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Jakaria Al-Mujahidy SM, Kryukov K, Ikeo K, Saito K, Uddin ME, Ibn Sina AA. Functional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains. Microbiol Spectr 2024:e0347023. [PMID: 38771133 DOI: 10.1128/spectrum.03470-23] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subsp. bulgaricus. During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against Escherichia coli ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus. IMPORTANCE This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic Lactobacillus delbrueckii subsp. indicus TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.
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Affiliation(s)
- Sk Md Jakaria Al-Mujahidy
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kei Saito
- Laboratory of Physics and Cell Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Md Ekhlas Uddin
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka, Bangladesh
| | - Abu Ali Ibn Sina
- Australian Institute for Bioengineering & Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
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2
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [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: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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Subspecies-level genome comparison of Lactobacillus delbrueckii. Sci Rep 2023; 13:3171. [PMID: 36823299 PMCID: PMC9950072 DOI: 10.1038/s41598-023-29404-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.
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Güley Z, Fallico V, Cabrera-Rubio R, Cotter PD, Beresford T. Identification of Streptococcus infantarius subsp. infantarius as the species primarily responsible for acid production in Izmir Brined Tulum Cheese from the Aegean Region of Türkiye. Food Res Int 2022; 160:111707. [DOI: 10.1016/j.foodres.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022]
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Lin ST, Guu JR, Wang HM, Tamura T, Mori K, Huang L, Watanabe K. Fructobacillus papyriferae sp. nov., Fructobacillus papyrifericola sp. nov., Fructobacillus broussonetiae sp. nov. and Fructobacillus parabroussonetiae sp. nov., isolated from paper mulberry in Taiwan. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005235] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five Gram-stain-positive strains (M1-10T, M1-13, M1-21T, M2-14T and S1-1T) were isolated from paper mulberry (Broussonetia papyrifera) in Taiwan. Cells were rod-shaped, non-motile, non-haemolytic, asporogenous, facultatively anaerobic, heterofermentative, and did not exhibit catalase and oxidase activities. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these novel strains belonged to the genus
Fructobacillus
. On the basis of 16S rRNA gene sequence similarities, the type strains of
Fructobacillus fructosus
and
Fructobacillus durionis
were the closest neighbours to strains M1-10T, M1-13, M1-21T, M2-14T and S1-1T. Sequence analyses of concatenated two partial housekeeping genes, the RNA polymerase beta subunit (rpoC) and recombinase A (recA) also indicated that the novel strains belonged to the genus
Fructobacillus
. The 16S rRNA and concatenated rpoC and recA gene sequence similarities between strains M1-10T and M1-13 were 100 %, respectively. The average nucleotide identity values of M1-10T, M1-21T, M2-14T and S1-1T with
F. fructosus
and
F. durionis
were 75.1–78.9% and 76.5–77.5 %, respectively. The digital DNA–DNA hybridization values were 19.7–21.5% and 19.6–20.4 %, respectively. Phenotypic and genotypic test results demonstrated that these strains represent four novel species of the genus
Fructobacillus
, for which the names Fructobacillus papyriferae sp. nov., Fructobacillus papyrifericola sp. nov., Fructobacillus broussonetiae sp. nov. and Fructobacillus parabroussonetiae sp. nov. are proposed with the type strains M1-10T (=BCRC 81237T=NBRC 114433T), M1-21T (=BCRC 81239T=NBRC 114435T), M2-14T (=BCRC 81240T=NBRC 114436T) and S1-1T (=BCRC 81241T=NBRC 114437T), respectively.
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Affiliation(s)
- Shih-Ting Lin
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, No. 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Jia-Rong Guu
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, No. 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Hsing-Min Wang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, No. 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, No. 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Taipei 10673, Taiwan, ROC
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, No. 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
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Oberg TS, McMahon DJ, Culumber MD, McAuliffe O, Oberg CJ. Invited review: Review of taxonomic changes in dairy-related lactobacilli. J Dairy Sci 2022; 105:2750-2770. [DOI: 10.3168/jds.2021-21138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]
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7
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IWAMOTO D, ISHIZAKI M, MIURA T, SASAKI Y. Novel shuttle vector pGMβ1 for conjugative chromosomal manipulation of <i>Lactobacillus delbrueckii</i> subsp. <i>bulgaricus</i>. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2022; 41:20-29. [PMID: 35036250 PMCID: PMC8727053 DOI: 10.12938/bmfh.2021-014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/22/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Daiki IWAMOTO
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Megumi ISHIZAKI
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Taiki MIURA
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yasuko SASAKI
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Tsuchihashi H, Ichikawa A, Takeda M, Koizumi A, Mizoguchi C, Ishida T, Kimura K. Genetic diversity of Lactobacillus delbrueckii isolated from raw milk in Hokkaido, Japan. J Dairy Sci 2021; 105:2082-2093. [PMID: 34955279 DOI: 10.3168/jds.2021-21135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022]
Abstract
Lactic acid bacteria (LAB) play important roles in acid production and flavor formation in fermented dairy products. Lactic acid bacteria strains with distinct characteristics confer unique features to products. Diverse LAB have been identified in raw milk and traditional fermented milk prepared from raw milk. However, little is known about LAB in raw milk in Japan. To preserve diverse LAB as potential starters or probiotics for future use, we have isolated and identified various kinds of LAB from raw milk produced in Japan. In this study, we focused on Lactobacillus delbrueckii, one of the most important species in the dairy industry. We identified L. delbrueckii subspecies isolated from raw milk in Hokkaido, Japan, by analyzing intraspecific diversity using 4 distinct methods, hsp60 cluster analysis, multilocus sequence analysis, core-genome analysis, and whole-genome analysis based on average nucleotide identity. The subspecies distribution and a new dominant subset of L. delbrueckii from raw milk in Japan were revealed. The discovery of new strains with different genotypes is important for understanding the geographic distribution and characteristics of the bacteria and further their use as a microbial resource with the potential to express unconventional flavors and functionalities. The strains identified in this study may have practical applications in the development of fermented dairy products.
