1
|
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] [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 anlaysis 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.
Collapse
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.
| |
Collapse
|
2
|
Sornsenee P, Surachat K, Kang DK, Mendoza R, Romyasamit C. Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap. Foods 2024; 13:1773. [PMID: 38891001 PMCID: PMC11172291 DOI: 10.3390/foods13111773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
This study focused on L. paracasei strains isolated from fermented palm sap in southern Thailand that exhibit potential probiotic characteristics, including antibiotic susceptibility, resistance to gastrointestinal stresses, and antimicrobial activity against various pathogens. However, a thorough investigation of the whole genome sequences of L. paracasei isolates is required to ensure their safety and probiotic properties for human applications. This study aimed to sequence the genome of L. paracasei isolated from fermented palm sap, to assess its safety profile, and to conduct a comprehensive comparative genomic analysis with other Lacticaseibacillus species. The genome sizes of the seven L. paracasei strains ranged from 3,070,747 bp to 3,131,129 bp, with a GC content between 46.11% and 46.17% supporting their classification as nomadic lactobacilli. In addition, the minimal presence of cloud genes and a significant number of core genes suggest a high degree of relatedness among the strains. Meanwhile, phylogenetic analysis of core genes revealed that the strains possessed distinct genes and were grouped into two distinct clades. Genomic analysis revealed key genes associated with probiotic functions, such as those involved in gastrointestinal, oxidative stress resistance, vitamin synthesis, and biofilm disruption. This study is consistent with previous studies that used whole-genome sequencing and bioinformatics to assess the safety and potential benefits of probiotics in various food fermentation processes. Our findings provide valuable insights into the potential use of seven L. paracasei strains isolated from fermented palm sap as probiotic and postbiotic candidates in functional foods and pharmaceuticals.
Collapse
Affiliation(s)
- Phoomjai Sornsenee
- Department of Family and Preventive Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Dae-Kyung Kang
- Department of Animal Biotechnology, Dankook University, Cheonan 31116, Republic of Korea; (D.-K.K.); (R.M.)
| | - Remylin Mendoza
- Department of Animal Biotechnology, Dankook University, Cheonan 31116, Republic of Korea; (D.-K.K.); (R.M.)
| | - Chonticha Romyasamit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Center of Excellence in Innovation of Essential Oil and Bioactive Compounds, Walailak University, Nakhon Si Thammarat 80160, Thailand
| |
Collapse
|
3
|
Huidrom S, Ngashangva N, Khumlianlal J, Sharma KC, Mukherjee PK, Devi SI. Genomic insights from Lactiplantibacillus plantarum BRD3A isolated from Atingba, a traditional fermented rice-based beverage and analysis of its potential for probiotic and antimicrobial activity against Methicillin-resistant Staphylococcus aureus. Front Microbiol 2024; 15:1357818. [PMID: 38628861 PMCID: PMC11019378 DOI: 10.3389/fmicb.2024.1357818] [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: 12/18/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Lactiplantibacillus plantarum BRD3A was isolated from Atingba, a traditional fermented rice-based beverage of Manipur. Its genomic sequence has 13 contigs and its genome size is 3,320,817 bp with a guanine-cytosine (GC) ratio of 44.6%. It comprises 3185 genes including 3112 coding sequences (CDSs), 73 RNAs (including 66 tRNAs and others), and one clustered regularly interspaced short palindromic repeat (CRISPR) array. A comparative and phylogenetic analysis with the Lp. plantarum genome shows that this strain has close similarity with other Lp. plantarum strains and about 99% average nucleotide identity. Functional annotation using evolutionary genealogy of genes-non-supervised orthologous groups (EggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) reveals genes associated with various biological processes such as metabolism, genetic information processing, and transport functions. Furthermore, the strain harbors bacteriocins like plantaricin E, Plantaricin F, and Enterocin X categorized under class IIb by the BAGEL4 database, indicating its potential antimicrobial properties. Additionally, AntiSMASH web server predicted four secondary regions-T3PKS, terpene, cyclic lactone inducer, and ribosomally synthesized and post-translationally modified peptide (RiPP)-suggesting an even higher antimicrobial potential. We validated the antimicrobial activity of Lp. plantarum BRD3A through in vitro experiments in which it exhibited promising bactericidal effects on methicillin-resistant Staphylococcus aureus, inhibiting their biofilm growth. These findings indicate the potential of Lp. plantarum BRD3A to be used as an alternative to conventional antibiotics.
Collapse
Affiliation(s)
- Surmani Huidrom
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Ng Ngashangva
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| | - Joshua Khumlianlal
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | | | - Pulok Kumar Mukherjee
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| | - Sarangthem Indira Devi
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| |
Collapse
|
4
|
Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [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: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
Collapse
Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| |
Collapse
|
5
|
Liu X, Wang M, Hu T, Lin X, Liang H, Li W, Zhao S, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Safety assessment of potential probiotic Lactobacillus acidophilus AM13-1 with high cholesterol-lowering capability isolated from human gut. Lett Appl Microbiol 2024; 77:ovad143. [PMID: 38126115 DOI: 10.1093/lambio/ovad143] [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: 07/04/2023] [Revised: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
An important risk factor for cardiovascular disease is dyslipidemia, especially abnormal cholesterol levels. The relation between probiotics and cholesterol-lowering capability has been extensively studied. Lactobacillus acidophilus plays a significant role in affecting host health, and produces multitudinous metabolites, which have prohibitory functions against pathogenic microorganisms. In this study, we identified a cholesterol-lowering strain AM13-1, isolated from a fecal sample obtained from a healthy adult male, and performed comprehensive function analysis by whole-genome analysis and in vitro experiments. Genome analyses of L. acidophilus AM13-1 revealed that carbohydrate and amino acid transport, metabolism, translation, ribosomal structure, and biogenesis are abundant categories of functional genes. No virulence factors or toxin genes with experimentally verified were found in the genome of strain AM13-1. Besides, plenty of probiotic-related genes were predicted from the L. acidophilus AM13-1 genome, such as cbh, atpA-D, and dltD, with functions related to cholesterol-lowering and acid resistance. And strain AM13-1 showed high-efficiency of bile salt hydrolase activity and the capacity for removing cholesterol with efficiency rates of 70%. These function properties indicate that strain AM13-1 can be considered as a probiotic candidate for use in food and health care products.
Collapse
Affiliation(s)
- Xudong Liu
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Wang
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongyuan Hu
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Xiaoqian Lin
- BGI Research, Shenzhen 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | - Hewei Liang
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Wenxi Li
- BGI Research, Shenzhen 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Yiyi Zhong
- BGI Research, Shenzhen 518083, China
- BGI Precision Nutrition, Shenzhen 518083, China
| | - Haifeng Zhang
- BGI Research, Shenzhen 518083, China
- BGI Precision Nutrition, Shenzhen 518083, China
| | - Lan Ge
- BGI Research, Shenzhen 518083, China
- BGI Precision Nutrition, Shenzhen 518083, China
| | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
- Lars Bolund Institute of Regenerative Medicine Qingdao-Europe Advanced Institute for LifeSciences, BGI Research, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen 518083, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
- Lars Bolund Institute of Regenerative Medicine Qingdao-Europe Advanced Institute for LifeSciences, BGI Research, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen 518083, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| |
Collapse
|
6
|
Kamarinou CS, Kiousi DE, Repanas P, Argyri AA, Chorianopoulos NG, Galanis A. Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10. Microorganisms 2024; 12:93. [PMID: 38257920 PMCID: PMC10820299 DOI: 10.3390/microorganisms12010093] [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: 12/09/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.
Collapse
Affiliation(s)
- Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Nikos G. Chorianopoulos
- Laboratory of Microbiology and Biotechnology of Foods, School of Food and Nutritional Sciences, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| |
Collapse
|
7
|
Sato K, Ikagawa Y, Niwa R, Nishioka H, Horie M, Iwahashi H. Genome Sequencing Unveils Nomadic Traits of Lactiplantibacillus plantarum in Japanese Post-Fermented Tea. Curr Microbiol 2023; 81:52. [PMID: 38155273 DOI: 10.1007/s00284-023-03566-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Post-fermented tea production involving microbial fermentation is limited to a few regions, such as Southeast Asia and Japan, with Japan's Shikoku island being particularly prominent. Lactiplantibacillus plantarum was the dominant species found in tea leaves after anaerobic fermentation of Awa-bancha in Miyoshi City, Tokushima, and Ishizuchi-kurocha in Ehime. Although the draft genome of L. plantarum from Japanese post-fermented tea has been previously reported, its genetic diversity requires further exploration. In this study, whole-genome sequencing was conducted on four L. plantarum strains isolated from Japanese post-fermented tea using nanopore sequencing. These isolates were then compared with other sources to examine their genetic diversity revealing that L. plantarum isolated from Japanese post-fermented tea contained several highly variable gene regions associated with sugar metabolism and transportation. However, no source-specific genes or clusters were identified within accessory or core gene regions. This study indicates that L. plantarum possesses high genetic diversity and that the unique environment of Japanese post-fermented tea does not appear to exert selective pressure on L. plantarum growth.
