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Altuntas EG, Celık AA, Sevım B, Tok KC, Gumustas M, Mergen H, Juneja VK. A Novel Bioprotective Strain of Lactiplantibacillus plantarum F2-Physiological, Genetical, and Antimicrobial Characterization. Foodborne Pathog Dis 2024. [PMID: 39258750 DOI: 10.1089/fpd.2024.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024] Open
Abstract
Lactiplantibacillus plantarum is a member of lactic acid bacteria that improves the quality of fermented foods while also having a positive impact on human health. In this study, L. plantarum F2 was studied for characteristics such as biochemical and genetic identification, metabolite production, antimicrobial activity, and plasmid content. This strain exerts antimicrobial activity against some Gram-positive and Gram-negative pathogens (Listeria monocytogenes, Staphylococcus aureus, Salmonella, and Escherichia coli) with inhibition zone diameters ranging between 17.0 and 29.0 mm; it can ferment glucose, arabinose, galactose, lactose, and demonstrated the ability to grow at high temperature (50°C). Another physiological specification of the strain was the morphology of the isolate in selective medium, the de Man, Rogosa, Sharpe medium (MRS medium containing triphenyl tetrazolium chloride), which exhibits a chromogenic colony (characterized as purple colonies) on the modified-MRS (mMRS) medium. Metabolites such as lactic acid and diacetyl production of the strain F2 were also investigated using chromatography and found to be 10.07 and 0.05 µg/mL, respectively. The peptides of the isolate's cell-free supernatant were determined to be ∼80 kDa, and finally, the plasmid isolated from the strain F2 was identified as L. plantarum strain KLDS1.0386 plasmid p4, which may be responsible for some characteristic properties, such as antimicrobial peptide production of the strain.
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Affiliation(s)
| | | | - Busra Sevım
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Kenan Can Tok
- Department of Forensic Toxicology, Ankara University, Institute of Forensic Sciences, Ankara, Turkey
| | - Mehmet Gumustas
- Department of Forensic Toxicology, Ankara University, Institute of Forensic Sciences, Ankara, Turkey
| | - Hatice Mergen
- Department of Biology, Hacettepe University Science Faculty, Ankara, Turkey
| | - Vijay K Juneja
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, USA
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Kingkaew E, Tanaka N, Shiwa Y, Sitdhipol J, Nuhwa R, Tanasupawat S. Genomic Assessment of Potential Probiotic Lactiplantibacillus plantarum CRM56-2 Isolated from Fermented Tea Leaves. Trop Life Sci Res 2024; 35:249-269. [PMID: 39234476 PMCID: PMC11371405 DOI: 10.21315/tlsr2024.35.2.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 02/19/2024] [Indexed: 09/06/2024] Open
Abstract
Lactiplantibacillus plantarum is a widely studied species known for its probiotic properties that can help alleviate serum cholesterol levels. Whole-genome sequencing provides genetic information on probiotic attributes, metabolic activities and safety assessment. This study investigates the probiotic properties of strain CRM56-2, isolated from Thai fermented tea leaves, using Whole-Genome Sequencing (WGS) to evaluate the safety, health-promoting genes and functional analysis. Strain CRM56-2 showed bile salt hydrolase (BSH) activity, assimilated cholesterol at a rate of 75.94%, tolerated acidic and bile environments and attached to Caco-2 cells. Based on ANIb (98.9%), ANIm (99.2%), and digital DNA-DNA hybridisation (98.3%), strain CRM56-2 was identified as L. plantarum. In silico analysis revealed that it was not pathogenic and contained no antibiotic-resistance genes or plasmids. L. plantarum CRM56-2 possessed genes linked to several probiotic properties and beneficial impacts. The genome of strain CRM56-2 suggested that L. plantarum CRM56-2 is non-hazardous, with potential probiotic characteristics and beneficial impacts, which could enhance its probiotic application. Consequently, L. plantarum CRM56-2 demonstrated excellent cholesterol-lowering activity and probiotic properties.
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Affiliation(s)
- Engkarat Kingkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Jaruwan Sitdhipol
- Biodiversity Research Centre, Research and Development Group for Bio-Industries, Thailand Institute of Scientific and Technological Research, Pathum Thani 12120, Thailand
| | - Rattanatda Nuhwa
- 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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Jawaid MZ, Ashfaq MY, Al-Ghouti M, Zouari N. Insights into population adaptation and biodiversity of lactic acid bacteria in challenged date palm leaves silaging, using MALDI-TOF MS. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100235. [PMID: 38660337 PMCID: PMC11039324 DOI: 10.1016/j.crmicr.2024.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
The study focused on isolating indigenous Qatari lactic acid bacteria (LAB) from various challenged date palm tree leaf silages to construct a comprehensive strain collection, useful to study the diversity of these strains following their adaptation to the uncommon silage. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was employed for strain identification and differentiation. The diversity of LAB populations and strains was assessed through principal component analysis (PCA) and dendrogram analyses. A total of 88 LAB isolates were obtained from silages of fresh palm leaves, silage of mixed leaves and dairy feed, along with fresh palm tree leaves, and dairy feed, adapted to local harsh environments. These isolates were categorized according to the new classification of 2020, belonging to genera of Pediococcus, Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Companilactobacillus farciminis, Limosilactobacillus oris, Limosilactobacillus vaginalis, Lactiplantibacillus pentosus and Lactobacillus johnsonii. Pediococcus was the most prevalent genus, falling mostly within the species Pediococcus lolii. MALDI-TOF MS protein profiles, PCA, and dendrogram analyses successfully grouped the LAB isolates into five distinctive clusters based on the protein's similarities. The high diversity of the indigenous LAB in spontaneous palm leaf silages demonstrated their adaptation and mutualistic interactions, forming robust consortia that ensure the quality of the silage. The straightforward, quick, and accurate identification of LAB in this silage using MALDI-TOF MS presents a valuable approach for formulating LAB consortia for silaging harsh agricultural by-products.
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Affiliation(s)
- Muhammad Zaid Jawaid
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha, Qatar
| | - Mohammad Yousaf Ashfaq
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha, Qatar
| | - Mohammad Al-Ghouti
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha, Qatar
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Abriouel H, Caballero Gómez N, Manetsberger J, Benomar N. Dual effects of a bacteriocin-producing Lactiplantibacillus pentosus CF-6HA, isolated from fermented aloreña table olives, as potential probiotic and antimicrobial agent. Heliyon 2024; 10:e28408. [PMID: 38560111 PMCID: PMC10981101 DOI: 10.1016/j.heliyon.2024.e28408] [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: 11/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The probiotic potential of Lactiplantibacillus pentosus CF-6HA isolated from traditionally fermented Aloreña table olives was analyzed in vitro and in silico. Results obtained suggested that this strain can be catalogued as "talented" bacterium exhibiting bacteriocin production with antimicrobial activity against human/animal and plant pathogens, such as Pseudomonas syringae and Verticillium dahliae. The robustness, safety and probiotic potential of L. pentosus CF-6HA was confirmed by in silico analysis. In addition, a plethora of coding genes for defense and adaptability to different life styles besides functional properties were identified. In this sense, defense mechanisms of L. pentosus CF-6HA consist of 17 ISI elements, 98 transposases and 13 temperate phage regions as well as a CRISPR (clustered regularly interspaced short palindromic repeats)/cas system. Moreover, the functionality of this strain was confirmed by the presence of genes coding for secondary metabolites, exopolysaccharides and other bioactive molecules. Finally, we demonstrated the ability of L. pentosus CF-6HA to biotransform selenite to nanoparticles (SeNPs) highlighting its potential role in selenium bioremediation to be exploited in foods, agriculture and the environment; but also for the bio-enrichment of fermented foods with selenium.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Julia Manetsberger
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
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Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
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Muradova M, Proskura A, Canon F, Aleksandrova I, Schwartz M, Heydel JM, Baranenko D, Nadtochii L, Neiers F. Unlocking Flavor Potential Using Microbial β-Glucosidases in Food Processing. Foods 2023; 12:4484. [PMID: 38137288 PMCID: PMC10742834 DOI: 10.3390/foods12244484] [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: 11/20/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Aroma is among of the most important criteria that indicate the quality of food and beverage products. Aroma compounds can be found as free molecules or glycosides. Notably, a significant portion of aroma precursors accumulates in numerous food products as nonvolatile and flavorless glycoconjugates, termed glycosidic aroma precursors. When subjected to enzymatic hydrolysis, these seemingly inert, nonvolatile glycosides undergo transformation into fragrant volatiles or volatiles that can generate odor-active compounds during food processing. In this context, microbial β-glucosidases play a pivotal role in enhancing or compromising the development of flavors during food and beverage processing. β-glucosidases derived from bacteria and yeast can be utilized to modulate the concentration of particular aroma and taste compounds, such as bitterness, which can be decreased through hydrolysis by glycosidases. Furthermore, oral microbiota can influence flavor perception by releasing volatile compounds that can enhance or alter the perception of food products. In this review, considering the glycosidic flavor precursors present in diverse food and beverage products, we underscore the significance of glycosidases with various origins. Subsequently, we delve into emerging insights regarding the release of aroma within the human oral cavity due to the activity of oral microbial glycosidases.
