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Doukaki A, Papadopoulou OS, Baraki A, Siapka M, Ntalakas I, Tzoumkas I, Papadimitriou K, Tassou C, Skandamis P, Nychas GJ, Chorianopoulos N. Effect of the Bioprotective Properties of Lactic Acid Bacteria Strains on Quality and Safety of Feta Cheese Stored under Different Conditions. Microorganisms 2024; 12:1870. [PMID: 39338544 PMCID: PMC11434416 DOI: 10.3390/microorganisms12091870] [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: 07/15/2024] [Revised: 08/26/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024] Open
Abstract
Lately, the inclusion of additional lactic acid bacteria (LAB) strains to cheeses is becoming more popular since they can affect cheese's nutritional, technological, and sensory properties, as well as increase the product's safety. This work studied the effect of Lactiplantibacillus pentosus L33 and Lactiplantibacillus plantarum L125 free cells and supernatants on feta cheese quality and Listeria monocytogenes fate. In addition, rapid and non-invasive techniques such as Fourier transform infrared (FTIR) and multispectral imaging (MSI) analysis were used to classify the cheese samples based on their sensory attributes. Slices of feta cheese were contaminated with 3 log CFU/g of L. monocytogenes, and then the cheese slices were sprayed with (i) free cells of the two strains of the lactic acid bacteria (LAB) in co-culture (F, ~5 log CFU/g), (ii) supernatant of the LAB co-culture (S) and control (C, UHT milk) or wrapped with Na-alginate edible films containing the pellet (cells, FF) or the supernatant (SF) of the LAB strains. Subsequently, samples were stored in air, in brine, or in vacuum at 4 and 10 °C. During storage, microbiological counts, pH, and water activity (aw) were monitored while sensory assessment was conducted. Also, in every sampling point, spectral data were acquired by means of FTIR and MSI techniques. Results showed that the initial microbial population of Feta was ca. 7.6 log CFU/g and consisted of LAB (>7 log CFU/g) and yeast molds in lower levels, while no Enterobacteriaceae were detected. During aerobic, brine, and vacuum storage for both temperatures, pathogen population was slightly postponed for S and F samples and reached lower levels compared to the C ones. The yeast mold population was slightly delayed in brine and vacuum packaging. For aerobic storage at 4 °C, an elongation in the shelf life of F samples by 4 days was observed compared to C and S samples. At 10 °C, the shelf life of both F and S samples was extended by 13 days compared to C samples. FTIR and MSI analyses provided reliable estimations of feta quality using the PLS-DA method, with total accuracy (%) ranging from 65.26 to 84.31 and 60.43 to 89.12, respectively. In conclusion, the application of bioprotective LAB strains can result in the extension of feta's shelf life and provide a mild antimicrobial action against L. monocytogenes and spoilage microbiota. Furthermore, the findings of this study validate the effectiveness of FTIR and MSI techniques, in tandem with data analytics, for the rapid assessment of the quality of feta samples.
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Affiliation(s)
- Angeliki Doukaki
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Olga S. Papadopoulou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, S. Venizelou 1, 14123 Lycovrissi, Greece; (O.S.P.); (C.T.)
| | - Antonia Baraki
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Marina Siapka
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Ioannis Ntalakas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Ioannis Tzoumkas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (K.P.); (P.S.)
| | - Chrysoula Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, S. Venizelou 1, 14123 Lycovrissi, Greece; (O.S.P.); (C.T.)
| | - Panagiotis Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (K.P.); (P.S.)
| | - George-John Nychas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
| | - Nikos Chorianopoulos
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (A.D.); (A.B.); (M.S.); (I.N.); (I.T.); (G.-J.N.)
