1
|
Wu J, Cheng X, Wu Z, Dong S, Zhong Q. In Vitro Cholesterol-Lowering Bioactivity, Synthetic Pathway, and Structural Characterization of Exopolysaccharide Synthesized by Schleiferilactobacillus harbinensis Z171. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:3737-3751. [PMID: 39818809 DOI: 10.1021/acs.jafc.4c09916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2025]
Abstract
A strain identified as Schleiferilactobacillus harbinensis was isolated from Chinese sauerkraut, and its exopolysaccharide (EPS) exhibited excellent in vitro cholesterol-lowering bioactivity. Besides, the whole genome of this strain and the structure characteristics of the purified EPS were investigated in this study. S. harbinensis Z171 presented a strong EPS production capacity, with five nucleotide sugar biosynthesis pathways regulated by an EPS synthesis gene cluster. Structural characterization revealed that the purified fraction F-EPS1A was a neutral polysaccharide with a molecular weight of 6.4 × 104 Da. The structure of F-EPS1A contained a backbone that comprised blocks of four 1,2-linked and three 1,3-linked alpha mannose units. Some 1,2-linked alpha mannose residues were branched at C6 with side chains formed by single alpha mannose or a disaccharide consisting of 1,6-linked alpha mannose residues. The structural characteristics endowed F-EPS1A with a high level of cholesterol-lowering bioactivity. In addition, whole genome analysis indicated that S. harbinensis Z171 possessed a strong EPS production capacity. These findings suggested that the EPS produced by S. harbinensis Z171 could be applied as a potential cholesterol-lowering prebiotic agent or supplement in functional food.
Collapse
Affiliation(s)
- Jinsong Wu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Department of Science, Henan University of Animal Husbandry and Economy, Henan, Zhengzhou 450001, China
| | - Xianbo Cheng
- Dietary Fiber Isolation and Structural Characterization Laboratory, Guangxi Vocational College of Technology and Business, Nanning 530003, China
| | - Ziyi Wu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Sashuang Dong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
2
|
Popović N, Veljović K, Radojević D, Brdarić E, Stevanović D, Živković M, Kojić M. Insight into the Probiogenomic Potential of Enterococcus faecium BGPAS1-3 and Application of a Potent Thermostable Bacteriocin. Foods 2024; 13:2637. [PMID: 39200563 PMCID: PMC11353538 DOI: 10.3390/foods13162637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/02/2024] Open
Abstract
This study aimed to investigate the probiogenomic features of artisanal bacteriocin-producing Enterococcus faecium BGPAS1-3 and the use of the improved pMALc5HisEk expression vector for overexpressing class II bacteriocins and the application of purified bacteriocin 31 in a milk model as a preservative against L. monocytogenes. The BGPAS1-3 strain was isolated from traditional fresh soft cheese manufactured in households on a small scale in rural locations surrounding Pale Mountain City in Bosnia and Herzegovina. The whole-genome sequencing approach and bioinformatics analyses revealed that the strain BGPAS1-3 was non-pathogenic to humans. The presence of bacteriocin operons suggested the ability of the isolate to suppress the growth of pathogens. Coding regions for three maturated bacteriocins (bacteriocin 31, bacteriocin 32, and enterocin P) produced by BGPAS1-3 were amplified and expressed in Escherichia coli ER2523 using the pMALc5HisEk system. All three bacteriocins were successfully overexpressed and purified after enterokinase cleavage but showed different antimicrobial activity. Bacteriocin 31 showed significantly stronger antimicrobial activity compared with bacteriocin 32. It was the only one that proved to be suitable for use as a food preservative against L. monocytogenes in a milk model.
Collapse
Affiliation(s)
- Nikola Popović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Katarina Veljović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Dušan Radojević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Emilija Brdarić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Dušan Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Milica Živković
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
| | - Milan Kojić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (K.V.); (D.R.); (E.B.); (D.S.); (M.Ž.)
