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Goel A, Halami PM. Safety assessment of probiotic Lactiplantibacillus plantarum MCC5231 and its persistence in gastrointestinal tract. Microb Pathog 2024; 194:106824. [PMID: 39067492 DOI: 10.1016/j.micpath.2024.106824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Probiotics are the health beneficial microorganisms and suitable for food industry if found fit for human consumption. In the present study, Lactiplantibacillus plantarum MCC5231, a probiotic bacterium included in vegetable-based beverages, was evaluated for its safety characteristics and gastrointestinal survival using a combined in silico and in vitro approach. The strain was found to be devoid of hemolytic, lecithinase and gelatinase activities. Additionally, it does not consist any transferable antibiotic resistance genes. Further, whole genome sequence analysis revealed the presence of three intact prophages and 14 virulence-associated genes, however, none of them posed a pathogenic threat. Importantly, MCC5231 do not possess any gene associated with toxin production. The strain harbored a CRISPR system, enhancing defense against prophages. Survival assays under simulated gastric and intestinal fluid conditions demonstrated viability rates of 71.4 % and 83.3 %, respectively. Genetic analysis of the mucin binding protein indicated possession of a type II mucin binding domain, suggesting moderate adhesion to intestinal cells. Furthermore, L. plantarum MCC5231 exhibited the ability to produce exopolysaccharides and form biofilms, which may confer additional protection in the gastrointestinal tract. Based on these findings, L. plantarum MCC5231 appears to be a safe probiotic candidate suitable for commercial use in the food industry.
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Affiliation(s)
- Aditi Goel
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India.
| | - Prakash M Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India.
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2
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Lemos MLP, do Monte DFM, Leite EL, Egito AS, Olbrich KM, Oliveira CJB. Genomic insights of Lactiplantibacillus plantarum CNPC024: a potential probiotic strain producing immune-boosting tryptophan-derived metabolites. Braz J Microbiol 2024:10.1007/s42770-024-01480-1. [PMID: 39222220 DOI: 10.1007/s42770-024-01480-1] [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: 10/04/2023] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Probiogenomics can provide important insights bout probiotic candidate bacteria. This study aimed to perform an in-depth genomic characterization of the probiotic candidate Lactiplantibacillus plantarum CNPC024 to investigate its probiosis mechanisms, identify metabolic pathways that might benefit the host, and improve the safety assessment for this strain to be effectively used as a probiotic. After whole-genome sequencing in Illumina MiSeq platform, the de novo genome assembly resulted in a 3.2 Mb draft genome. According to the Average Nucleotide Identity (ANI) analysis with 46 randomly validated probiotic LAB belonging to the Lactobacillaceae family, the strain showed a 99% nucleotide identity with other L. plantarum probiotic species. We identified a set of determinants conferring tolerance to bile salts and low pH conditions, as well as temperature, oxidative and osmotic stressors via the glutathione-glutaredoxin system (Grxs). As a β‑galactosidase‑producing strain, it has the potential to be used in fermented dairy products for lactose-intolerant individuals. There were no significant hits for transferable antibiotic-resistance genes. We also identified gene clusters associated with production of bacteriocins (plantaricins E, F and K). Lastly, we detected metabolic pathways associated with the production of tryptophan-derived metabolites that could potentially modulate the host's immune responses.
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Affiliation(s)
- Mateus L P Lemos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, 58397-000, Brazil
| | - Daniel F M do Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, 58397-000, Brazil
| | - Elma L Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, 58397-000, Brazil
| | - Antônio S Egito
- Embrapa Goats and Sheep, Northeast Regional Center, R. Osvaldo Cruz 1143, Campina Grande, PB, 58428-09, Brazil
| | - Karina M Olbrich
- Embrapa Food Agroindustry, Av. das Américas, nº 29.501, Guaratiba, Rio de Janeiro, RJ, 23020-470, Brazil
| | - Celso J B Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, 58397-000, Brazil.