Collapse
Affiliation(s)
- Kyoka Sato
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| | - Yuichiro Ikagawa
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Niwa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Hiroki Nishioka
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center, Tokushima, 770-8021, Japan
| | - Masanori Horie
- Health and Medical Research Institute (HMRI), National Institute of Advanced Industrial Science and Technology (AIST), Kagawa, 761-0395, Japan
| | - Hitoshi Iwahashi
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| |
Collapse
|
8
|
Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [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: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
Collapse
Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
| |
Collapse
|
9
|
Kingkaew E, Woraprayote W, Booncharoen A, Niwasabutra K, Janyaphisan T, Vilaichone RK, Yamaoka Y, Visessanguan W, Tanasupawat S. Functional genome analysis and anti-Helicobacter pylori activity of a novel bacteriocinogenic Lactococcus sp. NH2-7C from Thai fermented pork (Nham). Sci Rep 2023; 13:20362. [PMID: 37990119 PMCID: PMC10663479 DOI: 10.1038/s41598-023-47687-4] [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: 08/03/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Helicobacter pylori, linked to gastric diseases, is targeted for probiotic treatment through bacteriocin production. Bacteriocins have gained recognition for their non-toxic effects on host cells and their ability to combat a wide range of pathogens. This study aimed to taxonomically characterize and evaluate the safety and probiotic properties of the novel species of Lactococcus sp. NH2-7C isolated from fermented pork, as well as its bacteriocin NH2-7C, both in vitro and in silico. Comparative genotypic analysis revealed an average nucleotide identity of 94.96%, an average amino acid identity of 94.29%, and a digital DNA-DNA hybridization value of 63.80% when compared to Lactococcus lactis subsp. lactis JCM 5805T. These findings suggest that strain NH2-7C represents a novel species within the genus Lactococcus. In silico assessments confirmed the non-pathogenic nature of strain NH2-7C and the absence of genes associated with virulence and biogenic amine formation. Whole-genome analysis revealed the presence of the nisA gene responsible for nisin A production, indicating its potential as a beneficial compound with anti-Helicobacter pylori activity and non-toxic characteristics. Probiotic assessments indicated bile salt hydrolase and cholesterol assimilation activities, along with the modulation of interleukin-6 and tumour necrosis factor-α secretion. Strain NH2-7C demonstrated gastrointestinal tolerance and the ability to adhere to Caco-2 cells, affirming its safety and probiotic potential. Additionally, its ability to produce bacteriocins supports its suitability as a functional probiotic strain with therapeutic potential. However, further in vitro and in vivo investigations are crucial to ensure its safety and explore potential applications for Lactococcus sp. NH2-7C as a probiotic agent.
Collapse
Affiliation(s)
- Engkarat Kingkaew
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Weerapong Woraprayote
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Auttaporn Booncharoen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kanidta Niwasabutra
- Thailand Institute of Scientific and Technological Research (TISTR) Biodiversity Research Centre, Pathum Thani, 12120, Thailand
| | - Thitiphorn Janyaphisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Ratha-Korn Vilaichone
- GI Unit, Department of Medicine, and Center of Excellence in Digestive Diseases, Thammasat University, Thailand Science Research and Innovation Fundamental Fund, Bualuang ASEAN Chair Professorship at Thammasat University, Pathum Thani, 12120, Thailand
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine Oita University, Yufu, Oita, Japan
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
10
|
Ahmed NA, Khattab RA, Ragab YM, Hassan M. Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species. BMC Genomics 2023; 24:667. [PMID: 37932698 PMCID: PMC10626658 DOI: 10.1186/s12864-023-09749-9] [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: 03/31/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis. RESULTS The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value > 0.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species. CONCLUSIONS Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.
Collapse
Affiliation(s)
- Noha A Ahmed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt.
| | - Rania Abdelmonem Khattab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Yasser M Ragab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Mariam Hassan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, 43511, Egypt.
| |
Collapse
|
11
|
Kingkaew E, Konno H, Hosaka Y, Tanasupawat S. Probiogenomic Analysis of Lactiplantibacillus sp. LM14-2 from Fermented Mussel (Hoi-dong), and Evaluation of its Cholesterol-lowering and Immunomodulation Effects. Probiotics Antimicrob Proteins 2023; 15:1206-1220. [PMID: 35987935 DOI: 10.1007/s12602-022-09977-7] [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] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
Lactiplantibacillus sp. LM14-2, isolated from Thai-fermented mussel (Hoi-dong), showed attractive probiotic properties. This strain was identified as Lactiplantibacillus plantarum based on its phenotypic, chemotaxonomic, and genetic characteristics including whole-genome sequencing (WGS). The draft genome sequence was analyzed and annotated for the molecular mechanisms involved in the safety assessment, the adaptation and adhesion of L. plantarum LM14-2 to the gastrointestinal tract (GIT), and the beneficial genes involved in bacteria-host interactions. The L. plantarum LM14-2 exhibited bile salt hydrolase (BSH) activity, assimilated cholesterol at 86.07 ± 5.03%, stimulated the secretion of interleukin-12, interferon-gamma, and human beta defensin-2, and induced nitric oxide production. In addition, L. plantarum LM14-2 showed excellent gastrointestinal tolerance and adhesion ability to Caco-2 cells. Furthermore, the in silico analysis showed that L. plantarum LM14-2 was a non-human pathogen and did not contain antibiotic resistance genes or plasmids. L. plantarum LM14-2 also contained potential genes associated with various probiotic characteristics and health-promoting effects. Consequently, this study suggested that L. plantarum LM14-2 could be considered safe, with potential probiotic properties and health-promoting impacts, which could facilitate its probiotic application.
Collapse
Affiliation(s)
- Engkarat Kingkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Hiroshi Konno
- Akita Konno CO., LTD., 248 Aza Kariwano, Daisen-shi, Akita, 019-2112, Japan
| | - Yoshihito Hosaka
- Akita Konno CO., LTD., 248 Aza Kariwano, Daisen-shi, Akita, 019-2112, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
12
|
Liu S, Zhang ZF, Mao J, Zhou Z, Zhang J, Shen C, Wang S, Marco ML, Mao J. Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations. NPJ Biofilms Microbiomes 2023; 9:65. [PMID: 37726290 PMCID: PMC10509236 DOI: 10.1038/s41522-023-00432-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
Identification of the core functional microorganisms in food fermentations is necessary to understand the ecological and functional processes for making those foods. Wheat qu, which provides liquefaction and saccharifying power, and affects the flavor quality, is a key ingredient in ancient alcoholic huangjiu fermentation, while core microbiota of them still remains indistinct. In this study, metagenomics, metabolomics, microbial isolation and co-fermentation were used to investigate huangjiu. Although Aspergillus is usually regarded as core microorganism in wheat qu to initiate huangjiu fermentations, our metagenomic analysis showed that bacteria Saccharopolyspora are predominant in wheat qu and responsible for breakdown of starch and cellulose. Metabolic network and correlation analysis showed that Saccharopolyspora rectivirgula, Saccharopolyspora erythraea, and Saccharopolyspora hirsuta made the greatest contributions to huangjiu's metabolites, consisting of alcohols (phenylethanol, isoamylol and isobutanol), esters, amino acids (Pro, Arg, Glu and Ala) and organic acids (lactate, tartrate, acetate and citrate). S. hirsuta J2 isolated from wheat qu had the highest amylase, glucoamylase and protease activities. Co-fermentations of S. hirsuta J2 with S. cerevisiae HJ resulted in a higher fermentation rate and alcohol content, and huangjiu flavors were more similar to that of traditional huangjiu compared to co-fermentations of Aspergillus or Lactiplantibacillus with S. cerevisiae HJ. Genome of S. hirsuta J2 contained genes encoding biogenic amine degradation enzymes. By S. hirsuta J2 inoculation, biogenic amine content was reduced by 45%, 43% and 62% in huangjiu, sausage and soy sauce, respectively. These findings show the utility of Saccharopolyspora as a key functional organism in fermented food products.
