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Wu M, Pakroo S, Nadai C, Molinelli Z, Speciale I, De Castro C, Tarrah A, Yang J, Giacomini A, Corich V. Genomic and functional evaluation of exopolysaccharide produced by Liquorilactobacillus mali t6-52: technological implications. Microb Cell Fact 2024; 23:158. [PMID: 38812023 PMCID: PMC11138040 DOI: 10.1186/s12934-024-02431-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: 03/21/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND This study explores the biosynthesis, characteristics, and functional properties of exopolysaccharide produced by the strain Liquorilactobacillus mali T6-52. The strain demonstrated significant EPS production with a non-ropy phenotype. RESULTS The genomic analysis unveiled genes associated with EPS biosynthesis, shedding light on the mechanism behind EPS production. These genes suggest a robust EPS production mechanism, providing insights into the strain's adaptability and ecological niche. Chemical composition analysis identified the EPS as a homopolysaccharide primarily composed of glucose, confirming its dextran nature. Furthermore, it demonstrated notable functional properties, including antioxidant activity, fat absorption capacity, and emulsifying activity. Moreover, the EPS displayed promising cryoprotective activities, showing notable performance comparable to standard cryoprotective agents. The EPS concentration also demonstrated significant freeze-drying protective effects, presenting it as a potential alternative cryoprotectant for bacterial storage. CONCLUSIONS The functional properties of L. mali T6-52 EPS reveal promising opportunities across various industrial domains. The strain's safety profile, antioxidant prowess, and exceptional cryoprotective and freeze-drying characteristics position it as an asset in food processing and pharmaceuticals.
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Affiliation(s)
- Manyu Wu
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, Padova, Italy
| | - Shadi Pakroo
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Chiara Nadai
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
| | - Zeno Molinelli
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
| | - Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA, Italy
| | - Crisitina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA, Italy
| | - Armin Tarrah
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Jijin Yang
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, Padova, Italy
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, Padova, Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, Padova, Italy
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Fanelli F, Montemurro M, Chieffi D, Cho GS, Low HZ, Hille F, Franz CMAP, Fusco V. Motility in Periweissella Species: Genomic and Phenotypic Characterization and Update on Motility in Lactobacillaceae. Microorganisms 2023; 11:2923. [PMID: 38138067 PMCID: PMC10745875 DOI: 10.3390/microorganisms11122923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
The genus Weissella and the recently described genus Periweissella, to which some previously named Weissella species have been reclassified as a result of a taxogenomic assessment, includes lactic acid bacteria species with high biotechnological and probiotic potential. Only one species, namely, Periweissella (P.) beninensis, whose type strain has been shown to possess probiotic features, has so far been described to be motile. However, the availability of numerous genome sequences of Weissella and Periweissella species prompted the possibility to screen for the presence of the genetic determinants encoding motility in Weissella and Periweissellas spp. other than P. beninensis. Herein, we performed a comprehensive genomic analysis to identify motility-related proteins in all Weissella and Periweissella species described so far, and extended the analysis to the recently sequenced Lactobacillaceae spp. Furthermore, we performed motility assays and transmission electron microscopy (TEM) on Periweissella type strains to confirm the genomic prediction. The homology-based analysis revealed genes coding for motility proteins only in the type strains of P. beninensis, P. fabalis, P. fabaria and P. ghanensis genomes. However, only the P. beninensis type strain was positive in the motility assay and displayed run-and-tumble behavior. Many peritrichous and long flagella on bacterial cells were visualized via TEM, as well. As for the Lactobacillaceae, in addition to the species previously described to harbor motility proteins, the genetic determinants of motility were also found in the genomes of the type strains of Lactobacillus rogosae and Ligilactobacillus salitolerans. This study, which is one of the first to analyze the genomes of Weissella, Periweissella and the recently sequenced Lactobacillaceae spp. for the presence of genes coding for motility proteins and which assesses the associated motility phenotypes, provides novel results that expand knowledge on these genera and are useful in the further characterization of lactic acid bacteria.
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Affiliation(s)
- Francesca Fanelli
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), 70126 Bari, Italy; (F.F.); (M.M.); (D.C.)
| | - Marco Montemurro
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), 70126 Bari, Italy; (F.F.); (M.M.); (D.C.)
| | - Daniele Chieffi
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), 70126 Bari, Italy; (F.F.); (M.M.); (D.C.)
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (G.-S.C.); (H.-Z.L.); (F.H.)
| | - Hui-Zhi Low
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (G.-S.C.); (H.-Z.L.); (F.H.)
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (G.-S.C.); (H.-Z.L.); (F.H.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (G.-S.C.); (H.-Z.L.); (F.H.)
| | - Vincenzina Fusco
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), 70126 Bari, Italy; (F.F.); (M.M.); (D.C.)
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Qiao N, Bechtner J, Cnockaert M, Depoorter E, Díaz-Muñoz C, Vandamme P, De Vuyst L, Gänzle MG. Comparative genomic analysis of Periweissella and the characterization of novel motile species. Appl Environ Microbiol 2023; 89:e0103423. [PMID: 37728921 PMCID: PMC10617413 DOI: 10.1128/aem.01034-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 09/22/2023] Open
Abstract
The genus Periweissella was proposed as a novel genus in the Lactobacillaceae in 2022. However, the phylogenetic relationship between Periweissella and other heterofermentative lactobacilli, and the genetic and physiological properties of this genus remain unclear. This study aimed to determine the phylogenetic relationship between Periweissella and the two closest genera, Weissella and Furfurilactobacillus, by the phylogenetic analysis and calculation of (core gene) pairwise average amino acid identity. Targeted genomic analysis showed that fructose bisphosphate aldolase was only present in the genome of Pw. cryptocerci. Mannitol dehydrogenase was found in genomes of Pw. beninensis, Pw. fabaria, and Pw. fabalis. Untargeted genomic analysis identified the presence of flagellar genes in Periweissella but not in other closely related genera. Phenotypes related to carbohydrate fermentation and motility matched the genotypes. Motility genes were organized in a single operon and the proteins shared a high amino acid similarity in the genus Periweissella. The relatively low similarity of motility operons between Periweissella and other motile lactobacilli indicated the acquisition of motility by the ancestral species. Our findings facilitate the phylogenetic, genetic, and phenotypic understanding of the genus Periweissella.ImportanceThe genus Periweissella is a heterofermentative genus in the Lactobacillaceae which includes predominantly isolates from cocoa fermentations in tropical climates. Despite the relevance of the genus in food fermentations, genetic and physiological properties of the genus are poorly characterized and genome sequences became available only after 2020. This study characterized strains of the genus by functional genomic analysis, and by determination of metabolic and physiological traits. Phylogenetic analysis revealed that Periweissella is the evolutionary link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade with the genera Weissella and Furfurilactobacillus as closest relatives. Periweissella is the only heterofermentative genus in the Lactobacillaceae which comprises predominantly motile strains. The genomic, physiological, and metabolic characterization of Periweissella may facilitate the potential use of strains of the genus as starter culture in traditional or novel food fermentations.