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Affiliation(s)
- Mariam Muradova
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Alena Proskura
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Francis Canon
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Irina Aleksandrova
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Mathieu Schwartz
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Jean-Marie Heydel
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Denis Baranenko
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Liudmila Nadtochii
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Fabrice Neiers
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
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Kingkaew E, Woraprayote W, Booncharoen A, Niwasabutra K, Janyaphisan T, Vilaichone RK, Yamaoka Y, Visessanguan W, Tanasupawat S. Functional genome analysis and anti-Helicobacter pylori activity of a novel bacteriocinogenic Lactococcus sp. NH2-7C from Thai fermented pork (Nham). Sci Rep 2023; 13:20362. [PMID: 37990119 PMCID: PMC10663479 DOI: 10.1038/s41598-023-47687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Helicobacter pylori, linked to gastric diseases, is targeted for probiotic treatment through bacteriocin production. Bacteriocins have gained recognition for their non-toxic effects on host cells and their ability to combat a wide range of pathogens. This study aimed to taxonomically characterize and evaluate the safety and probiotic properties of the novel species of Lactococcus sp. NH2-7C isolated from fermented pork, as well as its bacteriocin NH2-7C, both in vitro and in silico. Comparative genotypic analysis revealed an average nucleotide identity of 94.96%, an average amino acid identity of 94.29%, and a digital DNA-DNA hybridization value of 63.80% when compared to Lactococcus lactis subsp. lactis JCM 5805T. These findings suggest that strain NH2-7C represents a novel species within the genus Lactococcus. In silico assessments confirmed the non-pathogenic nature of strain NH2-7C and the absence of genes associated with virulence and biogenic amine formation. Whole-genome analysis revealed the presence of the nisA gene responsible for nisin A production, indicating its potential as a beneficial compound with anti-Helicobacter pylori activity and non-toxic characteristics. Probiotic assessments indicated bile salt hydrolase and cholesterol assimilation activities, along with the modulation of interleukin-6 and tumour necrosis factor-α secretion. Strain NH2-7C demonstrated gastrointestinal tolerance and the ability to adhere to Caco-2 cells, affirming its safety and probiotic potential. Additionally, its ability to produce bacteriocins supports its suitability as a functional probiotic strain with therapeutic potential. However, further in vitro and in vivo investigations are crucial to ensure its safety and explore potential applications for Lactococcus sp. NH2-7C as a probiotic agent.
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Affiliation(s)
- Engkarat Kingkaew
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Weerapong Woraprayote
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Auttaporn Booncharoen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kanidta Niwasabutra
- Thailand Institute of Scientific and Technological Research (TISTR) Biodiversity Research Centre, Pathum Thani, 12120, Thailand
| | - Thitiphorn Janyaphisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Ratha-Korn Vilaichone
- GI Unit, Department of Medicine, and Center of Excellence in Digestive Diseases, Thammasat University, Thailand Science Research and Innovation Fundamental Fund, Bualuang ASEAN Chair Professorship at Thammasat University, Pathum Thani, 12120, Thailand
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine Oita University, Yufu, Oita, Japan
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Tsoungos A, Pemaj V, Slavko A, Kapolos J, Papadelli M, Papadimitriou K. The Rising Role of Omics and Meta-Omics in Table Olive Research. Foods 2023; 12:3783. [PMID: 37893676 PMCID: PMC10606081 DOI: 10.3390/foods12203783] [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: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.
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Affiliation(s)
- Anastasios Tsoungos
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Violeta Pemaj
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Aleksandra Slavko
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - John Kapolos
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Marina Papadelli
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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Kingkaew E, Konno H, Hosaka Y, Tanasupawat S. Probiogenomic Analysis of Lactiplantibacillus sp. LM14-2 from Fermented Mussel (Hoi-dong), and Evaluation of its Cholesterol-lowering and Immunomodulation Effects. Probiotics Antimicrob Proteins 2023; 15:1206-1220. [PMID: 35987935 DOI: 10.1007/s12602-022-09977-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
Lactiplantibacillus sp. LM14-2, isolated from Thai-fermented mussel (Hoi-dong), showed attractive probiotic properties. This strain was identified as Lactiplantibacillus plantarum based on its phenotypic, chemotaxonomic, and genetic characteristics including whole-genome sequencing (WGS). The draft genome sequence was analyzed and annotated for the molecular mechanisms involved in the safety assessment, the adaptation and adhesion of L. plantarum LM14-2 to the gastrointestinal tract (GIT), and the beneficial genes involved in bacteria-host interactions. The L. plantarum LM14-2 exhibited bile salt hydrolase (BSH) activity, assimilated cholesterol at 86.07 ± 5.03%, stimulated the secretion of interleukin-12, interferon-gamma, and human beta defensin-2, and induced nitric oxide production. In addition, L. plantarum LM14-2 showed excellent gastrointestinal tolerance and adhesion ability to Caco-2 cells. Furthermore, the in silico analysis showed that L. plantarum LM14-2 was a non-human pathogen and did not contain antibiotic resistance genes or plasmids. L. plantarum LM14-2 also contained potential genes associated with various probiotic characteristics and health-promoting effects. Consequently, this study suggested that L. plantarum LM14-2 could be considered safe, with potential probiotic properties and health-promoting impacts, which could facilitate its probiotic application.
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Affiliation(s)
- Engkarat Kingkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Hiroshi Konno
- Akita Konno CO., LTD., 248 Aza Kariwano, Daisen-shi, Akita, 019-2112, Japan
| | - Yoshihito Hosaka
- Akita Konno CO., LTD., 248 Aza Kariwano, Daisen-shi, Akita, 019-2112, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3-A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms 2023; 11:2440. [PMID: 37894099 PMCID: PMC10609609 DOI: 10.3390/microorganisms11102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacteria, contributing significantly to the establishment and constitution of infant gut microbiota. In light of this, our study attempted to conduct an initial investigation encompassing both genomic and phenotypic aspects of the L. plantarum PU3 strain, that holds potential as a probiotic agent. By employing the cutting-edge third-generation Nanopore sequencing technology, L. plantarum PU3 revealed a circular chromosome of 3,180,940 bp and nine plasmids of various lengths. The L. plantarum PU3 genome has a total of 2962 protein-coding and non-coding genes. Our in-depth investigations revealed more than 150 probiotic gene markers that unfold the genetic determinants for acid tolerance, bile resistance, adhesion, and oxidative and osmotic stress. The in vivo analysis showed the strain's proficiency in utilizing various carbohydrates as growth substrates, complementing the in silico analysis of the genes involved in metabolic pathways. Notably, the strain demonstrated a pronounced affinity for D-sorbitol, D-mannitol, and D-Gluconic acid, among other carbohydrate sources. The in vitro experimental verification of acid, osmotic and bile tolerance validated the robustness of the strain in challenging environments. Encouragingly, no virulence factors were detected in the genome of PU3, suggesting its safety profile. In search of beneficial properties, we found potential bacteriocin biosynthesis clusters, suggesting its capability for antimicrobial activity. The characteristics exhibited by L. plantarum PU3 pave the way for promising strain potential, warranting further investigations to unlock its full capacity and contributions to probiotic and therapeutic avenues.