Collapse
Affiliation(s)
- Shuangping Liu
- National Engineering Laboratory for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang, 312000, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, Zhejiang, 312000, China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jieqi Mao
- Department of Food Science and Technology, National University of Singapore, Science Drive 2, 117542, Singapore, Singapore
| | - Zhilei Zhou
- National Engineering Laboratory for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang, 312000, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, Zhejiang, 312000, China
| | - Jing Zhang
- National Engineering Laboratory for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Caihong Shen
- National Engineering Research Center of Solid-State Brewing, Luzhou, China
| | - Songtao Wang
- National Engineering Research Center of Solid-State Brewing, Luzhou, China
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, CA, USA.
| | - Jian Mao
- National Engineering Laboratory for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang, 312000, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, Zhejiang, 312000, China.
| |
Collapse
|
13
|
Ren F, Ji N, Zhu Y. Research Progress of α-Glucosidase Inhibitors Produced by Microorganisms and Their Applications. Foods 2023; 12:3344. [PMID: 37761053 PMCID: PMC10529981 DOI: 10.3390/foods12183344] [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: 08/24/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Based on the easy cultivation of microorganisms and their short cycle time, research on α-glucosidase inhibitors (α-GIs) of microbial origin is receiving extensive attention. Raw materials used in food production, such as cereals, dairy products, fruits, and vegetables, contain various bioactive components, like flavonoids, polyphenols, and alkaloids. Fermentation with specific bacterial strains enhances the nutritional value of these raw materials and enables the creation of hypoglycemic products rich in diverse active ingredients. Additionally, conventional food processing often results in significant byproduct generation, causing resource wastage and environmental issues. However, using bacterial strains to ferment these byproducts into α-GIs presents an innovative solution. This review describes the microbial-derived α-GIs that have been identified. Moreover, the production of α-GIs using industrial food raw materials and processing byproducts as a medium in fermentation is summarized. It is worth analyzing the selection of strains and raw materials, the separation and identification of key compounds, and fermentation broth research methods. Notably, the innovative ideas in this field are described as well. This review will provide theoretical guidance for the development of microbial-derived hypoglycemic foods.
Collapse
Affiliation(s)
- Fei Ren
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China; (F.R.); (N.J.)
| | - Nairu Ji
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China; (F.R.); (N.J.)
| | - Yunping Zhu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China; (F.R.); (N.J.)
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| |
Collapse
|
14
|
Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [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: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
Collapse
Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
| |
Collapse
|
15
|
Nitipan S, Saithong P. Characterization and sequencing analysis of pLP2.5-11 and pLP3.0-4 novel cryptic plasmids from Lactiplantibacillus plantarum WP72/27. 3 Biotech 2023; 13:263. [PMID: 37408733 PMCID: PMC10317920 DOI: 10.1007/s13205-023-03684-y] [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: 12/21/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
We sequenced and described two cryptic plasmids from Lactiplantibacillus plantarum strain WP72/27, termed pLP2.5-11 (OP831909) and pLP3.0-4 (OP831910). Nucleotide sequencing gave the sizes of pLP2.5-11 and pLP3.0-4 as 2754 and 3197 base pairs, with G + C contents 38.89% and 40.88% and predicted two and eight putative open reading frames, respectively. The RepA protein of pLP2.5-11 shared a 99% identity with pC30il, pLP1 and pC30il, whereas the RepB protein of pLP3.0-4 shared a 98% identity with pXY3, a member of the rolling-circle replication (RCR) pC194 family. The origin of plasmid replication was predicted to consist of inverted and directed repeat sequences upstream of the Rep genes. Sequence analysis predicted that both pLP2.5-11 and pLP3.0-4 plasmids replicate via a rolling-circle process. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03684-y.
Collapse
Affiliation(s)
- Supachai Nitipan
- Department of Biology, Faculty of Science, Thaksin University, Phattalung Campus, Phattalung, 93210 Thailand
- Microbial Technology for Agriculture, Food and Environment Research Center, Thaksin University, Phatthalung Campus, Phatthalung, 93210 Thailand
| | - Pramuan Saithong
- Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Bangkok, 10900 Thailand
| |
Collapse
|
16
|
Bae WY, Lee YJ, Jung WH, Shin SL, Kim TR, Sohn M. Draft genome sequence and probiotic functional property analysis of Lactobacillus gasseri LM1065 for food industry applications. Sci Rep 2023; 13:12212. [PMID: 37500806 PMCID: PMC10374649 DOI: 10.1038/s41598-023-39454-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Probiotics are defined as live organisms in the host that contribute to health benefits. Lactobacillus gasseri LM1065, isolated from human breast milk, was investigated for its probiotic properties based on its genome. Draft genome map and de novo assembly were performed using the PacBio RS II system and hierarchical genome assembly process (HGAP). Probiotic properties were determined by the resistance to gastric conditions, adherence ability, enzyme production, safety assessment and mobile genetic elements. The fungistatic effect and inhibition of hyphae transition were studied using the cell-free supernatant (CFS). L. gasseri LM1065 showed high gastric pepsin tolerance and mild tolerance to bile salts. Auto-aggregation and hydrophobicity were measured to be 61.21% and 61.55%, respectively. The adherence to the human intestinal epithelial cells was measured to be 2.02%. Antibiotic-resistance genes and putative virulence genes were not predicted in the genomic analysis, and antibiotic susceptibility was satisfied by the criteria of the European Food Safety Authority. CFS showed a fungistatic effect and suppressed the tricarboxylic acid cycle in Candida albicans (29.02%). CFS also inhibited the transition to true hyphae and damaged the blastoconidia. This study demonstrates the essential properties of this novel probiotic, L. gasseri LM1065, and potential to inhibit vaginal C. albicans infection.
Collapse
Affiliation(s)
- Won-Young Bae
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea.
| | - Young Jin Lee
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Woo-Hyun Jung
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - So Lim Shin
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Tae-Rahk Kim
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Minn Sohn
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| |
Collapse
|
17
|
Zinno P, Perozzi G, Devirgiliis C. Foodborne Microbial Communities as Potential Reservoirs of Antimicrobial Resistance Genes for Pathogens: A Critical Review of the Recent Literature. Microorganisms 2023; 11:1696. [PMID: 37512869 PMCID: PMC10383130 DOI: 10.3390/microorganisms11071696] [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: 06/01/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global and increasing threat to human health. Several genetic determinants of AMR are found in environmental reservoirs, including bacteria naturally associated with widely consumed fermented foods. Through the food chain, these bacteria can reach the gut, where horizontal gene transfer (HGT) can occur within the complex and populated microbial environment. Numerous studies on this topic have been published over the past decades, but a conclusive picture of the potential impact of the non-pathogenic foodborne microbial reservoir on the spread of AMR to human pathogens has not yet emerged. This review critically evaluates a comprehensive list of recent experimental studies reporting the isolation of AMR bacteria associated with fermented foods, focusing on those reporting HGT events, which represent the main driver of AMR spread within and between different bacterial communities. Overall, our analysis points to the methodological heterogeneity as a major weakness impairing determination or a causal relation between the presence of AMR determinants within the foodborne microbial reservoir and their transmission to human pathogens. The aim is therefore to highlight the main gaps and needs to better standardize future studies addressing the potential role of non-pathogenic bacteria in the spread of AMR.
