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Hu G, Naveed M, Shabbir MA, Sarwar A, Yousaf J, Zhennai Y, Aziz T, Alharbi M, Alshammari A. Revolutionizing the probiotic functionality, biochemical activity, antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H via in-vitro and in-silico approaches. Z NATURFORSCH C 2024; 0:znc-2024-0074. [PMID: 39026396 DOI: 10.1515/znc-2024-0074] [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: 04/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
This study presents a comprehensive genomic exploration, biochemical characterization, and the identification of antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H strain. The functional characterization, genetic makeup, biological activities, and other considerable parameters have been investigated in this study with a prime focus on antibiotic resistance and specialty gene profiles. The results of this study revealed the unique susceptibility patterns for antibiotic resistance and specialty genes. BCB1H had good in vitro probiotic properties, which survived well in simulated artificial gastrointestinal fluid, and exhibited acid and bile salt resistance. BCB1H didn't produce hemolysis and had certain antibiotic sensitivity, making it a relatively safe LAB strain. Simultaneously, it had good self-coagulation characteristics and antioxidant activity. The EPS produced by BCB1H also had certain antioxidant activity and hypoglycemic function. Moreover, the genome with a 42.4 % GC content and a size of roughly 1.92 million base pairs was analyzed in the genomic investigations. The genome annotation identified 192 subsystems and 1,895 genes, offering light on the metabolic pathways and functional categories found in BCB1H. The identification of specialty genes linked to the metabolism of carbohydrates, stress response, pathogenicity, and amino acids highlighted the strain's versatility and possible uses. This study establishes the groundwork for future investigations by highlighting the significance of using multiple strains to investigate genetic diversity and experimental validation of predicted genes. The results provide a roadmap for utilizing P. acidilactici BCB1H's genetic traits for industrial and medical applications, opening the door to real-world uses in industries including food technology and medicine.
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Affiliation(s)
- Gege Hu
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore 54590, Punjab, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Biological Sciences, Lahore University of Biological & Applied Sciences, Lahore 54800, Punjab, Pakistan
| | - Abid Sarwar
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Junaid Yousaf
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Yang Zhennai
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Tariq Aziz
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
- Laboratory of Animal Health Food Hygiene and Quality, 37796 University of Ioannina , Arta 47132, Greece
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, King Saud University, Riyadh, Saudi Arabia
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Wonglapsuwan M, Pahumunto N, Teanpaisan R, Surachat K. Unlocking the genetic potential of Lacticaseibacillus rhamnosus strains: Medical applications of a promising probiotic for human and animal health. Heliyon 2024; 10:e29499. [PMID: 38655288 PMCID: PMC11035056 DOI: 10.1016/j.heliyon.2024.e29499] [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] [Received: 08/26/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Lacticaseibacillus rhamnosus is a group of probiotic strains that have gained popularity for their potential health benefits such as promoting digestive health, boosting the immune system, improving lactose digestion, preventing and treating antibiotic-associated diarrhea, reducing the severity and duration of certain infections, and preventing the formation of dental plaque. In particular, L. rhamnosus strains SD4 and SD11 have promising human and animal health applications due to their ability to inhibit the growth of harmful pathogens. This study presents an in silico genomic analysis of L. rhamnosus strains SD4 and SD11. We analyzed draft genomes and conducted comparative genome analyses against several other probiotic strains, aiming to gain insights into the genomes of the two strains and to compare them to related strains isolated from other sources. We also aimed to clarify the functional mechanisms and adaptation of these strains to specific environments. Comprehensive insights into the genomes of L. rhamnosus SD4 and SD11 could enhance our understanding of their capacity to colonize, adapt, and exhibit probiotic properties after administration. This study holds significance in advancing our understanding of the potential health benefits associated with these strains and in elucidating the underlying mechanisms responsible for their effectiveness in humans and animals.
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Affiliation(s)
- Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Nuntiya Pahumunto
- Research Center of Excellence for Oral Health, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Department of Oral Diagnostic Sciences, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Rawee Teanpaisan
- Medical Science Research and Innovation Institute, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
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Zhao K, Qiu L, Tao X, Zhang Z, Wei H. Genome Analysis for Cholesterol-Lowing Action and Bacteriocin Production of Lactiplantibacillus plantarum WLPL21 and ZDY04 from Traditional Chinese Fermented Foods. Microorganisms 2024; 12:181. [PMID: 38258009 PMCID: PMC10820322 DOI: 10.3390/microorganisms12010181] [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: 12/18/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics.
