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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024; 931:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [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: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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Sarang S, Ernst L, Wefers D, Kulkarni R. Characterization of a novel inulosucrase from Lactiplantibacillus plantarum. Food Chem 2024; 453:139597. [PMID: 38788653 DOI: 10.1016/j.foodchem.2024.139597] [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: 10/01/2023] [Revised: 04/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Fructansucrases produce fructans by polymerizing the fructose moiety released from sucrose. Here, we describe the recombinant expression and characterization of a unique fructansucrase from Lactiplantibacillus plantarum DKL3 that showed low sequence similarity with previously characterized fructansucrases. The optimum pH and temperature of fructansucrase were found to be 4.0 and 35 °C, respectively. Enzyme activity increased in presence of Ca2+ and distinctly in presence of Mn2+. The enzyme was characterized as an inulosucrase (LpInu), based on the production of an inulin-type fructan as assessed byNMR spectroscopy and methylation analysis. In addition to β-2,1-linkages, the inulin contained a few β-2,1,6-linked branchpoints. High-performance size exclusion chromatography with refractive index detection (HPSEC-RI) revealed the production of inulin with a lower molecular weight compared to other characterized bacterial inulin. LpInu and its inulin product represent novel candidates to be explored for possible food and biomedical applications.
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Affiliation(s)
- Sahara Sarang
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune 412115, India.
| | - Luise Ernst
- Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany.
| | - Daniel Wefers
- Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany.
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune 412115, India.
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3
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Lugo-Zarate L, Delgado-Olivares L, Cruz-Cansino NDS, González-Olivares LG, Castrejón-Jiménez NS, Estrada-Luna D, Jiménez-Osorio AS. Blackberry Juice Fermented with Two Consortia of Lactic Acid Bacteria and Isolated Whey: Physicochemical and Antioxidant Properties during Storage. Int J Mol Sci 2024; 25:8882. [PMID: 39201566 PMCID: PMC11354321 DOI: 10.3390/ijms25168882] [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: 05/29/2024] [Revised: 08/01/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Fermenting fruit juices with lactic acid bacteria (LAB) is a sustainable method to enhance fruit harvests and extend shelf life. This study focused on blackberries, rich in antioxidants with proven health benefits. In this research, we examined the effects of fermentation (48 h at 37 °C) at 28 days on whey-supplemented (WH, 1:1) blackberry juice (BJ) inoculated with two LAB mixtures. Consortium 1 (BJWH/C1) included Levilactobacillus brevis, Lactiplantibacillus plantarum, and Pediococcus acidilactici, while consortium 2 (BJWH/C2) comprised Lacticaseibacillus casei and Lacticaseibacillus rhamnosus. All of the strains were previously isolated from aguamiel, pulque, and fermented milk. Throughout fermentation and storage, several parameters were evaluated, including pH, lactic acid production, viscosity, stability, reducing sugars, color, total phenolic content, anthocyanins, and antioxidant capacity. Both consortia showed a significant increase in LAB count (29-38%) after 16 h. Sample BJWH/C2 demonstrated the best kinetic characteristics, with high regression coefficients (R2 = 0.97), indicating a strong relationship between lactic acid, pH, and fermentation/storage time. Despite some fluctuations during storage, the minimum LAB count remained at 9.8 log CFU/mL, and lactic acid content increased by 95%, with good storage stability. Notably, sample BJWH/C2 increased the total phenolic content during storage. These findings suggest that adding whey enhances biomass and preserves physicochemical properties during storage.
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Affiliation(s)
- Liliana Lugo-Zarate
- Área Académica de Enfermería, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.L.-Z.); (D.E.-L.)