Collapse
Affiliation(s)
- Paola Zinno
- Institute for the Animal Production System in the Mediterranean Environment (ISPAAM), National Research Council, Piazzale Enrico Fermi 1, 80055 Portici, Italy
| | - Giuditta Perozzi
- Research Centre for Food and Nutrition, CREA (Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria), Via Ardeatina 546, 00178 Rome, Italy
| | - Chiara Devirgiliis
- Research Centre for Food and Nutrition, CREA (Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria), Via Ardeatina 546, 00178 Rome, Italy
| |
Collapse
|
18
|
Aziz T, Naveed M, Shabbir MA, Sarwar A, Ali Khan A, Zhennai Y, Alharbi M, Alsahammari A, Alasmari AF. Comparative genomics of food-derived probiotic Lactiplantibacillus plantarum K25 reveals its hidden potential, compactness, and efficiency. Front Microbiol 2023; 14:1214478. [PMID: 37455721 PMCID: PMC10346846 DOI: 10.3389/fmicb.2023.1214478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 07/18/2023] Open
Abstract
This study aimed to investigate the intricate genetic makeup of the Lactiplantibacillus plantarum K25 strain by conducting a comprehensive analysis of comparative genomics. The results of our study demonstrate that the genome exhibits a high-level efficiency and compactness, comprising a total of 3,199 genes that encode proteins and a GC content of 43.38%. The present study elucidates the evolutionary lineage of Lactiplantibacillus plantarum strains through an analysis of the degree of gene order conservation and synteny across a range of strains, thereby underscoring their closely interrelated evolutionary trajectories. The identification of various genetic components in the K25 strain, such as bacteriocin gene clusters and prophage regions, highlights its potential utility in diverse domains, such as biotechnology and medicine. The distinctive genetic elements possess the potential to unveil innovative therapeutic and biotechnological remedies in future. This study provides a comprehensive analysis of the L. plantarum K25 strain, revealing its remarkable genomic potential and presenting novel prospects for utilizing its unique genetic features in diverse scientific fields. The present study contributes to the existing literature on Lactiplantibacillus plantarum and sets the stage for prospective investigations and practical implementations that leverage the exceptional genetic characteristics of this adap organism.
Collapse
Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
- Laboratory of Animal Health, Food Hygiene, and Quality, Department of Agriculture, University of Ioannina, Arta, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center for Food Additives, Beijing Technology and Business University, Beijing, China
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alsahammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
19
|
Xie S, Wang C, Zeng T, Wang H, Suo H. Whole-genome and comparative genome analysis of Mucor racemosus C isolated from Yongchuan Douchi. Int J Biol Macromol 2023; 234:123397. [PMID: 36739051 DOI: 10.1016/j.ijbiomac.2023.123397] [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: 09/09/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Mucor racemosus is the predominant fungal in the zhiqu stage of the fermentation of Yongchuan Douchi (Mucor-type), which plays an important role in the fermentation process of Yongchuan Douchi. However, there is a lack of information on the genetic analysis of M. racemosus. In this study, we isolated and identified M. racemosus C (accession no JAPEHQ000000000) from Yongchuan Douchi and analyzed the physiological indicators, then genomic information of the strain to perform a comprehensive analysis of its fermentation capacity and safety. M. racemosus C had neutral protease activity up to 68.051 U/mL at 30 °C and alkaline protease activity up to 57.367 U/mL at 25 °C. In addition, comparing the genomic data with the COGs database (NCBI), it was predicted that M. racemosus C undergoes extensive amino acid metabolism, making C suitable for the production of fermented foods (e.g., Douchi, Syoyu, and sufu). Finally, we performed virulence genes and resistance genes analysis, hemolysis experiment, aflatoxins assay, antibiotic resistance assay to evaluate the safety of M. racemosus C, and the results showed that M. racemosus C was safe, non-toxin-producing and non-hemolytic.
Collapse
Affiliation(s)
- Shicai Xie
- College of Food Science, Southwest University, Chongqing 400715, China; Food Industry Innovation Research Institute of Modern Sichuan Cuisine & Chongqing Flavor, Chongqing 400715, China
| | - Chen Wang
- College of Food Science, Southwest University, Chongqing 400715, China; Food Industry Innovation Research Institute of Modern Sichuan Cuisine & Chongqing Flavor, Chongqing 400715, China
| | - Tao Zeng
- College of Food Science, Southwest University, Chongqing 400715, China; Food Industry Innovation Research Institute of Modern Sichuan Cuisine & Chongqing Flavor, Chongqing 400715, China
| | - Hongwei Wang
- College of Food Science, Southwest University, Chongqing 400715, China; Food Industry Innovation Research Institute of Modern Sichuan Cuisine & Chongqing Flavor, Chongqing 400715, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing 400715, China; Food Industry Innovation Research Institute of Modern Sichuan Cuisine & Chongqing Flavor, Chongqing 400715, China.
| |
Collapse
|
20
|
Hou H, Zhou W, Guo L, Jia S, Zhang X, Wang L. Effects of characteristics of douchi during rapid fermentation and antioxidant activity using different starter cultures. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2459-2472. [PMID: 36588174 DOI: 10.1002/jsfa.12419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 09/14/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND As a traditional Chinese condiment, douchi has attracted attention in Asian and European countries because of its high nutrient content and unique flavors. Douchi is currently produced mostly by natural fermentation. The quality of douchi produced in this way is affected by microbial species, temperature, humidity, and season, so the physical and chemical properties of the product, the content of flavor substances, and its safety vary. In this study, four safe strains with high protease activity, screened previously, namely Bacillus velezensis, Bacillus amyloliquefaciens, Lichtheimia ramosa, and Lichtheimia corymbifera, were used as starter cultures for douchi fermentation. RESULTS After 35 days, the results showed that the pH, titratable acids, free amino-type nitrogen, amino acids, the total number of colonies, and neutral protease activity of all samples had reached an average level. Through gas chromatography-mass spectrometry (GC-MS), the content of key aroma substances aldehydes and esters was higher than in commercial douchi and the free amino acid content of douchi fermented by the four strains was three to five times that of commercial douchi. Douchi fermented by Bacillus amyloliquefaciens had more flavor substances and the highest 2, 2-diphenyl-1-(2, 4, 6-trinitrophenyl) hydrazyl (DPPH) free radical scavenging rates of 92.4%. Four samples yielded total phenolic content and soy isoflavones in the range of 0.98-1.93 g kg-1 and 0.58-0.89 g kg-1 , respectively. CONCLUSION These findings indicate that the use of a high-protease activity starter to produce douchi can improve the quality of douchi to a certain extent. The douchi obtained using Bacillus amyloliquefaciens not only has a good flavor but also has a high level of antioxidant activity. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Hongwei Hou
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
| | - Wanting Zhou
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
| | - Lidan Guo
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
| | - Shuang Jia
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Zhang
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
| | - Liping Wang
- College of Food Science And Engineering, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| |
Collapse
|
21
|
Kruasuwan W, Jenjaroenpun P, Arigul T, Chokesajjawatee N, Leekitcharoenphon P, Foongladda S, Wongsurawat T. Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements. Sci Rep 2023; 13:4540. [PMID: 36941307 PMCID: PMC10027865 DOI: 10.1038/s41598-023-31626-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/15/2023] [Indexed: 03/23/2023] Open
Abstract
The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover, the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas, Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations, as well as antimicrobial resistance genes, and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry.
Collapse
Affiliation(s)
- Worarat Kruasuwan
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Tantip Arigul
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
22
|
Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
Collapse
|
23
|
Coelho-Rocha ND, de Jesus LCL, Barroso FAL, da Silva TF, Ferreira E, Gonçalves JE, Dos Santos Martins F, de Oliveira Carvalho RD, Barh D, Azevedo VADC. Evaluation of Probiotic Properties of Novel Brazilian Lactiplantibacillus plantarum Strains. Probiotics Antimicrob Proteins 2023; 15:160-174. [PMID: 36028786 DOI: 10.1007/s12602-022-09978-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 01/20/2023]
Abstract
Beneficial effects of Lactiplantibacillus plantarum strains have been widely reported. Knowing that the effects of probiotic bacteria are strain-dependent, this study aimed to characterize the probiotic properties and investigate the gastrointestinal protective effects of nine novel L. plantarum strains isolated from Bahia, Brazil. The probiotic functionality was first evaluated in vitro by characterizing bile salt and acidic tolerance, antibacterial activity, and adhesion to Caco-2 cells. Antibiotic resistance profile, mucin degradation, and hemolytic activity assays were also performed to evaluate safety features. In vivo analyses were conducted to investigate the anti-inflammatory effects of the strains on a mouse model of 5-Fluorouracil-induced mucositis. Our results suggest that the used L. plantarum strains have good tolerance to bile salts and low pH and can inhibit commonly gastrointestinal pathogens. Lp2 and Lpl1 strains also exhibited high adhesion rates to Caco-2 cells (13.64 and 9.05%, respectively). Phenotypical resistance to aminoglycosides, vancomycin, and tetracycline was observed for most strains. No strain showed hemolytic or mucolytic activity. Seven strains had a protective effect against histopathological and inflammatory damage induced by 5-FU. Gene expression analysis of inflammatory markers showed that five strains upregulated interleukin 10 (Il10), while four downregulated both interleukin 6 (Il6) and interleukin 1b (Il1b). Additionally, all strains reduced eosinophilic and neutrophilic infiltration; however, they could not prevent weight loss or reduced liquid/ food intake. Altogether, our study suggests these Brazilian L. plantarum strains present good probiotic characteristics and safety levels for future applications and can be therapeutically adjuvant alternatives to prevent/treat intestinal mucositis.