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Affiliation(s)
- Nanzhen Qiao
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Julia Bechtner
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Eliza Depoorter
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Christian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Michael G. Gänzle
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Suzuki S, Yokota K, Igimi S, Kajikawa A. Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances. Sci Rep 2023; 13:15632. [PMID: 37730901 PMCID: PMC10511705 DOI: 10.1038/s41598-023-42840-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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5
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Bnfaga AA, Lee KW, Than LTL, Amin-Nordin S. Antimicrobial and immunoregulatory effects of Lactobacillus delbrueckii 45E against genitourinary pathogens. J Biomed Sci 2023; 30:19. [PMID: 36959635 PMCID: PMC10037868 DOI: 10.1186/s12929-023-00913-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Lactobacilli are essential microbiota that maintain a healthy, balanced vaginal environment. Vaginitis is a common infection in women during their reproductive years. Many factors are associated with vaginitis; one of them is the imbalance of microbiota in the vaginal environment. This study aimed to evaluate the antimicrobial properties of Lactobacillus delbrueckii 45E (Ld45E) against several species of bacteria, namely, Group B Streptococcus (GBS), Escherichia coli, Klebsiella spp., and Candida parapsilosis, as well as to determine the concentration of interleukin-17 (IL-17) in the presence of Ld45E. METHODS The probiotic characteristics of Ld45E were evaluated by examining its morphology, pH tolerance, adhesive ability onto HeLa cells, hemolytic activity, antibiotic susceptibility, and autoaggregation ability. Then, the antimicrobial activity of Ld45E was determined using Ld45E culture, cell-free supernatant, and crude bacteriocin solution. Co-aggregation and competition ability assays against various pathogens were conducted. The immunoregulatory effects of Ld45E were analyzed by measuring the proinflammatory cytokine IL-17. A p-value less than 0.05 was considered statistical significance. RESULTS Ld45E is 3-5 mm in diameter and round with a flat-shaped colony. pH 4 and 4.5 were the most favorable range for Ld45E growth within 12 h of incubation. Ld45E showed a strong adhesion ability onto HeLa cells (86%) and negative hemolytic activities. Ld45E was also sensitive to ceftriaxone, cefuroxime, ciprofloxacin, and doxycycline. We found that it had a good autoaggregation ability of 80%. Regarding antagonistic properties, Ld45E culture showed strong antimicrobial activity against GBS, E. coli, and Klebsiella spp. but only a moderate effect on C. parapsilosis. Cell-free supernatant of Ld45E exerted the most potent inhibitory effects at 40 °C against all genital pathogens, whereas bacteriocin showed a robust inhibition at 37 °C and 40 °C. The highest co-aggregation affinity was observed with GBS (81%) and E. coli (40%). Competition ability against the adhesion of GBS (80%), E. coli (76%), Klebsiella (72%), and C. parapsilosis (58%) was found. Ld45E was able to reduce the induction of the proinflammatory protein IL-17. CONCLUSIONS Ld45E possessed antimicrobial and immunoregulatory properties, with better cell-on-cell activity than supernatant activity. Thus, Ld45E is a potential probiotic candidate for adjunct therapy to address vaginal infections.
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Affiliation(s)
- Ameda Abdullah Bnfaga
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Para-Clinic, Faculty of Medicine, Aden University, Aden, Yemen
| | - Kai Wei Lee
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Hospital Sultan Abdul Aziz Shah, Universiti Putra Malaysia, Persiaran MARDI-UPM, 43400, Serdang, Malaysia.
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Heng YC, Menon N, Chen B, Loo BZL, Wong GWJ, Lim ACH, Silvaraju S, Kittelmann S. Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit ( Durio zibethinus). Int J Syst Evol Microbiol 2023; 73. [PMID: 36920986 DOI: 10.1099/ijsem.0.005733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).
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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
| | - Nandita Menon
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Binbin Chen
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Zong Lin Loo
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Garrett Wei Jie Wong
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Amber Ching Han Lim
- 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
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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Jiang L, Seo J, Peng Y, Jeon D, Lee JH, Kim CY, Lee J. A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species. Front Microbiol 2023; 14:1101150. [PMID: 36846770 PMCID: PMC9950776 DOI: 10.3389/fmicb.2023.1101150] [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: 11/17/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
A novel, nostoxanthin-producing, endophytic bacterium, designated as AK-PDB1-5T, was isolated from the needle-like leaves of the Korean fir (Abies koreana Wilson) collected from Mt. Halla in Jeju, South Korea. A 16S rRNA sequence comparison indicated that the closest phylogenetic neighbors were Sphingomonas crusticola MIMD3T (95.6%) and Sphingomonas jatrophae S5-249T (95.3%) of the family Sphingomonadaceae. Strain AK-PDB1-5T had a genome size of 4,298,284 bp with a 67.8% G + C content, and digital DNA-DNA hybridization and OrthoANI values with the most closely related species of only 19.5-21% and 75.1-76.8%, respectively. Cells of the strain AK-PDB1-5T were Gram-negative, short rods, oxidase- and catalase-positive. Growth occurred at pH 5.0-9.0 (optimum pH 8.0) in the absence of NaCl at 4-37°C (optimum 25-30°C). Strain AK-PDB1-5T contained C14:0 2OH, C16:0 and summed feature 8 as the major cellular fatty acids (> 10%), while sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phospholipids and lipids were found to be the major polar lipids. The strain produces a yellow carotenoid pigment; natural products prediction via AntiSMASH tool found zeaxanthin biosynthesis clusters in the entire genome. Biophysical characterization by ultraviolet-visible absorption spectroscopy and ESI-MS studies confirmed the yellow pigment was nostoxanthin. In addition, strain AK-PDB1-5T was found significantly promote Arabidopsis seedling growth under salt conditions by reducing reactive oxygen species (ROS). Based on the polyphasic taxonomic analysis results, strain AK-PDB1-5T was determined to be a novel species in the genus Sphingomonas with the proposed name Sphingomonas nostoxanthinifaciens sp. nov. The type strain is AK-PDB1-5T (= KCTC 82822T = CCTCC AB 2021150T).