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.D.-O.); (N.d.S.C.-C.)
| | - Luis Delgado-Olivares
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.D.-O.); (N.d.S.C.-C.)
| | - Nelly del Socorro Cruz-Cansino
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.D.-O.); (N.d.S.C.-C.)
| | - Luis Guillermo González-Olivares
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico;
| | - Nayeli Shantal Castrejón-Jiménez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Ex Hacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Hidalgo, Mexico;
| | - Diego Estrada-Luna
- Área Académica de Enfermería, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.L.-Z.); (D.E.-L.)
| | - Angélica Saraí Jiménez-Osorio
- Área Académica de Enfermería, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Actopan Tilcuautla s/n. Ex Hacienda La Concepción, San Agustín Tlaxiaca 42160, Hidalgo, Mexico; (L.L.-Z.); (D.E.-L.)
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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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Yang C, Wang S, Li Q, Zhang R, Xu Y, Feng J. Effects of Probiotic Lactiplantibacillus plantarum HJLP-1 on Growth Performance, Selected Antioxidant Capacity, Immune Function Indices in the Serum, and Cecal Microbiota in Broiler Chicken. Animals (Basel) 2024; 14:668. [PMID: 38473053 DOI: 10.3390/ani14050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/20/2024] [Indexed: 03/14/2024] Open
Abstract
This research study aimed to investigate the effects of Lactiplantibacillus plantarum (L. plantarum) on growth performance, oxidation resistance, immunity, and cecal microbiota in broilers. This work classed three hundred and sixty 1-day-old male broilers into three groups randomly, including a control group (CON, basal diet) and antibiotic (ANT, 75 mg kg-1 chlortetracycline added into basal diet) and probiotic groups (LP, 5 × 108 CFU kg-1Lactiplantibacillus plantarum HJLP-1 contained within basal diet). Animals were then fed for 42 days, and each group comprised eight replicates with 15 broilers. Compared with CON, L. plantarum supplementation significantly improved the average daily weight gain (AWDG) (p < 0.05) while reducing the feed-gain ratio over the entire supplemental period (p < 0.05). Birds fed L. plantarum had markedly lower serum ammonia and xanthine oxidase levels (p < 0.05) than those in the ANT and CON groups. Significant improvements (p < 0.05) in superoxide dismutase, catalase, and serum IgM and IgY contents in broilers fed L. plantarum were also observed when compared with those in the CON and ANT groups. Both L. plantarum and antibiotics decreased pro-inflammatory factor IL-1β levels significantly (p < 0.05), while only L. plantarum promoted anti-inflammatory factor IL-10 levels in the serum (p < 0.05) compared with CON. L. plantarum (p < 0.05) increased acetic acid and butyric acid concentrations in cecal contents when compared to those in CON and ANT. Among the differences revealed via 16S rRNA analysis, L. plantarum markedly improved the community richness of the cecal microbiota. At the genus level, the butyric acid-producing bacteria Ruminococcus and Lachnospiraceae were found in higher relative abundance in samples of L. plantarum-treated birds. In conclusion, dietary L. plantarum supplementation promoted the growth and health of broilers, likely by inducing a shift in broiler gut microbiota toward short-chain fatty acid (SCFA)-producing bacteria. Therefore, L. plantarum has potential as an alternative to antibiotics in poultry breeding.
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Affiliation(s)
- Caimei Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Shuting Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Qing Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Ruiqiang Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yinglei Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Jie Feng
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Surve SV, Shinde DB, Fernandes JM, Sharma S, Vijayvargiya M, Kadam K, Kulkarni R. Laboratory domestication of Lactiplantibacillus plantarum alters some phenotypic traits but causes non-novel genomic impact. J Appl Microbiol 2024; 135:lxae035. [PMID: 38341274 DOI: 10.1093/jambio/lxae035] [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: 11/02/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024]
Abstract
AIMS Laboratory domestication has been negligibly examined in lactic acid bacteria (LAB). Lactiplantibacillus plantarum is a highly studied and industrially relevant LAB. Here, we passaged L. plantarum JGR2 in a complex medium to study the effects of domestication on the phenotypic properties and the acquisition of mutations. METHODS AND RESULTS Lactiplantibacillus plantarum JGR2 was passaged in mMRS medium (deMan Rogossa Sharpe supplemented with 0.05% w/v L-cysteine) in three parallel populations for 70 days. One pure culture from each population was studied for various phenotypic properties and genomic alterations. Auto-aggregation of the evolved strains was significantly reduced, and lactic acid production and ethanol tolerance were increased. Other probiotic properties and antibiotic sensitivity were not altered. Conserved synonymous and non-synonymous mutations were observed in mobile element proteins (transposases), β-galactosidase, and phosphoketolases in all three isolates. The evolved strains lost all the repeat regions and some of the functions associated with them. Most of the conserved mutations were found in the genomes of other wild-type strains available in a public database, indicating the non-novel genomic impact of laboratory passaging. CONCLUSIONS Laboratory domestication can affect the phenotypic and genotypic traits of L. plantarum and similar studies are necessary for other important species of LAB.