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Affiliation(s)
- H Tsuchihashi
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan.
| | - A Ichikawa
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
| | - M Takeda
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
| | - A Koizumi
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
| | - C Mizoguchi
- Applied Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
| | - T Ishida
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
| | - K Kimura
- Basic Microbiology Research Department, Food Microbiology Research Laboratories, R&D Division, Meiji Co. Ltd., Hachioji, Tokyo 192-0919, Japan
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9
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Kim E, Cho EJ, Yang SM, Kim HY. Identification and Monitoring of Lactobacillus delbrueckii Subspecies Using Pangenomic-Based Novel Genetic Markers. J Microbiol Biotechnol 2021; 31:280-289. [PMID: 33144553 PMCID: PMC9705890 DOI: 10.4014/jmb.2009.09034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun-Ji Cho
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea,Corresponding author Phone: +82-31-201-2123 Fax: +82-31-204-8116 E-mail:
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10
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Effects of a low allergenic soybean variety on gut permeability, microbiota composition, ileal digestibility of amino acids, and growth performance in pigs. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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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: 1480] [Impact Index Per Article: 370.0] [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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12
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The molecular and phenotypic characterization of fructophilic lactic acid bacteria isolated from the guts of Apis mellifera L. derived from a Polish apiary. J Appl Genet 2018; 59:503-514. [DOI: 10.1007/s13353-018-0467-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
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13
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Attar MA, Yavarmanesh M, Mortazavi A, Edalatian Dovom MR, Habibi Najafi MB. Antibacterial effects of Lactococcus lactis isolated from Lighvan cheese regarding the recognition of Nisin, Lacticin and Lactococcin structural genes. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Screening for proteolytically active lactic acid bacteria and bioactivity of peptide hydrolysates obtained with selected strains. Appl Microbiol Biotechnol 2017; 101:7621-7633. [PMID: 28695230 DOI: 10.1007/s00253-017-8369-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 10/19/2022]
Abstract
In a screening for proteolytically active lactic acid bacteria, three strains, Lactobacillus delbrueckii ssp. lactis 92202, Lactobacillus helveticus 92201, and Lactobacillus delbrueckii ssp. bulgaricus 92059, showed the highest activities following growth in milk. All three strains degraded α- and β-casein, but did not hydrolyse κ-casein. HPLC analysis of skim milk fermentation revealed increasing amounts of peptides after 5 and 10 h with Lb. d. ssp. bulgaricus 92059. Hydrolysates obtained with Lb. d. ssp. lactis 92202 and Lb. d. ssp. bulgaricus 92059 revealed the highest angiotensin-converting enzyme-inhibitory effect. The effect was dose dependent. Almost no effect (<10%) was seen for Lb. helveticus 92201. For Lb. d. ssp. bulgaricus 92059, maximal inhibition of approx. 65% was reached after 25 h of fermentation. In an in vitro assay measuring potential immunomodulation, hydrolysates of the three strains yielded anti-inflammatory activities in the presence of TNF-α. However, the effects were more pronounced at lower hydrolysate concentrations. In the absence of TNF-α, slight pro-inflammatory effects were observed. The hydrolysate of Lb. d. ssp. bulgaricus 92059, when purified by means of solid-phase extraction, exhibited pro-inflammatory activity. Sour whey containing Lb. d. ssp. bulgaricus 92059 cells showed pro-inflammatory activity while cell-free sour whey was clearly anti-inflammatory. In the purified hydrolysate, 20 different α- and β-casein (CN)-derived peptides could be identified by LC-MS. Most peptides originated from the central and C-terminal regions of β-casein. Peptide length was between 9 (β-CN(f 59-67)) and 22 amino acids (β-CN(f 117-138)).