- Department of Research and Development, Institute of Virology, Vaccines, and Sera “Torlak”, Vojvode Stepe 458, 11152 Belgrade, Serbia
| |
Collapse
|
3
|
Xiao J, Chen C, Fu Z, Wang S, Luo F. Assessment of the Safety and Probiotic Properties of Enterococcus faecium B13 Isolated from Fermented Chili. Microorganisms 2024; 12:994. [PMID: 38792822 PMCID: PMC11123876 DOI: 10.3390/microorganisms12050994] [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: 02/25/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety of B13 were evaluated at the genetic and phenotype levels in vitro and then confirmed in vivo. The genome of B13 contains one chromosome and two plasmids. The average nucleotide identity indicated that B13 was most closely related to the fermentation-plant-derived strain. The strain does not carry the major virulence genes of the clinical E. faecium strains but contains aac(6')-Ii, ant (6)-Ia, msrC genes. The strain had a higher tolerance to acid at pH 3.0, 4.0, and 0.3% bile salt and a 32.83% free radical DPPH clearance rate. It can adhere to Caco-2 cells and reduce the adhesion of E. coli to Caco-2 cells. The safety assessment revealed that the strain showed no hemolysis and did not exhibit gelatinase, ornithine decarboxylase, lysine decarboxylase, or tryptophanase activity. It was sensitive to twelve antibiotics but was resistant to erythromycin, rifampicin, tetracycline, doxycycline, and minocycline. Experiments in vivo have shown that B13 can be located in the ileum and colon and has no adverse effects on experiment animals. After 28 days of feeding, B13 did not remarkable change the α-diversity of the gut flora or increase the virulence genes. Our study demonstrated that E. faecium B13 may be used as a probiotic candidate.
Collapse
Affiliation(s)
- Jingmin Xiao
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Cai Chen
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Zhuxian Fu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Shumin Wang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China;
| | - Fan Luo
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China;
| |
Collapse
|
4
|
Huidrom S, Ngashangva N, Khumlianlal J, Sharma KC, Mukherjee PK, Devi SI. Genomic insights from Lactiplantibacillus plantarum BRD3A isolated from Atingba, a traditional fermented rice-based beverage and analysis of its potential for probiotic and antimicrobial activity against Methicillin-resistant Staphylococcus aureus. Front Microbiol 2024; 15:1357818. [PMID: 38628861 PMCID: PMC11019378 DOI: 10.3389/fmicb.2024.1357818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Lactiplantibacillus plantarum BRD3A was isolated from Atingba, a traditional fermented rice-based beverage of Manipur. Its genomic sequence has 13 contigs and its genome size is 3,320,817 bp with a guanine-cytosine (GC) ratio of 44.6%. It comprises 3185 genes including 3112 coding sequences (CDSs), 73 RNAs (including 66 tRNAs and others), and one clustered regularly interspaced short palindromic repeat (CRISPR) array. A comparative and phylogenetic analysis with the Lp. plantarum genome shows that this strain has close similarity with other Lp. plantarum strains and about 99% average nucleotide identity. Functional annotation using evolutionary genealogy of genes-non-supervised orthologous groups (EggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) reveals genes associated with various biological processes such as metabolism, genetic information processing, and transport functions. Furthermore, the strain harbors bacteriocins like plantaricin E, Plantaricin F, and Enterocin X categorized under class IIb by the BAGEL4 database, indicating its potential antimicrobial properties. Additionally, AntiSMASH web server predicted four secondary regions-T3PKS, terpene, cyclic lactone inducer, and ribosomally synthesized and post-translationally modified peptide (RiPP)-suggesting an even higher antimicrobial potential. We validated the antimicrobial activity of Lp. plantarum BRD3A through in vitro experiments in which it exhibited promising bactericidal effects on methicillin-resistant Staphylococcus aureus, inhibiting their biofilm growth. These findings indicate the potential of Lp. plantarum BRD3A to be used as an alternative to conventional antibiotics.
Collapse
Affiliation(s)
- Surmani Huidrom
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Ng Ngashangva
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| | - Joshua Khumlianlal
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | | | - Pulok Kumar Mukherjee
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| | - Sarangthem Indira Devi
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| |
Collapse
|
5
|
Tarek N, Azmy AF, Khairalla AS, Abdel-Fattah M, Jefri OA, Shaban M, El-Sayed AA, El-Gendy AO. Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens. Heliyon 2023; 9:e16253. [PMID: 37292348 PMCID: PMC10245172 DOI: 10.1016/j.heliyon.2023.e16253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Objective This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens. Methods The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools. Results Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion. Conclusion Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.
