- Equipe de Chimie Analytique des Molécules Bio-Actives; IPHC-DSA; Université de Strasbourg; CNRS; Illkirch-Graffenstaden France
| | | | - S. Ennahar
- Equipe de Chimie Analytique des Molécules Bio-Actives; IPHC-DSA; Université de Strasbourg; CNRS; Illkirch-Graffenstaden France
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Lactobacillus curieae sp. nov., isolated from stinky tofu brine. Int J Syst Evol Microbiol 2013; 63:2501-2505. [DOI: 10.1099/ijs.0.041830-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A lactic acid bacterium, strain CCTCC M 2011381T, isolated from the brine of the traditional Chinese snack, stinky tofu, was studied to determine its taxonomic position. It was a Gram-stain-positive, non-motile, facultatively anaerobic rod-shaped bacterium that did not exhibit catalase activity. The DNA G+C content of the strain was 44.1 % and its peptidoglycan was characterized by the presence of meso-diaminopimelic acid. Levels of 16S rRNA gene sequence similarity between strain CCTCC M 2011381T and the most closely related species
Lactobacillus senioris
JCM 17472T,
Lactobacillus parafarraginis
JCM 14109T and
Lactobacillus diolivorans
JCM 12183T were 96.5, 96.4 and 96.4 %, respectively. Combined with data from high-resolution genomic markers recA, rpoA and pheS, strain CCTCC M 2011381T was classified as representing a novel species. The strain could also be distinguished from other related species of the genus
Lactobacillus
by its physiological and biochemical characteristics. Based on the phylogenetic, physiological and biochemical data, it is proposed that the new isolate can be classified as representing a novel species of the genus
Lactobacillus
, for which the name Lactobacillus curieae sp. nov. (type strain CCTCC M 2011381T = S1L19T = JCM 18524T) is proposed.
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Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SAFT, Siezen RJ. Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. PLoS One 2013; 8:e59239. [PMID: 23527145 PMCID: PMC3602190 DOI: 10.1371/journal.pone.0059239] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 02/14/2013] [Indexed: 12/21/2022] Open
Abstract
The vaginal microbiota, in particular Lactobacillus species, play an important role in female health through modulation of immunity, countering pathogens and maintaining a pH below 4.7. We report the isolation and genome sequence of Lactobacillus pentosus strain KCA1 (formally known as L. plantarum) from the vagina of a healthy Nigerian woman. The genome was sequenced using Illumina GA II technology. The resulting 16,920,226 paired-end reads were assembled with the Velvet tool. Contigs were annotated using the RAST server, and manually curated. A comparative analysis with the available genomes of L. pentosus IG1 and L. plantarum WCFS1 showed that over 15% of the predicted functional activities are found only in this strain. The strain has a chromosome sequence of 3,418,159 bp with a G+C content of 46.4%, and is devoid of plasmids. Novel gene clusters or variants of known genes relative to the reference genomes were found. In particular, the strain has loci encoding additional putative mannose phosphotransferase systems. Clusters of genes include those for utilization of hydantoin, isopropylmalate, malonate, rhamnosides, and genes for assimilation of polyglycans, suggesting the metabolic versatility of L. pentosus KCA1. Loci encoding putative phage defense systems were also found including clustered regularly interspaced short palindromic repeats (CRISPRs), abortive infection (Abi) systems and toxin-antitoxin systems (TA). A putative cluster of genes for biosynthesis of a cyclic bacteriocin precursor, here designated as pentocin KCA1 (penA) were identified. These findings add crucial information for understanding the genomic and geographic diversity of vaginal lactobacilli.
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Affiliation(s)
- Kingsley C Anukam
- Department of Medical Laboratory Sciences, TWAS Research Unit, University of Benin, Benin City, Edo, Nigeria.
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Tohno M, Kobayashi H, Tajima K, Uegaki R. Strain-dependent effects of inoculation ofLactobacillus plantarumsubsp.plantarumon fermentation quality of paddy rice (Oryza sativaL. subsp.japonica) silage. FEMS Microbiol Lett 2012; 337:112-9. [DOI: 10.1111/1574-6968.12014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/25/2012] [Accepted: 09/20/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science; Nasushiobara; Tochigi; Japan
| | - Hisami Kobayashi
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science; Tsukuba; Ibaraki; Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science; Tsukuba; Ibaraki; Japan
| | - Ryuichi Uegaki
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science; Nasushiobara; Tochigi; Japan
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