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Quach NT, Nguyen TTA, Vu THN, Nguyen TTN, Tran XK, Chu NH, Ta TTT, Chu HH, Phi QT. New insight into protective effect against oxidative stress and biosynthesis of exopolysaccharides produced by Lacticaseibacillus paracasei NC4 from fermented eggplant. Curr Genet 2024; 70:7. [PMID: 38743270 DOI: 10.1007/s00294-024-01292-8] [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: 03/20/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Fermented eggplant is a traditional fermented food, however lactic acid bacteria capable of producing exopolysaccharide (EPS) have not yet been exploited. The present study focused on the production and protective effects against oxidative stress of an EPS produced by Lacticaseibacillus paracasei NC4 (NC4-EPS), in addition to deciphering its genomic features and EPS biosynthesis pathway. Among 54 isolates tested, strain NC4 showed the highest EPS yield and antioxidant activity. The maximum EPS production (2.04 ± 0.11 g/L) was achieved by culturing in MRS medium containing 60 g/L sucrose at 37 °C for 48 h. Under 2 mM H2O2 stress, the survival of a yeast model Saccharomyces cerevisiae treated with 0.4 mg/mL NC4-EPS was 2.4-fold better than non-treated cells, which was in agreement with the catalase and superoxide dismutase activities measured from cell lysates. The complete genome of NC4 composed of a circular chromosome of 2,888,896 bp and 3 circular plasmids. The NC4 genome comprises more genes with annotated function in nitrogen metabolism, phosphorus metabolism, cell division and cell cycle, and iron acquisition and metabolism as compared to other reported L. paracasei. Of note, the eps gene cluster is not conserved across L. paracasei. Pathways of sugar metabolism for EPS biosynthesis were proposed for the first time, in which gdp pathway only present in few plant-derived bacteria was identified. These findings shed new light on the cell-protective activity and biosynthesis of EPS produced by L. paracasei, paving the way for future efforts to enhance yield and tailor-made EPS production for food and pharmaceutical industries.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | - Thi Thanh Ngoc Nguyen
- Faculty of Food Technology, East Asia University of Technology, Hanoi, 100000, Vietnam
| | - Xuan Khoi Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | - Nhat Huy Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | | | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam
| | - Quyet-Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 100000, Vietnam.
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Makete G, Mamphogoro TP. De novo genome assembly of a probiotic Lacticaseibacillus rhamnosus ISO20, isolated from raw milk in South Africa. Microbiol Resour Announc 2024; 13:e0122723. [PMID: 38376337 DOI: 10.1128/mra.01227-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms including production of antimicrobial substances and bile salts tolerance. Here, we report a draft genome sequence of Lacticaseibacillus rhamnosus ISO20, a lactic acid bacterium isolated from raw goat's milk to provide genomic insight into its strategies as probiotic strain.
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Affiliation(s)
- Goitsemang Makete
- Gastro-Intestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production, Irene, Pretoria, South Africa
| | - Tshifhiwa Paris Mamphogoro
- Gastro-Intestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production, Irene, Pretoria, South Africa
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Guan W, Gong C, Wu S, Cui Z, Zheng Y, Li Z, Zhu S, Liu X. Instant Protection Spray for Anti-Infection and Accelerated Healing of Empyrosis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2306589. [PMID: 37703451 DOI: 10.1002/adma.202306589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/26/2023] [Indexed: 09/15/2023]
Abstract
Distinct from common injuries, deep burns often require a chronic recovery cycle for healing and long-term antibiotic treatment to prevent infection. The rise of drug-resistant bacteria has caused antibiotics to no longer be perfect, and continuous drug use can easily lead to repeated infection and even death. Inspired by wild animals that chew plants to prevent wound infection, probiotic extracts with a structure similar to the tailspike of phage are obtained from Lactobacillus casei and combined with different flavones to design a series of nonantibiotic bactericides. These novel antibacterial agents are combined with a rapid gelation spray with a novel cross-angle layout to form an instant protection spray (IPS) and provide a physical and anti-infectious barrier for burns within 30 s. This IPS is able to sterilize 100.00% and 96.14% of multidrug-resistant Staphylococcus aureus (MRSA) in vitro and in vivo, respectively. In addition, it is found to effectively reduce inflammation in MRSA-infected burns in rats and to promote tissue healing.
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Affiliation(s)
- Wei Guan
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135, Tianjin, 300072, China
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yi-He-Yuan Road 5, Beijing, 100871, China
| | - Caixin Gong
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan, 430062, China
| | - Shuilin Wu
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135, Tianjin, 300072, China
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yi-He-Yuan Road 5, Beijing, 100871, China
| | - Zhenduo Cui
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135, Tianjin, 300072, China
| | - Yufeng Zheng
- School of Materials Science & Engineering, Peking University, Yi-He-Yuan Road 5, Beijing, 100871, China
| | - Zhaoyang Li
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135, Tianjin, 300072, China
| | - Shengli Zhu
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135, Tianjin, 300072, China
| | - Xiangmei Liu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340, Tianjin, 300401, China
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Choksket S, Sharma S, Harshvardhan, Pal V, Jain A, Patil PB, Korpole S, Grover V. Evaluation of Human Dental Plaque Lactic Acid Bacilli for Probiotic Potential and Functional Analysis in Relevance to Oral Health. Indian J Microbiol 2023; 63:520-532. [PMID: 38031619 PMCID: PMC10682319 DOI: 10.1007/s12088-023-01108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
Members of the lactic acid bacillus group are well-known probiotics and primarily isolated from fermented food, dairy products, intestinal and gut environment of human. Since probiotics from the human source are preferred, there exists a huge repertoire of lactobacilli in the human oral cavity which could prove a much better niche to be exploited for these beneficial microorganisms. Therefore, in this study, four lactobacilli strains, including strain DISK7, reported earlier, isolated from dental plaque samples of a healthy humans were evaluated for their probiotic potential. Strains displayed 99.9% of 16S rRNA gene sequence identity with species of the genera Lactobacillus and Limosilactobacillus. All strains showed lactic acid production, tolerance to low pH and antibiotic sensitivity. Variations were observed among strains in their aggregation ability, biofilm formation, bile salt resistance and cholesterol degradation. Further, we analyzed the interaction of strains with other oral commensals and opportunistic pathogens in co-culture experiments. Isolates DISK7 and DISK26 exhibited high co-aggregation (> 70%) with secondary colonizers, Streptococcus pyogenes and Veillonella parvula, respectively, but their aggregation ability was decreased with opportunistic pathogens. Furthermore, strains showed a substantial increase in biofilm in co-culture with other Lactobacillus isolates, indicating their ability to proliferate commensal bacteria in the oral environment. These microbes continually evolve in terms of niche adaptation as evidenced in genome analysis. The highlight of the investigation is the isolation and evaluation of the probiotic lactobacilli from the human oral cavity, which could prove a much better niche to be exploited for the effective commercialization of these beneficial microbes. Taken together, probiotic properties and interaction with commensal bacteria, these isolates exhibit the huge potential to be developed as alternative bioresource agents for maintenance of oral health. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01108-2.