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Affiliation(s)
- Daniela Mollova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Ilia Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
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11
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Sha Y, Yan Q, Liu J, Yu J, Xu S, He Z, Ren J, Qu J, Zheng S, Wang G, Dong W. Homologous genes shared between probiotics and pathogens affect the adhesion of probiotics and exclusion of pathogens in the gut mucus of shrimp. Front Microbiol 2023; 14:1195137. [PMID: 37389343 PMCID: PMC10301755 DOI: 10.3389/fmicb.2023.1195137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
Clarifying mechanisms underlying the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine is a central theme for shrimp health. Under experimental manipulation of probiotic strain (i.e., Lactiplantibacillus plantarum HC-2) adhesion to the shrimp mucus, this study tested the core hypothesis that homologous genes shared between probiotic and pathogen would affect the adhesion of probiotics and exclusion of pathogens by regulating the membrane proteins of probiotics. Results indicated that the reduction of FtsH protease activity, which significantly correlated with the increase of membrane proteins, could increase the adhesion ability of L. plantarum HC-2 to the mucus. These membrane proteins mainly involved in transport (glycine betaine/carnitine/choline ABC transporter choS, ABC transporter, ATP synthase subunit a atpB, amino acid permease) and regulation of cellular processes (histidine kinase). The genes encoding the membrane proteins were significantly (p < 0.05) up-regulated except those encoding ABC transporters and histidine kinases in L. plantarum HC-2 when co-cultured with Vibrio parahaemolyticus E1, indicating that these genes could help L. plantarum HC-2 to competitively exclude pathogens. Moreover, an arsenal of genes predicted to be involved in carbohydrate metabolism and bacteria-host interactions were identified in L. plantarum HC-2, indicating a clear strain adaption to host's gastrointestinal tract. This study advances our mechanistic understanding of the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine, and has important implications for screening and applying new probiotics for maintaining gut stability and host health.
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Affiliation(s)
- Yujie Sha
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Jiafeng Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Shicai Xu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jing Ren
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Shiying Zheng
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Guomin Wang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Weiying Dong
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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12
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Wang M, Hu T, Lin X, Liang H, Li W, Zhao S, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Probiotic characteristics of Lactobacillus gasseri TF08-1: A cholesterol-lowering bacterium, isolated from human gut. Enzyme Microb Technol 2023; 169:110276. [PMID: 37321015 DOI: 10.1016/j.enzmictec.2023.110276] [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: 03/28/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Lactobacillus contribute to maintain the human healthy and use for nutritional additives as probiotics. In this study, a cholesterol-lowering bacterium, Lactobacillus gasseri TF08-1, was isolated from the feces of a healthy adolescent, and its probiotic potentials were evaluated through genomic mining and in vitro test. The assembled draft genome comprised of 1,974,590 bp and was predicted total of 1,940 CDSs. The annotation of the genome revealed that L. gasseri TF08-1 harbored abundant categories of functional genes in metabolic and information processing. Moreover, strain TF08-1 has capacity to utilize D-Glucose, Sucrose, D-Maltose, Salicin, D-Xylose, D-Cellobiose, D-Mannose, and D-Trehalose, as the carbon source. The safety assessment showed strain TF08-1 contained few antibiotic resistance genes and virulence factors and was only resistant to 2 antibiotics detected by antimicrobial susceptibility test. A high bile salt hydrolase activity was found and a cholesterol-reducing effect was determined in vitro, which the result showed a remarkable cholesterol removal capability of L. gasseri TF08-1 with an efficiency of 84.40 %. This study demonstrated that the strain showed great capability of exopolysaccharide production, and tolerance to acid and bile salt. Therefore, these results indicate that L. gasseri TF08-1 can be considered as a safe candidate for probiotic, especially its potential in biotherapeutic for metabolic diseases.
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Affiliation(s)
- Mengmeng Wang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiaoqian Lin
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Wenxi Li
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Yiyi Zhong
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Lan Ge
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China; Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China; BGI Research-Wuhan, BGI, Wuhan, 430074, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China; Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China; BGI Research-Wuhan, BGI, Wuhan, 430074, China.
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Sam-On MFS, Mustafa S, Hashim AM, Yusof MT, Zulkifly S, Malek AZA, Roslan MAH, Asrore MSM. Mining the genome of Bacillus velezensis FS26 for probiotic markers and secondary metabolites with antimicrobial properties against aquaculture pathogens. Microb Pathog 2023:106161. [PMID: 37207784 DOI: 10.1016/j.micpath.2023.106161] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/21/2023]
Abstract
Bacillus velezensis FS26 is a bacterium from the genus Bacillus that has been proven as a potential probiotic in aquaculture with a good antagonistic effect on Aeromonas spp. and Vibrio spp. Whole-genome sequencing (WGS) allows a comprehensive and in-depth analysis at the molecular level, and it is becoming an increasingly significant technique in aquaculture research. Although numerous probiotic genomes have been sequenced and investigated recently, there are minimal data on in silico analysis of B. velezensis as a probiotic bacterium isolated from aquaculture sources. Thus, this study aims to analyse the general genome characteristics and probiotic markers from the B. velezensis FS26 genome with secondary metabolites predicted against aquaculture pathogens. The B. velezensis FS26 genome (GenBank Accession: JAOPEO000000000) assembly proved to be of high quality, with eight contigs containing 3,926,371 bp and an average G + C content of 46.5%. According to antiSMASH analysis, five clusters of secondary metabolites from the B. velezensis FS26 genome showed 100% similarity. These clusters include Cluster 2 (bacilysin), Cluster 6 (bacillibactin), Cluster 7 (fengycin), Cluster 8 (bacillaene), and Cluster 9 (macrolactin H), which signify promising antibacterial, antifungal, and anticyanobacterial agents against pathogens in aquaculture. The probiotic markers of B. velezensis FS26 genome for adhesion capability in the hosts' intestine, as well as the acid and bile salt-tolerant genes, were also detected through the Prokaryotic Genome Annotation System (Prokka) annotation pipeline. These results are in agreement with our previous in vitro data, suggesting that the in silico investigation facilitates establishing B. velezensis FS26 as a beneficial probiotic for use in aquaculture.
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Affiliation(s)
- Muhamad Firdaus Syahmi Sam-On
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Shuhaimi Mustafa
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia; Halal Products Research Institute, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia.
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia; Halal Products Research Institute, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Shahrizim Zulkifly
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Ahmad Zuhairi Abdul Malek
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Muhamad Akhmal Hakim Roslan
- Halways Sdn Bhd, Jalan Satelit, Putra Science Park, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shaufi Mohd Asrore
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
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Aswal M, Singhal N, Kumar M. Comprehensive genomic analysis of hypocholesterolemic probiotic Enterococcus faecium LR13 reveals unique proteins involved in cholesterol-assimilation. Front Nutr 2023; 10:1082566. [PMID: 37081914 PMCID: PMC10110904 DOI: 10.3389/fnut.2023.1082566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Hypercholesterolemia is a major risk factor for cardiovascular diseases (CVDs). Chemotherapeutic agents for CVDs exhibit several side effects. Specific probiotics with hypocholesterolemic effects can be safe and effective alternatives to chemotherapeutics. Here, we have analyzed and compared the genome of a novel rhizospheric Enterococcus faecium LR13 cholesterol-assimilating probiotic with other probiotic/pathogenic E. faecium strains to discern genetic factors underlying probiotic efficacy and cholesterol-assimilation. Genomic analyses of E. faecium probiotic strains revealed that LR13 and WEFA23 (cholesterol-assimilating probiotics) harbored 21 unique proteins absent in non-cholesterol-assimilating probiotics. Of these, 14 proteins could directly help in cholesterol-assimilation by producing short chain fatty acids, lipid (sterol) transport and membrane stabilization, and bile salt hydrolase activity. This suggests that cholesterol-assimilation is an intrinsic, strain-specific trait exhibited by probiotics with a specific genetic constitution. Moreover, the unique proteins identified in this study can serve as biomarkers for discerning/characterizing cholesterol-assimilating probiotics as novel biotherapeutics against CVDs.