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Ahadaf S, Azzouz S, Galiou OE, Errahmouni MA, Mentag R, Arakrak A, Laglaoui A. Genomic Insights Into Enterococcus mundtii 203: A Promising Probiotic Candidate Isolated From Camel Feces. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10284-6. [PMID: 38733462 DOI: 10.1007/s12602-024-10284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Enterococcus, a common commensal organism in the human gut, exhibits a dual nature with certain strains offering probiotic benefits, while others are associated with nosocomial infections. In this study, we conducted a comprehensive examination of the genome of Enterococcus mundtii strain 203 to assess its probiotic potential and safety profile. The complete genome sequencing, assembly, and annotation were performed, followed by bioinformatics analysis. Our investigation reveals a detailed characterization of the Enterococcus mundtii 203 genome, originally isolated from camel feces, with a size of 3,053,234 bases and a GC content of 38.4%. Importantly, our analysis suggests that this strain poses no risk as a human pathogen due to the absence of antibiotic resistance determinants and virulence factors. The genome harbors a multitude of genes responsible for lactic acid production, bioactive peptide synthesis, adhesion molecule expression, resistance to harsh gut conditions, and enhancement of host metabolism. These findings underline the potential probiotic functionality of Enterococcus mundtii 203, positioning it as a promising candidate. Notably, our study did not identify any sequences related to insertion elements or CRISPR-Cas fragments.
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Affiliation(s)
- Soumaya Ahadaf
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Safae Azzouz
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Ouiam El Galiou
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Mohamed Akram Errahmouni
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Abdelhay Arakrak
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Amin Laglaoui
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco.
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Tian C, Wang L, Liu M, Liu J, Qiu M, Chen Y. Isolation and Identification of Chicken-Derived Lactic Acid Bacteria: In Vitro Probiotic Properties and Antagonistic Effects against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli. Microorganisms 2024; 12:795. [PMID: 38674739 PMCID: PMC11052321 DOI: 10.3390/microorganisms12040795] [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: 03/09/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The development of probiotics capable of quickly colonizing the intestines of animals is important in promoting the healthy growth of livestock. The aim of this study was to screen lactic acid bacteria (LAB) from the intestinal microbiota of chickens with potential applications, and to evaluate their probiotic properties and antagonistic abilities against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli. The results showed that a total of 79 strains with the characteristics of LAB were isolated from the chicken cecum microbiota, of which 7 strains exhibited strong inhibitory activity against S. pullorum, S. aureus, and E. coli. Performing 16s rDNA sequencing revealed that these seven strains were Lactiplantibacillus pentosus (n = 1), Lactiplantibacillus plantarum (n = 3), Lactiplantibacillus paraplantarum (n = 1), Lactiplantibacillus argentoratensis (n = 1), and Lactiplantibacillus fabifermentans (n = 1). Among them, L. pentosus R26 and L. plantarum R32 exhibited superior antibacterial activity. These two strains demonstrated high lactic acid production ability, with survival rates of 86.29% and 87.99% after 3 h of treatment at pH 1.5, 86.66% and 85.52% after 3 h of treatment with 0.5% bile salts, 90.03% and 88.16% after 2 h of treatment with simulated gastric fluid, and 98.92% and 98.22% after 2 h of treatment with simulated intestinal fluid, respectively. Co-cultivation with L. pentosus R26 for 24 h resulted in 50% of the pathogens being antagonized, while almost complete inhibition was observed following 72 h of co-cultivation. In conclusion, L. pentosus R26 and L. plantarum R32 exhibited high antibacterial activity and acid production capability, while also demonstrating satisfactory tolerance to low pH values and high concentrations of bile salts and digestive fluid. The probiotic characteristics and stress resistance of L. pentosus R26 were slightly superior to those of L. plantarum R32, indicating its potential for development as a probiotic.
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Affiliation(s)
| | | | | | | | | | - Yong Chen
- Xinjiang Key Laboratory of Herbivore Nutrition for Meat & Milk, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.T.); (L.W.); (M.L.); (J.L.); (M.Q.)
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Kahraman-Ilıkkan Ö. Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing. Mol Genet Genomics 2024; 299:31. [PMID: 38472540 DOI: 10.1007/s00438-024-02129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.