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Shikha Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Harshvardhan
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vijay Pal
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Ashish Jain
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
| | - Prabhu B. Patil
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vishakha Grover
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
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Aktas B, Budinich M, Hoza L, Rankin SA, Broadbent JR, Steele JL. Shelf-life studies of putative probiotic Lacticaseibacillus casei strains in milk and model yogurt. FOOD SCI TECHNOL INT 2023; 29:729-738. [PMID: 35790393 DOI: 10.1177/10820132221112260] [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] [Indexed: 11/17/2022]
Abstract
Lacticaseibacillus casei are commonly utilized as probiotic in a wide-range of fermented and unfermented dairy products. The stability of probiotics in fermented dairy products during shelf-life is of concern due to low pH and high level of organic acids. The objective of this study is to evaluate L. casei for their ability to survive in a model yogurt and fluid milk; additionally, their impact on the pH, organic acids, and sensory attributes of these products was examined. The strain-to-strain differences in cell densities in yogurt and milk inoculated at a therapeutic level at the end of shelf-life were 1.2 and 1.4 log CFU/mL, respectively. Five of the strains examined increased the pH of the yogurt, while two strains were observed to reduce the pH. In milk, one strain raised the pH, while eleven strains reduced the pH. The levels of lactate, acetate, and formate in both the yogurt and milk were altered in a strain-specific manner. The results suggested that the metabolism by these strains differed significantly during the shelf-life. Careful strain selection is required to identify probiotic L. casei strains that will survive through shelf-life in either yogurt or fluid milk and not impact product quality.
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Affiliation(s)
- Busra Aktas
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | - Mateo Budinich
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | - Lulu Hoza
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | - Scott A Rankin
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | - Jeff R Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, Utah State University, Logan, UT, USA
| | - James L Steele
- Department of Food Science, University of Wisconsin, Madison, WI, USA
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Pei Z, Li X, Cui S, Yang B, Lu W, Zhao J, Mao B, Chen W. Population genomics of Lacticaseibacillus paracasei: pan-genome, integrated prophage, antibiotic resistance, and carbohydrate utilization. World J Microbiol Biotechnol 2023; 39:280. [PMID: 37587248 DOI: 10.1007/s11274-023-03722-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 08/06/2023] [Indexed: 08/18/2023]
Abstract
Lacticaseibacillus paracasei has beneficial effects on human health and holds promising potential as a probiotic for use in the development of functional foods, especially dairy products. This species can adapt to a variety of ecological niches and presents fundamental carbohydrate metabolism and tolerance to environmental stresses. However, the population structure, ecology, and antibiotic resistance of Lc. paracasei in diverse ecological niches are poorly understood. Reclassification of Lc. paracasei as a separate species of Lacticaseibacillus has stimulated renewed interest in its research, and a deeper interpretation of it will be important for screening strains beneficial to human health. Here, we collected 121 self-isolated and 268 publicly available Lc. paracasei genomes discussed how genomic approaches have advanced our understanding of its taxonomy, ecology, evolution, diversity, integrated prophage-related element distribution, antibiotic resistance, and carbohydrate utilization. Moreover, for the Lc. paracasei strains isolated in this study, we assessed the inducibility of integrated prophages in their genomes and determined the phenotypes that presented tolerance to multiple antibiotics to provide evidence for safety evaluations of Lc. paracasei during the fermentation processes.
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Affiliation(s)
- Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Xiaoshu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
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Bonn CM, Rafiqullah IM, Crawford JA, Qian YM, Guthrie JL, Matuszewska M, Robinson DA, McGavin MJ. Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0074922. [PMID: 36744906 PMCID: PMC10019231 DOI: 10.1128/aac.00749-22] [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] [Indexed: 02/07/2023] Open
Abstract
Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarRE160G and FarRE93EE were exclusive to CC5, while FarRC116Y, FarRP165L, and FarRG166D also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarRC116Y and FarRG166D strains were polyphyletic, each exhibiting two emergence events. FarRC116Y and FarRE160G were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarRE93EE were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarRE93EE. Accumulation of pseudogenes and additional polymorphisms in FarRE93EE strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.
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Affiliation(s)
- Camryn M. Bonn
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - John A. Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yi Meng Qian
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Jennifer L. Guthrie
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Martin J. McGavin
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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Cappello C, Acin-Albiac M, Pinto D, Polo A, Filannino P, Rinaldi F, Gobbetti M, Di Cagno R. Do nomadic lactobacilli fit as potential vaginal probiotics? The answer lies in a successful selective multi-step and scoring approach. Microb Cell Fact 2023; 22:27. [PMID: 36774510 PMCID: PMC9921609 DOI: 10.1186/s12934-023-02030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/21/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND The goal of this study was to create a multi-strain probiotic gel that would foster a lactobacilli-dominated vaginal microbiota in pregnant women and ensure appropriate eubiosis for the newborn. Nomadic lactobacilli (95 strains), mostly isolated from food sources, were preliminarily screened for functional traits before being characterized for their capability to inhibit the two vaginal pathogens Streptococcus agalactiae and Candida albicans, which may lead to adverse pregnancy-related outcomes. Eight best-performing strains were chosen and furtherly investigated for their ability to produce biofilm. Lastly, the two selected potential probiotic candidates were analyzed in vitro for their ability to reduce the inflammation caused by C. albicans infection on the reconstituted human vaginal epithelium (HVE). RESULTS Lactiplantibacillus plantarum produced both isomers of lactic acid, while Lacticaseibacillus paracasei produced only L-isomer. The production of hydrogen peroxide was strain-dependent, with the highest concentrations found within Lact. paracasei strains. The auto-aggregation capacity and hydrophobicity traits were species-independent. S. agalactiae 88II3 was strongly inhibited both at pH 7.0 and 4.0, whereas the inhibition of C. albicans UNIBZ54 was less frequent. Overall, L. plantarum strains had the highest pathogen inhibition and functional scoring. L. plantarum C5 and POM1, which were selected as potential probiotic candidates also based on their ability to form biofilms, were able to counteract the inflammation process caused by C. albicans infection in the HVE model. CONCLUSIONS Our multi-step and cumulative scoring-based approach was proven successful in mining and highlighting the probiotic potential of two nomadic lactobacilli strains (L. plantarum C5 and POM1), being applicable to preserve and improve human vaginal health.