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Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Jiyoon Seo
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yuxin Peng
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Doeun Jeon
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Cha Young Kim
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
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Sun Z, Jiang X, Wang B, Tian F, Zhang H, Yu L. Novel Phocaeicola Strain Ameliorates Dextran Sulfate Sodium-induced Colitis in Mice. Curr Microbiol 2022; 79:393. [DOI: 10.1007/s00284-022-03054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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9
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Ledormand P, Desmasures N, Bernay B, Goux D, Rué O, Midoux C, Monnet C, Dalmasso M. Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages. Food Microbiol 2022; 107:104069. [DOI: 10.1016/j.fm.2022.104069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/12/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
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10
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Yu L, Zang X, Chen Y, Gao Y, Pei Z, Yang B, Zhang H, Narbad A, Tian F, Zhai Q, Chen W. Phenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems. Food Res Int 2022; 160:111640. [PMID: 36076376 DOI: 10.1016/j.foodres.2022.111640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
Abstract
The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.
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Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaojie Zang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuhang Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Arjan Narbad
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China; Gut Health and Microbiome Institute Strategic Programme, Quadram Institute Bioscience, Norwich 16 NR4 7UQ, UK
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
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Immunogenic Modification of Ligilactobacillus agilis by Specific Amino Acid Substitution of Flagellin. Appl Environ Microbiol 2022; 88:e0127722. [PMID: 36173204 PMCID: PMC9599256 DOI: 10.1128/aem.01277-22] [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: 12/01/2022] Open
Abstract
Ligilactobacillus agilis is a flagellated motile commensal microbe that resides in the gastrointestinal tract of mammals and birds. Flagellin, the major subunit protein of flagellar filament, from pathogenic bacteria is generally a proinflammatory molecule that stimulates immune cells via Toll-like receptor 5 (TLR5). Interestingly, the flagellins of L. agilis are known to be immunologically attenuated despite the fact that the structure of the proteins, including the TLR5 recognition site, is highly conserved among bacteria. The results of our previous study suggested that this is attributed to the differences in three specific amino acids within the conserved TLR5 recognition site; however, this hypothesis remains to be confirmed. In this study, a series of recombinant L. agilis flagellins, with amino acid substitutions at the TLR5 recognition site, were constructed, and their immunogenic activity was evaluated in vitro. Then, an L. agilis strain with an active immunogenic TLR5 recognition site was generated. In vitro and in vivo immunological studies revealed that the mutant L. agilis strain with the modified flagellin was more immunogenic than the wild-type strain. In conclusion, the specific amino acid residues in L. agilis flagellins likely contribute to the discrimination between pathogens and commensals by the host defense system. Additionally, the immunogenically potent L. agilis mutants may serve as a useful platform for oral vaccine delivery. IMPORTANCE The interactions between gut microbes and immune cells play an important role in the health and disease of hosts. Ligilactobacillus agilis is a flagellated commensal bacterium found in the gut of mammals and birds. However, the flagellin proteins of L. agilis are immunologically attenuated and barely induce TLR5-dependent inflammation, unlike the flagellins of several pathogenic bacteria. This study demonstrated that three specific amino acids in the flagellin protein are responsible for this low immunogenicity in L. agilis. The results obtained herein improve our understanding of the symbiosis between gut microbes and their hosts.
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Meza-Gutiérrez NN, Magallón-Servín P, Balois-Morales R, Pérez-Ramírez IF, López-Guzmán GG, Berumen-Varela G, Bautista-Rosales PU. Growth Promoting Activity of Annona muricata L. Leaf Extracts on Lactobacillus casei. PLANTS (BASEL, SWITZERLAND) 2022; 11:581. [PMID: 35270049 PMCID: PMC8912565 DOI: 10.3390/plants11050581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Soursop leaves are a source of phytochemical compounds, such as phenolic acids, flavonoids, hydrolyzable tannins, and acetogenins. These compounds can have several types of biological activities. Lactic acid bacteria can uptake phenolic compounds present in plants or fruits. The aim of the present work was to investigate the in vitro effect of hexane, acetone, methanolic, and aqueous extracts of soursop leaves (Annona muricata L.) on the growth, motility, and biofilm formation of Lactobacillus casei, and to determine compounds related to growth. The minimum concentration promoting growth, motility (swimming, swarming, and twitching), and biofilm-forming capacity (crystal violet) were evaluated. The results showed the growth-promoting capacity of acetone and aqueous extracts at low doses 25-50 mg/L, and an inhibition in the four extracts at higher doses of 100 mg/L. The L. casei growth is related to ellagic acid, quercetin rhamnoside, kaempferol dihexoside, quercetin hexoside, secoisolariciresinol, and kaempferol hexoside-rhamnoside. Hexane extract increased the three types of motility, while aqueous maintained swimming and twitching motility similar to control. The four extracts inhibited the biofilm formation capacity.
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Affiliation(s)
- Nimcy Noemí Meza-Gutiérrez
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Km 9 Carretera Tepic-Compostela, Xalisco C.P. 63180, Nayarit, Mexico; (N.N.M.-G.); (R.B.-M.)
- Unidad de Tecnología de Alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico;
| | - Paola Magallón-Servín
- Centro de Investigaciones Biológicas del Noroeste, Km 1 Carretera a San Juan de La Costa “El Comitan”, La Paz C.P. 23205, Baja California Sur, Mexico;
- Bashan Institure of Sciences, 1730 Post Oak Ct, Auburn, AL 36830, USA
| | - Rosendo Balois-Morales
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Km 9 Carretera Tepic-Compostela, Xalisco C.P. 63180, Nayarit, Mexico; (N.N.M.-G.); (R.B.-M.)