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Affiliation(s)
- Sarvesh V Surve
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Dasharath B Shinde
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Joyleen M Fernandes
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Sharoni Sharma
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Monty Vijayvargiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Komal Kadam
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
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Fatemi M, Meshkini A, Matin MM. A dual catalytic functionalized hollow mesoporous silica-based nanocarrier coated with bacteria-derived exopolysaccharides for targeted delivery of irinotecan to colorectal cancer cells. Int J Biol Macromol 2024; 259:129179. [PMID: 38181911 DOI: 10.1016/j.ijbiomac.2023.129179] [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: 10/14/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
In this study, we introduced a multifunctional hollow mesoporous silica-based nanocarrier (HMSN) for the targeted delivery of irinotecan (IRT) to colorectal cancer cells. Due to their large reservoirs, hollow mesoporous silica nanoparticles are suitable platforms for loading significant amounts of drugs for sustained drug release. To respond to pH and redox, HMSNs were functionalized with cerium and iron oxides. Additionally, they were coated with bacterial-derived exopolysaccharide (EPS) as a biocompatible polymer. In vitro analyses revealed that cytotoxicity induced in cancer cells through oxidative stress, mediated by mature nanocarriers (EPS.IRT.Ce/Fe.HMSN), was surprisingly greater than that caused by free drugs. Cerium and iron ions, in synergy with the drug, were found to generate reactive oxygen species when targeting the acidic pH within lysosomes and the tumor microenvironment. This, in turn, triggered cascade reactions, leading to cell death. In vivo experiments revealed that the proposed nanocarriers had no noticeable effect on healthy tissues. These findings indicate the selective delivery of the drug to cancerous tissue and the induction of antioxidant effects due to the dual catalytic properties of cerium in normal cells. Accordingly, this hybrid drug delivery system provides a more effective treatment for colorectal cancer with the potential for cost-effective scaling up.
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Affiliation(s)
- Mohsen Fatemi
- Biochemical Research Center, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Azadeh Meshkini
- Biochemical Research Center, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Maryam M Matin
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Sato K, Ikagawa Y, Niwa R, Nishioka H, Horie M, Iwahashi H. Genome Sequencing Unveils Nomadic Traits of Lactiplantibacillus plantarum in Japanese Post-Fermented Tea. Curr Microbiol 2023; 81:52. [PMID: 38155273 DOI: 10.1007/s00284-023-03566-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Post-fermented tea production involving microbial fermentation is limited to a few regions, such as Southeast Asia and Japan, with Japan's Shikoku island being particularly prominent. Lactiplantibacillus plantarum was the dominant species found in tea leaves after anaerobic fermentation of Awa-bancha in Miyoshi City, Tokushima, and Ishizuchi-kurocha in Ehime. Although the draft genome of L. plantarum from Japanese post-fermented tea has been previously reported, its genetic diversity requires further exploration. In this study, whole-genome sequencing was conducted on four L. plantarum strains isolated from Japanese post-fermented tea using nanopore sequencing. These isolates were then compared with other sources to examine their genetic diversity revealing that L. plantarum isolated from Japanese post-fermented tea contained several highly variable gene regions associated with sugar metabolism and transportation. However, no source-specific genes or clusters were identified within accessory or core gene regions. This study indicates that L. plantarum possesses high genetic diversity and that the unique environment of Japanese post-fermented tea does not appear to exert selective pressure on L. plantarum growth.