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Affiliation(s)
- Claudia Cappello
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Marta Acin-Albiac
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Daniela Pinto
- Human Microbiome Advanced Project, Research & Development, Milan, Italy.
| | - Andrea Polo
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Pasquale Filannino
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Fabio Rinaldi
- Human Microbiome Advanced Project, Research & Development, Milan, Italy
| | - Marco Gobbetti
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
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Extraction and Characterization of Cocoa Bean Shell Cell Wall Polysaccharides. Polymers (Basel) 2023; 15:polym15030745. [PMID: 36772046 PMCID: PMC9921167 DOI: 10.3390/polym15030745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Cocoa bean shells (CBS), a by-product of the cocoa industry, from two cacao varieties and obtained after selected processing conditions (fermentation, drying, roasting) were characterized in terms of their chemical composition, where they were found to be a great source of carbohydrates, specifically dietary fiber, protein, ash, and polyphenols, namely quercetin, epicatechin, and catechin. Cell wall polysaccharides were isolated by alkaline extraction (0.5 M or 4 M KOH) and were found to be enriched primarily in pectic polysaccharides (80.6-86%) namely rhamnogalacturonan and arabinogalactan as well as hemi- cellulosic polysaccharides (13.9-19.4%). Overall, 0.5 M KOH polysaccharides were favored having provided a diverse profile of neutral sugars and uronic acids. When tested for the promotion of the growth of selected probiotic strains, CBS cell wall polysaccharides performed similarly or more than inulin and rhamnogalacturonan based on the prebiotic activity scores. The short-chain fatty acid profiles were characterized by high amounts of lactic acid, followed by acetic and propionic acid.
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Genomic, probiotic, and metabolic potentials of Liquorilactobacillus nagelii AGA58, a novel bacteriocinogenic motile strain isolated from lactic acid-fermented shalgam. J Biosci Bioeng 2023; 135:34-43. [PMID: 36384719 DOI: 10.1016/j.jbiosc.2022.10.008] [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] [Received: 05/24/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/15/2022]
Abstract
This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and probiotic features. AGA58 is gram-positive, motile, catalase-negative and appears as short rods under the light-microscope. The AGA58 chromosome comprises a single linear chromosome of 2,294,635 bp that is predicted to carry 2135 coding sequences, including 45 tRNA genes, 3 mRNA, and 3 rRNA operons. The genome has a G+C content of 36.9%, including 55 pseudogenes and a single intact prophage. AGA58 is micro-anaerobic due to achieving a shorter doubling time and faster growth rate than micro-aerophilic conditions. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior, which was confirmed with the in vitro motility test. AGA58 is an obligatory homofermentative lactobacillus that can ferment hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N-acetyl glucosamine, maltose, and trehalose to lactate through glycolysis. No acid production from pentoses implies that five-carbon sugars are being utilized for purine and pyrimidine synthesis. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin, and lactate forms from pyruvate. AGA58 is predicted to encode the LuxS gene and biosynthesis of class IIa and Blp family class-II bacteriocins suggesting this bacterium's antimicrobial potential, linked to antagonism tests that AGA58 can inhibit Escherichia coli ATCC 43895, Salmonellaenterica serovar Typhimurium ATCC 14028, and Klebsiellapneumonia ATCC 13883. Moreover, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions depicting the probiotic potential of the organism as the first report in literature within the same species.
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Detection and identification of Lactobacillus acidophilus species and its commercial probiotic strains using CRISPR loci-based amplicon analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Gumustop I, Ortakci F. Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes. BMC Genom Data 2022; 23:61. [PMID: 35918643 PMCID: PMC9344693 DOI: 10.1186/s12863-022-01074-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Leuconostoc lactis forms a crucial member of the genus Leuconostoc and has been widely used in the fermentation industry to convert raw material into acidified and flavored products in dairy and plant-based food systems. Since the ecological niches that strains of Ln. lactis being isolated from were truly diverse such as the human gut, dairy, and plant environments, comparative genome analysis studies are needed to better understand the strain differences from a metabolic adaptation point of view across diverse sources of origin. We compared eight Ln. lactis strains of 1.2.28, aa_0143, BIOML-A1, CBA3625, LN19, LN24, WIKIM21, and WiKim40 using bioinformatics to elucidate genomic level characteristics of each strain for better utilization of this species in a broad range of applications in food industry. Results Phylogenomic analysis of twenty-nine Ln. lactis strains resulted in nine clades. Whole-genome sequence analysis was performed on eight Ln. lactis strains representing human gastrointestinal tract and fermented foods microbiomes. The findings of the present study are based on comparative genome analysis against the reference Ln. lactis CBA3625 genome. Overall, a ~ 41% of all CDS were conserved between all strains. When the coding sequences were assigned to a function, mobile genetic elements, mainly insertion sequences were carried by all eight strains. All strains except LN24 and WiKim40 harbor at least one intact putative prophage region, and two of the strains contained CRISPR-Cas system. All strains encoded Lactococcin 972 bacteriocin biosynthesis gene clusters except for CBA3625. Conclusions The findings in the present study put forth new perspectives on genomics of Ln. lactis via complete genome sequence based comparative analysis and further determination of genomic characteristics. The outcomes of this work could potentially pave the way for developing elements for future strain engineering applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01074-6.
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Wang J, Wang T, Li Y, Fan Z, Lv Z, Liu L, Li X, Li B. Comparative genomic analysis of Lacticaseibacillus paracasei SMN-LBK from koumiss. Front Microbiol 2022; 13:1042117. [DOI: 10.3389/fmicb.2022.1042117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Lacticaseibacillus paracasei SMN-LBK, which was isolated in Xinjiang, has been shown to be a probiotic strain and used as the auxiliary starter for dairy fermentation. Comparative genomic analysis was performed to investigate the metabolic preference and ethanol tolerance mechanisms of L. paracasei SMN-LBK. The results of comparative genomics showed that L. paracasei strains had high conservation and genetic diversity. SMN-LBK encoded various genes related to carbohydrate and amino acid metabolism pathways, which endow this strain with good fermentation potential. In addition, 6 CRISPR sequences and 8 cas proteins were found in SMN-LBK, and these could play vital roles in the immune system. Furthermore, a unique cluster of potential secondary metabolism genes related to bacteriocins was detected in the genome of SMN-LBK, and this could be important for the preservation of fermented foods. Multiple genes related to alcohol tolerance were also identified. In conclusion, our study explained the traits that were previously demonstrated for SMN-LBK as phenotypes and provided a theoretical basis for the application of SMN-LBK in the food industry.