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15
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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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16
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Abriouel H, Manetsberger J, Caballero Gómez N, Benomar N. In silico genomic analysis of the potential probiotic Lactiplantibacillus pentosus CF2-10N reveals promising beneficial effects with health promoting properties. Front Microbiol 2022; 13:989824. [PMID: 36406402 PMCID: PMC9670130 DOI: 10.3389/fmicb.2022.989824] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/04/2022] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus pentosus CF2-10 N, isolated from brines of naturally fermented Aloreña green table olives, exhibited high probiotic potential. High throughput sequencing and annotation of genome sequences underline the potential of L. pentosus CF2-10 N as excellent probiotic candidate of vegetable origin. In a previous study we could show the probiotic potential of CF2-10 N in vitro, while in this study in silico analysis of its genome revealed new insights into its safety and functionality. Our findings highlight the microorganism's ecological flexibility and adaptability to a broad range of environmental niches, food matrices and the gastrointestinal tract. These features are shared by both phylogenetically very close L. pentosus strains (CF2-10 N and MP-10) isolated from the same ecological niche with respect to their genome size (≅ 3.6 Mbp), the presence of plasmids (4-5) and several other properties. Nonetheless, additional and unique features are reported in the present study for L. pentosus CF2-10 N. Notably, the safety of L. pentosus CF2-10 N was shown by the absence of virulence determinants and the determination of acquired antibiotic resistance genes, i.e., resistome, which is mostly represented by efflux-pump resistance genes responsible for the intrinsic resistance. On the other hand, defense mechanisms of L. pentosus CF2-10 N include eight prophage regions and a CRISPR/cas system (CRISPR-I and CRISPR-II) as acquired immune system against mobile elements. Finally, the probiotic potential of this strain was further demonstrated by the presence of genes coding for proteins involved in adhesion, exopolysaccharide biosynthesis, tolerance to low pH and bile salts, immunomodulation, and vitamin and enzyme production. Taken together these results, we propose the use of L. pentosus CF2-10 N as a potential and promising probiotic candidate able to colonize several niches and adapt to different lifestyles. The strain can provide attractive functional and probiotic features necessary for its application as starter culture and probiotic.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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17
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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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Hove PR, Nealon NJ, Chan SHJ, Boyer SM, Haberecht HB, Ryan EP. Integrated Profiling of Gram-Positive and Gram-Negative Probiotic Genomes, Proteomes and Metabolomes Revealed Small Molecules with Differential Growth Inhibition of Antimicrobial-Resistant Pathogens. J Diet Suppl 2022; 20:788-810. [PMID: 36099186 PMCID: PMC10008781 DOI: 10.1080/19390211.2022.2120146] [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] [Indexed: 10/14/2022]
Abstract
Probiotics produce small molecules that may serve as alternatives to conventional antibiotics by suppressing growth of antimicrobial resistant (AMR) pathogens. The objective of this study was to identify and examine antimicrobials produced and secreted by probiotics using 'omics' profiling with computer-based metabolic flux analyses. The cell-free supernatant of Gram-positive Lacticaseibacillus rhamnosus GG (LGG) and Gram-negative Escherichia coli Nissle (ECN) probiotics inhibited growth of AMR Salmonella Typhimurium, Escherichia coli, and Klebsiella oxytoca ranging between 28.85 - 41.20% (LGG) and 11.48 - 29.45% (ECN). A dose dependent analysis of probiotic supernatants showed LGG was 6.27% to 20.55% more effective at reducing AMR pathogen growth when compared to ECN. Principal component analysis showed clear separation of ECN and LGG cell free supernatant metabolomes. Among 667 metabolites in the supernatant, 304 were differentially abundant between LGG and ECN probiotics. Proteomics identified 87 proteins, whereby 67 (ECN) and 14 (LGG) showed differential expression as enzymes related to carbohydrate and energy metabolic pathways. The whole genomes and metabolomes were next used for in-silico metabolic network analysis. The model predicted the production of 166 metabolites by LGG and ECN probiotics across amino acid, carbohydrate/energy, and nucleotide metabolism with antimicrobial functions. The predictive accuracy of the metabolic flux analysis highlights the novel utility for profiling probiotic supplements as dietary-based antimicrobial alternatives in the control of AMR pathogen growth.
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Affiliation(s)
- Petronella R. Hove
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Nora Jean Nealon
- Department of Environmental and Radiological Health Sciences, Colorado State University. Fort Collins, CO, USA
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Shea M. Boyer
- Department of Environmental and Radiological Health Sciences, Colorado State University. Fort Collins, CO, USA
| | - Hannah B. Haberecht
- Department of Environmental and Radiological Health Sciences, Colorado State University. Fort Collins, CO, USA
| | - Elizabeth P. Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University. Fort Collins, CO, USA
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Heat, cold, acid, and bile salt induced differential proteomic responses of a novel potential probiotic Lactococcus garvieae C47 isolated from camel milk. Food Chem 2022; 397:133774. [PMID: 35905615 DOI: 10.1016/j.foodchem.2022.133774] [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: 02/19/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022]
Abstract
Probiotics encounter various stresses during food processing and digestion. This study evaluated the differential proteomic responses of a newly identified potential probiotic lactic acid bacteria, Lactococcus garvieae, isolated from camel milk. Lc. garvieae C47 was exposed to heat, cold, acid, and bile conditions, and stress-responsive proteins were identified. The proteomic analysis was done using 2D-IEF SDS PAGE and nano-LC-MS/MS. Out of 91 differentially expressed proteins, 20 upregulated and 27 downregulated proteins were shared among the stresses. The multivariate data analysis revealed abundance of elongation factor Ts (spot C42), uridine phosphorylase, fructose-bisphosphate aldolase, peptidase T, cobalt ECF transporter T component CbiQ, UDP-N-acetylmuramate-l-alanine ligase, uncharacterized protein, aspartokinase, chaperone protein DnaK, IGP synthase cyclase subunit, probable nicotinate-nucleotide adenylyltransferase, NADH-quinone oxidoreductase, holo-[acyl-carrier-protein] synthase, l-lactate dehydrogenase, and uncharacterized protein. The maximum number of differentially expressed proteins belonged to carbohydrate and protein metabolism, which indicates Lc. garvieae shifts towards growth and energy metabolism for resistance against stress conditions.
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Namrak T, Raethong N, Jatuponwiphat T, Nitisinprasert S, Vongsangnak W, Nakphaichit M. Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5. BIOLOGY 2022; 11:biology11020294. [PMID: 35205160 PMCID: PMC8869380 DOI: 10.3390/biology11020294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
Limosilactobacillus reuteri KUB-AC5 displays the hallmark features of probiotic properties for food and feed industries. Optimization of cultivation condition for the industrial production is important to reach cell concentration and cost reduction. Considering the strain-specific growth physiology, metabolic capability, and essential nutrients of L. reuteri KUB-AC5, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5 was developed. Hereby, the GSMM of iTN656 was successfully constructed which contained 656 genes, 831 metabolites, and 953 metabolic reactions. The iTN656 model could show a metabolic capability under various carbon sources and guide potentially 14 essential single nutrients (e.g., vitamin B complex and amino acids) and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth through single and double omission analysis. Promisingly, the iTN656 model was further integrated with transcriptome data suggesting that putative metabolic routes as preferable paths e.g., sucrose uptake, nucleotide biosynthesis, urea cycle, and glutamine transporter for L. reuteri KUB-AC5 growth. The developed GSMM offers a powerful tool for multi-level omics analysis, enabling probiotic strain optimization for biomass overproduction on an industrial scale.
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Affiliation(s)
- Thanawat Namrak
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Theeraphol Jatuponwiphat
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Sunee Nitisinprasert
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| | - Massalin Nakphaichit
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
- Correspondence: (W.V.); (M.N.)