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Affiliation(s)
- Kyoka Sato
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| | - Yuichiro Ikagawa
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Niwa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Hiroki Nishioka
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center, Tokushima, 770-8021, Japan
| | - Masanori Horie
- Health and Medical Research Institute (HMRI), National Institute of Advanced Industrial Science and Technology (AIST), Kagawa, 761-0395, Japan
| | - Hitoshi Iwahashi
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
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Dekham K, Jones SM, Jitrakorn S, Charoonnart P, Thadtapong N, Intuy R, Dubbs P, Siripattanapipong S, Saksmerprome V, Chaturongakul S. Functional and genomic characterization of a novel probiotic Lactobacillus johnsonii KD1 against shrimp WSSV infection. Sci Rep 2023; 13:21610. [PMID: 38062111 PMCID: PMC10703779 DOI: 10.1038/s41598-023-47897-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
White Spot syndrome virus (WSSV) causes rapid shrimp mortality and production loss worldwide. This study demonstrates potential use of Lactobacillus johnsonii KD1 as an anti-WSSV agent for post larva shrimp cultivation and explores some potential mechanisms behind the anti-WSSV properties. Treatment of Penaeus vannamei shrimps with L. johnsonii KD1 prior to oral challenge with WSSV-infected tissues showed a significantly reduced mortality. In addition, WSSV copy numbers were not detected and shrimp immune genes were upregulated. Genomic analysis of L. johnsonii KD1 based on Illumina and Nanopore platforms revealed a 1.87 Mb chromosome and one 15.4 Kb plasmid. Only one antimicrobial resistance gene (ermB) in the chromosome was identified. Phylogenetic analysis comparing L. johnsonii KD1 to other L. johnsonii isolates revealed that L. johnsonii KD1 is closely related to L. johnsonii GHZ10a isolated from wild pigs. Interestingly, L. johnsonii KD1 contains isolate-specific genes such as genes involved in a type I restriction-modification system and CAZymes belonging to the GT8 family. Furthermore, genes coding for probiotic survival and potential antimicrobial/anti-viral metabolites such as a homolog of the bacteriocin helveticin-J were found. Protein-protein docking modelling suggests the helveticin-J homolog may be able to block VP28-PmRab7 interactions and interrupt WSSV infection.
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Affiliation(s)
- Kanokwan Dekham
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Samuel Merryn Jones
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT2 7NZ, UK
| | - Sarocha Jitrakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Patai Charoonnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nalumon Thadtapong
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, 12120, Thailand
| | - Rattanaporn Intuy
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Padungsri Dubbs
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Vanvimon Saksmerprome
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Soraya Chaturongakul
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [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] [Received: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
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11
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Davray D, Kulkarni R. In-silico functional analysis of hypothetical proteins from Lactiplantibacillus plantarum plasmids reveals enrichment of cell envelope proteins. Plasmid 2023; 127:102693. [PMID: 37257733 DOI: 10.1016/j.plasmid.2023.102693] [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: 12/09/2022] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Lactiplantibacillus plantarum is one of the important species of lactic acid bacterium (LAB) found in diverse environments, with many strains exhibiting probiotic properties. In our previous study, 41.6% of protein families (PFs) encoded by 395 plasmids from several L. plantarum strains were found to be hypothetical proteins with no predicted function. This study aimed at predicting the functions of these 647 hypothetical proteins using 21 different bioinformatics methods. As a result, 160 PFs could be newly annotated. A lower proportion of plasmid-specific functions was annotated as compared to the functions shared between plasmids and chromosomes. Also, hypothetical proteins were less conserved than the annotated proteins across L.plantarum plasmids. Based on the subcellular localization, cell envelope proteins represented the biggest category in the newly annotated proteins. Transporters (112 PFs) which was a part of cell envelop proteins represented the largest functional group. Additionally, 40 and 25 other PFs were predicted to contain signal peptides and transmembrane helices, respectively. We speculate that such hypothetical proteins might be involved in the transport of various chemicals and environmental interactions in L. plantarum. In the future, functional characterization of these proteins through wet-lab experimental approach can provide novel insights into their contribution to the physiology, probiotic properties, and industrial utility of these bacteria.