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Gushgari-Doyle S, Lui LM, Nielsen TN, Wu X, Malana RG, Hendrickson AJ, Carion H, Poole FL, Adams MWW, Arkin AP, Chakraborty R. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions. ISME COMMUNICATIONS 2022; 2:32. [PMID: 37938300 PMCID: PMC9723602 DOI: 10.1038/s43705-022-00113-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 07/04/2023]
Abstract
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
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Affiliation(s)
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ria G Malana
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Heloise Carion
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
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15
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Oberg TS, McMahon DJ, Culumber MD, McAuliffe O, Oberg CJ. Invited review: Review of taxonomic changes in dairy-related lactobacilli. J Dairy Sci 2022; 105:2750-2770. [DOI: 10.3168/jds.2021-21138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]
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16
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Dobreva L, Koprinarova M, Bratchkova A, Danova S. Antibiotic susceptibility of Lactobacillus plantarum strains, isolated from katak. BULGARIAN JOURNAL OF VETERINARY MEDICINE 2022. [DOI: 10.15547/bjvm.2020-0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several Lactobacillus species are accepted as microorganisms with Qualified Presumption of Safety (QPS) in the EFSA’s list. One of them, Lactobacillus plantarum is a widely distributed species with a proven probiotic potential and technological relevance. In addition, every strain must complete several requirements, before implementation. Antibiotic susceptibility is one of EFSA’s important criteria regarding the safety of probiotics. The reason is to avoid any possibility of antibiotic resistance genes transfer to opportunistic pathogens in the gut. In the present study 14 Lactobacillus plantarum strains were assessed for susceptibility to 21 antibiotics from different groups. A high number of resistant strains was determined toward 12 antibiotics (penicillins – penicillin, piperacillin; IIIth generation cephalosporins – cefotaxime, ceftriaxone, ceftazidime; glycopeptides – vancomycin; tetracyclines – tetracycline; aminoglycosides – gentamicin; macrolides – clarithromycin; quinolones – nalidixic acid, ciprofloxacin, levofloxacin). Concerning the other tested antibiotics, strain-specific antibiotic-sensitivity patterns were observed. Antibiotic resistance was also discussed as an advantage in the selection of probiotic strains, however only when it is not transferable. Estimated susceptibility patterns of some of tested candidate probiotic strains are also important, considering the use of the latter as agents accompanying antibiotic therapy
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Affiliation(s)
- L. Dobreva
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiolo-gy, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - M. Koprinarova
- Institute of Molecular Biology “Acad. Roumen Tsanev”, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - A. Bratchkova
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiolo-gy, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - S. Danova
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiolo-gy, Bulgarian Academy of Sciences, Sofia, Bulgaria
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17
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Bisson G, Marino M, Poletti D, Innocente N, Maifreni M. Turbidimetric definition of growth limits in probiotic Lactobacillus strains from the perspective of an adaptation strategy. J Dairy Sci 2021; 104:12236-12248. [PMID: 34600710 DOI: 10.3168/jds.2021-20888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 11/19/2022]
Abstract
The application of an adaptation strategy for probiotics, which may improve their stress tolerance, requires the identification of the growth range for each parameter tested. In this study, 4 probiotics (Lactobacillus acidophilus, Lacticaseibacillus casei, Lacticaseibacillus rhamnosus, and Lactiplantibacillus plantarum) were grown under different pH, NaCl, and sucrose concentrations at 25°C, 30°C, and 37°C. Turbidimetric growth curves were carried out and lag phase duration, maximum growth rate, and amplitude (i.e., the difference between initial and stationary phase optical density) were estimated. Moreover, cell morphology was observed, and cell length measured. The growth response, as well as the morphological changes, were quite different within the 4 species. The L. acidophilus was the most sensitive strain, whereas L. plantarum was shown to better tolerate a wide range of stressful conditions. Frequently, morphological changes occurred when the growth curve was delayed. Based on the results, ranges of environmental parameters are proposed that can be considered suboptimal for each strain, and therefore could be tested. The quantitative evaluation of the growth kinetics as well as the morphological observation of the cells can constitute useful support to the choice of the parameters to be used in an adaptation strategy, notwithstanding the need to verify the effect on viability both in model systems and in foods.
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Affiliation(s)
- Giulia Bisson
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2/A, 33100 Udine, Italy
| | - Marilena Marino
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2/A, 33100 Udine, Italy.
| | - Denise Poletti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2/A, 33100 Udine, Italy
| | - Nadia Innocente
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2/A, 33100 Udine, Italy
| | - Michela Maifreni
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2/A, 33100 Udine, Italy
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18
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Feruloylation of polysaccharides from cranberry and characterization of their prebiotic properties. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches. Foods 2021; 10:foods10081717. [PMID: 34441495 PMCID: PMC8393274 DOI: 10.3390/foods10081717] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.
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20
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Pujato S, Galliani V, Irazoqui JM, Amadío A, Quiberoni A, Mercanti D. Analysis of CRISPR systems of types II-A, I-E and I-C in strains of Lacticaseibacillus. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems. mSystems 2021; 6:e0121120. [PMID: 34060909 PMCID: PMC8269257 DOI: 10.1128/msystems.01211-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Prophage integration, release, and dissemination exert various effects on host bacteria. In the genus Lactobacillus, they may cause bacteriophage contamination during fermentation and even regulate bacterial populations in the gut. However, little is known about their distribution, genetic architecture, and relationships with their hosts. Here, we conducted prophage prediction analysis on 1,472 genomes from 16 different Lactobacillus species and found prophage fragments in almost all lactobacilli (99.8%), with 1,459 predicted intact prophages identified in 64.1% of the strains. We present an uneven prophage distribution among Lactobacillus species; multihabitat species retained more prophages in their genomes than restricted-habitat species. Characterization of the genome features, average nucleotide identity, and landscape visualization presented a high genome diversity of Lactobacillus prophages. We detected antibiotic resistance genes in more than 10% of Lactobacillus prophages and validated that the occurrence of resistance genes conferred by prophage integration was possibly associated with phenotypic resistance in Lactobacillus plantarum. Furthermore, our broad and comprehensive examination of the distribution of CRISPR-Cas systems across the genomes predicted type I and type III systems as potential antagonistic elements of Lactobacillus prophage. IMPORTANCE Lactobacilli are inherent microorganisms in the human gut and are widely used in the food processing industries due to their probiotic properties. Prophages were reportedly hidden in numerous Lactobacillus genomes and can potentially contaminate entire batches of fermentation or modulate the intestinal microecology once they are released. Therefore, a comprehensive scanning of prophages in Lactobacillus is essential for the safety evaluation and application development of probiotic candidates. We show that prophages are widely distributed among lactobacilli; however, intact prophages are more common in multihabitat species and display wide variations in genome feature, integration site, and genomic organization. Our data of the prophage-mediated antibiotic resistance genes (ARGs) and the resistance phenotype of lactobacilli provide evidence for deciphering the putative role of prophages as vectors of the ARGs. Furthermore, understanding the association between prophages and CRISPR-Cas systems is crucial to appreciate the coevolution of phages and Lactobacillus.