- Unidad de Tecnología de Alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico;
| | - Iza Fernanda Pérez-Ramírez
- Facultad de Química, Universidad Autónoma de Querétaro, C.U., Cerro de las Campanas S/N, Querétaro C.P. 76010, Querétaro, Mexico;
| | - Graciela Guadalupe López-Guzmán
- Unidad Académica de Agricultura, Universidad Autónoma de Nayarit, Km 9 Carretera Tepic-Compostela, Xalisco C.P. 63780, Nayarit, Mexico;
| | - Guillermo Berumen-Varela
- Unidad de Tecnología de Alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico;
| | - Pedro Ulises Bautista-Rosales
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Km 9 Carretera Tepic-Compostela, Xalisco C.P. 63180, Nayarit, Mexico; (N.N.M.-G.); (R.B.-M.)
- Unidad de Tecnología de Alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico;
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13
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Shi C, Maktabdar M. Lactic Acid Bacteria as Biopreservation Against Spoilage Molds in Dairy Products - A Review. Front Microbiol 2022; 12:819684. [PMID: 35154045 PMCID: PMC8826399 DOI: 10.3389/fmicb.2021.819684] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
Mold spoilage of dairy products such as yogurt is a concern in dairy industry. Not only does it lead to substantial food waste, economic losses, and even brand image damage, but it may also cause public health concern due to the potential production of mycotoxin. Good hygiene practices are necessary to prevent contamination, but contamination may nevertheless occur at the production site and, not least, at the site of the consumer. In recent years, there has been a growing interest from consumers for "clean label" food products, which are natural, less-processed, and free of added, chemical preservatives, and a wish for shelf lives of considerable length in order to minimize food waste. This has sparked an interest in using lactic acid bacteria (LAB) or their metabolites as biopreservatives as a way to limit the growth of spoilage organisms in dairy products. A range of compounds produced by LAB with potential antifungal activity have been described as contributing factors to the inhibitory effect of LAB. More recently, growth inhibition effects caused by specific competitive exclusion have been elucidated. It has also become clear that the sensitivity toward both individual antifungal compounds and competition mechanisms differ among molds. In this review, the main spoilage molds encountered in dairy products are introduced, and an overview of the antifungal activity of LAB against different spoilage molds is presented including the main antifungal compounds derived from LAB cultures and the sensitivity of the spoilage molds observed toward these compounds. The recent findings of the role of competitive exclusion with emphasis on manganese depletion and the possible implications of this for biopreservation are described. Finally, some of the knowledge gaps, future challenges, and trends in the application of LAB biopreservation in dairy products are discussed.
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Affiliation(s)
- Ce Shi
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Luchan J, Choi C, Carrier RL. Reactive oxygen species limit intestinal mucosa-bacteria homeostasis in vitro. Sci Rep 2021; 11:23727. [PMID: 34887444 PMCID: PMC8660821 DOI: 10.1038/s41598-021-02080-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Interactions between epithelial and immune cells with the gut microbiota have wide-ranging effects on many aspects of human health. Therefore, there is value in developing in vitro models capable of performing highly controlled studies of such interactions. However, several critical factors that enable long term homeostasis between bacterial and mammalian cultures have yet to be established. In this study, we explored a model consisting of epithelial and immune cells, as well as four different bacterial species (Bacteroides fragilis KLE1958, Escherichia coli MG1655, Lactobacillus rhamnosus KLE2101, or Ruminococcus gnavus KLE1940), over a 50 hour culture period. Interestingly, both obligate and facultative anaerobes grew to similar extents in aerobic culture environments during the co-culture period, likely due to measured microaerobic oxygen levels near the apical surface of the epithelia. It was demonstrated that bacteria elicited reactive oxygen species (ROS) production, and that the resulting oxidative damage heavily contributed to observed epithelial barrier damage in these static cultures. Introduction of a ROS scavenger significantly mitigated oxidative damage, improving cell monolayer integrity and reducing lipid peroxidation, although not to control (bacteria-free culture) levels. These results indicate that monitoring and mitigating ROS accumulation and oxidative damage can enable longer term bacteria-intestinal epithelial cultures, while also highlighting the significance of additional factors that impact homeostasis in mammalian cell-bacteria systems.
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Affiliation(s)
- Joshua Luchan
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Christian Choi
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Rebecca L Carrier
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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15
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Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation. Appl Environ Microbiol 2021; 87:e0058421. [PMID: 34105982 DOI: 10.1128/aem.00584-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.
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16
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Eguchi N, Suzuki S, Yokota K, Igimi S, Kajikawa A. Ligilactobacillus agilis BKN88 possesses thermo-/acid-stable heteropolymeric flagellar filaments. MICROBIOLOGY-SGM 2021; 167. [PMID: 33502302 DOI: 10.1099/mic.0.001020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many flagellated bacteria possess multiple flagellins, but the roles and the compositions of each flagellin are diverse and poorly understood. In Ligilactobacillus agilis BKN88, there are two active flagellin gene paralogues but their function and composition in its flagellar filaments have not been described. The aim of this study is to find the function and composition of the flagellins by employing mutant strains each of which expresses a single flagellin or a modified flagellin. Two single flagellin-expressing strains were both flagellated while the number of flagella per cell in the single flagellin-expressing derivatives was lower than that in the wild type. Nonetheless, these derivative strains were apparently equally motile as the wild type. This indicates that either flagellin is sufficient for cell motility. The immunological activity via Toll-like receptor 5 of the single flagellin-expressing strains or purified single flagellins was readily detectable but mostly variably weaker than that of the wild type. The flagellar filaments of wild type L. agilis BKN88 were more acid-/thermo-stable than those of single flagellin-expressing derivatives. Using a combination of immunoprecipitation and flagellin-specific staining, wild type BKN88 appeared to possess heteropolymeric flagellar filaments consisting of both flagellins and each flagellin appeared to be equally distributed throughout the filaments. The results of this study suggest that the two flagellins together form a more robust filament than either alone and are thus functionally complementary.