Collapse
Affiliation(s)
- Nina Dias Coelho-Rocha
- Department of Genetics, Ecology, and Evolution, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fernanda Alvarenga Lima Barroso
- Department of Genetics, Ecology, and Evolution, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Tales Fernando da Silva
- Department of Genetics, Ecology, and Evolution, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Enio Ferreira
- Department of General Pathology, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - José Eduardo Gonçalves
- Department of Pharmaceutic Products, Pharmacy Faculty, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Flaviano Dos Santos Martins
- Department of Microbiology, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo Dias de Oliveira Carvalho
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40110-909, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), West Bengal, Nonakuri, Purba Medinipur, 721172, India
| | - Vasco Ariston de Carvalho Azevedo
- Department of Genetics, Ecology, and Evolution, Biological Sciences Institute, Federal University of Minas Gerais, Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| |
Collapse
|
24
|
Riangrungroj P, Visessanguan W, Leartsakulpanich U. Production of Lactobacillus plantarum ghosts by conditional expression of a prophage-encoded holin. FEMS Microbiol Lett 2023; 370:fnad095. [PMID: 37738444 DOI: 10.1093/femsle/fnad095] [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: 05/03/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
Bacterial ghosts (BGs) are nonviable empty bacterial cell envelopes with intact cellular morphology and native surface structure. BGs made from pathogenic bacteria are used for biomedical and pharmaceutical applications. However, incomplete pathogenic cell inactivation during BG preparation raises safety concerns that could limit the intended use. Therefore, safer bacterial cell types are needed for BG production. Here, we produced BGs from the food-grade Gram-positive bacterium Lactobacillus plantarum TBRC 2-4 by conditional expression of a prophage-encoded holin (LpHo). LpHo expression was regulated using the pheromone-inducible pSIP system and LpHo was localized to the cell membrane. Upon LpHo induction, a significant growth retardation and a drastic decrease in cell viability were observed. LpHo-induced cells also showed membrane pores by scanning electron microscopy, membrane depolarization by flow cytometry, and release of nucleic acid contents in the cell culture supernatant, consistent with the role of LpHo as a pore-forming protein and L. plantarum ghost formation. The holin-induced L. plantarum BG platform could be developed as a safer alternative vehicle for the delivery of biomolecules.
Collapse
Affiliation(s)
- Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani 12120, Thailand
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
25
|
Pulido-Mateos EC, Lessard-Lord J, Guyonnet D, Desjardins Y, Roy D. Comprehensive analysis of the metabolic and genomic features of tannin transforming Lactiplantibacillus plantarum strains. Sci Rep 2022; 12:22406. [PMID: 36575241 PMCID: PMC9794748 DOI: 10.1038/s41598-022-26005-4] [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: 09/09/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Extracellular tannase Lactiplantibacillus plantarum-producing strains (TanA+) release bioactive metabolites from dietary tannins. However, there is a paucity of knowledge of TanA+ strains and their hydrolyzing capacities. This study aimed to shed light on the metabolic and genomic features of TanA+ L. plantarum strains and to develop a screening technique. The established spectrophotometric was validated by UPLC-UV-QToF. Eight of 115 screened strains harbored the tanA gene, and six presented TanA activity (PROBI S126, PROBI S204, RKG 1-473, RKG 1-500, RKG 2-219, and RKG 2-690). When cultured with tannic acid (a gallotannin), TanA+ strains released 3.2-11 times more gallic acid than a lacking strain (WCFS1) (p < 0.05). TanA+ strains with gallate decarboxylase (n = 5) transformed this latter metabolite, producing 2.2-4.8 times more pyrogallol than the TanA lacking strain (p < 0.05). However, TanA+ strains could not transform punicalagin (an ellagitannin). Genomic analysis revealed high similarity between TanA+ strains, as only two variable regions of phage and polysaccharide synthesis were distinguished. A phylogenetic analysis of 149 additional genome sequences showed that tanA harboring strains form a cluster and present two bacteriocin coding sequences profile. In conclusion, TanA+ L. plantarum strains are closely related and possess the ability to resist and transform gallotannins. TanA can be screened by the method proposed herein.
Collapse
Affiliation(s)
- Elena C. Pulido-Mateos
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada ,grid.23856.3a0000 0004 1936 8390Laboratoire de Génomique Microbienne, Département des Sciences des Aliments, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | - Jacob Lessard-Lord
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | | | - Yves Desjardins
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | - Denis Roy
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada ,grid.23856.3a0000 0004 1936 8390Laboratoire de Génomique Microbienne, Département des Sciences des Aliments, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| |
Collapse
|
26
|
Comparative Genomics Analysis Provides New Insights into High Ethanol Tolerance of Lactiplantibacillus pentosus LTJ12, a Novel Strain Isolated from Chinese Baijiu. Foods 2022; 12:foods12010035. [PMID: 36613254 PMCID: PMC9818588 DOI: 10.3390/foods12010035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lactic acid bacteria have received a significant amount of attention due to their probiotic characteristics. The species Lactiplantibacillus plantarum and Lactiplantibacillus pentosus are genotypically closely related, and their phenotypes are so similar that they are easily confused and mistaken. In the previous study, an ethanol-resistant strain, LTJ12, isolated from the fermented grains of soy sauce aroma type baijiu in North China, was originally identified as L. plantarum through a 16S rRNA sequence analysis. Here, the genome of strain LTJ12 was further sequenced using PacBio and Illumina sequencing technology to obtain a better understanding of the metabolic pathway underlying its resistance to ethanol stress. The results showed that the genome of strain LTJ12 was composed of one circular chromosome and three circular plasmids. The genome size is 3,512,307 bp with a GC content of 46.37%, and the number of predicted coding genes is 3248. Moreover, by comparing the coding genes with the GO (Gene Ontology), COG (Cluster of Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, the functional annotation of the genome and an assessment of the metabolic pathways were performed, with the results showing that strain LTJ12 has multiple genes that may be related to alcohol metabolism and probiotic-related genes. Antibiotic resistance gene analysis showed that there were few potential safety hazards. Further, after conducting the comparative genomics analysis, it was found that strain LTJ12 is L. pentosus but not L. plantarum, but it has more functional genes than other L. pentosus strains that are mainly related to carbohydrate transport and metabolism, transcription, replication, recombination and repair, signal transduction mechanisms, defense mechanisms and cell wall/membrane/envelope biogenesis. These unique functional genes, such as gene 2754 (encodes alcohol dehydrogenase), gene 3093 (encodes gamma-D-glutamyl-meso-diaminopimelate peptidase) and some others may enhance the ethanol tolerance and alcohol metabolism of the strain. Taken together, L. pentosus LTJ12 might be a potentially safe probiotic with a high ethanol tolerance and alcohol metabolism. The findings of this study will also shed light on the accurate identification and rational application of the Lactiplantibacillus species.