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Affiliation(s)
- Kui Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Liang Qiu
- Centre for Translational Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, China;
| | - Xueying Tao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Zhihong Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Hua Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
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Fusco V, Fanelli F, Chieffi D. Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages. Foods 2023; 12:3782. [PMID: 37893675 PMCID: PMC10606304 DOI: 10.3390/foods12203782] [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: 09/11/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.
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Affiliation(s)
- Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy; (F.F.); (D.C.)
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Kim JA, Jang HJ, Kim DH, Son YK, Kim Y. Complete genome sequence of Pediococcus acidilactici CACC 537 isolated from canine. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:1105-1109. [PMID: 37969339 PMCID: PMC10640928 DOI: 10.5187/jast.2022.e102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/03/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2023]
Abstract
Pedi coccus acidilactici CACC 537 was isolated from canine feces and reported to have probiotic properties. We aimed to characterize the potential probiotic properties of this strain by functional genomic analysis. Complete genome sequencing of P. acidilactici CACC 537 was performed using a PacBio RSII and Illumina platform, and contained one circular chromosome (2.0 Mb) with a 42% G + C content. The sequences were annotation revealed 1,897 protein-coding sequences, 15 rRNAs, and 56 tRNAs. It was determined that P. acidilactici CACC 537 genome carries genes known to be involved in the immune system, defense mechanisms, restriction-modification (R-M), and the CRISPR system. CACC 537 was shown to be beneficial in preventing pathogen infection during the fermentation process, help host immunity, and maintain intestinal health. These results provide for a comprehensive understanding of P. acidilactici and the development of industrial probiotic feed additives that can help improve host immunity and intestinal health.
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Affiliation(s)
- Jung-Ae Kim
- Department of Research and Development,
Center for Industrialization of Agricultural and Livestock
Microorganisms, Jeongeup 56212, Korea
- Department of Bioactive Material Science,
Jeonbuk National University, Jeonju 54896, Korea
| | - Hyun-Jun Jang
- Department of Research and Development,
Center for Industrialization of Agricultural and Livestock
Microorganisms, Jeongeup 56212, Korea
| | - Dae-Hyuk Kim
- Department of Research and Development,
Center for Industrialization of Agricultural and Livestock
Microorganisms, Jeongeup 56212, Korea
- Department of Molecular Biology,
Department of Bioactive Material Science, Institute for Molecular Biology
and Genetics, Jeonbuk National University, Jeonju 54896,
Korea
| | - Youn Kyoung Son
- Biologicla and Genetic Reources Assessment
Division, National Institute of Biological Resources, Incheon
22689, Korea
| | - Yangseon Kim
- Department of Research and Development,
Center for Industrialization of Agricultural and Livestock
Microorganisms, Jeongeup 56212, Korea
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Chukamnerd A, Jeenkeawpiam K, Chusri S, Pomwised R, Singkhamanan K, Surachat K. BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes. Microorganisms 2023; 11:1769. [PMID: 37512941 PMCID: PMC10385524 DOI: 10.3390/microorganisms11071769] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Whole-genome sequencing (WGS) of bacterial pathogens is widely conducted in microbiological, medical, and clinical research to explore genetic insights that could impact clinical treatment and molecular epidemiology. However, analyzing WGS data of bacteria can pose challenges for microbiologists, clinicians, and researchers, as it requires the application of several bioinformatics pipelines to extract genetic information from raw data. In this paper, we present BacSeq, an automated bioinformatic pipeline for the analysis of next-generation sequencing data of bacterial genomes. BacSeq enables the assembly, annotation, and identification of crucial genes responsible for multidrug resistance, virulence factors, and plasmids. Additionally, the pipeline integrates comparative analysis among isolates, offering phylogenetic tree analysis and identification of single-nucleotide polymorphisms (SNPs). To facilitate easy analysis in a single step and support the processing of multiple isolates, BacSeq provides a graphical user interface (GUI) based on the JAVA platform. It is designed to cater to users without extensive bioinformatics skills.