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Affiliation(s)
- Naoto Eguchi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
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17
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Mandal A, Mandal RK, Yang Y, Khatri B, Kong BW, Kwon YM. In vitro characterization of chicken gut bacterial isolates for probiotic potentials. Poult Sci 2020; 100:1083-1092. [PMID: 33518067 PMCID: PMC7858158 DOI: 10.1016/j.psj.2020.11.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/18/2022] Open
Abstract
Probiotics often play an important role in improving gut health in chickens through multiple mechanisms, including enhancement of tight junctions, nutrient acquisition, niche colonization, or coaggregation with enteric pathogens. The objective of this study was to characterize lactic acid bacteria (LAB) isolated from the gut of healthy broiler chickens for a number of phenotypes that might be indicative of good probiotic potentials. A total 40 bacterial isolates were isolated from 3-week-old chickens using Man, Rogosa and Sharpe (MRS) agar plates. The bacterial isolates were evaluated in vitro for motility, autoaggregation, pathogen inhibition, pH of overnight culture, growth on different agar plates, and their impact on gut integrity. Selected isolates were genotyped by sequencing the 16S-23S rRNA gene intergenic region. Based on the phenotype and genotype, we identified 20 potential probiotic (PP) isolates that belong to LAB. Multivariate analysis showed that PP isolates were positively correlated with parameters such as growth on MRS agar plate (pH 5.5), pathogen inhibition, and autoaggregation. However, growth on MacConkey agar plates, supernatant pH, motility, and transepithelial electrical resistance were negatively correlated with the PP isolates. Furthermore, in vivo study needs to be performed for evaluation of the utility of these probiotic candidates in poultry production.
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Affiliation(s)
- Anita Mandal
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701
| | - Rabindra K Mandal
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701
| | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701
| | - Bhuwan Khatri
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701
| | - Byung-Whi Kong
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701.
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Latilactobacillus curvatus: A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits. Foods 2020; 9:foods9101366. [PMID: 32993033 PMCID: PMC7600897 DOI: 10.3390/foods9101366] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 02/02/2023] Open
Abstract
Latilactobacillus curvatus is a candidate probiotic that has been included in the list of recommended biological agents for certification by the European Food Safety Authority. According to the published genomic information, L. curvatus has several genes that encode metabolic pathways of carbohydrate utilization. In addition, there are some differences in cell surface complex related genes of L. curvatus from different sources. L. curvatus also has several genes that encode bacteriocin production, which can produce Curvacin A and Sakacin P. Due to its ability to produce bacteriocin, it is often used as a bioprotective agent in fermented meat products, to inhibit the growth of a variety of pathogenic and spoilage bacteria. L. curvatus exerts some probiotic effects, such as mediating the production of IL-10 by dendritic cells through NF-κB and extracellular regulated protein kinases (ERK) signals to relieve colitis in mice. This review is the first summary of the genomic and biological characteristics of L. curvatus. Our knowledge on its role in the food industry and human health is also discussed, with the aim of providing a theoretical basis for the development of applications of L. curvatus.
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Bechtner J, Ludwig C, Kiening M, Jakob F, Vogel RF. Living the Sweet Life: How Liquorilactobacillus hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose. Foods 2020; 9:foods9091150. [PMID: 32825547 PMCID: PMC7555045 DOI: 10.3390/foods9091150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Liquorilactobacillus (L.) hordei (formerly Lactobacillus hordei) is one of the dominating lactic acid bacteria within the water kefir consortium, being highly adapted to survive in this environment, while producing high molecular weight dextrans from sucrose. In this work, we extensively studied the physiological response of L. hordei TMW 1.1822 to sucrose compared to glucose, applying label-free, quantitative proteomics of cell lysates and exoproteomes. This revealed the differential expression of 53 proteins within cellular proteomes, mostly associated with carbohydrate uptake and metabolism. Supported by growth experiments, this suggests that L. hordei TMW 1.1822 favors fructose over other sugars. The dextransucrase was expressed irrespectively of the present carbon source, while it was significantly more released in the presence of sucrose (log2FC = 3.09), being among the most abundant proteins within exoproteomes of sucrose-treated cells. Still, L. hordei TMW 1.1822 expressed other sucrose active enzymes, predictively competing with the dextransucrase reaction. While osmolysis appeared to be unlikely, sucrose led to increased release of a multitude of cytoplasmic proteins, suggesting that biofilm formation in L. hordei is not only composed of a polysaccharide matrix but is also of proteinaceous nature. Therefore, our study highlights the intrinsic adaptation of water kefir-borne L. hordei to sucrose-rich habitats and provides fundamental knowledge for its use as a starter culture in plant-based food fermentations with in situ dextran formation.
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Affiliation(s)
- Julia Bechtner
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), 85354 Freising, Germany;
| | - Michael Kiening
- Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München (TUM), 85354 Freising, Germany;
| | - Frank Jakob
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; (J.B.); (F.J.)
- Correspondence:
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Suzuki S, Fujita K, Maeno S, Shiwa Y, Endo A, Yokota K, Igimi S, Kajikawa A. PCR-based screening, isolation, and partial characterization of motile lactobacilli from various animal feces. BMC Microbiol 2020; 20:142. [PMID: 32493209 PMCID: PMC7268542 DOI: 10.1186/s12866-020-01830-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Most lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that Lactobacillus agilis BKN88, which is a highly motile strain originating from a chicken, takes advantage of motility in gut colonization in murine models, and thus motile lactobacilli likely have unique ecological characteristics conferred by motility. However, the ecology and habitat of gut-derived motile lactobacilli are still rarely understood. In addition, the limited availability of motile Lactobacillus isolates is one of the major obstacles for further studies. To gain insight into the ecology and habitat of the motile lactobacilli, we established a routinely applicable detection method for motile lactobacilli using PCR and subsequent selective isolation in semi-solid MRS medium for the collection of additional motile lactobacilli from animal feces. RESULTS We applied the PCR detection using motile lactobacilli-specific primers, based on the motor switch protein gene (fliG) of flagella, to 120 animal feces, followed by selective isolation performed using 45 animal feces. As a result, motile lactobacilli were detected in 44 animal feces. In the selective isolation, 29 isolates of L. agilis and 2 isolates of L. ruminis were obtained from 8 animal species. CONCLUSIONS These results indicated that motile lactobacilli are distributed in different animal species. Moreover, phylogenetic analysis of the L. agilis isolates suggests co-evolution with the host, and adaptation to a particular environmental niche.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