Collapse
Affiliation(s)
- Nashwa Tarek
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt
- Basic Science Department, Faculty of Oral and Dental Medicine, Nahda University Beni-Suef (NUB), Beni Suef, Egypt
| | - Ahmed F. Azmy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
| | - Ahmed S. Khairalla
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Medhat Abdel-Fattah
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt
| | - Ohoud A. Jefri
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mohamed Shaban
- Department of Physics, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawarah, 42351, Saudi Arabia
- Nanophotonics and Applications (NPA) Lab, Physics Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Abdelaziz A.A. El-Sayed
- Biology Department, Faculty of Science, Islamic University of Madinah, Al-Madinah Al- Munawarah, 42351, Saudi Arabia
- Zoology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Ahmed O. El-Gendy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Egypt
| |
Collapse
|
6
|
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: 0.5] [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.
Collapse
|
7
|
Zhao X, Liang Q, Song X, Zhang Y. Whole genome sequence of Lactiplantibacillus plantarum MC5 and comparative analysis of eps gene clusters. Front Microbiol 2023; 14:1146566. [PMID: 37200914 PMCID: PMC10185785 DOI: 10.3389/fmicb.2023.1146566] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction Probiotic Lactiplantibacillus plantarum MC5 produces large amounts of exopolysaccharides (EPS), and its use as a compound fermentor can greatly improve the quality of fermented milk. Methods To gain insight into the genomic characteristics of probiotic MC5 and reveal the relationship between its EPS biosynthetic phenotype and genotype, we analyzed the carbohydrate metabolic capacity, nucleotide sugar formation pathways, and EPS biosynthesis-related gene clusters of strain MC5 based on its whole genome sequence. Finally, we performed validation tests on the monosaccharides and disaccharides that strain MC5 may metabolize. Results Genomic analysis showed that MC5 has seven nucleotide sugar biosynthesis pathways and 11 sugar-specific phosphate transport systems, suggesting that the strain can metabolize mannose, fructose, sucrose, cellobiose, glucose, lactose, and galactose. Validation results showed that strain MC5 can metabolize these seven sugars and produce significant amounts of EPS (> 250 mg/L). In addition, strain MC5 possesses two typical eps biosynthesis gene clusters, which include the conserved genes epsABCDE, wzx, and wzy, six key genes for polysaccharide biosynthesis, and one MC5-specific epsG gene. Discussion These insights into the mechanism of EPS-MC5 biosynthesis can be used to promote the production of EPS through genetic engineering.
Collapse
|
8
|
Singh A, Husein A, Singh S, Ghattargi V, Dhotre D, Shouche YS, Colaco S, Abhyankar V, Patekar S, Chhabria K, Kumar S, Urhekar AD, Modi D. False-positive detection of Group B Streptococcus (GBS) in chromogenic media (Strep B Carrot Broth) due to presence of Enterococcus faecalis in High Vaginal swabs. J Med Microbiol 2022; 71. [PMID: 35972461 DOI: 10.1099/jmm.0.001577] [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: 11/18/2022] Open
Abstract
Introduction. Vaginal colonization of Group B Streptococcus (GBS) is associated with preterm births and neonatal sepsis. Thus routine screening of GBS in prenatal care is recommended.Hypothesis. Chromogenic media (carrot broth) aids in specific and rapid detection of GBS.Aim. To investigate the efficiency of Strep B Carrot Broth for detection of GBS in high vaginal swabs from pregnant women.Methods. In this study 201 vaginal swab samples were collected from pregnant women. Swabs were inoculated in chromogenic media (Strep B Carrot Broth). The positive and negative cultures were inoculated on blood agar and crome agar plates. The colonies were subjected to 16S rRNA sequencing and gene-specific PCR for confirmation. The Christie Atkins Munch Peterson (CAMP) and bile esculin agar (BEA) tests were used for biochemical confirmation. PCR was performed on genomic DNA isolated from uncultured vaginal swabs.Results. It was found that 20/201 (9.9 %) vaginal swab samples were positive in the Strep B Carrot Broth and 17/20 (85 %) and 19/20 (95 %) of these samples yielded colonies on blood agar and crome agar, respectively. Of the 181 carrot broth-negative samples, 1 (0.5 %) and 38 (20.9 %) yielded colonies on blood agar and crome agar plates, respectively. However, 16 s rRNA sequencing revealed that none of the 20 carrot broth-positive cultures were GBS and had sequence similarities to Enterococcus faecalis. This was also confirmed by using gene-specific PCR and BEA positivity. Furthermore, E. faecalis was detected by PCR in DNA isolated from 57 uncultured vaginal swabs samples, GBS could only be detected by PCR in four samples.Conclusion. Carrot broth-based culture can lead to false-positive detection due to the presence of E. faecalis. Thus GBS-positive results in carrot broth must be confirmed by the other molecular and biochemical tests before making a final diagnosis.