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Affiliation(s)
- Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kongpop Jeenkeawpiam
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, 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
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
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Phuengjayaem S, Pakdeeto A, Kingkaew E, Tunvongvinis T, Somphong A, Tanasupawat S. Genome sequences and functional analysis of Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 from fermented fish cake (Som-fak) with gamma-aminobutyric acid (GABA) production. Funct Integr Genomics 2023; 23:158. [PMID: 37171680 DOI: 10.1007/s10142-023-01085-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Gamma-aminobutyric acid (GABA) is a crucial inhibitory neurotransmitter in the sympathetic nervous system that exerts regulatory effects on the blood, immune, and nervous systems. GABA production in som-fak, a traditional fermented fish of Thailand, has been attributed to the activity of lactic acid bacteria (LAB). The present study aims to characterize the LAB isolates and compare the genomes and GABA synthesis genes of selected isolates capable of GABA production. Thirteen isolates demonstrating GABA synthesis capability were identified based on their phenotypic and genotypic characteristics. Seven isolates (group I: LSF3-3, LSF8-3, LSF9-1, LSF9-3, LSF9-6, LSF9-7, and LSF10-14) were identified as Levilactobacillus brevis with 99.78-100% similarity. LSF2-1, LSF3-2, LSF5-4, and LSF6-5 (group II) were identified as Lactiplantibacillus pentosus with 99.86-100% similarity. Strain LSF1-1 (group III) was identified as Pediococcus acidilactici (99.47%), and LSF10-4 (group IV) was identified as Pediococcus pentosaceus with 99.93% similarity. The GABA production of isolates ranged from 0.087 to 16.935 g/L. The maximum production of 16.935 g/L from 3% monosodium glutamate was obtained from strain LSF9-1. Gene and genome analysis revealed that L. brevis LSF9-1 has multiple gad genes in the genome, such as gadB1, gadB2, gadC1, and gadC2, making it the potential strain for GABA production. Additionally, the genome analysis of P. acidilactici LSF1-1 consists of gadA, gadB, and gadC, which respond to controlling GABA production and export. Furthermore, strain LSF1-1 was considered safe, containing no virulence factors. Thus, Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 have the potential for GABA production and probiotic use in future studies.
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Affiliation(s)
- Sukanya Phuengjayaem
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Amnat Pakdeeto
- Program in Food Science and Technology, Faculty of Agriculture and Life Sciences, Chandrakasem Rajabhat University, Bangkok, 10900, Thailand
| | - Engkarat Kingkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tuangrat Tunvongvinis
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Beneficial features of pediococcus: from starter cultures and inhibitory activities to probiotic benefits. World J Microbiol Biotechnol 2023; 39:4. [PMID: 36344843 PMCID: PMC9640849 DOI: 10.1007/s11274-022-03419-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/18/2022] [Indexed: 11/09/2022]
Abstract
Pediococci are lactic acid bacteria (LAB) which have been used for centuries in the production of traditional fermented foods. There fermentative abilities were explored by the modern food processing industry in use of pediococci as starter cultures, enabling the production of fermented foods with distinct characteristics. Furthermore, some pediococci strains can produce bacteriocins and other antimicrobial metabolites (AMM), such as pediocins, which are increasingly being explored as bio-preservatives in various food matrices. Due to their versatility and inhibitory spectrum, pediococci bacteriocins and AMM are being extensively researched not only in the food industry, but also in veterinary and human medicine. Some of the pediococci were evaluated as potential probiotics with different beneficial areas of application associated with human and other animals' health. The main taxonomic characteristics of pediococci species are presented here, as well as and their potential roles and applications as starter cultures, as bio-preservatives and as probiotic candidates.
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Woraprayote W, Janyaphisan T, Adunphatcharaphon S, Sonhom N, Showpanish K, Rumjuankiat K, Visessanguan W, Elliott CT, Petchkongkaew A. Bacteriocinogenic lactic acid bacteria from Thai fermented foods: Potential food applications. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections. Sci Rep 2022; 12:20429. [PMID: 36443433 PMCID: PMC9705362 DOI: 10.1038/s41598-022-24791-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Lactic acid bacteria are the well acknowledged probiotics that can cure a variety of diseases. In this study, we observed the in vivo potentials of Pediococcus to treat hyperglycemia, hypercholesterolemia and gastrointestinal infections. A total of 77 Lactobacillus were isolated from the milk of 10 cows and 10 goats, four of those strains inhibited both carbohydrates-hydrolyzing enzymes, α-glucosidase, and α-amylase. They all showed antagonistic effects on pathogenic E. coli and S. Typhimurium which were confirmed by performing pathogen challenge test and visualizing on Electron microscopy. 16S rRNA gene sequence identified that all four strains belong to Pediococcus genus which were further distinguished as Pediococcus acidilactici by pheS gene sequence. Whole genome sequence analysis revealed their non-pathogenic properties for human and the presence of probiotic genes responsible for stress resistance, immunomodulation, adhesion, metal and drug resistance. In vivo trial with diabetes-induced mice ascertained that all Pediococcus acidilactici had significant potentials to reduce elevated glucose and low-density lipoprotein level in blood. Interestingly, two out of four strains were significantly more effective (p < 0.0001 each) than metformin in reducing the blood glucose level. This in vivo study demonstrated that Pediococcus acidilactici might be a promising probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections.