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Niu D, Feng N, Xi S, Xu J, Su Y. Genomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics. Mol Genet Genomics 2024; 299:24. [PMID: 38438804 DOI: 10.1007/s00438-024-02101-0] [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: 06/28/2023] [Accepted: 11/16/2023] [Indexed: 03/06/2024]
Abstract
The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301 bp to 2,318,470 bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics. The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.
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Affiliation(s)
- Dekai Niu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, China
| | - Ni Feng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, China
| | - Siteng Xi
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, China
| | - Jianjian Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, China.
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Wiull K, Hagen LH, Rončević J, Westereng B, Boysen P, Eijsink VGH, Mathiesen G. Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2. Microb Cell Fact 2024; 23:19. [PMID: 38212746 PMCID: PMC10782763 DOI: 10.1186/s12934-024-02296-2] [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: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins. RESULTS Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences. CONCLUSION All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.
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Affiliation(s)
- Kamilla Wiull
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Jelena Rončević
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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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.
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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.)
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Sevillano E, Lafuente I, Peña N, Cintas LM, Muñoz-Atienza E, Hernández PE, Borrero J. Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S. Foods 2023; 13:107. [PMID: 38201135 PMCID: PMC10778751 DOI: 10.3390/foods13010107] [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: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production.
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Affiliation(s)
| | | | | | | | | | | | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Spain; (E.S.); (I.L.); (N.P.); (L.M.C.); (E.M.-A.); (P.E.H.)
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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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Kiousi DE, Karadedos DM, Sykoudi A, Repanas P, Kamarinou CS, Argyri AA, Galanis A. Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers. Microorganisms 2023; 11:2553. [PMID: 37894211 PMCID: PMC10609308 DOI: 10.3390/microorganisms11102553] [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: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Dimitrios M. Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Anastasia Sykoudi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
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Dhanya Raj CT, Suryavanshi MV, Kandaswamy S, Ramasamy KP, James RA. Whole genome sequence analysis and in-vitro probiotic characterization of Bacillus velezensis FCW2 MCC4686 from spontaneously fermented coconut water. Genomics 2023; 115:110637. [PMID: 37150228 DOI: 10.1016/j.ygeno.2023.110637] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/23/2023] [Accepted: 05/03/2023] [Indexed: 05/09/2023]
Abstract
In this study, the probiotic potential of B. velezensis FCW2, isolated from naturally fermented coconut water, was investigated by in vitro and genomic characterization. Our findings highlight key features of the bacterium which includes, antibacterial activity, high adhesive potential, aggregation capacity, production of nutrient secondary metabolites. In vivo safety assessment revealed no adverse effects on zebrafish. WGS data of B. velezensis FCW2 revealed a complete circular genome of 4,147,426 nucleotides and a GC content of 45.87%. We have identified 4059 coding sequence (CDS) genes that encode proteins involved in stress resistance, adhesion and micronutrient production. The genes responsible for producing secondary metabolites, exopolysaccharides, and other beneficial nutrients were identified. The KEGG and COG databases revealed that genes mainly involved amino acid metabolism, carbohydrate utilization, vitamin and cofactor metabolism, and biological adhesion. These findings suggest that B. velezensis FCW2 could be a putative probiotic in the development of fermented foods.
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Affiliation(s)
- C T Dhanya Raj
- Department of Marine Science, Bharathidasan University, Tiruchirappalli 620024, Tamilnadu, India
| | - Mangesh V Suryavanshi
- Cardiovascular and Metabolic Sciences Department, Lerner Research Institute, Cleveland Clinic, OH 44195, USA
| | - Surabhi Kandaswamy
- Manchester Centre for Genomic Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, 6th Floor, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK; School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK..
| | | | - Rathinam Arthur James
- Department of Marine Science, Bharathidasan University, Tiruchirappalli 620024, Tamilnadu, India.