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Characterization of two new strains of Lactococcus lactis for their probiotic efficacy over commercial synbiotics consortia. Braz J Microbiol 2022; 53:903-920. [PMID: 35138631 PMCID: PMC9151986 DOI: 10.1007/s42770-022-00685-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 01/02/2022] [Indexed: 02/01/2023] Open
Abstract
Lactococcus spp. are industrially crucial lactic acid bacteria (LAB) used to manufacture lactic acid, pickled vegetables, buttermilk, cheese, and many kinds of delicious dairy foods and drinks. In addition to these, they are also being used as probiotics in specific formulations. However, their uses as probiotics are comparatively less than the other LAB genera. The present communication hypothesizes to validate the probiotic potentiality of two new Lactococcus lactis subsp. lactis strains for their future uses. These native food fermenting strains were characterized for in vitro acid tolerance, tolerance to simulated gastric and pancreatic juices, autoaggregation and co-aggregation, hydrophobicity, haemolytic activity, bile salt deconjugation, cholesterol removal, antimicrobial spectrum, and antibiotic sensitivity. The in vivo live bacterial feeding of these strains for 30 days was done in Swiss albino mice either singly or in combination with prebiotic inulin and evaluated for hypocholesterolemic activity, immune enhancement, and gut colonization efficiency and compared with the commercial probiotic consortia. The study revealed that the strains could survive in human gut bile concentration, gastric pH conditions at pH 2.0, 3.0, and 8.0 for 6 h, had a broad antibacterial spectrum, and cholesterol binding efficacy. The strains could survive with higher colony-forming units (CFU/mL) when amended with sodium caseinate. The strains had autoaggregation ranges from 15 to 25% over 24 h and had a significant co-aggregation with both lactic acid and Gram-positive and Gram-negative bacterial strains related to human illness. The strains also showed solvent and media-specific hydrophobicity against n-hexane and xylene. The live bacterial feeding either singly or in combination with prebiotic inulin resulted in a significant reduction of LDL (low-density lipoprotein), VLDL (very low-density lipoprotein) cholesterol and triglyceride (TG), and a significant increase in HDL (high-density lipoprotein) cholesterol level, and improved gut colonization and gut immunomodulation. The results prove that these non-haemolytic, non-toxic strains had significant health benefits than the commercial probiotics consortium with the recommended prebiotics mix. Thus, these new Lactococcus lactis subsp. lactis strains could be trialled as a new probiotic combination for human and animal feeds.
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22
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Rai R, Tamang JP. In vitro and genetic screening of probiotic properties of lactic acid bacteria isolated from naturally fermented cow-milk and yak-milk products of Sikkim, India. World J Microbiol Biotechnol 2022; 38:25. [PMID: 34989904 DOI: 10.1007/s11274-021-03215-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
A total of 272 isolates of lactic acid bacteria (LAB) were isolated from 22 samples of naturally fermented milk products of Sikkim in India viz. dahi, soft-variety chhurpi, hard-variety chhurpi, mohi and philu, out of which, 68 LAB isolates were randomly grouped on the basis of phenotypic characteristics, and were identified by 16S rRNA gene sequence analysis. Leuconostoc mesenteroides was the most dominant genus, followed by Leuc. mesenteroides subsp. jonggajibkimchii, Lactococcus lactis subsp. cremoris, Lc. lactis, Lc. lactis subsp. hordniae, Lc. lactis subsp. tructae, Enterococcus faecalis, E. italicus and E. pseudoavium. LAB strains were tested for probiotics attributes by in vitro and genetic screening, based on marker genes. LAB strains showed tolerance to pH 3.0, bile salt, resistance to lysozyme and β-galactosidase activity. Enterococcus faecalis YS4-11 and YS4-14 and Lactococcus lactis subsp. cremoris SC3 showed more than 85% of hydrophobicity. Genes clp L and tdc encoding for low pH tolerance, agu A and Ir1516 encoding for bile tolerance, LBA1446 gene encoding for BSH activity, map A, apf, mub 1 and msa encoding for mucosal binding property were detected. Gene mesY for bacteriocin production was detected only in Leuconostoc spp. Based on the in vitro and genetic screening of probiotic attributes, Leuc. mesenteroides; Leuc. mesenteroides subsp. jonggajibkimchii and Lc. lactis subsp. cremoris were tentatively selected for possible probiotic candidates.
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Affiliation(s)
- Ranjita Rai
- Department of Microbiology, School of Life Sciences, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Sikkim University, Gangtok, 737102, Sikkim, India.
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23
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Enriching Lactobacilli from Fermented Pulse Dal Flour-Analyzing its Efficacy in Utilizing Carbohydrates and Production of α-galactosidase Enzyme During Pigeon Pea Fermentation. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pigeon peas are an excellent source of carbohydrates, proteins and other nutrients. Many traditional fermented foods are prepared from cereals and combinations of cereals and pulses that usually contain Lactic acid bacteria (LAB), Bacillus, Enterococcus and yeast. Lactobacillus can be used as a starter culture for such fermentation using pulses, as very few reports are available on fermented pulse-based products. Hence, pulse dal flour was used as a source for isolation of Lactobacillus to maintain their functionality, growth characteristics and activity during food processing. In this study, we investigated the potential of lactobacilli from fermented pigeon pea to utilize carbohydrates, the ability to degrade non-digestible oligosaccharides and the production of the α-galactosidase enzyme. Lactobacillus isolated from six different pulse dal flour grew well during fermentation with carbohydrates in mMRS medium. Among Lactobacillus species, only Lactobacillus brevis displayed the highest α-galactosidase activity (1.24 U/ml), where raffinose was added as the sole carbohydrate source in the medium. The isolate was further tested in pigeon pea fermentation, where it showed maximum activity (1.86 U/ml) and complete hydrolysis of non-digestible oligosaccharides was observed. Overall, usage of Lactobacilli could be an excellent opportunity to design and develop a novel pulse-based fermented product contributing to beneficial bioactive compounds and improving the properties of food.
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Mehra Y, Viswanathan P. High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain. PLoS One 2021. [DOI: https://doi.org/10.1371/journal.pone.0260116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lactobacillus paragasseri was identified as a novel sister taxon of L. gasseri in 2018. Since the reclassification of L. paragasseri, there has been hardly any report describing the probiotic properties of this species. In this study, an L. paragasseri strain UBLG-36 was sequenced and analyzed to determine the molecular basis that may confer the bacteria with probiotic potential. UBLG-36 was previously documented as an L. gasseri strain. Average nucleotide identity and phylogenomic analysis allowed accurate taxonomic identification of UBLG-36 as an L. paragasseri strain. Analysis of the draft genome (~1.94 Mb) showed that UBLG-36 contains 5 contigs with an average G+C content of 34.85%. Genes essential for the biosynthesis of bacteriocins, adhesion to host epithelium, stress resistance, host immunomodulation, defense, and carbohydrate metabolism were identified in the genome. Interestingly, L. paragasseri UBLG-36 also harbored genes that code for enzymes involved in oxalate catabolism, such as formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). In vitro oxalate degradation assay showed that UBLG-36 is highly effective in degrading oxalate (averaging more than 45% degradation), a feature that has not been reported before. As a recently identified bacterium, there are limited genomic reports on L. paragasseri, and our draft genome sequence analysis is the first to describe and emphasize the probiotic potential and oxalate degrading ability of this species. With results supporting the probiotic functionalities and oxalate catabolism of UBLG-36, we propose that this strain is likely to have immense biotechnological applications upon appropriate characterization.
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Stergiou OS, Tegopoulos K, Kiousi DE, Tsifintaris M, Papageorgiou AC, Tassou CC, Chorianopoulos N, Kolovos P, Galanis A. Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages. Front Microbiol 2021; 12:746659. [PMID: 34764945 PMCID: PMC8576124 DOI: 10.3389/fmicb.2021.746659] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/08/2021] [Indexed: 01/11/2023] Open
Abstract
Lactobacillus is a diverse genus that includes species of industrial and biomedical interest. Lactiplantibacillus pentosus, formerly known as Lactobacillus pentosus, is a recently reclassified species, that contains strains isolated from diverse environmental niches, ranging from fermented products to mammalian gut microbiota. Importantly, several L. pentosus strains present health-promoting properties, such as immunomodulatory and antiproliferative activities, and are regarded as potential probiotic strains. In this study, we present the draft genome sequence of the potential probiotic strain L. pentosus L33, originally isolated from fermented sausages. Comprehensive bioinformatic analysis and whole-genome annotation were performed to highlight the genetic loci involved in host-microbe interactions and the probiotic phenotype. Consequently, we found that this strain codes for bile salt hydrolases, adhesins and moonlighting proteins, and for Class IIb bacteriocin peptides lacking the GxxxG and GxxxG-like motifs, crucial for their inhibitory activity. Its adhesion ability was also validated in vitro, on human cancer cells. Furthermore, L. pentosus L33 contains an exopolysaccharide (EPS) biosynthesis cluster, and it does not carry transferable antibiotic resistance genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and CAZymes analyses showed that L. pentosus L33 possesses biosynthetic pathways for seven amino acids, while it can degrade a wide array of carbohydrates. In parallel, Clusters of Orthologous Groups (COGs) and KEGG profiles of L. pentosus L33 are similar to those of 26 L. pentosus strains, as well as of two well documented L. plantarum probiotic strains. Conclusively, L. pentosus L33 exhibits good probiotic potential, although further studies are needed to elucidate the extent of its biological properties.