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Levante A, Lazzi C, Vatsellas G, Chatzopoulos D, Dionellis VS, Makrythanasis P, Neviani E, Folli C. Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution. Microorganisms 2021; 9:microorganisms9030648. [PMID: 33800997 PMCID: PMC8003834 DOI: 10.3390/microorganisms9030648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022] Open
Abstract
The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in lactic acid bacteria. In this work, genome sequences of Lacticaseibacillus strains of dairy origin were compared, focusing on the distribution of type I TA systems homologous to Lpt/RNAII and of the most common type II TA systems. A high number of TA systems have been identified spread in all the analyzed strains, with type I TA systems mainly located on plasmid DNA. The type II TA systems identified in these strains highlight the diversity of encoded toxins and antitoxins and their organization. This study opens future perspectives on the use of genomic data as a resource for the study of TA systems distribution and prevalence in microorganisms of industrial relevance.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Giannis Vatsellas
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Dimitris Chatzopoulos
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Vasilis S. Dionellis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Periklis Makrythanasis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
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Huang D, Yang B, Chen Y, Stanton C, Ross RP, Zhao J, Zhang H, Chen W. Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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Zhang Q, Zhang L, Ross P, Zhao J, Zhang H, Chen W. Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation. Genes (Basel) 2020; 11:genes11040360. [PMID: 32230824 PMCID: PMC7230607 DOI: 10.3390/genes11040360] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human feces (n = 11), and chicken feces (n = 9), and used comparative genomics to explore the genetic information of L. crispatus from the feces and vagina. No significant difference was found in the three sources of genomic features such as genome size, GC content, and number of protein coding sequences (CDS). However, in a phylogenetic tree constructed based on core genes, vagina-derived L. crispatus and feces-derived strains were each clustered separately. Therefore, the niche exerted an important impact on the evolution of L. crispatus. According to gene annotation, the L. crispatus derived from the vagina possessed a high abundance of genes related to acid tolerance, redox reactions, pullulanase, and carbohydrate-binding modules (CBMs). These genes helped L. crispatus to better adapt to the acidic environment of the vagina and obtain more nutrients, maintaining its dominance in the vagina in competition with other strains. In feces-derived bacteria, more genes encoding CRISPR/Cas system, glycoside hydrolases (GHs) family, and tetracycline/lincomycin resistance genes were found to adapt to the complex intestinal environment. This study highlights the evolutionary relationship of L. crispatus strains isolated from the vagina and feces, and the adaptation of L. crispatus to the host environment.
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Affiliation(s)
- Qiuxiang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
| | - Lili Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: ; Tel.: +86-510-859-12155
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Zhou X, Yang B, Stanton C, Ross RP, Zhao J, Zhang H, Chen W. Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa. BMC Genomics 2020; 21:119. [PMID: 32013858 PMCID: PMC6998098 DOI: 10.1186/s12864-020-6527-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. RESULTS In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. CONCLUSIONS This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.
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Affiliation(s)
- Xingya Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.
| | - Catherine Stanton
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - R Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China. .,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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Yu AO, Leveau JHJ, Marco ML. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:16-29. [PMID: 31573142 DOI: 10.1111/1758-2229.12794] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g-1 to over 108.5 CFU g-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
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28
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Phenotypic Diversity of Lactobacillus casei Group Isolates as a Selection Criterion for Use as Secondary Adjunct Starters. Microorganisms 2020; 8:microorganisms8010128. [PMID: 31963444 PMCID: PMC7022476 DOI: 10.3390/microorganisms8010128] [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: 12/19/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Autochthonous lactic acid bacteria (LAB) play a key role in the development of cheese flavor. As the pasteurization treatment on raw milk causes the elimination of LAB, secondary starter cultures are used in cheese manufacture to obtain cheeses with improved and standardized flavors. In this work, strains of the L. casei group isolated from traditional Italian cheeses were screened for their phenotypic features of technological interest for use as secondary starters. Their milk acidifying performance and the production of volatile compounds when grown in milk were evaluated. Simultaneously, the acetoin metabolic pathway presence was screened in the strains and assessed for its transcriptional activation. The results showed that the analyzed strains, despite belonging to taxonomically-related species, vary greatly according to the measured phenotypes. Four strains among the fourteen screened could be potentially used as adjunct cultures for cheese-making processes. The strain that showed the highest production of acetoin upregulated the aspartate pathway. An increased knowledge of volatile compounds’ production and acidifying properties of LAB strains isolated from traditional dairy products might guide the selection of strains for industrial applications.
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29
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Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches. Genes (Basel) 2020; 11:genes11010070. [PMID: 31936280 PMCID: PMC7016997 DOI: 10.3390/genes11010070] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 01/14/2023] Open
Abstract
Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.
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30
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Welker DL, Coburn BM, McClatchy JH, Broadbent JR. Multiple pulse electroporation of lactic acid bacteria Lactococcus lactis and Lactobacillus casei. J Microbiol Methods 2019; 166:105741. [PMID: 31634499 DOI: 10.1016/j.mimet.2019.105741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022]
Abstract
Genetic manipulation of lactic acid bacteria is often difficult due to the inability to transform them with high efficiency. Multi-pulse electroporation offers a simple approach to increase transformation efficiencies. Using cells grown with 1% glycine and pretreated with lithium acetate and dithiothreitol, multi-pulse electroporation (five pulses of 12.5 kV cm-1) of Lactococcus lactis JB704 cells resulted in a transformation efficiency of up to 1.2 × 106 colony forming units (CFU) μg-1 pGK13, an 8-fold increase in the transformation efficiency compared to single pulse electroporation. Other cell growth and pretreatment conditions with JB704 resulted in lower transformation efficiencies but had 4-fold to 27-fold higher transformation efficiencies with the five pulse electroporations. With similarly grown and pretreated Lactobacillus casei 32G cells, multi-pulse electroporation (five pulses of 7.5 kV cm-1) resulted in a mean transformation efficiency of 7.3 × 103 CFU μg-1 pTRKH2, a 4-fold increase in the transformation efficiency compared to single pulse electroporation.