| | - Koki Fujita
- Department of Agricultural Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
| | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Graduate School of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099-2493 Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099-2493 Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502 Japan
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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: 1448] [Impact Index Per Article: 362.0] [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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22
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Funck GD, Marques JDL, Cruxen CEDS, Sehn CP, Haubert L, Dannenberg GDS, Klajn VM, Silva WP, Fiorentini ÂM. Probiotic potential of Lactobacillus curvatusP99 and viability in fermented oat dairy beverage. J FOOD PROCESS PRES 2019. [DOI: 10.1111/jfpp.14286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Graciele Daiana Funck
- Department of Agroindustrial Science and Technology Federal University of Pelotas Pelotas Brazil
| | | | | | - Carla Pohl Sehn
- Laboratory of Pharmacological and Toxicological Reviews Applied to Bioactive Molecules – LaftamBio Pampa Federal University of Pampa Itaqui Brazil
| | - Louise Haubert
- Technology Development Center Federal University of Pelotas Pelotas Brazil
| | | | - Vera Maria Klajn
- Farroupilha Federal Institute of Education, Science and Technology Santa Rosa Brazil
| | - Wladimir Padilha Silva
- Department of Agroindustrial Science and Technology Federal University of Pelotas Pelotas Brazil
- Technology Development Center Federal University of Pelotas Pelotas Brazil
| | - Ângela Maria Fiorentini
- Department of Agroindustrial Science and Technology Federal University of Pelotas Pelotas Brazil
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23
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Tan H, Wang C, Zhang Q, Tang X, Zhao J, Zhang H, Zhai Q, Chen W. Preliminary safety assessment of a new Bacteroides fragilis isolate. Food Chem Toxicol 2019; 135:110934. [PMID: 31682931 DOI: 10.1016/j.fct.2019.110934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 01/16/2023]
Abstract
The novel commensal strain of Bacteroides fragilis HCK-B3 isolated from a healthy Chinese donor was discovered beneficial effects of attenuating lipopolysaccharides-induced inflammation. In order to contribute to the development of natural next-generation probiotic strains, the safety assessment was carried out with in vitro investigations of its morphology, potential virulence genes and antimicrobial resistance, and an in vivo acute toxicity study based on both healthy and immunosuppressed mice by cyclophosphamide injection. Consequently, the potential virulence genes in the genome of B. fragilis HCK-B3 have yet been identified as toxicity-associated. The absence of plasmids prevents the possibility of transferring antibiotic resistance features to other intestinal commensals. No intracorporal pathogenic properties were observed according to the body weight, hematological and liver parameters, cytokine secretions and tissue integrity. In addition, B. fragilis HCK-B3 performed alleviations on part of the side effects caused by the cyclophosphamide treatment. Thus, the novel strain of B. fragilis HCK-B3 was confirmed to be non-toxigenic and did not display adverse effects in both healthy and immune-deficient mice at a routinely applicable dose.
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Affiliation(s)
- Huizi Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Xiaoshu Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, PR China
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24
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Schwimmer JB, Johnson JS, Angeles JE, Behling C, Belt PH, Borecki I, Bross C, Durelle J, Goyal NP, Hamilton G, Holtz ML, Lavine JE, Mitreva M, Newton KP, Pan A, Simpson PM, Sirlin CB, Sodergren E, Tyagi R, Yates KP, Weinstock G, Salzman NH. Microbiome Signatures Associated With Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease. Gastroenterology 2019; 157:1109-1122. [PMID: 31255652 PMCID: PMC6756995 DOI: 10.1053/j.gastro.2019.06.028] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The intestinal microbiome might affect the development and severity of nonalcoholic fatty liver disease (NAFLD). We analyzed microbiomes of children with and without NAFLD. METHODS We performed a prospective, observational, cross-sectional study of 87 children (age range, 8-17 years) with biopsy-proven NAFLD and 37 children with obesity without NAFLD (controls). Fecal samples were collected and microbiome composition and functions were assessed using 16S ribosomal RNA amplicon sequencing and metagenomic shotgun sequencing. Microbial taxa were identified using zero-inflated negative binomial modeling. Genes contributing to bacterial pathways were identified using gene set enrichment analysis. RESULTS Fecal microbiomes of children with NAFLD had lower α-diversity than those of control children (3.32 vs 3.52, P = .016). Fecal microbiomes from children with nonalcoholic steatohepatitis (NASH) had the lowest α-diversity (control, 3.52; NAFLD, 3.36; borderline NASH, 3.37; NASH, 2.97; P = .001). High abundance of Prevotella copri was associated with more severe fibrosis (P = .036). Genes for lipopolysaccharide biosynthesis were enriched in microbiomes from children with NASH (P < .001). Classification and regression tree model with level of alanine aminotransferase and relative abundance of the lipopolysaccharide pathway gene encoding 3-deoxy-d-manno-octulosonate 8-phosphate-phosphatase identified patients with NASH with an area under the receiver operating characteristic curve value of 0.92. Genes involved in flagellar assembly were enriched in the fecal microbiomes of patients with moderate to severe fibrosis (P < .001). Classification and regression tree models based on level of alanine aminotransferase and abundance of genes encoding flagellar biosynthesis protein had good accuracy for identifying case children with moderate to severe fibrosis (area under the receiver operating characteristic curve, 0.87). CONCLUSIONS In an analysis of fecal microbiomes of children with NAFLD, we associated NAFLD and NASH with intestinal dysbiosis. NAFLD and its severity were associated with greater abundance of genes encoding inflammatory bacterial products. Alterations to the intestinal microbiome might contribute to the pathogenesis of NAFLD and be used as markers of disease or severity.