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Tarek N, Azmy AF, Khairalla AS, Abdel-Fattah M, Jefri OA, Shaban M, El-Sayed AA, El-Gendy AO. Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens. Heliyon 2023; 9:e16253. [PMID: 37292348 PMCID: PMC10245172 DOI: 10.1016/j.heliyon.2023.e16253] [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: 08/28/2022] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Objective This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens. Methods The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools. Results Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion. Conclusion Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.
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Affiliation(s)
- Nashwa Tarek
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt
- Basic Science Department, Faculty of Oral and Dental Medicine, Nahda University Beni-Suef (NUB), Beni Suef, Egypt
| | - Ahmed F. Azmy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
| | - Ahmed S. Khairalla
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Medhat Abdel-Fattah
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt
| | - Ohoud A. Jefri
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mohamed Shaban
- Department of Physics, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawarah, 42351, Saudi Arabia
- Nanophotonics and Applications (NPA) Lab, Physics Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Abdelaziz A.A. El-Sayed
- Biology Department, Faculty of Science, Islamic University of Madinah, Al-Madinah Al- Munawarah, 42351, Saudi Arabia
- Zoology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Ahmed O. El-Gendy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
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Kiousi DE, Kouroutzidou AZ, Neanidis K, Karavanis E, Matthaios D, Pappa A, Galanis A. The Role of the Gut Microbiome in Cancer Immunotherapy: Current Knowledge and Future Directions. Cancers (Basel) 2023; 15:cancers15072101. [PMID: 37046762 PMCID: PMC10093606 DOI: 10.3390/cancers15072101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Cancer immunotherapy is a treatment modality that aims to stimulate the anti-tumor immunity of the host to elicit favorable clinical outcomes. Immune checkpoint inhibitors (ICIs) gained traction due to the lasting effects and better tolerance in patients carrying solid tumors in comparison to conventional treatment. However, a significant portion of patients may present primary or acquired resistance (non-responders), and thus, they may have limited therapeutic outcomes. Resistance to ICIs can be derived from host-related, tumor-intrinsic, or environmental factors. Recent studies suggest a correlation of gut microbiota with resistance and response to immunotherapy as well as with the incidence of adverse events. Currently, preclinical and clinical studies aim to elucidate the unique microbial signatures related to ICI response and anti-tumor immunity, employing metagenomics and/or multi-omics. Decoding this complex relationship can provide the basis for manipulating the malleable structure of the gut microbiota to enhance therapeutic success. Here, we delve into the factors affecting resistance to ICIs, focusing on the intricate gut microbiome–immunity interplay. Additionally, we review clinical studies and discuss future trends and directions in this promising field.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Antonia Z. Kouroutzidou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Konstantinos Neanidis
- Oncology Department, 424 General Military Training Hospital, 56429 Thessaloniki, Greece
| | - Emmanuel Karavanis
- Oncology Department, 424 General Military Training Hospital, 56429 Thessaloniki, Greece
| | | | - Aglaia Pappa
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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Ma N, Sun J, Li S, Shao M, Ying N, Liu W, Zhu L. A Potential Risk Comprehensive Evaluation Model of Probiotic Species Based on Complete Genome Sequences. FOOD ANAL METHOD 2023. [DOI: 10.1007/s12161-023-02456-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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15
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Dhanya Raj CT, Kandaswamy S, Suryavanshi MV, Ramasamy KP, Rajasabapathy R, Arthur James R. Genomic and metabolic properties of Staphylococcus gallinarum FCW1 MCC4687 isolated from naturally fermented coconut water towards GRAS assessment. Gene 2023; 867:147356. [PMID: 36907276 DOI: 10.1016/j.gene.2023.147356] [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: 10/19/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Staphylococcus gallinarum FCW1 was isolated from naturally fermented coconut-water and identified by biochemical and molecular methods. Probiotic characterization and safety assessment were conducted through a series of in vitro tests. A high survival rate was observed when the strain was tested for resistance to bile, lysozyme, simulated gastric and intestinal fluid, phenol, and different temperature and salt concentrations. The strain showed antagonism against some pathogens, was susceptible to all antibiotics tested except penicillin, and showed no hemolytic and DNase activity. Hydrophobicity, autoaggregation, biofilm formation, and antioxidation tests indicated that the strain possessed a high adhesive and antioxidant ability. Enzymatic activity was used to evaluate the metabolic capacities of the strain. In-vivo experiment on zebrafish was performed to check its safety status. The whole-genome sequencing indicated that the genome contained 2,880,305 bp with a GC content of 33.23%. The genome annotation confirmed the presence of probiotic-associated genes and genes for oxalate degradation, sulfate reduction, acetate metabolism, and ammonium transport in the FCW1 strain, adding to the theory that this strain may be helpful in treating kidney stones. This study revealed that the strain FCW1 might be an excellent potential probiotic in developing fermented coconut beverages and treating and preventing kidney stone disease.