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Affiliation(s)
- Dennis L Welker
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322-5305, United States.
| | - Bryan M Coburn
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322-5305, United States
| | - John H McClatchy
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322-5305, United States
| | - Jeff R Broadbent
- Department of Nutrition, Dietetics and Food Science, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, United States
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31
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Expression of DinJ-YafQ System of Lactobacillus casei Group Strains in Response to Food Processing Stresses. Microorganisms 2019; 7:microorganisms7100438. [PMID: 31614503 PMCID: PMC6843646 DOI: 10.3390/microorganisms7100438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 11/19/2022] Open
Abstract
Toxin-antitoxin (TA) systems are widely distributed in bacterial genomes and are involved in the adaptive response of microorganisms to stress conditions. Few studies have addressed TA systems in Lactobacillus and their role in the adaptation to food environments and processes. In this work, for six strains belonging to L. casei group isolated from dairy products, the expression of DinJ-YafQ TA system was investigated after exposure to various food-related stresses (nutrient starvation, low pH, high salt concentration, oxidative stress, and high temperature), as well as to the presence of antibiotics. In particular, culturability and DinJ-YafQ expression were evaluated for all strains and conditions by plate counts and RT qPCR. Among all the food-related stress conditions, only thermal stress was capable to significantly affect culturability. Furthermore, exposure to ampicillin significantly decreased the culturability of two L. rhamnosus strains. The regulation of DinJ-YafQ TA system resulted strain-specific; however, high temperature was the most significant stress condition able to modulate DinJ-YafQ expression. The increasing knowledge about TA systems activity and regulation might offer new perspectives to understand the mechanisms that L. casei group strains exploit to adapt to different niches or production processes.
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32
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Bravo M, Combes T, Martinez FO, Cerrato R, Rey J, Garcia-Jimenez W, Fernandez-Llario P, Risco D, Gutierrez-Merino J. Lactobacilli Isolated From Wild Boar ( Sus scrofa) Antagonize Mycobacterium bovis Bacille Calmette-Guerin (BCG) in a Species-Dependent Manner. Front Microbiol 2019; 10:1663. [PMID: 31417502 PMCID: PMC6683848 DOI: 10.3389/fmicb.2019.01663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/04/2019] [Indexed: 01/06/2023] Open
Abstract
Background: Wildlife poses a significant burden for the complete eradication of bovine tuberculosis (bTB). In particular, wild boar (Sus scrofa) is one of the most important reservoirs of Mycobacterium bovis, the causal agent of bTB. Wild boar can display from mild TB lesions, usually found in head lymph nodes, to generalized TB lesions distributed in different anatomical regions; but rarely clinical signs, which complicates the diagnosis of Mycobacterium bovis infection and bTB control. Among the possibilities for this variability in lesion distribution is the influence of the host-beneficial commensal-primed immune barrier. In this respect, beneficial microbes may delay bTB dissemination as a consequence of an antagonistic competition for nutrients and phagocytes. In order to explore this possibility, we have tested whether typical commensals such as lactobacilli have the capacity to reduce the survival rate of the surrogate M. bovis strain Bacillus Calmette-Guerin (BCG); and to modulate its phagocyte intake. Results: Three Lactobacillus species, L. casei, L. plantarum, and L. salivarius, isolated from wild boar feces displayed a pH-dependent inhibitory activity against BCG and influenced its intake by porcine blood phagocytes in a species-dependent manner. All lactobacilli showed a very significant bactericidal effect against BCG at low pH, but only isolates of L. plantarum and L. casei displayed such antimycobacterial activity at neutral pH. The genomes of these isolates revealed the presence of two-peptide bacteriocins whose precursor genes up-regulate in the presence of BCG cells. Furthermore, L. plantarum reduced significantly the BCG phagocytic intake, whereas L. casei had the opposite effect. L. salivarius had no significant influence on the phagocytic response to BCG. Conclusions: Our in vitro results show that lactobacilli isolated from wild boar antagonize BCG as a consequence of their antimycobacterial activity and a competitive phagocytic response. These findings suggest that commensal bacteria could play a beneficial role in influencing the outcome of bTB dissemination. Further work with lactobacilli as a potential competitive pressure to control bTB will need to take into account the complex nature of the commensal microbiome, the specific immunity of the wild boar and the in vivo infection context with pathogenic strains of M. bovis.
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Affiliation(s)
- Maria Bravo
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Theo Combes
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Fernando O Martinez
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Rosario Cerrato
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain
| | - Joaquín Rey
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - David Risco
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain
| | - Jorge Gutierrez-Merino
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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33
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Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes. Appl Microbiol Biotechnol 2019; 103:3135-3152. [PMID: 30830251 PMCID: PMC6447522 DOI: 10.1007/s00253-019-09701-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Owing to their unique potential to ferment carbohydrates, both homo- and heterofermentative lactic acid bacteria (LAB) are widely used in the food industry. Deciphering the genetic basis that determine the LAB fermentation type, and hence carbohydrate utilization, is paramount to optimize LAB industrial processes. Deep sequencing of 24 LAB species and comparison with 32 publicly available genome sequences provided a comparative data set including five major LAB genera for further analysis. Phylogenomic reconstruction confirmed Leuconostoc and Pediococcus species as independently emerging from the Lactobacillus genus, within one of the three phylogenetic clades identified. These clades partially grouped LABs according to their fermentation types, suggesting that some metabolic capabilities were independently acquired during LAB evolution. In order to apply a genome-wide association study (GWAS) at the multigene family level, utilization of 49 carbohydrates was also profiled for these 56 LAB species. GWAS results indicated that obligately heterofermentative species lack 1-phosphofructokinase, required for d-mannose degradation in the homofermentative pathway. Heterofermentative species were found to often contain the araBAD operon, involved in l-arabinose degradation, which is important for heterofermentation. Taken together, our results provide helpful insights into the genetic determinants of LAB carbohydrate metabolism, and opens for further experimental research, aiming at validating the role of these candidate genes for industrial applications.
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34
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Campedelli I, Mathur H, Salvetti E, Clarke S, Rea MC, Torriani S, Ross RP, Hill C, O'Toole PW. Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp. Appl Environ Microbiol 2019; 85:e01738-18. [PMID: 30366997 PMCID: PMC6293106 DOI: 10.1128/aem.01738-18] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of Lactobacillus species and their carriage of antibiotic resistance (AR) genes is under continuing ad hoc review. To comprehensively update the identification of AR in the genus Lactobacillus, we determined the antibiotic susceptibility patterns of 182 Lactobacillus type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes aac(3) and lsa, involved in resistance to aminoglycosides and clindamycin, respectively, were found in Lactobacillus spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in Lactobacillus ingluviei, Lactobacillus amylophilus, and Lactobacillus amylotrophicus, flanked in the genome by mobile genetic elements with potential for horizontal transfer.IMPORTANCELactobacillus species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.