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Rodrigues Blanco I, José Luduverio Pizauro L, Victor dos Anjos Almeida J, Miguel Nóbrega Mendonça C, de Mello Varani A, Pinheiro de Souza Oliveira R. Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins. Comput Struct Biotechnol J 2022; 20:5595-5606. [PMID: 36284702 PMCID: PMC9568690 DOI: 10.1016/j.csbj.2022.09.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteriocins are antimicrobial peptides produced by different species of bacteria, especially the Gram-positive lactic acid bacteria (LAB). Pediococcus pentosaceus is widely applied in the industry and stands out as Bacteriocin-Like Inhibitory Substances (BLIS) producer known to inhibit pathogens commonly considered a concern in the food industries. This study aimed to perform in silico comparisons of P. pentosaceus genomes available in the public GenBank database focusing on their pediocin-like bacteriocins repertoire. The pan-genome analysis evidenced a temporal signal in the pattern of gene gain and loss, supporting the hypothesis that the complete genetic repertoire of this group of bacteria is still uncovered. Thirteen bacteriocin genes from Class II and III were predicted in the accessory genome. Four pediocin-like bacteriocins (54% of the detected bacteriocin repertoire) and their accompanying immunity genes are highlighted; penocin A, coagulin A, pediocin PA-1, and plantaricin 423. Additionally, in silico, modeling of the pediocin-like bacteriocins revealed different configurations of the helix motif compared to other physically determined pediocin-like structures. Comparative and phylogenomic analyses support the hypothesis that a dynamic mechanism of bacteriocin acquisition and purging is not dependent on the bacterial isolation source origin. Synteny analysis revealed that while coagulin A, pediocin PA-1, and Plantaricin 423 loci are associated with insertion sequences mainly from the IS30 family and are likely of plasmid origin, penocin A lies in a conserved chromosomal locus. The results presented here provide insights into the unique pediocin-like bacteriocin peptide fold, genomic diversity, and the evolution of the bacteriocin genetic repertoire of P. pentosaceus, shedding new insights into the role of these biomolecules for application in inhibiting bacterial pathogens, and suggesting that prospecting and sequencing new strains is still an alternative to mining for new probiotic compounds.
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Affiliation(s)
- Iago Rodrigues Blanco
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lucas José Luduverio Pizauro
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
| | - João Victor dos Anjos Almeida
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
| | - Carlos Miguel Nóbrega Mendonça
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alessandro de Mello Varani
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
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Surachat K, Kantachote D, Wonglapsuwan M, Chukamnerd A, Deachamag P, Mittraparp-arthorn P, Jeenkeawpiam K. Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. Front Microbiol 2022; 13:826683. [PMID: 35663880 PMCID: PMC9161744 DOI: 10.3389/fmicb.2022.826683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- *Correspondence: Komwit Surachat,
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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13
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Na N, Qili M, Wu N, Sun L, Xu H, Zhao Y, Wei X, Xue Y, Tao Y. Bacterial Community and Fermentation Quality of Ensiling Alfalfa With Commercial Lactic Acid Bacterial Additives. Front Microbiol 2022; 13:836899. [PMID: 35531295 PMCID: PMC9073077 DOI: 10.3389/fmicb.2022.836899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the effects of six common commercial lactic acid bacteria (LAB) additives [A1, Lactobacillus plantarum, L. buchneri, and Enterococcus faecalis; A2, L. plantarum and L. casei; A3, L. plantarum and L. buchneri; A4, L. plantarum, L. buchneri, L. casei, and Pediococcus acidilactici; A5, L. plantarum (producing feruloyl esterase); and A6, L. buchneri, P. acidilactici, β-glucanase, and xylanase] on the bacterial community and fermentation quality of alfalfa silage. Alfalfa was harvested at the squaring stage, wilted in the field for 24 h, and ensiled without any additives (Control) or with A1, A2, A3, A4, A5, or A6. Microbial counts, bacterial community, fermentation parameters, and nutritional composition were determined after ensiling for 90 days. The total abundance of LAB genera on alfalfa pre-ensiling was 0.38% in bacterial community. The abundances of Lactobacillus, Enterococcus, and Pediococcus in the Control silage were 42.18, 40.18, and 8.09% of abundance, respectively. The abundances of Lactobacillus in A1-, A2-, A3-, A4-, and A5-treatments were 89.32, 92.93, 92.87, 81.12, and 80.44%, respectively. The abundances of Pediococcus and Lactobacillus in A6-treatment were 70.14 and 24.86%, respectively. Compared with Control silage, LAB-treated