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3
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Bongaerts D, Bouchez A, De Roos J, Cnockaert M, Wieme AD, Vandamme P, Weckx S, De Vuyst L. Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production. Appl Environ Microbiol 2024; 90:e0186923. [PMID: 38446583 PMCID: PMC11022581 DOI: 10.1128/aem.01869-23] [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: 10/18/2023] [Accepted: 02/04/2024] [Indexed: 03/08/2024] Open
Abstract
The production of gueuze beers through refermentation and maturation of blends of lambic beer in bottles is a way for lambic brewers to cope with the variability among different lambic beer batches. The resulting gueuze beers are more carbonated than lambic beers and are supposed to possess a unique flavor profile that varies over time. To map this refermentation and maturation process for gueuze production, a blend of lambic beers was made and bottled, whereby one of them was produced with the old wheat landrace Zeeuwse Witte. Through the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and high-throughput sequencing of bacterial and fungal amplicons, in combination with metabolite target analysis, new insights into gueuze production were obtained. During the initial stages of refermentation, the conditions in the bottles were similar to those encountered during the maturation phase of lambic beer productions in wooden barrels, which was also reflected microbiologically (presence of Brettanomyces species, Pediococcus damnosus, and Acetobacter lambici) and biochemically (ethanol, higher alcohols, lactic acid, acetic acid, volatile phenolic compounds, and ethyl esters). However, after a few weeks of maturation, a switch from a favorable environment to one with nutrient and dissolved oxygen depletion resulted in several changes. Concerning the microbiology, a sequential prevalence of three lactic acid bacterial species occurred, namely, P. damnosus, Lentilactobacillus buchneri, and Lactobacillus acetotolerans, while the diversity of the yeasts decreased. Concerning the metabolites produced, mainly those of the Brettanomyces yeasts determined the metabolic profiles encountered during later stages of the gueuze production.IMPORTANCEGueuze beers are the result of a refermentation and maturation process of a blend of lambic beers carried out in bottles. These gueuze beers are known to have a long shelf life, and their quality typically varies over time. However, knowledge about gueuze production in bottles is scarce. The present study provided more insights into the varying microbial and metabolite composition of gueuze beers during the first 2 years of this refermentation and maturation process. This will allow gueuze producers to gain more information about the influence of the refermentation and maturation time on their beers. These insights can also be used by gueuze producers to better inform their customers about the quality of young and old gueuze beers.
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Affiliation(s)
- Dries Bongaerts
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Arne Bouchez
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonas De Roos
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anneleen D. Wieme
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Stefan Weckx
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Whole genome sequence analysis of bacteriophage P1 that infects the Lactobacillus plantarum. Virus Genes 2022; 58:570-583. [DOI: 10.1007/s11262-022-01929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/12/2022] [Indexed: 10/15/2022]
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Kim SH, Park JH. Characterization of Prophages in Leuconostoc Derived from Kimchi and Genomic Analysis of the Induced Prophage in Leuconostoc lactis. J Microbiol Biotechnol 2022; 32:333-340. [PMID: 34949750 PMCID: PMC9628853 DOI: 10.4014/jmb.2110.10046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
Leuconostoc has been used as a principal starter in natural kimchi fermentation, but limited research has been conducted on its phages. In this study, prophage distribution and characterization in kimchi-derived Leuconostoc strains were investigated, and phage induction was performed. Except for one strain, 16 Leuconostoc strains had at least one prophage region with questionable and incomplete regions, which comprised 0.5-6.0% of the bacterial genome. Based on major capsid protein analysis, ten intact prophages and an induced incomplete prophage of Leu. lactis CBA3626 belonged to the Siphoviridae family and were similar to Lc-Nu-like, sha1-like, phiMH1-like, and TPA_asm groups. Bacterial immunology genes, such as superinfection exclusion proteins and methylase, were found on several prophages. One prophage of Leu. lactis CBA3626 was induced using mitomycin C and was confirmed as belonging to the Siphoviridae family. Homology of the induced prophage with 21 reported prophages was not high (< 4%), and 47% identity was confirmed only with TPA_asm from Siphoviridae sp. isolate ct3pk4. Therefore, it is suggested that Leuconostoc from kimchi had diverse prophages with less than 6% genome proportion and some immunological genes. Interestingly, the induced prophage was very different from the reported prophages of other Leuconostoc species.