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Affiliation(s)
| | - Harsh Mathur
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Elisa Salvetti
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Siobhán Clarke
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Mary C Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Verona, Italy
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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35
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Konieczna C, Słodziński M, Schmidt MT. Exopolysaccharides Produced by Lactobacillus rhamnosus KL 53A and Lactobacillus casei Fyos Affect Their Adhesion to Enterocytes. Pol J Microbiol 2018; 67:273-281. [PMID: 30451443 PMCID: PMC7256689 DOI: 10.21307/pjm-2018-032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 11/11/2022] Open
Abstract
Probiotics promote and help to maintain beneficial microbiota composition of the gastrointestinal tract ecosystem and have a positive impact on the host’s health. Production of exopolysaccharides is an important feature of probiotic lactobacilli. It increases the chance of their survival in the gastrointestinal tract and promotes adhesion to the epithelium; therefore, exopolysaccharides are important for the process of colonization. Two lactic acid bacteria strains were used in this study: Lactobacillus rhamnosus KL 53A and Lactobacillus casei Fyos. Exopolysaccharides were isolated from bacterial cells and their monosaccharide composition was examined using liquid chromatography. The influence of exopolysaccharides on lactobacilli adhesion to enterocytes was studied after deglycosylation of the bacterial cells and incubation with the selected intestinal microbiota strains that metabolize polysaccharides – Faecalibacterium prausnitzii DSM 17677 and Blautia luti DSM 14534. Both deglycosylation and incubation with polysaccharide metabolizing strains influenced the ability of probiotic strains to adhere to enterocytes. Enzymatic deglycosylation decreased adhesion efficiency of L. rhamnosus KL 53A; however, co-incubation of both lactobacillus strains with F. prausnitzii DSM 17677 resulted in an increase of their adhesion efficiency. Exopolysaccharides are important adhesins of Lactobacillus spp. that influence their ability to colonize gut epithelium. Other members of gut microbiota can modify the adhesion property in situ; therefore the composition and metabolic state of commensal bacteria may influence their probiotic action.
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Affiliation(s)
- Corinna Konieczna
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Michał Słodziński
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Marcin T Schmidt
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
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36
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Zhao X, Wang W, Blaine A, Kane ST, Zijlstra RT, Gänzle MG. Impact of probiotic Lactobacillus sp. on autochthonous lactobacilli in weaned piglets. J Appl Microbiol 2018; 126:242-254. [PMID: 30276941 DOI: 10.1111/jam.14119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022]
Abstract
AIMS This study aimed to determine whether host-adapted lactobacilli exhibit superior survival during intestinal transit relative to nomadic and free-living organisms, and to characterize the impact of probiotic lactobacilli on autochthonous lactobacilli. METHODS AND RESULTS Mixed cultures of Lactobacillus casei K9-1 and Lactobacillus fermentum K9-2, or reutericyclin producing Lactobacillus reuteri and its isogenic mutant were fed to piglets as freeze-dried culture, or as part of fermented feed. Lactobacilli in digesta and faecal samples were quantified by strain-specific quantitative PCR (qPCR), high-resolution-melting curve qPCR, and high-throughput sequencing of 16S rRNA gene sequence tags. The abundance of the host adapted L. reuteri in digesta and faeces was higher (P < 0·05) when compared to L. casei or L. fermentum. Feed fermentation or chemical acidification of feed reduced (P < 0·05) cell counts of Lactobacillus salivarius in colonic digesta. The reutericyclin producing L. reuteri TMW1.656 transiently reduced (P < 0·05) the faecal abundance of lactobacilli. However, the overall impact of probiotic intervention on autochthonous lactobacilli was minor. CONCLUSIONS The vertebrate host-adapted L. reuteri survives better during intestinal transit of piglets compared to L. casei and L. fermentum. SIGNIFICANCE AND IMPACT OF THE STUDY Ecology and lifestyle of Lactobacillus strains may be suitable criteria for selection of probiotic strains for use in swine production.
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Affiliation(s)
- X Zhao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - W Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - A Blaine
- CanBiocin Inc., Edmonton, AB, Canada
| | - S T Kane
- CanBiocin Inc., Edmonton, AB, Canada
| | - R T Zijlstra
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - M G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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37
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Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates. Curr Microbiol 2018; 76:37-47. [DOI: 10.1007/s00284-018-1581-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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38
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Wüthrich D, Irmler S, Berthoud H, Guggenbühl B, Eugster E, Bruggmann R. Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster. Front Microbiol 2018; 9:2415. [PMID: 30386310 PMCID: PMC6200037 DOI: 10.3389/fmicb.2018.02415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei – a flavor-enhancing adjunct culture species – can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster – consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase – is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.
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Affiliation(s)
- Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | | | | | | | - Elisabeth Eugster
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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39
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Filannino P, De Angelis M, Di Cagno R, Gozzi G, Riciputi Y, Gobbetti M. How Lactobacillus plantarum
shapes its transcriptome in response to contrasting habitats. Environ Microbiol 2018; 20:3700-3716. [DOI: 10.1111/1462-2920.14372] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Pasquale Filannino
- Department of Soil, Plant and Food Sciences; University of Bari Aldo Moro; Bari Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences; University of Bari Aldo Moro; Bari Italy
| | | | - Giorgia Gozzi
- Department of Agricultural and Food Sciences; Alma Mater Studiorum, University of Bologna; Bologna Italy
| | - Ylenia Riciputi
- Department of Agricultural and Food Sciences; Alma Mater Studiorum, University of Bologna; Bologna Italy
| | - Marco Gobbetti
- Faculty of Science and Technology; Free University of Bozen Italy
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40
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Hill D, Sugrue I, Tobin C, Hill C, Stanton C, Ross RP. The Lactobacillus casei Group: History and Health Related Applications. Front Microbiol 2018; 9:2107. [PMID: 30298055 PMCID: PMC6160870 DOI: 10.3389/fmicb.2018.02107] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/20/2018] [Indexed: 01/16/2023] Open
Abstract
The Lactobacillus casei group (LCG), composed of the closely related Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are some of the most widely researched and applied probiotic species of lactobacilli. The three species have been extensively studied, classified and reclassified due to their health promoting properties. Differentiation is often difficult by conventional phenotypic and genotypic methods and therefore new methods are being continually developed to distinguish the three closely related species. The group remain of interest as probiotics, and their use is widespread in industry. Much research has focused in recent years on their application for health promotion in treatment or prevention of a number of diseases and disorders. The LCG have the potential to be used prophylactically or therapeutically in diseases associated with a disturbance to the gut microbiota. The group have been extensively researched with regard to stress responses, which are crucial for their survival and therefore application as probiotics.