silage had lower pH and less ammonia nitrogen and water-soluble carbohydrates concentrations (p < 0.05). Further, the A5- and A6-treatments contained lower neutral detergent fiber, acid detergent fiber, and hemicellulose than other treatments (p < 0.05). Overall, LAB genera were presented as minor taxa in alfalfa pre-ensiling and as dominant taxa in alfalfa silage. Adding LAB additives improved the fermentation quality and altered the bacterial community of alfalfa silage. The main bacterial genera in Control silage were Lactobacillus, Enterococcus, and Pediococcus. Lactobacillus dominated the bacterial communities of A1-, A2-, A3-, A4-, and A5-treatments, while Pediococcus and Lactobacillus were dominant bacterial genera in A6-treatment. Inoculating A5 and A6 degraded the fiber in alfalfa silage. It is necessary to ensile alfalfa with LAB inoculants.
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Affiliation(s)
- Na Na
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Moge Qili
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Nier Wu
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Lin Sun
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Haiwen Xu
- College of Foreign Languages, Inner Mongolia University of Finance and Economics, Hohhot, China
| | - Yi Zhao
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Xiaobin Wei
- Inner Mongolia Youran Animal Husbandry Co., Ltd., Hohhot, China
| | - Yanlin Xue
- Inner Mongolia Key Laboratory of Microbial Ecology of Silage, Inner Mongolia Engineering Research Center of Development and Utilization of Microbial Resources in Silage, Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, China
| | - Ya Tao
- Inner Mongolia Youran Animal Husbandry Co., Ltd., Hohhot, China
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
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14
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Queiroz LL, Hoffmann C, Lacorte GA, de Melo Franco BDG, Todorov SD. Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage. Sci Rep 2022; 12:1460. [PMID: 35087086 PMCID: PMC8795150 DOI: 10.1038/s41598-022-05086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0-10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage β-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.
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Affiliation(s)
- Luciano Lopes Queiroz
- Microbiology Graduate Program, Department of Microbiology, Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Christian Hoffmann
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Gustavo Augusto Lacorte
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto Federal de Minas Gerais, Bambuí, MG, Brazil
| | | | - Svetoslav Dimitrov Todorov
- Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil.
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk, 37554, Republic of Korea.
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15
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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: 10] [Impact Index Per Article: 5.0] [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.
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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.
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16
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Surachat K, Deachamag P, Kantachote D, Wonglapsuwan M, Jeenkeawpiam K, Chukamnerd A. In silico comparative genomics analysis of Lactiplantibacillus plantarum DW12, a potential gamma-aminobutyric acid (GABA)-producing strain. Microbiol Res 2021; 251:126833. [PMID: 34352473 DOI: 10.1016/j.micres.2021.126833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023]
Abstract
Gamma-aminobutyric acid (GABA) is an amino that plays a major role as a neurotransmitter. It iscommonly produced by lactic acid bacteria (LAB) naturally found in fermented food and fruit. Lactiplantibacillus plantarum DW12 is a high potential GABA-producing strain isolated from a fermented beverage. In this study, to highlight its ability to produce GABA, we sequenced the genome of L. plantarum DW12 and then performed comprehensive bioinformatics and meta-analysis to compare the genomic data of previously published genomes. Also, the evolutionary analysis among L. plantarum species was demonstrated using pan-genome analysis against 576 genomes from the database. As a result, the DW12 genome comprises one circular chromosome of 3,217,574 bp. It contains several genes that encode for the production of antimicrobial compounds including plantaricin A, E, F, J, K, and N. The glutamic acid decarboxylase (GAD) operon was found in the DW12 genome, suggests a high potential of producing GABA in this strain. Therefore, L. plantarum DW12 could be a good candidate as a starter culture in the beverage and food industries due to its safety aspects and ability to produce GABA.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Arnon Chukamnerd
- Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
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