Collapse
|
27
|
Kandasamy S, Yoo J, Yun J, Lee KH, Kang HB, Kim JE, Oh MH, Ham JS. Probiogenomic In-Silico Analysis and Safety Assessment of Lactiplantibacillus plantarum DJF10 Strain Isolated from Korean Raw Milk. Int J Mol Sci 2022; 23:ijms232214494. [PMID: 36430971 PMCID: PMC9699202 DOI: 10.3390/ijms232214494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The whole genome sequence of Lactiplantibacillus plantarum DJF10, isolated from Korean raw milk, is reported, along with its genomic analysis of probiotics and safety features. The genome consists of 29 contigs with a total length of 3,385,113 bp and a GC content of 44.3%. The average nucleotide identity and whole genome phylogenetic analysis showed the strain belongs to Lactiplantibacillus plantarum with 99% identity. Genome annotation using Prokka predicted a total of 3235 genes, including 3168 protein-coding sequences (CDS), 59 tRNAs, 7 rRNAs and 1 tmRNA. The functional annotation results by EggNOG and KEGG showed a high number of genes associated with genetic information and processing, transport and metabolism, suggesting the strain's ability to adapt to several environments. Various genes conferring probiotic characteristics, including genes related to stress adaptation to the gastrointestinal tract, biosynthesis of vitamins, cell adhesion and production of bacteriocins, were identified. The CAZyme analysis detected 98 genes distributed under five CAZymes classes. In addition, several genes encoding carbohydrate transport and metabolism were identified. The genome also revealed the presence of insertion sequences, genomic islands, phage regions, CRISPR-cas regions, and the absence of virulence and toxin genes. However, the presence of hemolysin and antibiotic-resistance-related genes detected in the KEGG search needs further experimental validation to confirm the safety of the strain. The presence of two bacteriocin clusters, sactipeptide and plantaricin J, as detected by the BAGEL 4 webserver, confer the higher antimicrobial potential of DJF10. Altogether, the analyses in this study performed highlight this strain's functional characteristics. However, further in vitro and in vivo studies are required on the safety assurance and potential application of L. plantarum DJF10 as a probiotic agent.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Jun-Sang Ham
- Correspondence: ; Tel.: +82-63-238-7366; Fax: +82-63-238-7397
| |
Collapse
|
28
|
Tenea GN, Ascanta P. Fortification of cocoa semi-skimmed milk formulations with native lactic acid bacteria: Cell viability, physicochemical and functional properties for developing novel foods. Front Nutr 2022; 9:1008871. [PMID: 36313091 PMCID: PMC9608143 DOI: 10.3389/fnut.2022.1008871] [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: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
This study aimed to evaluate several cocoa semi-skimmed milk formulations (CSMFs) as potential carriers of native lactic acid bacteria (LAB) strains to obtain novel probiotic beverages (PBs) with improved technological and functional characteristics, and satisfactorily organoleptic acceptance. The viability of two native LAB (Lactiplantibacillus plantarum UTNGt2 and Lactiplantibacillus pentosus UTNGt5) was assessed in comparison with two references (Lactococcus lactis subsp. lactis ATCC11474 and Limosilactobacillus reuteri DSM17938) strains in supplemented CSMFs throughout storage with refrigeration. The optimum conditions to produce novel beverages supplemented with native LAB were pH 6.6, 42°C, and 1 h of fermentation. Moreover, the effect of LAB strains fortification on pH, titratable acidity, total solids (°Brix), total polyphenolic compounds (TPC), antioxidant capacity (AOX), and ascorbic acid content (AAC), total proteins and fat, at initial and final storage was evaluated. The addition of two native LAB strains did alter the physicochemical quality of CSMFs to a lesser extent, where the bioactive molecules improved significantly (p < 0.05) with the increase of cocoa concentration and depending on the supplied strain. Although a statistically significant (p < 0.05) decrease in cell counts was recorded during storage, the LAB cells were found to be viable up to 21 days of storage at 4°C (>6 logCFU/ml), which is sufficient in number to prove their stability in vitro. Overall organoleptic results suggested that LAB supplementation had a significant impact on sensory attributes with satisfactory acceptability (>78%) of PBs containing the native strains and 1-2% cocoa, while CSMFs counterparts were less appreciated (40%) as perceived off-flavor. It appears that supplying bacteria to CSMF preserves flavor in the final product. Furthermore, the final beverages were free of harmful bacteria; thus, they comply with consumer safety regulations. This study concludes that CSMF can be used as a carrier of native LAB strains, maintaining cell viability, unaltered physicochemical properties, and improved functional and sensory characteristics, for which final beverages can be regarded as functional food. From the application standpoint, these formulations are an alternative to delivering native LAB strains and could help the cocoa and dairy industry to develop more attractive products for the growing regional market.
Collapse
|
29
|
Oh YJ, Kim SA, Yang SH, Kim DH, Cheng YY, Kang JI, Lee SY, Han NS. Integrated genome-based assessment of safety and probiotic characteristics of Lactiplantibacillus plantarum PMO 08 isolated from kimchi. PLoS One 2022; 17:e0273986. [PMID: 36190947 PMCID: PMC9529155 DOI: 10.1371/journal.pone.0273986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Lactiplantibacillus plantarum PMO 08 has been used as a probiotic starter culture for plant-based fermented beverages, with various health-promoting effects such as cholesterol-lowering and anti-inflammatory activities. This study aimed to analyze the genome sequence of Lp. plantarum PMO 08 and identify its safety and probiotic characteristics at the genomic level. For this, complete genome sequencing was conducted to investigate the genes associated with risk and probiotic characteristics by using Pacbio combined with Illumina HiSeq. This bacterial strain has one circular chromosome of 3,247,789 bp with 44.5% G + C content and two plasmids of 50,296 bp with 39.0% G + C content and 19,592 bp with 40.5% G + C content. Orthologous average nucleotide identity analysis showed that PMO 08 belongs to the Lp. plantarum group with 99.14% similarity to Lp. plantarum WCFS1. No deleterious genes were determined in the virulence factor analysis, and no hemolysin activity or secondary bile salt synthesis were detected in vitro test. In the case of antibiotic resistance analysis, PMO 08 was resistant to ampicillin in vitro test, but these genes were not transferable. In addition, the strain showed same carbohydrate utilization with Lp. plantarum WCFS1, except for mannopyranoside, which only our strain can metabolize. The strain also harbors a gene for inositol monophosphatase family protein related with phytate hydrolysis and have several genes for metabolizing various carbohydrate which were rich in plant environment. Furthermore, in probiotic characteristics several genes involved in phenotypes such as acid/bile tolerance, adhesion ability, and oxidative stress response were detected in genome analysis. This study demonstrates that Lp. plantarum PMO 08 harbors several probiotic-related genes (with no deleterious genes) and is a suitable probiotic starter for plant-based fermentation.
Collapse
Affiliation(s)
| | - Seul-Ah Kim
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Soo Hwi Yang
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Da Hye Kim
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Ya-Yun Cheng
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | | | | | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
- * E-mail:
| |
Collapse
|
30
|
Raethong N, Santivarangkna C, Visessanguan W, Santiyanont P, Mhuantong W, Chokesajjawatee N. Whole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3, a gamma-aminobutyric acid (GABA)-producing strain isolated from Thai pickled weed. Front Microbiol 2022; 13:969548. [PMID: 36212812 PMCID: PMC9539741 DOI: 10.3389/fmicb.2022.969548] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Lactiplantibacillus pentosus 9D3, a prominent gamma-aminobutyric acid (GABA)-producing bacteria isolated from Thai pickled weed was characterized for its safety and probiotic properties via whole-genome analysis and in vitro testing. The whole-genome sequence of L. pentosus 9D3 was determined using a hybrid-sequencing approach, combining PacBio and Illumina technologies. A 3.81-Mbp genome of L. pentosus 9D3 consisting of one 3.65-Mbp chromosome and six plasmids (1.9–71.9 Kbp) was identified with an estimated GC content of 46.09% and 3,456 predicted genes. The strain was confirmed to be Lactiplantibacillus pentosus according to the high average nucleotide identity value of >95% and digital DNA–DNA hybridization scores of >70% to the L. pentosus type strain. Comparative genome analysis with other L. pentosus strains showed that the GABA-producing capability was specific to the strain 9D3. Genes related to GABA biosynthesis and transport were identified on a plasmid, pLPE-70K, indicating the acquired nature of this property. The safety of L. pentosus 9D3 was demonstrated through the lack of genes related to the production of toxins, biogenic amines, and antimicrobial drugs. Although the strain exhibited resistance to ampicillin and chloramphenicol, none of the antimicrobial resistance (AMR) genes were associated with mobile elements, i.e., plasmids and prophages. Therefore, the strain is considered to have low risk of transferring the AMR genes to other, potentially pathogenic bacteria. In addition, L. pentosus 9D3 showed good survivability in the gastrointestinal tract environment and was able to adhere to the intestinal cell in vitro. Therefore, L. pentosus 9D3 is concluded to be safe, with the potential to be used as a probiotic, exerting its health benefit through GABA production in the food system. The GABA-producing capability of the strain in vivo is the subject of further investigation.
Collapse
Affiliation(s)
- Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
- *Correspondence: Nachon Raethong, ; Nipa Chokesajjawatee,
| | | | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Pannita Santiyanont
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
- *Correspondence: Nachon Raethong, ; Nipa Chokesajjawatee,
| |
Collapse
|
31
|
Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
Collapse
Affiliation(s)
- Frédéric Borges
- Université de Lorraine, LIBio, Nancy, France
- *Correspondence: Frédéric Borges,
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | | |
Collapse
|
32
|
Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence. Microbiol Spectr 2022; 10:e0236021. [PMID: 35579444 PMCID: PMC9241834 DOI: 10.1128/spectrum.02360-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the “Lactobacterin” probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.