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15
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Zanni E, Schifano E, Motta S, Sciubba F, Palleschi C, Mauri P, Perozzi G, Uccelletti D, Devirgiliis C, Miccheli A. Combination of Metabolomic and Proteomic Analysis Revealed Different Features among Lactobacillus delbrueckii Subspecies bulgaricus and lactis Strains While In Vivo Testing in the Model Organism Caenorhabditis elegans Highlighted Probiotic Properties. Front Microbiol 2017; 8:1206. [PMID: 28702021 PMCID: PMC5487477 DOI: 10.3389/fmicb.2017.01206] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
Lactobacillus delbrueckii represents a technologically relevant member of lactic acid bacteria, since the two subspecies bulgaricus and lactis are widely associated with fermented dairy products. In the present work, we report the characterization of two commercial strains belonging to L. delbrueckii subspecies bulgaricus, lactis and a novel strain previously isolated from a traditional fermented fresh cheese. A phenomic approach was performed by combining metabolomic and proteomic analysis of the three strains, which were subsequently supplemented as food source to the model organism Caenorhabditis elegans, with the final aim to evaluate their possible probiotic effects. Restriction analysis of 16S ribosomal DNA revealed that the novel foodborne strain belonged to L. delbrueckii subspecies lactis. Proteomic and metabolomic approaches showed differences in folate, aminoacid and sugar metabolic pathways among the three strains. Moreover, evaluation of C. elegans lifespan, larval development, brood size, and bacterial colonization capacity demonstrated that L. delbrueckii subsp. bulgaricus diet exerted beneficial effects on nematodes. On the other hand, both L. delbrueckii subsp. lactis strains affected lifespan and larval development. We have characterized three strains belonging to L. delbrueckii subspecies bulgaricus and lactis highlighting their divergent origin. In particular, the two closely related isolates L. delbrueckii subspecies lactis display different galactose metabolic capabilities. Moreover, the L. delbrueckii subspecies bulgaricus strain demonstrated potential probiotic features. Combination of omic platforms coupled with in vivo screening in the simple model organism C. elegans is a powerful tool to characterize industrially relevant bacterial isolates.
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Affiliation(s)
- Elena Zanni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of RomeRome, Italy
| | - Emily Schifano
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of RomeRome, Italy
| | - Sara Motta
- Institute of Biomedical Technologies, National Research CouncilMilan, Italy
| | - Fabio Sciubba
- Department of Chemistry, Sapienza University of RomeRome, Italy
| | - Claudio Palleschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of RomeRome, Italy
| | - Pierluigi Mauri
- Institute of Biomedical Technologies, National Research CouncilMilan, Italy
| | - Giuditta Perozzi
- Food and Nutrition Research Center, Council for Agricultural Research and EconomicsRome, Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of RomeRome, Italy
| | - Chiara Devirgiliis
- Food and Nutrition Research Center, Council for Agricultural Research and EconomicsRome, Italy
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16
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Song Y, Sun Z, Guo C, Wu Y, Liu W, Yu J, Menghe B, Yang R, Zhang H. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods. Sci Rep 2016; 6:22704. [PMID: 26940047 PMCID: PMC4778129 DOI: 10.1038/srep22704] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/18/2016] [Indexed: 11/30/2022] Open
Abstract
Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2–CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1–L6, with various homologous recombination rates. Although L2–L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.
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Affiliation(s)
- Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Chenyi Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
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17
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Miyashita M, Yukphan P, Chaipitakchonlatarn W, Malimas T, Sugimoto M, Yoshino M, Kamakura Y, Potacharoen W, Tanasupawat S, Tanaka N, Nakagawa Y, Suzuki KI. Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods. Int J Syst Evol Microbiol 2015; 65:2485-2490. [DOI: 10.1099/ijs.0.000290] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA–DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.
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Affiliation(s)
- Mika Miyashita
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Pattaraporn Yukphan
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Winai Chaipitakchonlatarn
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Taweesak Malimas
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Masako Sugimoto
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mayumi Yoshino
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yuki Kamakura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Wanchern Potacharoen
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyoshi Nakagawa
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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18
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Koirala R, Ricci G, Taverniti V, Ferrario C, Malla R, Shrestha S, Fortina MG, Guglielmetti S. Isolation and molecular characterization of lactobacilli from traditional fermented Dahi produced at different altitudes in Nepal. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13594-014-0167-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Phenotypic and genotypic characterization of non-starter Lactobacillus species diversity in Indian Cheddar cheese. Lebensm Wiss Technol 2014. [DOI: 10.1016/j.lwt.2013.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Chen YS, Lin YH, Pan SF, Ji SH, Chang YC, Yu CR, Liou MS, Wu HC, Otoguro M, Yanagida F, Liao CC, Chiu CM, Huang BQ. Enterococcus saccharolyticus subsp. taiwanensis subsp. nov., isolated from broccoli. Int J Syst Evol Microbiol 2013; 63:4691-4697. [DOI: 10.1099/ijs.0.052761-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A coccal strain isolated from fresh broccoli was initially identified as
Enterococcus saccharolyticus
; however, molecular identification and phenotypic traits did not support this identification. DNA–DNA hybridization with the type strain of
E. saccharolyticus
(76.4 % relatedness), DNA G+C content (35.7 mol%), phylogenetic analysis based on 16S rRNA, pheS and rpoA gene sequences, rep-PCR fingerprinting and profiles of cellular fatty acids, whole-cell proteins and enzyme activities, together with carbohydrate metabolism characteristics, indicated that this strain is distinct and represents a novel subspecies, for which the name Enterococcus saccharolyticus subsp. taiwanensis subsp. nov. is proposed. The type strain is 812T ( = NBRC 109476T = BCRC 80575T). Furthermore, we present an emended description of
Enterococcus saccharolyticus
and proposal of Enterococcus saccharolyticus subsp. saccharolyticus subsp. nov. (type strain ATCC 43076T = CCUG 27643T = CCUG 33311T = CIP 103246T = DSM 20726T = JCM 8734T = LMG 11427T = NBRC 100493T = NCIMB 702594T).