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Affiliation(s)
- Daragh Hill
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.,Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Ivan Sugrue
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Tobin
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
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41
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Diversity and evolution of Lactobacillus casei group isolated from fermented dairy products in Tibet. Arch Microbiol 2018; 200:1111-1121. [DOI: 10.1007/s00203-018-1528-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/30/2017] [Accepted: 05/18/2018] [Indexed: 12/16/2022]
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42
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Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche. BMC Genomics 2018; 19:205. [PMID: 29554864 PMCID: PMC5859408 DOI: 10.1186/s12864-018-4586-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities. Results Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident. Conclusions The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.
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43
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Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH. Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. Front Microbiol 2018; 9:63. [PMID: 29441050 PMCID: PMC5797582 DOI: 10.3389/fmicb.2018.00063] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/10/2018] [Indexed: 11/20/2022] Open
Abstract
Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.
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Affiliation(s)
- Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Jonathan Muri
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Damianos Melidis
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Adrian Wicki
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Marc Bourqui
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Claudia Wenzel
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Elisabeth Eugster-Meier
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
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44
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Morovic W, Roper JM, Smith AB, Mukerji P, Stahl B, Rae JC, Ouwehand AC. Safety evaluation of HOWARU ® Restore ( Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium animalis subsp. lactis Bl-04 and B. lactis Bi-07) for antibiotic resistance, genomic risk factors, and acute toxicity. Food Chem Toxicol 2017; 110:316-324. [DOI: 10.1016/j.fct.2017.10.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 12/30/2022]
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45
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Xing Z, Geng W, Li C, Sun Y, Wang Y. Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments. Sci Rep 2017; 7:12827. [PMID: 28993659 PMCID: PMC5634458 DOI: 10.1038/s41598-017-12916-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/11/2017] [Indexed: 01/18/2023] Open
Abstract
It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production. Reverse transcription-qPCR (RT-qPCR) revealed significant increases in the relative expression of pgm, ugp, and uge during the mid-logarithmic phase, whereas the expression of pgi was higher at the beginning of the stationary phase. The enzymes encoded by these four genes concertedly regulated carbon flux, which in turn modulated the production of EPS precursors. Moreover, ZW3 tolerated pH 3.5 and 3% bile salt and retained cell surface hydrophobicity and auto-aggregation. In conclusion, we explored the potential of ZW3 for utilization in both the dairy industry and in probiotic applications. Additionally, we elucidated the regulation of the relevant genes involved in EPS production.
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Affiliation(s)
- Zhuqing Xing
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China.,Chinese medical college of TJUTCM, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Weitao Geng
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Chao Li
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ye Sun
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yanping Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China.
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46
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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47
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Hidalgo-Cantabrana C, Crawley AB, Sanchez B, Barrangou R. Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum. Front Microbiol 2017; 8:1851. [PMID: 29033911 PMCID: PMC5626976 DOI: 10.3389/fmicb.2017.01851] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Alexandra B. Crawley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Borja Sanchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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von Ossowski I. Novel Molecular Insights about Lactobacillar Sortase-Dependent Piliation. Int J Mol Sci 2017; 18:ijms18071551. [PMID: 28718795 PMCID: PMC5536039 DOI: 10.3390/ijms18071551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023] Open
Abstract
One of the more conspicuous structural features that punctuate the outer cell surface of certain bacterial Gram-positive genera and species is the sortase-dependent pilus. As these adhesive and variable-length protrusions jut outward from the cell, they provide a physically expedient and useful means for the initial contact between a bacterium and its ecological milieu. The sortase-dependent pilus displays an elongated macromolecular architecture consisting of two to three types of monomeric protein subunits (pilins), each with their own specific function and location, and that are joined together covalently by the transpeptidyl activity of a pilus-specific C-type sortase enzyme. Sortase-dependent pili were first detected among the Gram-positive pathogens and subsequently categorized as an essential virulence factor for host colonization and tissue invasion by these harmful bacteria. However, the sortase-dependent pilus was rebranded as also a niche-adaptation factor after it was revealed that “friendly” Gram-positive commensals exhibit the same kind of pilus structures, which includes two contrasting gut-adapted species from the Lactobacillus genus, allochthonous Lactobacillus rhamnosus and autochthonous Lactobacillus ruminis. This review will highlight and discuss what has been learned from the latest research carried out and published on these lactobacillar pilus types.
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Affiliation(s)
- Ingemar von Ossowski
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki FIN-00014, Finland.
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49
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Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez-Muñoz ME, Leulier F, Gänzle M, Walter J. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 2017; 41:S27-S48. [DOI: 10.1093/femsre/fux030] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 02/07/2023] Open
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50
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A "Ct contrast"-based strain-specific real-time quantitative PCR system for Lactobacilllus paracasei subsp. paracasei NTU 101. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:535-544. [PMID: 28693925 DOI: 10.1016/j.jmii.2017.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 06/18/2016] [Accepted: 05/24/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND/PURPOSES Routine cell number determination for specific Lactobacillus strain by cultivation requires at least 4-7 days. Thus rapid and specific cell number determine methods such as strain-specific quantitative PCR (qPCR) are valuable. However, qPCR method is vulnerable to difficult PCR target such as dimer/secondary structure forming sequence. METHODS In this study, a two-component, "Ct contrast" approach was applied to strain-specific qPCR system following the development of Lactobacillus paracasei subsp. paracasei NTU 101 (NTU 101) strain-specific PCR with random amplification of polymorphic DNA (RAPD)-derived strain-specific sequences. RESULTS The quantitative range of the NTU 101 strain-specific qPCR system was 3.0 × 101 to 3.0 × 105 copies for pure cultures, and 3.0 × 102 to 3.0 × 105 copies for multi-strain or unknown food samples. The results of spike in test and real sample testing suggested that non-specific weak background signals did not compromise test specificity, and demonstrated the potential of the NTU 101 strain-specific qPCR system in food samples. CONCLUSION The two-component, "Ct contrast" approach is useful for qPCR discrimination when no ideal PCR target is available or the variance of the target site is unpredictable. The Ct contrast approach might provide a simple and robust solution for other challenging qPCR targets.
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