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Affiliation(s)
- Odysseas Sotirios Stergiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Margaritis Tsifintaris
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aristotelis C Papageorgiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chrysoula C Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, Athens, Greece
| | - Nikos Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, Athens, Greece
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
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Alonso García E, de la Fuente Ordoñez JJ, Lavilla Lerma L, Estudillo-Martínez MD, Castillo-Gutiérrez S, Benomar N, Knapp CW, Abriouel H. Transcriptomic Profile and Probiotic Properties of Lactiplantibacillus pentosus Pre-adapted to Edible Oils. Front Microbiol 2021; 12:747043. [PMID: 34721347 PMCID: PMC8553220 DOI: 10.3389/fmicb.2021.747043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils improved their robustness and functionality; this may have great importance on their stress response during fermentation, storage, and digestion. Pre-adapting the strains to the corresponding oils significantly increased their probiotic functionality (e.g., auto-aggregation, co-aggregation with pathogens, and mucin adhesion), although results depended on the strain and the oil used for pre-adaptation. As such, we selected olive-adapted (TO) L. pentosus AP2-16, which exhibited improved functionality, and subjected it to transcriptomic profiling with the aim to understand the molecular mechanisms involved in the adaptation and the increased functionality. Global transcriptomic analysis of oil-adapted (olive or almond) and non-adapted (control) L. pentosus AP2-16 realized that 3,259 genes were expressed, with 2,779 mapped to the reference database. Comparative transcriptomic analysis showed that 125 genes (olive vs. control) and 108 genes (olive vs. almond) became significantly differentially expressed. TO L. pentosus AP2-16 responded by rerouting its metabolic pathways to balance energy production and storage, cell growth and survivability, host interactions (glycoconjugates), and other physiological features. As such, the pre-adaptation of lactobacilli with olive oil switches their transcriptional network to regulate robustness and functionality, possibly representing a novel approach toward the design and manufacture of probiotic products with improved stability and functionality.
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Affiliation(s)
- Esther Alonso García
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Juan José de la Fuente Ordoñez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - María D Estudillo-Martínez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Sonia Castillo-Gutiérrez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability and Public Health, Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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27
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Baig MA, Turner MS, Liu SQ, Al-Nabulsi AA, Shah NP, Ayyash MM. Potential Probiotic Pediococcus pentosaceus M41 Modulates Its Proteome Differentially for Tolerances Against Heat, Cold, Acid, and Bile Stresses. Front Microbiol 2021; 12:731410. [PMID: 34721329 PMCID: PMC8548654 DOI: 10.3389/fmicb.2021.731410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/13/2021] [Indexed: 01/01/2023] Open
Abstract
Probiotics containing functional food confer health benefits in addition to their nutritional properties. In this study, we have evaluated the differential proteomic responses of a potential novel probiotic Pediococcus pentosaceus M41 under heat, cold, acid, and bile stress conditions. We identified stress response proteins that could provide tolerances against these stresses and could be used as probiotic markers for evaluating stress tolerance. Pediococcus pentosaceus M41 was exposed for 2 h to each condition: 50°C (heat stress), 4°C (cold stress), pH 3.0 (acid stress) and 0.05% bile (bile stress). Proteomic analysis was carried out using 2D-IEF SDS PAGE and LC-MS/MS. Out of 60 identified proteins, 14 upregulated and 6 downregulated proteins were common among all the stress conditions. These proteins were involved in different biological functions such as translation-related proteins, carbohydrate metabolism (phosphoenolpyruvate phosphotransferase), histidine biosynthesis (imidazole glycerol phosphate synthase) and cell wall synthesis (tyrosine-protein kinase CapB). Proteins such as polysaccharide deacetylase, lactate oxidase, transcription repressor NrdR, dihydroxyacetone kinase were upregulated under three out of the four stress conditions. The differential expression of these proteins might be responsible for tolerance and protection of P. pentosaceus M41 against different stress conditions.
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Affiliation(s)
- Mohd Affan Baig
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mark S. Turner
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Shao-Quan Liu
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Anas A. Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, Jordan
| | - Nagendra P. Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
| | - Mutamed M. Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
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28
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Khangwal I, Skariyachan S, Uttarkar A, Muddebihalkar AG, Niranjan V, Shukla P. Understanding the Xylooligosaccharides Utilization Mechanism of Lactobacillus brevis and Bifidobacterium adolescentis: Proteins Involved and Their Conformational Stabilities for Effectual Binding. Mol Biotechnol 2021; 64:75-89. [PMID: 34542815 DOI: 10.1007/s12033-021-00392-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/08/2021] [Indexed: 11/26/2022]
Abstract
Xylooligosaccharides having various degrees of polymerization such as xylobiose, xylotriose, and xylotetraose positively affect human health by interacting with gut proteins. The present study aimed to identify proteins present in gut microflora, such as xylosidase, xylulokinase, etc., with the help of retrieved whole-genome annotations and find out the mechanistic interactions of those with the above substrates. The 3D structures of proteins, namely Endo-1,4-beta-xylanase B (XynB) from Lactobacillus brevis and beta-D-xylosidase (Xyl3) from Bifidobacterium adolescentis, were computationally predicted and validated with the help of various bioinformatics tools. Molecular docking studies identified the effectual binding of these proteins to the xylooligosaccharides, and the stabilities of the best-docked complexes were analyzed by molecular dynamic simulation. The present study demonstrated that XynB and Xyl3 showed better effectual binding toward Xylobiose with the binding energies of - 5.96 kcal/mol and - 4.2 kcal/mol, respectively. The interactions were stabilized by several hydrogen bonding having desolvation energy (- 6.59 and - 7.91). The conformational stabilities of the docked complexes were observed in the four selected complexes of XynB-xylotriose, XynB-xylotetraose, Xyl3-xylobiose, and Xyn3-xylotriose by MD simulations. This study showed that the interactions of these four complexes are stable, which means they have complex metabolic activities among each other. Extending these studies of understanding, the interaction between specific probiotics enzymes and their ligands can explore the detailed design of synbiotics in the future.
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Affiliation(s)
- Ishu Khangwal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Sinosh Skariyachan
- Department of Microbiology, St. Pius X College, Rajapuram, Kasaragod, Kerala, India
| | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | | | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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29
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Safety Evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: a Health-Promoting Bacteria. Probiotics Antimicrob Proteins 2021; 14:816-829. [PMID: 34403080 DOI: 10.1007/s12602-021-09826-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Lactobacillus delbrueckii subsp. lactis CIDCA is a new potential probiotic strain whose molecular basis attributed to the host's benefit has been reported. This study investigated the safety aspects of Lactobacillus delbrueckii subsp. lactis CIDCA 133 based on whole-genome sequence and phenotypic analysis to avoid future questions about the harmful effects of this strain consumption. Genomic analysis showed that L. delbrueckii subsp. lactis CIDCA 133 harbors virulence, harmful metabolites, and antimicrobial resistance-associated genes. However, none of these genetic elements is flanked or located within prophage regions and plasmid sequence. At a phenotypic level, it was observed L. delbrueckii subsp. lactis CIDCA 133 antimicrobial resistance to aminoglycosides streptomycin and gentamicin antibiotics, but no hemolytic and mucin degradation activity was exhibited by strain. Furthermore, no adverse effects were observed regarding mice clinical and histopathological analysis after the strain consumption (5 × 107 CFU/mL). Overall, these findings reveal the safety of Lactobacillus delbrueckii subsp. lactis CIDCA 133 for consumption and future probiotic applications.