Collapse
|
33
|
The Impacts of Lactiplantibacillus plantarum on the Functional Properties of Fermented Foods: A Review of Current Knowledge. Microorganisms 2022; 10:microorganisms10040826. [PMID: 35456875 PMCID: PMC9026118 DOI: 10.3390/microorganisms10040826] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/17/2022] Open
Abstract
One of the most varied species of lactic acid bacteria is Lactiplantibacillus plantarum (Lb. plantarum), formerly known as Lactobacillus plantarum. It is one of the most common species of bacteria found in foods, probiotics, dairy products, and beverages. Studies related to genomic mapping and gene locations of Lb. plantarum have shown the novel findings of its new strains along with their non-pathogenic or non-antibiotic resistance genes. Safe strains obtained with new technologies are a pioneer in the development of new probiotics and starter cultures for the food industry. However, the safety of Lb. plantarum strains and their bacteriocins should also be confirmed with in vivo studies before being employed as food additives. Many of the Lb. plantarum strains and their bacteriocins are generally safe in terms of antibiotic resistance genes. Thus, they provide a great opportunity for improving the nutritional composition, shelf life, antioxidant activity, flavour properties and antimicrobial activities in the food industry. Moreover, since some Lb. plantarum strains have the ability to reduce undesirable compounds such as aflatoxins, they have potential use in maintaining food safety and preventing food spoilage. This review emphasizes the impacts of Lb. plantarum strains on fermented foods, along with novel approaches to their genomic mapping and safety aspects.
Collapse
|
34
|
A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. Int J Mol Sci 2022; 23:ijms23052487. [PMID: 35269627 PMCID: PMC8910486 DOI: 10.3390/ijms23052487] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.
Collapse
|
35
|
Oliveira FS, da Silva Rodrigues R, de Carvalho AF, Nero LA. Genomic Analyses of Pediococcus pentosaceus ST65ACC, a Bacteriocinogenic Strain Isolated from Artisanal Raw-Milk Cheese. Probiotics Antimicrob Proteins 2022; 15:630-645. [PMID: 34984631 DOI: 10.1007/s12602-021-09894-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Pediococcus pentosaceus ST65ACC was obtained from a Brazilian artisanal cheese (BAC) and characterized as bacteriocinogenic. This strain presented beneficial properties in previous studies, indicating its potential as a probiotic candidate. In this study, we aimed to carry out a genetic characterization based on whole-genome sequencing (WGS), including taxonomy, biotechnological properties, bacteriocin clusters and safety-related genes. WGS was performed using the Illumina MiSeq platform and the genome was annotated with the Prokaryotic Genome Annotation (Prokka). P. pentosaceus ST65ACC taxonomy was investigated and bacteriocin genes clusters were identified by BAGEL4, metabolic pathways were analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG) and safety-related genes were checked. P. pentosaceus ST65ACC had a total draft genome size of 1,933,194 bp with a GC content of 37.00%, and encoded 1950 protein coding sequences (CDSs), 6 rRNA, 55 tRNA, 1 tmRNA and no plasmids were detected. The analysis revealed absence of a CRISPR/Cas system, bacteriocin gene clusters for pediocin PA-1/AcH and penocin-A were identified. Genes related to beneficial properties, such as stress adaptation genes and adhesion genes, were identified. Furthermore, genes related to biogenic amines and virulence-related genes were not detected. Genes related to antibiotic resistance were identified, but not in prophage regions. Based on the obtained results, the beneficial potential of P. pentosaceus ST65ACC was confirmed, allowing its characterization as a potential probiotic candidate.
Collapse
Affiliation(s)
- Francielly Soares Oliveira
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.,Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Rafaela da Silva Rodrigues
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.,Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Antônio Fernandes de Carvalho
- Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Luís Augusto Nero
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.
| |
Collapse
|
36
|
Stergiou OS, Tegopoulos K, Kiousi DE, Tsifintaris M, Papageorgiou AC, Tassou CC, Chorianopoulos N, Kolovos P, Galanis A. Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages. Front Microbiol 2021; 12:746659. [PMID: 34764945 PMCID: PMC8576124 DOI: 10.3389/fmicb.2021.746659] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/08/2021] [Indexed: 01/11/2023] Open
Abstract
Lactobacillus is a diverse genus that includes species of industrial and biomedical interest. Lactiplantibacillus pentosus, formerly known as Lactobacillus pentosus, is a recently reclassified species, that contains strains isolated from diverse environmental niches, ranging from fermented products to mammalian gut microbiota. Importantly, several L. pentosus strains present health-promoting properties, such as immunomodulatory and antiproliferative activities, and are regarded as potential probiotic strains. In this study, we present the draft genome sequence of the potential probiotic strain L. pentosus L33, originally isolated from fermented sausages. Comprehensive bioinformatic analysis and whole-genome annotation were performed to highlight the genetic loci involved in host-microbe interactions and the probiotic phenotype. Consequently, we found that this strain codes for bile salt hydrolases, adhesins and moonlighting proteins, and for Class IIb bacteriocin peptides lacking the GxxxG and GxxxG-like motifs, crucial for their inhibitory activity. Its adhesion ability was also validated in vitro, on human cancer cells. Furthermore, L. pentosus L33 contains an exopolysaccharide (EPS) biosynthesis cluster, and it does not carry transferable antibiotic resistance genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and CAZymes analyses showed that L. pentosus L33 possesses biosynthetic pathways for seven amino acids, while it can degrade a wide array of carbohydrates. In parallel, Clusters of Orthologous Groups (COGs) and KEGG profiles of L. pentosus L33 are similar to those of 26 L. pentosus strains, as well as of two well documented L. plantarum probiotic strains. Conclusively, L. pentosus L33 exhibits good probiotic potential, although further studies are needed to elucidate the extent of its biological properties.
Collapse
Affiliation(s)
- Odysseas Sotirios Stergiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Margaritis Tsifintaris
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aristotelis C Papageorgiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chrysoula C Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, Athens, Greece
| | - Nikos Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, Athens, Greece
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| |
Collapse
|
37
|
Kwon YJ, Chun BH, Jung HS, Chu J, Joung H, Park SY, Kim BK, Jeon CO. Safety Assessment of Lactiplantibacillus (formerly Lactobacillus) plantarum Q180. J Microbiol Biotechnol 2021; 31:1420-1429. [PMID: 34373437 PMCID: PMC9705903 DOI: 10.4014/jmb.2106.06066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
The safety of the probiotic strain Q180, which exerts postprandial lipid-lowering effects, was bioinformatically and phenotypically evaluated. The genome of strain Q180 was completely sequenced, and single circular chromosome of 3,197,263 bp without any plasmid was generated. Phylogenetic and related analyses using16S rRNA gene and whole-genome sequences revealed that strain Q180 is a member of Lactiplantibacillus (Lp., formerly Lactobacillus) plantarum. Antimicrobial resistance (AMR) genes were bioinformatically analyzed using all Lp. plantarum genomes available in GenBank, which showed that AMR genes are present differently depending on Lp. plantarum strains. Bioinformatic analysis demonstrated that some mobile genetic elements such as prophages and insertion sequences were identified in the genome of strain Q180, but because they did not contain harmful genes such as AMR genes and virulence factor (VF)- and toxin-related genes, it was suggested that there is no transferability of harmful genes. The minimum inhibition concentrations of seven tested antibiotics suggested by the European Food Safety Authority guidelines were slightly lower than or equal to the microbiological cut-off values for Lp. plantarum. Strain Q180 did not show hemolytic and gelatinase activities and biogenic amine-producing ability. Taken together, this study demonstrated the safety of strain Q180 in terms of absence of AMR genes and VF- and toxin-related genes as a probiotic strain.