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Affiliation(s)
- Song-Hee Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea,Corresponding author J.H. Park Phone: +82-31-750-5523 Fax: +82-31-750-5283 E-mail:
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Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi. Food Microbiol 2021; 102:103913. [PMID: 34809939 DOI: 10.1016/j.fm.2021.103913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/28/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.
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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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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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Sunthornthummas S, Doi K, Fujino Y, Rangsiruji A, Sarawaneeyaruk S, Insian K, Pringsulaka O. Genomic characterisation of Lacticaseibacillus paracasei phage ΦT25 and preliminary analysis of its derived endolysin. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2020.104968] [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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10
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Kwak W, Han YH, Seol D, Kim H, Ahn H, Jeong M, Kang J, Kim H, Kim TH. Complete Genome of Lactobacillus iners KY Using Flongle Provides Insight Into the Genetic Background of Optimal Adaption to Vaginal Econiche. Front Microbiol 2020; 11:1048. [PMID: 32528446 PMCID: PMC7264367 DOI: 10.3389/fmicb.2020.01048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/28/2020] [Indexed: 12/02/2022] Open
Abstract
Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited. In this study, the first complete genome of L. iners was constructed using a cost-effective long-read sequencing platform, Flongle from Oxford Nanopore, and comparative genome analysis was conducted using a total of 1,046 strain genomes from 10 vaginal Lactobacillus species. Single-molecule sequencing using Flongle effectively resolved the limitation of the 2nd generation sequencing technologies in dealing with genomic regions of high GC contents, and comparative genome analysis identified three potential core genes (INY, ZnuA, and hsdR) of L. iners which was related to its specific adaption to the vaginal environment. In addition, we performed comparative prophage analysis for 1,046 strain genomes to further identify the species specificity. The number of prophages in L. iners genomes was significantly smaller than other vaginal Lactobacillus species, and one of the specific genes (hsdR) was suggested as the means for defense against bacteriophage. The first complete genome of L. iners and the three specific genes identified in this study will provide useful resources to further expand our knowledge of L. iners and its specific adaption to the vaginal econiche.
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Affiliation(s)
| | - Young-Hyun Han
- Priority Research Center, Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Jaeku Kang
- Priority Research Center, Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea.,Department of Pharmacology, College of Medicine, Konyang University, Daejeon, South Korea
| | - Heebal Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Tae Hyun Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea.,Department of Obstetrics and Gynecology, Konyang University Hospital, Daejeon, South Korea
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Pei Z, Sadiq FA, Han X, Zhao J, Zhang H, Ross RP, Lu W, Chen W. Identification, characterization, and phylogenetic analysis of eight new inducible prophages in Lactobacillus. Virus Res 2020; 286:198003. [PMID: 32450182 DOI: 10.1016/j.virusres.2020.198003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
Abstract
Lysogenic bacterial strains abound in the Lactobacillus genus and contain dormant prophages inserted within their genomes. To evaluate the prophage-induction potential of the Lactobacillus strains of six species, 142 randomly selected strains from these species were induced with Mitomycin C. Eight newly-induced phages were identified and found to be diverse in morphology. Among the six species assessed, Lactobacillus plantarum and Lactobacillus rhamnosus strains were generally insensitive to induction. The genomic characterizations of eight phages were performed via whole genome sequencing and protein prediction. Meanwhile, genome comparison of the induced phages and predicted prophages demonstrated that the prediction software PHASTER can accurately locate major prophage regions in Lactobacillus. A phylogenetic tree of the Lactobacillus phage population was constructed to obtain further insights into the clustering of individuals, two major groups were found, one of which consisted mostly of L. plantarum virulent phages, the other was represented by Lactobacillus casei/paracasei temperate phages. Finally, it was confirmed via genomic collinear analysis, which seven of the eight Lactobacillus temperate phages were newly discovered, and two Lactobacillus brevis temperate phages belonged to a novel lineage.
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Affiliation(s)
- Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiao Han
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 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 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China
| | - R Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China; Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China.