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Affiliation(s)
- C T Dhanya Raj
- Department of Marine Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Surabhi Kandaswamy
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire PR1 2HE, United Kingdom; Manchester Centre for Genomic Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, 6(th) Floor, St Mary's Hospital, Oxford Road, Manchester M13 9WL, United Kingdom
| | - Mangesh V Suryavanshi
- Cardiovascular and Metabolic Sciences Department, Lerner Research Institute, Cleveland Clinic, OH 44195, United States.
| | | | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Rathinam Arthur James
- Department of Marine Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
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In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms. Foods 2023; 12:foods12050938. [PMID: 36900455 PMCID: PMC10000683 DOI: 10.3390/foods12050938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations.
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Kiousi DE, Efstathiou C, Tzampazlis V, Plessas S, Panopoulou M, Koffa M, Galanis A. Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria. Front Cell Infect Microbiol 2023; 13:1127256. [PMID: 36844407 PMCID: PMC9944596 DOI: 10.3389/fcimb.2023.1127256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Lactobacilli are avid producers of antimicrobial compounds responsible for their adaptation and survival in microbe-rich matrices. The bactericidal or bacteriostatic ability of lactic acid bacteria (LAB) can be exploited for the identification of novel antimicrobial compounds to be incorporated in functional foodstuffs or pharmaceutical supplements. In this study, the antimicrobial and antibiofilm properties of Lactiplantibacillus pentosus L33, Lactiplantibacillus plantarum L125 and Lacticaseibacillus paracasei SP5, previously isolated form fermented products, were examined, against clinical isolates of Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Enteritidis and Escherichia coli. Methods The ability of viable cells to inhibit pathogen colonization on HT-29 cell monolayers, as well as their co-aggregation capacity, were examined utilizing the competitive exclusion assay. The antimicrobial activity of cell-free culture supernatants (CFCS) was determined against planktonic cells and biofilms, using microbiological assays, confocal microscopy, and gene expression analysis of biofilm formation-related genes. Furthermore, in vitro analysis was supplemented with in silico prediction of bacteriocin clusters and of other loci involved in antimicrobial activity. Results The three lactobacilli were able to limit the viability of planktonic cells of S. aureus and E. coli in suspension. Greater inhibition of biofilm formation was recorded after co-incubation of S. enterica with the CFCS of Lc. paracasei SP5. Predictions based on sequence revealed the ability of strains to produce single or two-peptide Class II bacteriocins, presenting sequence and structural conservation with functional bacteriocins. Discussion The efficiency of the potentially probiotic bacteria to elicit antimicrobial effects presented a strain- and pathogen-specific pattern. Future studies, utilizing multi-omic approaches, will focus on the structural and functional characterization of molecules involved in the recorded phenotypes.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Efstathiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vasilis Tzampazlis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stavros Plessas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Maria Panopoulou
- Department of Medicine, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Koffa
- 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
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Wang J, Lu C, Xu Q, Li Z, Song Y, Zhou S, Guo L, Zhang T, Luo X. Comparative Genomics Analysis Provides New Insights into High Ethanol Tolerance of Lactiplantibacillus pentosus LTJ12, a Novel Strain Isolated from Chinese Baijiu. Foods 2022; 12:35. [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] [Grants] [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.