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30
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de Jesus LCL, Drumond MM, Aburjaile FF, Sousa TDJ, Coelho-Rocha ND, Profeta R, Brenig B, Mancha-Agresti P, Azevedo V. Probiogenomics of Lactobacillus delbrueckii subsp. lactis CIDCA 133: In Silico, In Vitro, and In Vivo Approaches. Microorganisms 2021; 9:microorganisms9040829. [PMID: 33919849 PMCID: PMC8070793 DOI: 10.3390/microorganisms9040829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Lactobacillus delbrueckii subsp. lactis CIDCA 133 (CIDCA 133) has been reported as a potential probiotic strain, presenting immunomodulatory properties. This study investigated the possible genes and molecular mechanism involved with a probiotic profile of CIDCA 133 through a genomic approach associated with in vitro and in vivo analysis. Genomic analysis corroborates the species identification carried out by the classical microbiological method. Phenotypic assays demonstrated that the CIDCA 133 strain could survive acidic, osmotic, and thermic stresses. In addition, this strain shows antibacterial activity against Salmonella Typhimurium and presents immunostimulatory properties capable of upregulating anti-inflammatory cytokines Il10 and Tgfb1 gene expression through inhibition of Nfkb1 gene expression. These reported effects can be associated with secreted, membrane/exposed to the surface and cytoplasmic proteins, and bacteriocins-encoding genes predicted in silico. Furthermore, our results showed the genes and the possible mechanisms used by CIDCA 133 to produce their beneficial host effects and highlight its use as a probiotic microorganism.
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Affiliation(s)
- Luís Cláudio Lima de Jesus
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
| | - Mariana Martins Drumond
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET/MG), Departamento de Ciências Biológicas, Belo Horizonte 31421-169, Brazil;
| | - Flávia Figueira Aburjaile
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Thiago de Jesus Sousa
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
| | - Nina Dias Coelho-Rocha
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
| | - Rodrigo Profeta
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, D-37077 Göttingen, Germany;
| | | | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular (LGCM), Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.C.L.d.J.); (F.F.A.); (T.d.J.S.); (N.D.C.-R.); (R.P.)
- Correspondence:
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Mehra Y, Viswanathan P. High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain. PLoS One 2021; 16:e0260116. [PMID: 34797858 PMCID: PMC8604369 DOI: 10.1371/journal.pone.0260116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/02/2021] [Indexed: 02/05/2023] Open
Abstract
Lactobacillus paragasseri was identified as a novel sister taxon of L. gasseri in 2018. Since the reclassification of L. paragasseri, there has been hardly any report describing the probiotic properties of this species. In this study, an L. paragasseri strain UBLG-36 was sequenced and analyzed to determine the molecular basis that may confer the bacteria with probiotic potential. UBLG-36 was previously documented as an L. gasseri strain. Average nucleotide identity and phylogenomic analysis allowed accurate taxonomic identification of UBLG-36 as an L. paragasseri strain. Analysis of the draft genome (~1.94 Mb) showed that UBLG-36 contains 5 contigs with an average G+C content of 34.85%. Genes essential for the biosynthesis of bacteriocins, adhesion to host epithelium, stress resistance, host immunomodulation, defense, and carbohydrate metabolism were identified in the genome. Interestingly, L. paragasseri UBLG-36 also harbored genes that code for enzymes involved in oxalate catabolism, such as formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). In vitro oxalate degradation assay showed that UBLG-36 is highly effective in degrading oxalate (averaging more than 45% degradation), a feature that has not been reported before. As a recently identified bacterium, there are limited genomic reports on L. paragasseri, and our draft genome sequence analysis is the first to describe and emphasize the probiotic potential and oxalate degrading ability of this species. With results supporting the probiotic functionalities and oxalate catabolism of UBLG-36, we propose that this strain is likely to have immense biotechnological applications upon appropriate characterization.
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Affiliation(s)
- Yogita Mehra
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
- * E-mail:
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Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ, Barton W, Finnegan L, Crispie F, O'Sullivan O, Claesson MJ, Cotter PD. Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants. mSystems 2020; 5:e00522-20. [PMID: 33172966 PMCID: PMC7657593 DOI: 10.1128/msystems.00522-20] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.
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Affiliation(s)
- John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Guerrino Macori
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Wiley Barton
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Laura Finnegan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiol 2020; 92:103606. [PMID: 32950142 DOI: 10.1016/j.fm.2020.103606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023]
Abstract
Table olives are considered the most widespread fermented food in the Mediterranean area and their consumption is expanding all over the world. This fermented vegetable can be considered as a natural functional food thanks to their high nutritional value and high content of bioactive compounds that contribute to the health and well-being of consumers. The presence of bioactive compounds is strongly influenced by a complex microbial consortium, traditionally exploited through culture-dependent approaches. Recently, the rapid spread of omics technologies has represented an important challenge to better understand the function, the adaptation and the exploitation of microbial diversity in different complex ecosystems, such as table olives. This review provides an overview of the potentiality of omics technologies to in depth investigate the microbial composition and the metabolic processes that drive the table olives fermentation, affecting both sensorial profile and safety properties of the final product. Finally, the review points out the role of omics approaches to raise at higher sophisticated level the investigations on microbial, gene, protein, and metabolite, with huge potential for the integration of table olives composition with functional assessments.
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Torres S, Verón H, Contreras L, Isla MI. An overview of plant-autochthonous microorganisms and fermented vegetable foods. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Chileshe J, van den Heuvel J, Handema R, Zwaan BJ, Talsma EF, Schoustra S. Nutritional Composition and Microbial Communities of Two Non-alcoholic Traditional Fermented Beverages from Zambia: A Study of Mabisi and Munkoyo. Nutrients 2020; 12:nu12061628. [PMID: 32492891 PMCID: PMC7352844 DOI: 10.3390/nu12061628] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023] Open
Abstract
Traditional fermented foods and beverages are common in many countries, including Zambia. While the general (nutritional) benefits of fermented foods are widely recognised, the nutritional composition of most traditional fermented foods is unknown. Furthermore, fermentation is known to add nutritional value to raw materials, mainly by adding B-vitamins and removing anti-nutritional factors. In the case of traditional fermentation, the composition of microbial communities responsible for fermentation varies from producer to producer and this may also be true for the nutritional composition. Here, we characterized the nutrient profile and microbial community composition of two traditional fermented foods: milk-based Mabisi and cereal-based Munkoyo. We found that the two products are different with respect to their nutritional parameters and their microbial compositions. Mabisi was found to have higher nutritional values for crude protein, fat, and carbohydrates than Munkoyo. The microbial community composition was also different for the two products, while both communities were dominated by lactic acid bacteria. Our analyses showed that variations in nutritional composition, defined as the amount of consumption that would contribute to the estimated average requirement (EAR), might be explained by variations in microbial community composition. Consumption of Mabisi appeared to contribute more than Munkoyo to the EAR and its inclusion in food-based recommendations is warranted. Our results show the potential of traditional fermented foods such as Mabisi and Munkoyo to add value to current diets and suggests that variations in microbial composition between specific product samples can result in variations in nutritional composition.
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Affiliation(s)
- Justin Chileshe
- Laboratory of Genetics, Wageningen University and Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (J.C.); (J.v.d.H.); (B.J.Z.)
- Tropical Diseases Research Centre, Department of Biomedical Sciences, P.O. Box 71769, Ndola 10101, Zambia;
- Division of Human Nutrition and Health, Wageningen University, P.O. Box 57, 6700AB Wageningen, The Netherlands;
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University and Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (J.C.); (J.v.d.H.); (B.J.Z.)
| | - Ray Handema
- Tropical Diseases Research Centre, Department of Biomedical Sciences, P.O. Box 71769, Ndola 10101, Zambia;
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University and Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (J.C.); (J.v.d.H.); (B.J.Z.)
| | - Elise F. Talsma
- Division of Human Nutrition and Health, Wageningen University, P.O. Box 57, 6700AB Wageningen, The Netherlands;
| | - Sijmen Schoustra
- Laboratory of Genetics, Wageningen University and Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (J.C.); (J.v.d.H.); (B.J.Z.)
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
- Correspondence: ; Tel.: +31-317-483142
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36
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Kim E, Chang HC, Kim HY. Complete Genome Sequence of Lactobacillus plantarum EM, A Putative Probiotic Strain with the Cholesterol-Lowering Effect and Antimicrobial Activity. Curr Microbiol 2020; 77:1871-1882. [DOI: 10.1007/s00284-020-02000-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
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Perpetuini G, Prete R, Garcia-Gonzalez N, Khairul Alam M, Corsetti A. Table Olives More than a Fermented Food. Foods 2020; 9:E178. [PMID: 32059387 PMCID: PMC7073621 DOI: 10.3390/foods9020178] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/31/2022] Open
Abstract
Table olives are one of the oldest vegetable fermented foods in the Mediterranean area. Beside their economic impact, fermented table olives represent also an important healthy food in the Mediterranean diet, because of their high content of bioactive and health-promoting compounds. However, olive fermentation is still craft-based following traditional processes, which can lead to a not fully predictable final product with the risk of spontaneous alterations. Nowadays, food industries have to face consumer demands for safe and healthy products. This review offers an overview about the main technologies used for olive fermentation and the role of lactic acid bacteria and yeasts characterizing this niche during the fermentation. Particular attention is offered to the selection and use of microorganisms as starter cultures to fasten and improve the safety of table olives. The development and implementation of multifunctional starter cultures in order to obtain heath-oriented table olives is also discussed.