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Affiliation(s)
- Jeffrey B. Schwimmer
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA,Department of Gastroenterology, Rady Children’s
Hospital San Diego, San Diego, CA
| | | | - Jorge E. Angeles
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA
| | - Cynthia Behling
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA,Department of Pathology, Sharp Medical Center, San Diego,
CA
| | | | - Ingrid Borecki
- The McDonnell Genome Institute, Washington University in
St. Louis, St. Louis, MO
| | - Craig Bross
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA
| | - Janis Durelle
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA
| | - Nidhi P. Goyal
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA
| | - Gavin Hamilton
- Liver Imaging Group, Department of Radiology, University
of California, San Diego, CA
| | - Mary L. Holtz
- Department of Pediatrics, Division of Gastroenterology;
and Center for Microbiome Research, Medical College of Wisconsin, Milwaukee,
WI
| | - Joel E. Lavine
- Department of Pediatrics, Division of Pediatric
Gastroenterology, Hepatology and Nutrition, Columbia University, New York NY
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University in
St. Louis, St. Louis, MO
| | - Kimberly P. Newton
- Division of Gastroenterology, Hepatology, and Nutrition,
Department of Pediatrics, University of California, San Diego School of Medicine, La
Jolla, CA,Department of Gastroenterology, Rady Children’s
Hospital San Diego, San Diego, CA
| | - Amy Pan
- Department of Pediatrics, Division of Quantitative
Health Sciences; and Center for Microbiome Research, The Medical College of
Wisconsin, Milwaukee, WI
| | - Pippa M. Simpson
- Department of Pediatrics, Division of Quantitative
Health Sciences; and Center for Microbiome Research, The Medical College of
Wisconsin, Milwaukee, WI
| | - Claude B. Sirlin
- Liver Imaging Group, Department of Radiology, University
of California, San Diego, CA
| | | | - Rahul Tyagi
- The McDonnell Genome Institute, Washington University in
St. Louis, St. Louis, MO
| | | | | | - Nita H. Salzman
- Department of Pediatrics, Division of Gastroenterology;
and Center for Microbiome Research, Medical College of Wisconsin, Milwaukee,
WI
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25
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Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Khoruts A, Staley C. Specific gut microbiota changes heralding bloodstream infection and neutropenic fever during intensive chemotherapy. Leukemia 2019; 34:312-316. [PMID: 31439944 DOI: 10.1038/s41375-019-0547-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/10/2019] [Accepted: 06/26/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Thomas Kaiser
- Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Carolyn Graiziger
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Shernan G Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tauseef Ur Rehman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander Khoruts
- BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christopher Staley
- Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
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26
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Lauté-Caly DL, Raftis EJ, Cowie P, Hennessy E, Holt A, Panzica DA, Sparre C, Minter B, Stroobach E, Mulder IE. The flagellin of candidate live biotherapeutic Enterococcus gallinarum MRx0518 is a potent immunostimulant. Sci Rep 2019; 9:801. [PMID: 30692549 PMCID: PMC6349862 DOI: 10.1038/s41598-018-36926-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/01/2018] [Indexed: 12/13/2022] Open
Abstract
Many links between gut microbiota and disease development have been established in recent years, with particular bacterial strains emerging as potential therapeutics rather than causative agents. In this study we describe the immunostimulatory properties of Enterococcus gallinarum MRx0518, a candidate live biotherapeutic with proven anti-tumorigenic efficacy. Here we demonstrate that strain MRx0518 elicits a strong pro-inflammatory response in key components of the innate immune system but also in intestinal epithelial cells. Using a flagellin knock-out derivative and purified recombinant protein, MRx0518 flagellin was shown to be a TLR5 and NF-κB activator in reporter cells and an inducer of IL-8 production by HT29-MTX cells. E. gallinarum flagellin proteins display a high level of sequence diversity and the flagellin produced by MRx0518 was shown to be more potent than flagellin from E. gallinarum DSM100110. Collectively, these data infer that flagellin may play a role in the therapeutic properties of E. gallinarum MRx0518.
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Affiliation(s)
- Delphine L Lauté-Caly
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Emma J Raftis
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom.
| | - Philip Cowie
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Emma Hennessy
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Amy Holt
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - D Alessio Panzica
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Christina Sparre
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Beverley Minter
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Eline Stroobach
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
| | - Imke E Mulder
- 4D Pharma Research Ltd, Life Science Innovation Building, Cornhill Road, Aberdeen, AB25 2ZS, United Kingdom
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27
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Kurbakov KA, Konorov EA, Minaev MY, Kuznetsova OA. Multiplex Real-Time PCR with HRM for Detection of Lactobacillus sakei and Lactobacillus curvatus in Food Samples. Food Technol Biotechnol 2019; 57:97-104. [PMID: 31316281 PMCID: PMC6600297 DOI: 10.17113/ftb.57.01.19.5983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Optimization of fermentation processes requires monitoring the species composition of starter cultures and their growth during fermentation. Most starter cultures contain closely related species. Nowadays, high-resolution melting (HRM) analysis is extensively used for multiplex identification of closely related species. In the present paper, we applied real-time polymerase chain reaction (PCR) with HRM analysis for the detection and differentiation of Lactobacillus sakei and L. curvatus. A primer pair was selected for the site of the rpoA gene of Lactobacillus spp. Eleven starter cultures and fifteen fermented sausages with a known bacterial composition were successfully tested using real-time PCR with HRM analysis with the developed primer pair.
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Affiliation(s)
- Konstantin A Kurbakov
- V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Talalikhina 26, 109316, Moscow, Russian Federation
| | - Evgenii A Konorov
- V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Talalikhina 26, 109316, Moscow, Russian Federation.,Vavilov Institute of General Genetics, Gubkina 3, 119333, Moscow, Russian Federation.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Malaya Pirogovskaya 20-1, 119435 Moscow, Russian Federation
| | - Mikhail Y Minaev
- V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Talalikhina 26, 109316, Moscow, Russian Federation
| | - Oksana A Kuznetsova
- V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Talalikhina 26, 109316, Moscow, Russian Federation
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28
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Comparative genomics of Lactobacillus curvatus enables prediction of traits relating to adaptation and strategies of assertiveness in sausage fermentation. Int J Food Microbiol 2018; 286:37-47. [DOI: 10.1016/j.ijfoodmicro.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/12/2018] [Accepted: 06/29/2018] [Indexed: 11/23/2022]
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29
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George F, Daniel C, Thomas M, Singer E, Guilbaud A, Tessier FJ, Revol-Junelles AM, Borges F, Foligné B. Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective. Front Microbiol 2018; 9:2899. [PMID: 30538693 PMCID: PMC6277688 DOI: 10.3389/fmicb.2018.02899] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called "transionts" microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.
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Affiliation(s)
- Fanny George
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Catherine Daniel
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Muriel Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elisabeth Singer
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Axel Guilbaud
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Frédéric J. Tessier
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Anne-Marie Revol-Junelles
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Frédéric Borges
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Benoît Foligné
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
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30
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Tan H, Yu Z, Wang C, Zhang Q, Zhao J, Zhang H, Zhai Q, Chen W. Pilot Safety Evaluation of a Novel Strain of Bacteroides ovatus. Front Genet 2018; 9:539. [PMID: 30459813 PMCID: PMC6232662 DOI: 10.3389/fgene.2018.00539] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/24/2018] [Indexed: 12/16/2022] Open
Abstract
Bacteroides ovatus ELH-B2 is considered as a potential next-generation probiotic due to its preventive effects on lipopolysaccharides-associated inflammation and intestinal microbiota disorders in mice. To study safety issues associated with B. ovatus ELH-B2, we conducted comprehensive and systematic experiments, including in vitro genetic assessments of potential virulence and antimicrobial resistance genes, and an in vivo acute toxicity study of both immunocompetent and immunosuppressed mice via cyclophosphamide treatment. The results indicated that this novel strain is non-toxigenic, fragilysin is not expressed, and most of potential virulence genes are correlated with cellular structures such as capsular polysaccharide and polysaccharide utilizations. The antibiotic resistance features are unlikely be transferred to other intestinal microorganisms as no plasmids nor related genomic islands were identified. Side effects were not observed in mice. B. ovatus ELH-B2 also alleviated the damages caused by cyclophosphamide injection.