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Affiliation(s)
- Dimple Davray
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India.
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12
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Zhang J, Xiao Y, Wang H, Zhang H, Chen W, Lu W. Lactic acid bacteria-derived exopolysaccharide: Formation, immunomodulatory ability, health effects, and structure-function relationship. Microbiol Res 2023; 274:127432. [PMID: 37320895 DOI: 10.1016/j.micres.2023.127432] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
Exopolysaccharides (EPSs) synthesized by lactic acid bacteria (LAB) have implications for host health and act as food ingredients. Due to the variability of LAB-EPS (lactic acid bacteria-derived exopolysaccharide) gene clusters, especially the glycosyltransferase genes that determine monosaccharide composition, the structure of EPS is very rich. EPSs are synthesized by LAB through the extracellular synthesis pathway and the Wzx/Wzy-dependent pathway. LAB-EPS has a strong immunomodulatory ability. The EPSs produced by different genera of LAB, especially Lactobacillus, Leuconostoc, and Streptococcus, have different immunomodulatory abilities because of their specific structures. LAB-EPS possesses other health effects, including antitumor, antioxidant, intestinal barrier repair, antimicrobial, antiviral, and cholesterol-lowering activities. The bioactivities of LAB-EPS are tightly related to their structures such us monosaccharide composition, glycosidic bonds, and molecular weight (MW). For the excellent physicochemical property, LAB-EPS acts as product improvers in dairy, bakery food, and meat in terms of stability, emulsification, thickening, and gelling. We systematically summarize the detailed process of EPS from synthesis to application, with emphasis on physiological mechanisms of EPS, and specific structure-function relationship, which provides theoretical support for the potential commercial value in the pharmaceutical, chemical, food, and cosmetic industries.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
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13
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Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
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Echegaray N, Yilmaz B, Sharma H, Kumar M, Pateiro M, Ozogul F, Lorenzo JM. A novel approach to Lactiplantibacillus plantarum: From probiotic properties to the omics insights. Microbiol Res 2023; 268:127289. [PMID: 36571922 DOI: 10.1016/j.micres.2022.127289] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) strains are one of the lactic acid bacteria (LAB) commonly used in fermentation and their probiotic and functional properties along with their health-promoting roles come to the fore. Food-derived L. plantarum strains have shown good resistance and adhesion in the gastrointestinal tract (GI) and excellent antioxidant and antimicrobial properties. Furthermore, many strains of L. plantarum can produce bacteriocins with interesting antimicrobial activity. This probiotic properties of L. plantarum and existing in different niches give a great potential to have beneficial effects on health. It is also has been shown that L. plantarum can regulate the intestinal microbiota composition in a good way. Recently, omics approaches such as metabolomics, secretomics, proteomics, transcriptomics and genomics try to understand the roles and mechanisms of L. plantarum that are related to its functional characteristics. This review provides an overview of the probiotic properties, including the specific interactions between microbiota and host, and omics insights of L. plantarum.
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Affiliation(s)
- Noemí Echegaray
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia nº 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain
| | - Birsen Yilmaz
- Department of Nutrition and Dietetics, Cukurova University, Sarıcam, 01330 Adana, Turkey
| | - Heena Sharma
- Dairy Technology Division, ICAR-National Dairy Research Institute, Karnāl, Haryana, 132001, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, Central Institute for Research on Cotton Technology, Mumbai 400019, India
| | - Mirian Pateiro
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia nº 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain
| | - Fatih Ozogul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, 01330, Adana, Turkey
| | - Jose Manuel Lorenzo
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia nº 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; Universidade de Vigo, Área de Tecnoloxía dos Alimentos, Facultade de Ciencias de Ourense, 32004 Ourense, Spain.