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Affiliation(s)
- Yi-sheng Chen
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Yu-hsuan Lin
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Shwu-fen Pan
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Si-hua Ji
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Yu-chung Chang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Chi-rong Yu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Min-shiuan Liou
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Hui-chung Wu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Misa Otoguro
- The Institute of Enology and Viticulture, Yamanashi University, 1-13-1, Kitashin, Kofu, Yamanashi 400-0005, Japan
| | - Fujitoshi Yanagida
- The Institute of Enology and Viticulture, Yamanashi University, 1-13-1, Kitashin, Kofu, Yamanashi 400-0005, Japan
| | - Chen-chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chi-ming Chiu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
| | - Bi-qiang Huang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Road, Gui-Shan Township, Taoyuan County 333, Taiwan
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21
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Adimpong DB, Nielsen DS, Sørensen KI, Vogensen FK, Sawadogo-Lingani H, Derkx PMF, Jespersen L. Lactobacillus delbrueckii
subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso. Int J Syst Evol Microbiol 2013; 63:3720-3726. [DOI: 10.1099/ijs.0.048769-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus delbrueckii
is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9T, was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA–DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species
L. delbrueckii
. The genome sequence of isolate ZN7a-9T was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9T together with 41 additional
L. delbrueckii
strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of
L. delbrueckii
represented by strain ZN7a-9T as it clustered with
L. delbrueckii
strains unassigned to any of the recognized subspecies of
L. delbrueckii
. Strain ZN7a-9T additionally differed from the recognized type strains of the subspecies of
L. delbrueckii
with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9T represents a novel subspecies of
L. delbrueckii
closely related to
Lactobacillus delbrueckii subsp. lactis
and
Lactobacillus delbrueckii subsp. delbrueckii
for which the name
Lactobacillus delbrueckii
subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9T = DSM 26046T = LMG 27067T.
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Affiliation(s)
- David B. Adimpong
- Chr. Hansen A/S, Discovery Department, 10-12 Bøge Allé, DK-2970 Hørsholm, Denmark
- University of Copenhagen, Faculty of Science, Department of Food Science, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark
| | - Dennis S. Nielsen
- University of Copenhagen, Faculty of Science, Department of Food Science, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark
| | - Kim I. Sørensen
- Chr. Hansen A/S, Discovery Department, 10-12 Bøge Allé, DK-2970 Hørsholm, Denmark
| | - Finn K. Vogensen
- University of Copenhagen, Faculty of Science, Department of Food Science, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark
| | - Hagrétou Sawadogo-Lingani
- Département Technologie Alimentaire/IRSAT/CNRST, 03 BP 7047, Ouagadougou, Burkina Faso
- University of Copenhagen, Faculty of Science, Department of Food Science, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark
| | - Patrick M. F. Derkx
- Chr. Hansen A/S, Discovery Department, 10-12 Bøge Allé, DK-2970 Hørsholm, Denmark
| | - Lene Jespersen
- University of Copenhagen, Faculty of Science, Department of Food Science, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark
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22
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Cousin S, Motreff L, Gulat-Okalla ML, Gouyette C, Spröer C, Schumann P, Begaud E, Bouchier C, Clermont D, Bizet C. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. Int J Syst Evol Microbiol 2013; 63:53-59. [DOI: 10.1099/ijs.0.036665-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains 1517T and 61DT were characterized by phenotypic and molecular taxonomic methods. These Gram-positive lactic acid bacteria were homo-fermentative, facultatively anaerobic short rods. They were phylogenetically related to the genus
Lactobacillus
according to 16S rRNA gene sequence analysis, with 99 % similarity between strain 1517T and the type strain of
Lactobacillus gigeriorum
, and 98.6, 98.5 and 98.4 % between strain 61DT and
Lactobacillus gasseri
,
Lactobacillus taiwanensis
and
Lactobacillus johnsonii
, respectively. Multilocus sequence analysis and metabolic analysis of both strains showed variation between the two strains and their close relatives, with variation in the position of the pheS and rpoA genes. The DNA–DNA relatedness of 43.5 % between strain 1517T and
L. gigeriorum
, and 38.6, 29.9 and 39.7 % between strain 61DT and
L. johnsonii
,
L. taiwanensis
and
L. gasseri
, respectively, confirmed their status as novel species. Based on phenotypic and genotypic characteristics, two novel species of
Lactobacillus
are proposed: Lactobacillus pasteurii sp. nov., with 1517T ( = CRBIP 24.76T = DSM 23907T) as the type strain, and Lactobacillus hominis sp. nov., with 61DT ( = CRBIP 24.179T = DSM 23910T) as the type strain.