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Affiliation(s)
| | | | | | | | - Aldo Corsetti
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, 641000 Teramo, Italy; (G.P.); (R.P.); (N.G.-G.); (M.K.A.)
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Jatuponwiphat T, Namrak T, Supataragul A, Nitisinprasert S, Nakphaichit M, Vongsangnak W. Comparative genome analysis reveals metabolic traits associated with probiotics properties in Lactobacillus reuteri KUB-AC5. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Cubas-Cano E, González-Fernández C, Tomás-Pejó E. Evolutionary engineering of Lactobacillus pentosus improves lactic acid productivity from xylose-rich media at low pH. BIORESOURCE TECHNOLOGY 2019; 288:121540. [PMID: 31174085 DOI: 10.1016/j.biortech.2019.121540] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Since xylose is the second most abundant sugar in lignocellulose, using microorganisms able to metabolize it into bio-based chemicals like lactic acid is an attractive approach. In this study, Lactobacillus pentosus CECT4023T was evolved to improve its xylose fermentation capacity even at acid pH by adaptive laboratory evolution in repeated anaerobic batch cultures at increasing xylose concentration. The resulting strain (named MAX2) presented between 1.5 and 2-fold more xylose consumption and lactic acid production than the parental strain in 20 g L-1 xylose defined media independently of the initial pH value. When the pH was controlled in bioreactor, lactic acid productivity at 16 h increased 1.4-fold when MAX2 was grown both in xylose defined media and in wheat straw hydrolysate. These results demonstrated the potential of this new strain to produce lactic acid from hemicellulosic substrates at low pH, reducing the need of using neutralizing agents in the process.
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Affiliation(s)
- Enrique Cubas-Cano
- IMDEA Energy Institute, Biotechnological Processes for Energy Production Unit, 28935 Móstoles, Spain.
| | | | - Elia Tomás-Pejó
- IMDEA Energy Institute, Biotechnological Processes for Energy Production Unit, 28935 Móstoles, Spain
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40
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Pérez Montoro B, Benomar N, Caballero Gómez N, Ennahar S, Horvatovich P, Knapp CW, Gálvez A, Abriouel H. Proteomic analysis of Lactobacillus pentosus for the identification of potential markers involved in acid resistance and their influence on other probiotic features. Food Microbiol 2018; 72:31-38. [DOI: 10.1016/j.fm.2017.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/16/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022]
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41
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Pérez Montoro B, Benomar N, Caballero Gómez N, Ennahar S, Horvatovich P, Knapp CW, Alonso E, Gálvez A, Abriouel H. Proteomic analysis of Lactobacillus pentosus for the identification of potential markers of adhesion and other probiotic features. Food Res Int 2018; 111:58-66. [PMID: 30007721 DOI: 10.1016/j.foodres.2018.04.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 11/19/2022]
Abstract
We analyzed the adhesion capacity to mucus of 31 Lactobacillus pentosus strains isolated from naturally fermented Aloreña green table olives using an immobilized mucin model. On the basis of their adhesive capacity to mucin, three phenotypes were selected for cell-wall protein proteomic analysis to pinpoint proteins involved in the adhesion process: the highly adhesive L. pentosus CF1-43 N (73.49% of adhesion ability), the moderately adhesive L. pentosus CF1-37 N (49.56% of adhesion ability) and the poorly adhesive L. pentosus CF2-20P (32.79% of adhesion ability). The results revealed four moonlighting proteins over-produced in the highly adhesive L. pentosus CF1-43 N, which were under/not produced in the other two L. pentosus strains (CF1-37 N and CF2-20P). These proteins were involved in glycolytic pathway (phosphoglycerate mutase and glucosamine-6-phosphate deaminase), stress response (small heat shock protein) and transcription (transcription elongation factor GreA). Furthermore, the relative fold change in gene expression analysis showed significant up-regulation of the genes coding for these four moonlighting proteins in the highly adhesive L. pentosus CF1-43 N versus the poorly adhesive L. pentosus CF2-20P and also in response to mucin for 20 h which clearly indicate the significant role of these genes in the adhesion capacity of L. pentosus. Thus, these proteins could be used as biomarkers for mucus adhesion in L. pentosus. On the other hand, mucin exposure induced other probiotic effects in L. pentosus strains, enhancing their co-aggregation ability with pathogens and possible inactivation.
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Affiliation(s)
- Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Said Ennahar
- Equipe de Chimie Analytique des Molécules Bio-Actives, UMR 7178, IPHC-DSA, CNRS, Université de Strasbourg, Illkirch-Graffenstaden 67400, France
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Esther Alonso
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain.
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Guantario B, Zinno P, Schifano E, Roselli M, Perozzi G, Palleschi C, Uccelletti D, Devirgiliis C. In Vitro and in Vivo Selection of Potentially Probiotic Lactobacilli From Nocellara del Belice Table Olives. Front Microbiol 2018; 9:595. [PMID: 29643848 PMCID: PMC5882814 DOI: 10.3389/fmicb.2018.00595] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/15/2018] [Indexed: 12/23/2022] Open
Abstract
Table olives are increasingly recognized as a vehicle as well as a source of probiotic bacteria, especially those fermented with traditional procedures based on the activity of indigenous microbial consortia, originating from local environments. In the present study, we report characterization at the species level of 49 Lactic Acid Bacteria (LAB) strains deriving from Nocellara del Belice table olives fermented with the Spanish or Castelvetrano methods, recently isolated in our previous work. Ribosomal 16S DNA analysis allowed identification of 4 Enterococcus gallinarum, 3 E. casseliflavus, 14 Leuconostoc mesenteroides, 19 Lactobacillus pentosus, 7 L. coryniformis, and 2 L. oligofermentans. The L. pentosus and L. coryniformis strains were subjected to further screening to evaluate their probiotic potential, using a combination of in vitro and in vivo approaches. The majority of them showed high survival rates under in vitro simulated gastro-intestinal conditions, and positive antimicrobial activity against Salmonella enterica serovar Typhimurium, Listeria monocytogenes and enterotoxigenic Escherichia coli (ETEC) pathogens. Evaluation of antibiotic resistance to ampicillin, tetracycline, chloramphenicol, or erythromycin was also performed for all selected strains. Three L. coryniformis strains were selected as very good performers in the initial in vitro testing screens, they were antibiotic susceptible, as well as capable of inhibiting pathogen growth in vitro. Parallel screening employing the simplified model organism Caenorhabditis elegans, fed the Lactobacillus strains as a food source, revealed that one L. pentosus and one L. coryniformis strains significantly induced prolongevity effects and protection from pathogen-mediated infection. Moreover, both strains displayed adhesion to human intestinal epithelial Caco-2 cells and were able to outcompete foodborne pathogens for cell adhesion. Overall, these results are suggestive of beneficial features for novel LAB strains, which renders them promising candidates as starters for the manufacturing of fermented table olives with probiotic added value.
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Affiliation(s)
- Barbara Guantario
- Food & Nutrition Research Centre, Council for Agricultural Research and Economics, Rome, Italy
| | - Paola Zinno
- Food & Nutrition Research Centre, Council for Agricultural Research and Economics, Rome, Italy
| | - Emily Schifano
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Italy
| | - Marianna Roselli
- Food & Nutrition Research Centre, Council for Agricultural Research and Economics, Rome, Italy
| | - Giuditta Perozzi
- Food & Nutrition Research Centre, Council for Agricultural Research and Economics, Rome, Italy
| | - Claudio Palleschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Italy
| | - Chiara Devirgiliis
- Food & Nutrition Research Centre, Council for Agricultural Research and Economics, Rome, Italy
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Rohani M, Papizadeh M, Pourshafie MR. Correlation of Biofilm Formation and Caco-2 Cell Attachment Properties in Colonization Ability of Acid-Bile Resistant Fecal Lactobacillus plantarum Isolates. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2018. [DOI: 10.29252/jommid.6.1.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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