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15
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Aziz T, Naveed M, Makhdoom SI, Ali U, Mughal MS, Sarwar A, Khan AA, Zhennai Y, Sameeh MY, Dablool AS, Alharbi AA, Shahzad M, Alamri AS, Alhomrani M. Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens. Molecules 2023; 28:molecules28020491. [PMID: 36677548 PMCID: PMC9862464 DOI: 10.3390/molecules28020491] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites’ characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Urooj Ali
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Muhammad Saad Mughal
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
| | - Manal Y. Sameeh
- Chemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia
| | - Anas S. Dablool
- Department of Public Health, Health Sciences College Al-Leith, Umm Al-Qura University, Makkah al-Mukarramah 24382, Saudi Arabia
| | - Amnah A. Alharbi
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif 21944, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif 21944, Saudi Arabia
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16
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Aziz T, Naveed M, Jabeen K, Shabbir MA, Sarwar A, Zhennai Y, Alharbi M, Alshammari A, Alasmari AF. Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir. Front Microbiol 2023; 14:1157615. [PMID: 37152722 PMCID: PMC10158936 DOI: 10.3389/fmicb.2023.1157615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- *Correspondence: Yang Zhennai,
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Pulido-Mateos EC, Lessard-Lord J, Guyonnet D, Desjardins Y, Roy D. Comprehensive analysis of the metabolic and genomic features of tannin transforming Lactiplantibacillus plantarum strains. Sci Rep 2022; 12:22406. [PMID: 36575241 PMCID: PMC9794748 DOI: 10.1038/s41598-022-26005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Extracellular tannase Lactiplantibacillus plantarum-producing strains (TanA+) release bioactive metabolites from dietary tannins. However, there is a paucity of knowledge of TanA+ strains and their hydrolyzing capacities. This study aimed to shed light on the metabolic and genomic features of TanA+ L. plantarum strains and to develop a screening technique. The established spectrophotometric was validated by UPLC-UV-QToF. Eight of 115 screened strains harbored the tanA gene, and six presented TanA activity (PROBI S126, PROBI S204, RKG 1-473, RKG 1-500, RKG 2-219, and RKG 2-690). When cultured with tannic acid (a gallotannin), TanA+ strains released 3.2-11 times more gallic acid than a lacking strain (WCFS1) (p < 0.05). TanA+ strains with gallate decarboxylase (n = 5) transformed this latter metabolite, producing 2.2-4.8 times more pyrogallol than the TanA lacking strain (p < 0.05). However, TanA+ strains could not transform punicalagin (an ellagitannin). Genomic analysis revealed high similarity between TanA+ strains, as only two variable regions of phage and polysaccharide synthesis were distinguished. A phylogenetic analysis of 149 additional genome sequences showed that tanA harboring strains form a cluster and present two bacteriocin coding sequences profile. In conclusion, TanA+ L. plantarum strains are closely related and possess the ability to resist and transform gallotannins. TanA can be screened by the method proposed herein.