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Affiliation(s)
- Sylvie Cousin
- Institut Pasteur, Plate-forme Génomique, Dept Génomes et Génétique, F-75015 Paris, France
| | - Laurence Motreff
- Institut Pasteur, CRBIP (Centre de Ressources Biologiques de l’Institut Pasteur), Dept Microbiologie, F-75015 Paris, France
| | - Marie-Laure Gulat-Okalla
- Institut Pasteur, CRBIP (Centre de Ressources Biologiques de l’Institut Pasteur), Dept Microbiologie, F-75015 Paris, France
| | - Catherine Gouyette
- Institut Pasteur, Plate-forme Génomique, Dept Génomes et Génétique, F-75015 Paris, France
| | - Cathrin Spröer
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures), D-38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures), D-38124 Braunschweig, Germany
| | - Evelyne Begaud
- Institut Pasteur, CRBIP (Centre de Ressources Biologiques de l’Institut Pasteur), Dept Microbiologie, F-75015 Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Plate-forme Génomique, Dept Génomes et Génétique, F-75015 Paris, France
| | - Dominique Clermont
- Institut Pasteur, CRBIP (Centre de Ressources Biologiques de l’Institut Pasteur), Dept Microbiologie, F-75015 Paris, France
| | - Chantal Bizet
- Institut Pasteur, CRBIP (Centre de Ressources Biologiques de l’Institut Pasteur), Dept Microbiologie, F-75015 Paris, France
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23
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Satish Kumar R, Kanmani P, Yuvaraj N, Paari KA, Pattukumar V, Arul V. Traditional Indian fermented foods: a rich source of lactic acid bacteria. Int J Food Sci Nutr 2012. [PMID: 23181843 DOI: 10.3109/09637486.2012.746288] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the diversity of Indian fermented food and its significance as a potential source of lactic acid bacteria (LAB). Fermented foods consumed in India are categorized based upon their base material. Fermented foods such as dahi, gundruk, sinki, iniziangsang, iromba, fermented rai, kanjika and handua were reported to have significant medicinal properties. Some fermented products such as koozh, dahi and kanjika are consumed unknowingly as, probiotic drinks, by local people. There are very few reports regarding isolation of LAB from Indian fermented foods available in the past; however, due to growing consciousness about potential health benefits of LAB, we now have scores of reports in this field. There is an abundant opportunity available for food microbiologists to explore the Indian fermented foods for the isolation of new LAB strains for their potential role in probiotic research.
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Affiliation(s)
- R Satish Kumar
- Department of Biotechnology, Pondicherry University, Puducherry, India
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24
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Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 2012; 62:2643-2649. [DOI: 10.1099/ijs.0.037051-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as
Lactobacillus delbrueckii
, the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of
L. delbrueckii
. Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of
L. delbrueckii
were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T = DSM 24966T).
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25
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Chen L, Teasdale MT, Kaczmarczyk MM, Freund GG, Miller MJ. Development of a Lactobacillus specific T-RFLP method to determine lactobacilli diversity in complex samples. J Microbiol Methods 2012; 91:262-8. [PMID: 22981747 DOI: 10.1016/j.mimet.2012.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/06/2012] [Accepted: 08/07/2012] [Indexed: 11/29/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis has been widely used for studying microbial communities. However, most T-RFLP assays use 16S rDNA as the target and are unable to accurately characterize a microbial subpopulation. In this study, we developed a novel T-RFLP protocol based on Lactobacillus hsp60 to rapidly characterize and compare lactobacilli composition. The theoretical terminal restriction fragment (TRF) profiles were calculated from 769 Lactobacillus hsp60 sequences from online databases. In silico digestion with restriction endonucleases AluI and TacI on hsp60 amplicons generated 83 distinct TRF patterns, of which, 70 were species specific. To validate the assay, five previously sequenced lactobacilli were cultured independently, mixed at known concentrations and subjected to analysis by T-RFLP. All five strains generated the predicted TRFs and a qualitative consistent relationship was revealed. We performed the T-RFLP protocol on fecal samples from mice fed 6 different diets (n=4). Principal component analysis and agglomerative hierarchical clustering revealed that the lactobacilli community was strongly connected to dietary supplementation. Our study demonstrates the potential for using Lactobacillus specific T-RFLP to characterize lactobacilli communities in complex samples.
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Affiliation(s)
- Long Chen
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, United States
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Lee SH, Park MS, Jung JY, Jeon CO. Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi. Int J Syst Evol Microbiol 2012; 62:1098-1103. [PMID: 21705441 DOI: 10.1099/ijs.0.032367-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, non-motile and non-spore-forming lactic acid bacterium, designated strain M2(T), was isolated from fermented brown algae (Undaria pinnatifida) kimchi in South Korea. Cells of the isolate were facultatively anaerobic ovoids and showed catalase- and oxidase-negative reactions. Growth of strain M2(T) was observed at 4-35 °C and at pH 5.0-9.0. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M2(T) belonged to the genus Leuconostoc and was most closely related to Leuconostoc inhae IH003(T), Leuconostoc kimchii IH25(T), Leuconostoc gasicomitatum LMG 18811(T), Leuconostoc gelidum DSM 5578(T), Leuconostoc palmae TMW2.694(T) and Leuconostoc holzapfelii BFE 7000(T) with 98.9 %, 98.8 %, 98.8 %, 98.7 %, 98.5 % and 98.2 % sequence similarity, respectively. DNA-DNA hybridization values between strain M2(T) and Leuconostoc inhae KACC 12281(T), Leuconostoc kimchii IH25(T), Leuconostoc gelidum KACC 12256(T), Leuconostoc gasicomitatum KACC 13854(T), Leuconostoc palmae DSM 21144(T) and Leuconostoc holzapfelii DSM 21478(T) were 13.8±3.2 %, 14.3±3.4 %, 9.9±1.0 %, 13.2±0.8 %, 22.4±4.9 % and 16.2±4.6 %, respectively, which allowed differentiation of strain M2(T) from the closely related species of the genus Leuconostoc. On the basis of phenotypic and molecular properties, strain M2(T) represents a novel species in the genus Leuconostoc, for which the name Leuconostoc miyukkimchii sp. nov. is proposed. The type strain is M2(T) ( = KACC 15353(T) = JCM 17445(T)).