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12
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Wei B, Peng Z, Huang T, Guan Q, Xie M, Xiong T. Stability of potential prophages in commercial strain Lactobacillus plantarum NCU116 under various stressors. Arch Microbiol 2020; 202:1241-1250. [PMID: 32112122 DOI: 10.1007/s00203-020-01813-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/10/2020] [Accepted: 01/18/2020] [Indexed: 01/21/2023]
Abstract
Genetic stability of bacterium as a starter culture is vital for product quality in fermentation industry. The commercial strain Lactobacillus plantarum NCU116 widely used in fruit and vegetable fermentation was induced with various stressors to investigate the stability of potential prophages. PHAge Search Tool (PHAST) identified three potential prophages in bacterial genome. By spectrophotometric analysis, mitomycin C (MMC), lactic acid, and bile salt were found to inhibit the growth of L. plantarum NCU116 while ethanol and hydrogen peroxide had no notable impacts. Transcriptions of four phage-synthesizing genes (phaR, phacap, phaada, phatail) and four phage-resistant genes (cas116, helR, hsd1, hsd2) under stressors were investigated by quantitative reverse transcription PCR. MMC was found to most significantly upregulated transcriptions of phage-synthesizing genes, followed by lactic acid and bile salt. By transmission electron microscopy, no virus particles from the lysates of strain NCU116 treated by MMC were observed, corresponding to the result that no phage nucleic acids could be extracted from the supernatants of strain NCU116 treated by MMC. This study suggested that no prophages could be induced from L. plantarum NCU116 by strong inducer MMC, indicating its genetic stability, which supports the comprehensive application of strain NCU116 in industry without causing fermentation failure.
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Affiliation(s)
- Benliang Wei
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zhen Peng
- School of Food Science and Technology, Nanchang University, Nanchang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Tao Huang
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Qianqian Guan
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Mingyong Xie
- School of Food Science and Technology, Nanchang University, Nanchang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Tao Xiong
- School of Food Science and Technology, Nanchang University, Nanchang, China. .,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China.
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13
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Comparative Genomic Analysis of Lactobacillus plantarum: An Overview. Int J Genomics 2019; 2019:4973214. [PMID: 31093491 PMCID: PMC6481158 DOI: 10.1155/2019/4973214] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 01/21/2023] Open
Abstract
Background Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics. Results The finding of the current study indicates that the core genome of L. plantarum presents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes of L. pentosus KCA1 and L. plantarum WCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat. Conclusions Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains.
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Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain-Specific Viability Quantitative PCR Method. Appl Environ Microbiol 2018. [PMID: 29523544 PMCID: PMC5930365 DOI: 10.1128/aem.00107-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity. The nucleic acid-binding dye PEMAX was used to selectively detect and enumerate viable bacteria by v-qPCR. The primer set amplifying a 188-bp DNA fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed on apple blossoms, pear, strawberry, and kiwifruit leaves in potted plants under controlled environmental conditions, as well as pear and apple blossoms under field conditions, by comparing v-qPCR population estimations to those obtained by qPCR and specific plate counting on de Man-Rogosa-Sharpe (MRS)-rifampin. The population estimation did not differ significantly between methods when conditions were conducive to bacterial survival. However, under stressful conditions, differences between methods were observed due to cell death or viable-but-nonculturable state induction. While qPCR overestimated the population level, plate counting underestimated this value in comparison to v-qPCR. PM411 attained stable population levels of viable cells on the flower environment under high relative humidity. However, the unfavorable conditions on the leaf surface and the relatively dryness in the field caused an important decrease in the viable population. IMPORTANCE The v-qPCR method in combination with plate counting and qPCR is a powerful tool for studies of colonization and survival under field conditions, to improve formulations and delivery strategies of PM411, and to optimize the dose and timing of spray schedules. It is expected that PEMAX v-qPCR could also be developed for monitoring other strains on plant surfaces not only as biological control agents but also beneficial bacteria useful in the sustainable management of crop production.