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Affiliation(s)
- Elena C. Pulido-Mateos
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada ,grid.23856.3a0000 0004 1936 8390Laboratoire de Génomique Microbienne, Département des Sciences des Aliments, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | - Jacob Lessard-Lord
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | | | - Yves Desjardins
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
| | - Denis Roy
- grid.23856.3a0000 0004 1936 8390Institut sur la Nutrition et les Aliments Fonctionnels de l’Université Laval, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada ,grid.23856.3a0000 0004 1936 8390Laboratoire de Génomique Microbienne, Département des Sciences des Aliments, Faculté des Sciences de l’agriculture et de l’alimentation, Université Laval, Quebec, QC Canada
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Characterization of the recombinant PepX peptidase from Lactobacillus fermentum and its effect on gliadin protein hydrolysis in vitro. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01273-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kandasamy S, Yoo J, Yun J, Lee KH, Kang HB, Kim JE, Oh MH, Ham JS. Probiogenomic In-Silico Analysis and Safety Assessment of Lactiplantibacillus plantarum DJF10 Strain Isolated from Korean Raw Milk. Int J Mol Sci 2022; 23:ijms232214494. [PMID: 36430971 PMCID: PMC9699202 DOI: 10.3390/ijms232214494] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The whole genome sequence of Lactiplantibacillus plantarum DJF10, isolated from Korean raw milk, is reported, along with its genomic analysis of probiotics and safety features. The genome consists of 29 contigs with a total length of 3,385,113 bp and a GC content of 44.3%. The average nucleotide identity and whole genome phylogenetic analysis showed the strain belongs to Lactiplantibacillus plantarum with 99% identity. Genome annotation using Prokka predicted a total of 3235 genes, including 3168 protein-coding sequences (CDS), 59 tRNAs, 7 rRNAs and 1 tmRNA. The functional annotation results by EggNOG and KEGG showed a high number of genes associated with genetic information and processing, transport and metabolism, suggesting the strain's ability to adapt to several environments. Various genes conferring probiotic characteristics, including genes related to stress adaptation to the gastrointestinal tract, biosynthesis of vitamins, cell adhesion and production of bacteriocins, were identified. The CAZyme analysis detected 98 genes distributed under five CAZymes classes. In addition, several genes encoding carbohydrate transport and metabolism were identified. The genome also revealed the presence of insertion sequences, genomic islands, phage regions, CRISPR-cas regions, and the absence of virulence and toxin genes. However, the presence of hemolysin and antibiotic-resistance-related genes detected in the KEGG search needs further experimental validation to confirm the safety of the strain. The presence of two bacteriocin clusters, sactipeptide and plantaricin J, as detected by the BAGEL 4 webserver, confer the higher antimicrobial potential of DJF10. Altogether, the analyses in this study performed highlight this strain's functional characteristics. However, further in vitro and in vivo studies are required on the safety assurance and potential application of L. plantarum DJF10 as a probiotic agent.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun-Sang Ham
- Correspondence: ; Tel.: +82-63-238-7366; Fax: +82-63-238-7397
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20
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Sharma R, Diwan B, Singh BP, Kulshrestha S. Probiotic fermentation of polyphenols: potential sources of novel functional foods. FOOD PRODUCTION, PROCESSING AND NUTRITION 2022. [DOI: 10.1186/s43014-022-00101-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractFermented functional food products are among the major segments of food processing industry. Fermentation imparts several characteristic effects on foods including the enhancement of organoleptic characteristics, increased shelf-life, and production of novel health beneficial compounds. However, in addition to macronutrients present in the food, secondary metabolites such as polyphenols are also emerging as suitable fermentable substrates. Despite the traditional antimicrobial view of polyphenols, accumulating research shows that polyphenols exert differential effects on bacterial communities by suppressing the growth of pathogenic microbes while concomitantly promoting the proliferation and survival of probiotic bacteria. Conversely, probiotic bacteria not only survive among polyphenols but also induce their fermentation which often leads to improved bioavailability of polyphenols, production of novel metabolic intermediates, increased polyphenolic content, and thus enhanced functional capacity of the fermented food. In addition, selective fermentation of combinations of polyphenol-rich foods or fortification with polyphenols can result in novel functional foods. The present narrative review specifically explores the potential of polyphenols as fermentable substrates in functional foods. We discuss the emerging bidirectional relationship between polyphenols and probiotic bacteria with an aim at promoting the development of novel functional foods based on the amalgamation of probiotic bacteria and polyphenols.
Graphical abstract
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Kiousi DE, Efstathiou C, Tegopoulos K, Mantzourani I, Alexopoulos A, Plessas S, Kolovos P, Koffa M, Galanis A. Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Front Microbiol 2022; 13:922689. [PMID: 35783439 PMCID: PMC9244547 DOI: 10.3389/fmicb.2022.922689] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022] Open
Abstract
The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Efstathiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Mantzourani
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Athanasios Alexopoulos
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Stavros Plessas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
- *Correspondence: Stavros Plessas,
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Koffa
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
- Alex Galanis,
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