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Affiliation(s)
- Seung Hyeon Lee
- Schools of Biological Sciences & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Moon Su Park
- Schools of Biological Sciences & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Ji Young Jung
- Schools of Biological Sciences & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Che Ok Jeon
- Schools of Biological Sciences & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, 156-756, Republic of Korea
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Shevtsov AB, Kushugulova AR, Tynybaeva IK, Kozhakhmetov SS, Abzhalelov AB, Momynaliev KT, Stoyanova LG. Identification of phenotypically and genotypically related Lactobacillus strains based on nucleotide sequence analysis of the groEL, rpoB, rplB, and 16S rRNA genes. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711050134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Shin SG, Yoo S, Hwang K, Song M, Kim W, Han G, Hwang S. Dynamics of transitional acidogenic community along with methanogenic population during anaerobic digestion of swine wastewater. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tanigawa K, Watanabe K. Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii. Microbiology (Reading) 2011; 157:727-738. [DOI: 10.1099/mic.0.043240-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080T, was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.
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Affiliation(s)
- Kana Tanigawa
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Koichi Watanabe
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
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Botina SG, Klimina KM, Koroban NV, Amerkhanova AM, Zinchenko VV, Danilenko VN. Revised classification of native probiotic strains of Lactobacillus used in Russian Federation. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410110050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Endo A, Mizuno H, Okada S. Monitoring the bacterial community during fermentation of sunki, an unsalted, fermented vegetable traditional to the Kiso area of Japan. Lett Appl Microbiol 2009; 47:221-6. [PMID: 19552789 DOI: 10.1111/j.1472-765x.2008.02404.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the microbial community in sunki, an indigenous, unsalted, fermented vegetable, made from the leaves of red beet. METHODS AND RESULTS Fermenting samples were collected at 1- to 2-day intervals from four houses and investigated by culture-dependent and culture-independent techniques. PCR-Denaturing-Gradient-Gel-Electrophoresis profiles indicated that the bacterial community was stable and Lactobacillus delbrueckii, Lact. fermentum and Lact. plantarum were dominant during the fermentation. This result agreed well with that obtained by the culturing technique. Moulds, yeasts or bacteria other than lactic acid bacteria (LAB) were not detected. CONCLUSIONS The bacterial community was stable throughout the fermentation, and Lact. delbrueckii, Lact. fermentum and Lact. plantarum were dominant. The acidic pH and lactic acid produced by LAB probably preserve the sunki from spoilage. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report on the use of both culture-dependent and culture-independent techniques to study the bacterial community in sunki. A combination of culture-dependent and culture-independent techniques is necessary for the analysis of complex microbial communities.
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Affiliation(s)
- A Endo
- NODAI Culture Collection Center, Tokyo University of Agriculture, Tokyo, Japan.
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Ehrmann MA, Freiding S, Vogel RF. Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine. Int J Syst Evol Microbiol 2009; 59:943-7. [PMID: 19406772 DOI: 10.1099/ijs.0.005983-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel lactic acid bacterium, strain TMW 2.694(T), was isolated among other lactic acid bacteria from palm wine, an alcoholic beverage produced from the sap of various palm tree species. Strain TMW 2.694(T) is a Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming coccus, occurring in long chains. Phylogenetic analysis based on 16S rRNA gene sequencing positioned strain TMW 2.694(T) in a distinct line of descent within the genus Leuconostoc, with the closest neighbours being Leuconostoc lactis JCM 6123(T) (98.7 % sequence similarity) and Leuconostoc citreum DSM 5577(T) (98.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers dnaK and recA confirmed the 16S rRNA gene tree topology. Genomic DNA-DNA similarities of strain TMW 2.694(T) to L. lactis DSM 20202(T) and L. citreum DSM 5577(T) were 45.1 and 17.7 %, respectively. The DNA G+C content is 36.4 mol%. Thus, we propose a novel species within the genus Leuconostoc, with the name Leuconostoc palmae sp. nov. and the type strain TMW 2.694(T) (=DSM 21144(T) =LMG 24510(T)).
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Affiliation(s)
- Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany.
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Endo A, Okada S. Reclassification of the genus Leuconostoc and proposals of Fructobacillus fructosus gen. nov., comb. nov., Fructobacillus durionis comb. nov., Fructobacillus ficulneus comb. nov. and Fructobacillus pseudoficulneus comb. nov. Int J Syst Evol Microbiol 2008; 58:2195-205. [PMID: 18768629 DOI: 10.1099/ijs.0.65609-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was made of the genus Leuconostoc. The species in the genus were divided into three subclusters by phylogenetic analysis based on the 16S rRNA gene sequences. The three subclusters were the Leuconostoc mesenteroides subcluster (comprising L. carnosum, L. citreum, L. gasicomitatum, L. gelidum, L. inhae, L. kimchii, L. lactis, L. mesenteroides and L. pseudomesenteroides), the L. fructosum subcluster (L. durionis, L. ficulneum, L. fructosum and L. pseudoficulneum) and the L. fallax subcluster (L. fallax). Phylogenetic trees based on the sequences of the 16S-23S rRNA gene intergenic spacer region, the rpoC gene or the recA gene indicated a good correlation with the phylogenetic tree based on 16S rRNA gene sequences. The species in the L. fructosum subcluster were morphologically distinguishable from the species in the L. mesenteroides subcluster and L. fallax as species in the L. fructosum subcluster had rod-shaped cells. In addition, the four species in the L. fructosum subcluster needed an electron acceptor for the dissimilation of d-glucose and produced acetic acid from d-glucose rather than ethanol. On the basis of evidence presented in this study, it is proposed that the four species in the L. fructosum subcluster, Leuconostoc durionis, Leuconostoc ficulneum, Leuconostoc fructosum and Leuconostoc pseudoficulneum, should be transferred to a novel genus, Fructobacillus gen. nov., as Fructobacillus durionis comb. nov. (type strain D-24(T)=LMG 22556(T)=CCUG 49949(T)), Fructobacillus ficulneus comb. nov. (type strain FS-1(T)=DSM 13613(T)=JCM 12225(T)), Fructobacillus fructosus comb. nov. (type strain IFO 3516(T)=DSM 20349(T)=JCM 1119(T)=NRIC 1058(T)) and Fructobacillus pseudoficulneus comb. nov. (type strain LC-51(T)=DSM 15468(T)=CECT 5759(T)). The type species of the genus Fructobacillus is Fructobacillus fructosus gen. nov., comb. nov.. No significant physiological and biochemical differences were found between the species in the L. mesenteroides subcluster and L. fallax in the present study and thus L. fallax remains as a member of the genus Leuconostoc.