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Abriouel H, Pérez Montoro B, Casado Muñoz MDC, Knapp CW, Gálvez A, Benomar N. In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives. PLoS One 2017; 12:e0176801. [PMID: 28651019 PMCID: PMC5484467 DOI: 10.1371/journal.pone.0176801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/17/2017] [Indexed: 12/22/2022] Open
Abstract
Lactobacillus pentosus MP-10, isolated from brines of naturally fermented Aloreña green table olives, exhibited high probiotic potential. The genome sequence of L. pentosus MP-10 is currently considered the largest genome among lactobacilli, highlighting the microorganism's ecological flexibility and adaptability. Here, we analyzed the complete genome sequence for the presence of acquired antibiotic resistance and virulence determinants to understand their defense mechanisms and explore its putative safety in food. The annotated genome sequence revealed evidence of diverse mobile genetic elements, such as prophages, transposases and transposons involved in their adaptation to brine-associated niches. In-silico analysis of L. pentosus MP-10 genome sequence identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) as an immune system against foreign genetic elements, which consisted of six arrays (4-12 repeats) and eleven predicted cas genes [CRISPR1 and CRISPR2 consisted of 3 (Type II-C) and 8 (Type I) genes] with high similarity to L. pentosus KCA1. Bioinformatic analyses revealed L. pentosus MP-10 to be absent of acquired antibiotic resistance genes, and most resistance genes were related to efflux mechanisms; no virulence determinants were found in the genome. This suggests that L. pentosus MP-10 could be considered safe and with high-adaptation potential, which could facilitate its application as a starter culture and probiotic in food preparations.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - María del Carmen Casado Muñoz
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W. Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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Chen X, Xi Y, Zhang H, Wang Z, Fan M, Liu Y, Wu W. Characterization and adsorption of Lactobacillus virulent phage P1. J Dairy Sci 2016; 99:6995-7001. [PMID: 27372579 DOI: 10.3168/jds.2016-11332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022]
Abstract
Bacteriophage infection of lactic acid bacteria is considered an important problem worldwide in the food fermentation industry, as it may produce low quality or unsafe foods, cause fermentation failure, and result in economic losses. To increase current knowledge on the properties of Lactobacillus virulent phages, we evaluated the effect of divalent cations, temperature, pH, and chloramphenicol on the adsorption ability of Lactobacillus virulent phage P1. Phage P1 was isolated from the abnormal fermentation liquid of Lactobacillus plantarum IMAU10120. The results showed that this phage belonged to the Siphoviridae family. The latent period of this phage was 45min, and the burst time was 90min. Burst size was 132.88±2.37 phage counts expressed per milliliter per infective center. This phage showed good tolerance at different temperatures, but incubation at 50°C only affected its adsorption. Adsorption rate reached a maximum value between 30 and 42°C. A high adsorption value of phage infectivity was obtained from pH 6 to 8. Moreover, calcium ions promoted and increased the adsorption capacity of phage P1, but magnesium ions had negative effects. Chloramphenicol had no effect on phage adsorption. This study increased current knowledge on the characterization and biological aspects of Lactobacillus virulent phages, and may provide some basic information that can be used to design successful antiphage strategies in the food industry.
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Affiliation(s)
- X Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China.
| | - Y Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
| | - H Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
| | - Z Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
| | - M Fan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
| | - Y Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
| | - W Wu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, 010018, P. R. China
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Genomic Diversity of Phages Infecting Probiotic Strains of Lactobacillus paracasei. Appl Environ Microbiol 2015; 82:95-105. [PMID: 26475105 DOI: 10.1128/aem.02723-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/11/2015] [Indexed: 01/21/2023] Open
Abstract
Strains of the Lactobacillus casei group have been extensively studied because some are used as probiotics in foods. Conversely, their phages have received much less attention. We analyzed the complete genome sequences of five L. paracasei temperate phages: CL1, CL2, iLp84, iLp1308, and iA2. Only phage iA2 could not replicate in an indicator strain. The genome lengths ranged from 34,155 bp (iA2) to 39,474 bp (CL1). Phages iA2 and iLp1308 (34,176 bp) possess the smallest genomes reported, thus far, for phages of the L. casei group. The GC contents of the five phage genomes ranged from 44.8 to 45.6%. As observed with many other phages, their genomes were organized as follows: genes coding for DNA packaging, morphogenesis, lysis, lysogeny, and replication. Phages CL1, CL2, and iLp1308 are highly related to each other. Phage iLp84 was also related to these three phages, but the similarities were limited to gene products involved in DNA packaging and structural proteins. Genomic fragments of phages CL1, CL2, iLp1308, and iLp84 were found in several genomes of L. casei strains. Prophage iA2 is unrelated to these four phages, but almost all of its genome was found in at least four L. casei strains. Overall, these phages are distinct from previously characterized Lactobacillus phages. Our results highlight the diversity of L. casei phages and indicate frequent DNA exchanges between phages and their hosts.