Collapse
Affiliation(s)
- Yoo Jin Kwon
- Probiotics Research Laboratory, Chong Kun Dang Bio Research Institute (CKDBIO), Gyeonggi 15064, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaeryang Chu
- Probiotics Research Laboratory, Chong Kun Dang Bio Research Institute (CKDBIO), Gyeonggi 15064, Republic of Korea
| | - Hyunchae Joung
- Probiotics Research Laboratory, Chong Kun Dang Bio Research Institute (CKDBIO), Gyeonggi 15064, Republic of Korea
| | - Sung Yurb Park
- Probiotics Research Laboratory, Chong Kun Dang Bio Research Institute (CKDBIO), Gyeonggi 15064, Republic of Korea
| | - Byoung Kook Kim
- Probiotics Research Laboratory, Chong Kun Dang Bio Research Institute (CKDBIO), Gyeonggi 15064, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea,Corresponding author Phone: +82-2-820-5864 E-mail:
| |
Collapse
|
38
|
Zhang L, Ma H, Kulyar MFEA, Pan H, Li K, Li A, Mo Q, Wang Y, Dong H, Bao Y, Li J. Complete genome analysis of Lactobacillus fermentum YLF016 and its probiotic characteristics. Microb Pathog 2021; 162:105212. [PMID: 34597776 DOI: 10.1016/j.micpath.2021.105212] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 02/07/2023]
Abstract
Lactobacillus fermentum (L. fermentum) YLF016 is a well-characterized probiotic with several favorable characteristics. This study aimed to analyze the probiotic characteristics of L. fermentum and uncover the genes implicated in its potential probiotic ability on the base of its genomics features. The complete genome of L. fermentum YLF016 was found to have a circular chromosome of 2,094,354 bp, and 51.46% G + C content without any plasmid. Its chromosome contained 2,130 predicted protein-encoding genes, 58 tRNA, and 15 rRNA-encoding genes. Also, it was found to have many other probiotic properties, such as a high survival rate in the gastrointestinal tract with strong adherence to intestinal cells, antibacterial activity against pathogens, and antioxidant activity. Moreover, the genome sequence analysis demonstrated specific genes coding for carbon metabolism pathway, genetic adaption, stress resistance, and adhesive ability. Further analysis revealed its non-hemolytic activity and its non-functional ability of virulence factors. In conclusion, L. fermentum YLF016 possesses many valuable probiotic properties that refer to its potential probiotic ability.
Collapse
Affiliation(s)
- Lihong Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hongcai Ma
- Tibet Livestock Research Institute, Tibet Academy of Agriculture And Animal Science, Lhasa 850009, Tibet, People's Republic of China
| | | | - Huachun Pan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kewei Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Quan Mo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hailong Dong
- Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China
| | - Yuhua Bao
- Tibet Biological Pharmaceutical Factory, Lhasa 850009, People's Republic of China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China; Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China.
| |
Collapse
|
39
|
Ahmed S, Ashraf F, Tariq M, Zaidi A. Aggrandizement of fermented cucumber through the action of autochthonous probiotic cum starter strains of Lactiplantibacillus plantarum and Pediococcus pentosaceus. ANN MICROBIOL 2021; 71:33. [PMID: 34483789 PMCID: PMC8406656 DOI: 10.1186/s13213-021-01645-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose Cucumber fermentation is traditionally done using lactic acid bacteria. The involvement of probiotic cultures in food fermentation guarantees enhanced organoleptic properties and protects food from spoilage. Methods Autochthonous lactic acid bacteria were isolated from spontaneously fermented cucumber and identified to species level. Only strains adjudged as safe for human consumption were examined for their technological and functional characteristics. Strain efficiency was based on maintaining high numbers of viable cells during simulated GIT conditions and fermentation, significant antioxidant activity, EPS production, nitrite degradation, and antimicrobial ability against Gram-positive and Gram-negative foodborne pathogens. Result Two strains, Lactiplantibacillus plantarum NPL 1258 and Pediococcus pentosaceus NPL 1264, showing a suite of promising functional and technological attributes, were selected as a mixed-species starter for carrying out a controlled lactic acid fermentations of a native cucumber variety. This consortium showed a faster lactic acid-based acidification with more viable cells, at 4% NaCl and 0.2% inulin (w/v) relative to its constituent strains when tested individually. Sensory evaluation rated the lactofermented cucumber acceptable based on texture, taste, aroma, and aftertaste. Conclusion The results suggest that the autochthonous LAB starter cultures can shorten the fermentation cycle and reduce pathogenic organism’ population, thus improving the shelf life and quality of fermented cucumber. The development of these new industrial starters would increase the competitiveness of production and open the country’s frontiers in the fermented vegetable market.
Collapse
Affiliation(s)
- Sadia Ahmed
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000 Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650 Pakistan
| | - Fatima Ashraf
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000 Pakistan
| | - Muhammad Tariq
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000 Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650 Pakistan
| | - Arsalan Zaidi
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000 Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650 Pakistan
| |
Collapse
|
40
|
Safety Evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: a Health-Promoting Bacteria. Probiotics Antimicrob Proteins 2021; 14:816-829. [PMID: 34403080 DOI: 10.1007/s12602-021-09826-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Lactobacillus delbrueckii subsp. lactis CIDCA is a new potential probiotic strain whose molecular basis attributed to the host's benefit has been reported. This study investigated the safety aspects of Lactobacillus delbrueckii subsp. lactis CIDCA 133 based on whole-genome sequence and phenotypic analysis to avoid future questions about the harmful effects of this strain consumption. Genomic analysis showed that L. delbrueckii subsp. lactis CIDCA 133 harbors virulence, harmful metabolites, and antimicrobial resistance-associated genes. However, none of these genetic elements is flanked or located within prophage regions and plasmid sequence. At a phenotypic level, it was observed L. delbrueckii subsp. lactis CIDCA 133 antimicrobial resistance to aminoglycosides streptomycin and gentamicin antibiotics, but no hemolytic and mucin degradation activity was exhibited by strain. Furthermore, no adverse effects were observed regarding mice clinical and histopathological analysis after the strain consumption (5 × 107 CFU/mL). Overall, these findings reveal the safety of Lactobacillus delbrueckii subsp. lactis CIDCA 133 for consumption and future probiotic applications.
Collapse
|
41
|
Oliveira de Almeida M, Carvalho R, Figueira Aburjaile F, Malcher Miranda F, Canário Cerqueira J, Brenig B, Ghosh P, Ramos R, Kato RB, de Castro Soares S, Silva A, Azevedo V, Canário Viana MV. Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil. PeerJ 2021; 9:e11079. [PMID: 33854845 PMCID: PMC7955673 DOI: 10.7717/peerj.11079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/17/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Lactobacillus crispatus is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of L. crispatus involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four L. crispatus genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome. METHODS The four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain (L. crispatus CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions. RESULTS Genes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes csn2 and cas9. No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use.
Collapse
Affiliation(s)
- Marcelle Oliveira de Almeida
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Carvalho
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flavia Figueira Aburjaile
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fabio Malcher Miranda
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Janaína Canário Cerqueira
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Rommel Ramos
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Rodrigo Bentes Kato
- Post-graduation Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology, and Parasitology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcus Vinicius Canário Viana
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
42
|
Surachat K, Kantachote D, Deachamag P, Wonglapsuwan M. Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang. Microorganisms 2020; 9:microorganisms9010050. [PMID: 33375492 PMCID: PMC7823806 DOI: 10.3390/microorganisms9010050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022] Open
Abstract
Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.
Collapse
Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
- Correspondence:
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
| |
Collapse
|
43
|
Pornputtapong N, Acheampong DA, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Jun SR, Yongkiettrakul S, Chokesajjawatee N, Nookaew I. KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. Front Bioeng Biotechnol 2020; 8:556413. [PMID: 33072720 PMCID: PMC7538862 DOI: 10.3389/fbioe.2020.556413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
Genomic DNA is the best “unique identifier” for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification. Although this approach is not novel, selecting the appropriate k-mer length to obtain the optimal resolution is rather arbitrary. However, it is a very important parameter for achieving the appropriate resolution for genome/sequence distances to infer biologically meaningful phylogenetic relationships. Thus, there is a need for a systematic approach to identify the appropriate k-mer from whole-genome sequences. We present K-mer–length Iterative Selection for UNbiased Ecophylogenomics (KITSUNE), a tool for assessing the empirically optimal k-mer length of any given set of genomes of interest for phylogenomic analysis via a three-step approach based on (1) cumulative relative entropy (CRE), (2) average number of common features (ACF), and (3) observed common features (OCF). Using KITSUNE, we demonstrated the feasibility and reliability of these measurements to obtain empirically optimal k-mer lengths of 11, 17, and ∼34 from large genome datasets of viruses, bacteria, and fungi, respectively. Moreover, we demonstrated a feature of KITSUNE for accurate species identification for the two de novo assembled bacterial genomes derived from error-prone long-reads sequences, and for a published yeast genome. In addition, KITSUNE was used to identify the shortest species-specific k-mer accurately identifying viruses. KITSUNE is freely available at https://github.com/natapol/kitsune.
Collapse
Affiliation(s)
- Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, and Research Unit of DNA Barcoding of Thai Medicinal Plants, Chulalongkorn University, Bangkok, Thailand
| | - Daniel A Acheampong
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Preecha Patumcharoenpol
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Suganya Yongkiettrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|