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MESH Headings
- Acetic Acid/metabolism
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- DNA-Directed RNA Polymerases/genetics
- Ethanol/metabolism
- Genes, rRNA
- Genotype
- Glucose/metabolism
- Leuconostoc/classification
- Leuconostoc/cytology
- Leuconostoc/genetics
- Leuconostoc/metabolism
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rec A Recombinases/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Akihito Endo
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan.
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34
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Evaluation of biodiversity of lactic acid bacteria microbiota in the calf intestinal tracts. Antonie van Leeuwenhoek 2008; 94:145-55. [DOI: 10.1007/s10482-008-9220-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
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35
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Batdorj B, Trinetta V, Dalgalarrondo M, Prévost H, Dousset X, Ivanova I, Haertlé T, Chobert JM. Isolation, taxonomic identification and hydrogen peroxide production by Lactobacillus delbrueckii subsp. lactis T31, isolated from Mongolian yoghurt: inhibitory activity on food-borne pathogens. J Appl Microbiol 2007; 103:584-93. [PMID: 17714391 DOI: 10.1111/j.1365-2672.2007.03279.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The aim of this work was to isolate lactic acid bacteria (LAB) strains from Mongolian tarag (a traditionally homemade yoghurt) displaying antimicrobial activities against food-borne pathogens, identify inhibitory substances and study the kinetics of their production. METHODS AND RESULTS Inhibitory substance-producing bacterial strains were isolated from tarag. From 300 bacterial clones, 31 were able to inhibit the growth of the indicator strain Lactobacillus bulgaricus 340. One of the most active strains was identified as Lactobacillus delbrueckii subsp. lactis strain T31 by using cluster analysis of amplified fragment length polymorphism (AFLP) DNA fingerprints. The antimicrobial substance was inactivated by catalase, demonstrating the production of hydrogen peroxide (H(2)O(2)). Production of H(2)O(2) was studied under aerated and nonaerated culture conditions. The amount of H(2)O(2) in the culture supernatant increased during bacterial growth and reached a maximum (5.12 mmol l(-1)) at the early stationary phase under aerated conditions (agitated cultures). H(2)O(2) was not detected in the culture performed without agitation. In mixed cultures performed in milk with either Lact. delbrueckii subsp. lactis T31 in the presence of Escherichia coli, or Lact. delbrueckii subsp. lactis T31 in the presence of Listeria innocua under aerated and nonaerated conditions, a significant decrease in pathogen count was observed in aerated cultures. SIGNIFICANCE AND IMPACT OF THE STUDY The significant decrease in Listeria viability observed in aerated mixed cultures of Lact. delbrueckii subsp. lactis T31 is mainly because of H(2)O(2) production. Lactobacillus delbrueckii subsp. lactis T31 could be used as a protective culture in food industries or as a probiotic to prevent intestinal and urogenital infections.
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Affiliation(s)
- B Batdorj
- INRA, Unité de Recherche Biopolymères, Interactions, Assemblages, Fonctions et Interactions des Protéines Laitières (BIA-FIPL), rue de la Géraudière, Nantes Cedex 3, France
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36
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Mikkelsen L, Højberg O, Jensen B. Coarse structured feed stimulates members of the genera Lactobacillus and Mitsuokella as well as propionate and butyrate producers in the pig stomach. Livest Sci 2007. [DOI: 10.1016/j.livsci.2007.01.130] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Batdorj B, Trinetta V, Dalgalarrondo M, Prévost H, Dousset X, Ivanova I, Haertlé T, Chobert JM. Isolation, taxonomic identification and hydrogen peroxide production by Lactobacillus delbrueckii subsp. lactis T31, isolated from Mongolian yoghurt: inhibitory activity on food-borne pathogens. J Appl Microbiol 2007. [DOI: 10.1111/j.1365-2672.2006.03279.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Botina SG, Tsygankov YD, Sukhodolets VV. Identification of industrial strains of lactic acid bacteria by methods of molecular genetic typing. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406120039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Li Y, Raftis E, Canchaya C, Fitzgerald GF, van Sinderen D, O'Toole PW. Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and Lactobacillus salivarius subsp. salicinius do not merit separate subspecies status. Int J Syst Evol Microbiol 2006; 56:2397-2403. [PMID: 17012569 DOI: 10.1099/ijs.0.64426-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus salivarius Rogosa et al. 1953 was described as a homofermentative lactobacillus with two varieties: salivarius, typified inter alia by the ability to ferment rhamnose, and salicinius, characterized by the ability to ferment the glucoside salicin. These varieties have become accepted as subspecies divisions. We have examined the relatedness of 32 L. salivarius strains by a polyphasic approach. Carbohydrate fermentation profile analysis did not support clear distinction of the two subspecies. L. salivarius UCC118 was shown to be facultatively heterofermentative, confirming in silico genome analysis. 16S rRNA gene sequences and 16S-23S rRNA intergenic spacer region sequences provided no discrimination between any of the strains or subspecies. Broad subdivisions were distinguishable by pulsed-field gel genomic digest patterns, but they did not allow subspecific or phenotypic distinctions. A phylogeny based upon groEL gene sequences was discordant with rhamnose or salicin fermentation data for many taxa, and no reliable phenotypic correlations could be established. In the absence of meaningful taxonomic criteria, we therefore propose that Lactobacillus salivarius comprises a single species with no infraspecific taxa. Based on the present study and literature data, an emended description of the species Lactobacillus salivarius is provided.