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Snauwaert I, Stragier P, De Vuyst L, Vandamme P. Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment. BMC Genomics 2015; 16:267. [PMID: 25880122 PMCID: PMC4394401 DOI: 10.1186/s12864-015-1438-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 03/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions. It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. The molecular mechanisms underlying its metabolic capabilities and niche adaptations were unknown up to now. In the present study, whole-genome sequencing and comparative genome analysis were used to investigate this strain's mechanisms to reside in the beer niche, with special focus on not only stress and hop resistances but also folate biosynthesis and exopolysaccharide (EPS) production. RESULTS The draft genome sequence of P. damnosus LMG 28219 harbored 183 contigs, including an intact prophage region and several coding sequences involved in plasmid replication. The annotation of 2178 coding sequences revealed the presence of many transporters and transcriptional regulators and several genes involved in oxidative stress response, hop resistance, de novo folate biosynthesis, and EPS production. Comparative genome analysis of P. damnosus LMG 28219 with Pediococcus claussenii ATCC BAA-344(T) (beer origin) and Pediococcus pentosaceus ATCC 25745 (plant origin) revealed that various hop resistance genes and genes involved in de novo folate biosynthesis were unique to the strains isolated from beer. This contrasted with the genes related to osmotic stress responses, which were shared between the strains compared. Furthermore, transcriptional regulators were enriched in the genomes of bacteria capable of growth in beer, suggesting that those cause rapid up- or down-regulation of gene expression. CONCLUSIONS Genome sequence analysis of P. damnosus LMG 28219 provided insights into the underlying mechanisms of its adaptation to the beer niche. The results presented will enable analysis of the transcriptome and proteome of P. damnosus LMG 28219, which will result in additional knowledge on its metabolic activities.
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Affiliation(s)
- Isabel Snauwaert
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium.
| | - Pieter Stragier
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium.
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium.
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Zamani I, Bouzari M, Emtiazi G, Ghasemi SM, Chang HI. Complete genome sequence of a novel phage, vB_MoxS-ISF9, infecting methylotrophic Microbacterium: first report of a virulent Microbacterium phage. Arch Virol 2014; 159:2537-40. [PMID: 24777828 DOI: 10.1007/s00705-014-2092-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/17/2014] [Indexed: 11/24/2022]
Abstract
Here, we report the first genome sequence of a new virulent phage of Microbacterium oxydans, termed vB_MoxS-ISF9, which was isolated from sewage. Transmission electron microscopy showed that the isolated phage, which has a hexagonal head of about 80 nm in diameter and a long non-contractile tail of about 240 nm, belongs to the family Siphoviridae. The vB_MoxS-ISF9 DNA was completely sequenced and found to be 59,254 bp in length, with a G+C content of 62.76% and 120 putative open reading frames (ORFs). The predicted protein products of the ORFs were identified, and their sequences were analyzed. In a comparison with all available phage genomes, vB_MoxS-ISF9 did not show any significant similarity to other previously reported bacteriophages. To the beast of our knowledge, this is the first report of the isolation and complete genomic sequencing of a virulent phage against a member of the genus Microbacterium.
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Affiliation(s)
- Isaac Zamani
- Department of Biology, Faculty of Science, University of Isfahan, Hezar Jereeb Street, 81746-73441, Isfahan, Iran
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Characterization of two virulent phages of Lactobacillus plantarum. Appl Environ Microbiol 2012; 78:8719-34. [PMID: 23042172 DOI: 10.1128/aem.02565-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We characterized two Lactobacillus plantarum virulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eight L. plantarum strains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least two L. plantarum strains, LMG9211 and WCSF1. The linear double-stranded DNA genome of the pac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that of Pediococcus damnosus phage clP1 and 77% identity with that of L. plantarum phage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of the cos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those of Bacillus and Lactobacillus strains as well as phages. Some phage B2 genes were similar to ORFs from L. plantarum phage LP65 of the Myoviridae family. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.
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