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Affiliation(s)
- Huizi Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Zhiming Yu
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
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31
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Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
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Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
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32
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Chaudhari NM, Gautam A, Gupta VK, Kaur G, Dutta C, Paul S. PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features. Front Microbiol 2018; 9:2322. [PMID: 30349509 PMCID: PMC6187978 DOI: 10.3389/fmicb.2018.02322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/11/2018] [Indexed: 01/07/2023] Open
Abstract
The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) – a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Anupam Gautam
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Vinod Kumar Gupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Gagneet Kaur
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Chitra Dutta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sandip Paul
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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33
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Kazou M, Alexandraki V, Blom J, Pot B, Tsakalidou E, Papadimitriou K. Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. Front Microbiol 2018; 9:1244. [PMID: 29942291 PMCID: PMC6004923 DOI: 10.3389/fmicb.2018.01244] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/23/2018] [Indexed: 02/05/2023] Open
Abstract
Lactobacillus acidipiscis belongs to the Lactobacillus salivarius clade and it is found in a variety of fermented foods. Strain ACA-DC 1533 was isolated from traditional Greek Kopanisti cheese and among the available L. acidipiscis genomes it is the only one with a fully sequenced chromosome. L. acidipiscis strains exhibited a high degree of conservation at the genome level. Investigation of the distribution of prophages and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) among the three strains suggests the potential existence of lineages within the species. Based on the presence/absence patterns of these genomic traits, strain ACA-DC 1533 seems to be more related to strain JCM 10692T than strain KCTC 13900. Interestingly, strains ACA-DC 1533 and JCM 10692T which lack CRISPRs, carry two similar prophages. In contrast, strain KCTC 13900 seems to have acquired immunity to these prophages according to the sequences of spacers in its CRISPRs. Nonetheless, strain KCTC 13900 has a prophage that is absent from strains ACA-DC 1533 and JCM 10692T. Furthermore, comparative genomic analysis was performed among L. acidipiscis ACA-DC 1533, L. salivarius UCC118 and Lactobacillus ruminis ATCC 27782. The chromosomes of the three species lack long-range synteny. Important differences were also determined in the number of glycobiome related proteins, proteolytic enzymes, transporters, insertion sequences and regulatory proteins. Moreover, no obvious genomic traits supporting a probiotic potential of L. acidipiscis ACA-DC 1533 were detected when compared to the probiotic L. salivarius UCC118. However, the existence of more than one glycine-betaine transporter within the genome of ACA-DC 1533 may explain the ability of L. acidipiscis to grow in fermented foods containing high salt concentrations. Finally, in silico analysis of the L. acidipiscis ACA-DC 1533 genome revealed pathways that could underpin the production of major volatile compounds during the catabolism of amino acids that may contribute to the typical piquant flavors of Kopanisti cheese.
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Affiliation(s)
- Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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Variation of mucin adhesion, cell surface characteristics, and molecular mechanisms among Lactobacillus plantarum isolated from different habitats. Appl Microbiol Biotechnol 2017; 101:7663-7674. [DOI: 10.1007/s00253-017-8482-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 10/18/2022]
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35
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Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere. GENOME ANNOUNCEMENTS 2017; 5:5/26/e00584-17. [PMID: 28663298 PMCID: PMC5638282 DOI: 10.1128/genomea.00584-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This strain was isolated from beef carpaccio packaged in a modified atmosphere. The draft genome will contribute to understanding the role of L. curvatus strains in food products (fermentation, biopreservation, or spoilage) through comparative genomics with other strains.
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36
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Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533. GENOME ANNOUNCEMENTS 2017; 5:5/4/e01533-16. [PMID: 28126948 PMCID: PMC5270707 DOI: 10.1128/genomea.01533-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactobacillus acidipiscis is a Gram-positive lactic acid bacterium belonging to the Lactobacillus salivarius clade. Here, we present the first complete genome sequence of L. acidipiscis isolated from traditional Greek Kopanisti cheese. Strain ACA-DC 1533 may play a key role in the strong organoleptic characteristics of Kopanisti cheese.
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37
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Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria. Nat Ecol Evol 2016; 1:9. [PMID: 28812570 DOI: 10.1038/s41559-016-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/14/2016] [Indexed: 11/08/2022]
Abstract
Functional morphological adaptation is an implicit assumption across many ecological studies. However, despite a few pioneering attempts to link bacterial form and function, functional morphology is largely unstudied in prokaryotes. One intriguing candidate for analysis is bacterial shape, as multiple lines of theory indicate that cell shape and motility should be strongly correlated. Here we present a large-scale use of modern phylogenetic comparative methods to explore this relationship across 325 species of the phylum Firmicutes. In contrast to clear predictions from theory, we show that cell shape and motility are not coupled, and that transitions to and from flagellar motility are common and strongly associated with lifestyle (free-living or host-associated). We find no association between shape and lifestyle, and contrary to recent evidence, no indication that shape is associated with pathogenicity. Our results suggest that the independent evolution of shape and motility in this group might allow a greater evolutionary flexibility.
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38
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First Complete Genome Sequence of the Skin-Improving Lactobacillus curvatus Strain FBA2, Isolated from Fermented Vegetables, Determined by PacBio Single-Molecule Real-Time Technology. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00884-16. [PMID: 27587811 PMCID: PMC5009968 DOI: 10.1128/genomea.00884-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II. The single circular chromosome (1,848,756 bp, G+C content of 42.1%) of L. curvatus FBA2, isolated from fermented vegetables, contained low G+C regions (26.9% minimum) and 43 sets of >1,000-bp identical sequence pairs. No plasmids were detected.
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