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Affiliation(s)
- Jiali Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chengshun Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qiang Xu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhongyuan Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajian Song
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Sa Zhou
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Le Guo
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuegang Luo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
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Liu X, Lv X, Sun Y, Liu C, Wang R, Liu R, Ma Y, Li Q. Probiotic properties of Lacticaseibacillus rhamnosus grx10 revolved with complete genome. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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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.
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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,
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Dutta B, Lahiri D, Nag M, Abukhader R, Sarkar T, Pati S, Upadhye V, Pandit S, Amin MFM, Al Tawaha ARMS, Kumar M, Ray RR. Multi-Omics Approach in Amelioration of Food Products. Front Microbiol 2022; 13:955683. [PMID: 35903478 PMCID: PMC9315205 DOI: 10.3389/fmicb.2022.955683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Determination of the quality of food products is an essential key factor needed for safe-guarding the quality of food for the interest of the consumers, along with the nutritional and sensory improvements that are necessary for delivering better quality products. Bacteriocins are a group of ribosomally synthesized antimicrobial peptides that help in maintaining the quality of food. The implementation of multi-omics approach has been important for the overall enhancement of the quality of the food. This review uses various recent technologies like proteomics, transcriptomics, and metabolomics for the overall enhancement of the quality of food products. The matrix associated with the food products requires the use of sophisticated technologies that help in the extraction of a large amount of information necessary for the amelioration of the food products. This review would provide a wholesome view of how various recent technologies can be used for improving the quality food products and for enhancing their shelf-life.
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Affiliation(s)
- Bandita Dutta
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Rose Abukhader
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, India
| | - Siddhartha Pati
- NatNov Bioscience Private Limited, Balasore, India
- Skills Innovation & Academic Network (SIAN) Institute, Association for Biodiversity Conservation & Research (ABC), Balasore, India
| | - Vijay Upadhye
- Center of Research for Development (CR4D), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Soumya Pandit
- Department of Life Sciences, Sharda University, Noida, India
| | | | | | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, India
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
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Kiousi DE, Efstathiou C, Tegopoulos K, Mantzourani I, Alexopoulos A, Plessas S, Kolovos P, Koffa M, Galanis A. Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Front Microbiol 2022; 13:922689. [PMID: 35783439 PMCID: PMC9244547 DOI: 10.3389/fmicb.2022.922689] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022] Open
Abstract
The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Efstathiou
- 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
| | - Ioanna Mantzourani
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Athanasios Alexopoulos
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Stavros Plessas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
- *Correspondence: Stavros Plessas,
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Koffa
- 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
- Alex Galanis,
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The Clash of Microbiomes: From the Food Matrix to the Host Gut. Microorganisms 2022; 10:microorganisms10010116. [PMID: 35056566 PMCID: PMC8780850 DOI: 10.3390/microorganisms10010116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific community. Therefore, several studies have been conducted in animal and human hosts to decipher which of these products may have a beneficial outcome against specific ailments. However, despite the accumulating literature, a relatively small number of products have been authorized as ‘functional foods’ by regulatory bodies. Data inconsistency and lack of in-depth preclinical characterization of functional products could heavily contribute to this issue. Today, the increased availability of omics platforms and bioinformatic algorithms for comprehensive data analysis can aid in the systematic characterization of microbe–microbe, microbe–matrix, and microbe–host interactions, providing useful insights about the maximization of their beneficial effects. The incorporation of these platforms in food science remains a challenge; however, coordinated efforts and interdisciplinary collaboration could push the field toward the dawn of a new era.
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