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Affiliation(s)
- Yin Li
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Emma Raftis
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Carlos Canchaya
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Gerald F Fitzgerald
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Paul W O'Toole
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Ireland
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40
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Dellaglio F, Vancanneyt M, Endo A, Vandamme P, Felis GE, Castioni A, Fujimoto J, Watanabe K, Okada S. Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983. Int J Syst Evol Microbiol 2006; 56:1721-1724. [PMID: 16901998 DOI: 10.1099/ijs.0.64316-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.
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Affiliation(s)
- Franco Dellaglio
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Akihito Endo
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Giovanna E Felis
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - Anna Castioni
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - Junji Fujimoto
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Koichi Watanabe
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Sanae Okada
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
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41
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Felis GE, Vancanneyt M, Snauwaert C, Swings J, Torriani S, Castioni A, Dellaglio F. Reclassification of Lactobacillus thermotolerans Niamsup et al. 2003 as a later synonym of Lactobacillus ingluviei Baele et al. 2003. Int J Syst Evol Microbiol 2006; 56:793-795. [PMID: 16585696 DOI: 10.1099/ijs.0.63992-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The relatedness of the speciesLactobacillus ingluvieiandLactobacillus thermotoleranswas investigated by comparing partial sequences of the 16S rRNA gene (99·9 % similarity over 1504 bp), thehsp60gene (98·8 % similarity over 954 bp) and therecAgene (98·5 % similarity over 452 bp) and by determining DNA–DNA binding levels (79±3 %) and genomic DNA G+C contents (50 and 49 mol%, respectively). These data, in addition to their similar biochemical characteristics, suggest that the two taxa constitute a single species. According to Rules 38 and 42 of theBacteriological Code, they should be united under the nameLactobacillus ingluviei, with the nameLactobacillus thermotoleransas a later heterotypic synonym.
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Affiliation(s)
- G E Felis
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Viale San Pietro 43b, I-07100 Sassari, Italy
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - M Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - C Snauwaert
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - J Swings
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - S Torriani
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - A Castioni
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
| | - F Dellaglio
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy
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Naser SM, Hagen KE, Vancanneyt M, Cleenwerck I, Swings J, Tompkins TA. Lactobacillus suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla-Jensen 1919) Bergey et al. 1925 (Approved Lists 1980). Int J Syst Evol Microbiol 2006; 56:355-360. [PMID: 16449439 DOI: 10.1099/ijs.0.64001-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain R0052, isolated from a North American dairy starter culture, was initially identified as Lactobacillus acidophilus based on phenotypic analyses. However, upon sequencing the 16S rRNA gene, it became clear that the isolate was very highly related to Lactobacillus suntoryeus, Lactobacillus helveticus and Lactobacillus gallinarum, as similarities ranging from 99·3 to 99·8 % were observed. As an initial screening test to investigate the relatedness of strain R0052 and reference strains of L. suntoryeus, L. helveticus and L. gallinarum, the partial sequences for the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), the translational elongation factor Tu (tuf), a surface-layer protein (slp) and the Hsp60 chaperonins (groEL) were determined and they revealed high relatedness between all of the strains. The determination of the 16S–23S rRNA internally transcribed spacer (ITS) sequences revealed 98·3–100 % similarity between L. suntoryeus and L. helveticus strains. SDS-PAGE of whole-cell proteins did not distinguish between these species. Fluorescent amplified fragment length polymorphism (FAFLP) could distinguish between these taxa, but they still constituted a single cluster within the L. acidophilus group. Finally, DNA–DNA hybridization experiments between strain R0052 and the type strains of L. helveticus and L. suntoryeus yielded reassociation values above 70 % and confirmed that these names are synonyms.
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Affiliation(s)
- Sabri M Naser
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Karen E Hagen
- Institut Rosell Inc., Research and Development, 6100 Royalmount Ave, Montreal, Quebec, Canada, H4P 2R2
| | - Marc Vancanneyt
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Ilse Cleenwerck
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Thomas A Tompkins
- Institut Rosell Inc., Research and Development, 6100 Royalmount Ave, Montreal, Quebec, Canada, H4P 2R2
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