Collapse
Affiliation(s)
- Abhishek Singh
- Department of Microbiology, MGM Institute of Health Sciences, Kamothe Navi Mumbai, India.,Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Atahar Husein
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Salomi Singh
- Department of Obstetrics and Gynaecology, MGM Institute of Health Sciences, Kalamboli, Navi Mumbai, India
| | - Vikas Ghattargi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Sciences, Pune, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Sciences, Pune, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Sciences, Pune, India
| | - Stacy Colaco
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Vivek Abhyankar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Sciences, Pune, India
| | - Suyash Patekar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Sciences, Pune, India
| | - Karisma Chhabria
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Sushil Kumar
- Department of Obstetrics and Gynaecology, MGM Institute of Health Sciences, Kalamboli, Navi Mumbai, India
| | - A D Urhekar
- Department of Microbiology, MGM Institute of Health Sciences, Kamothe Navi Mumbai, India
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| |
Collapse
|
9
|
Wang T, Ishikawa T, Sasaki M, Chiba T. Oral and Gut Microbial Dysbiosis and Non-alcoholic Fatty Liver Disease: The Central Role of Porphyromonas gingivalis. Front Med (Lausanne) 2022; 9:822190. [PMID: 35308549 PMCID: PMC8924514 DOI: 10.3389/fmed.2022.822190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota play many important roles, such as the regulation of immunity and barrier function in the intestine, and are crucial for maintaining homeostasis in living organisms. The disruption in microbiota is called dysbiosis, which has been associated with various chronic inflammatory conditions, food allergies, colorectal cancer, etc. The gut microbiota is also affected by several other factors such as diet, antibiotics and other medications, or bacterial and viral infections. Moreover, there are some reports on the oral-gut-liver axis indicating that the disruption of oral microbiota affects the intestinal biota. Non-alcoholic fatty liver disease (NAFLD) is one of the systemic diseases caused due to the dysregulation of the oral-gut-liver axis. NAFLD is the most common liver disease reported in the developed countries. It includes liver damage ranging from simple steatosis to nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. Recently, accumulating evidence supports an association between NAFLD and dysbiosis of oral and gut microbiota. Periodontopathic bacteria, especially Porphyromonas gingivalis, have been correlated with the pathogenesis and development of NAFLD based on the clinical and basic research, and immunology. P. gingivalis was detected in the liver, and lipopolysaccharide from this bacteria has been shown to be involved in the progression of NAFLD, thereby indicating a direct role of P. gingivalis in NAFLD. Moreover, P. gingivalis induces dysbiosis of gut microbiota, which promotes the progression of NAFLD, through disrupting both metabolic and immunologic pathways. Here, we review the roles of microbial dysbiosis in NAFLD. Focusing on P. gingivalis, we evaluate and summarize the most recent advances in our understanding of the relationship between oral-gut microbiome symbiosis and the pathogenesis and progression of non-alcoholic fatty liver disease, as well as discuss novel strategies targeting both P. gingivalis and microbial dysbiosis.
Collapse
Affiliation(s)
- Ting Wang
- Division of Internal Medicine, Department of Oral Medicine, Iwate Medical University, Morioka, Japan
| | - Taichi Ishikawa
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Morioka, Japan
| | - Minoru Sasaki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Morioka, Japan
| | - Toshimi Chiba
- Division of Internal Medicine, Department of Oral Medicine, Iwate Medical University, Morioka, Japan
| |
Collapse
|
10
|
Jani K, Sharma A. Targeted amplicon sequencing reveals the probiotic potentials of microbial communities associated with traditional fermented foods of northeast India. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
11
|
El Jeni R, Ghedira K, El Bour M, Abdelhak S, Benkahla A, Bouhaouala-Zahar B. High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus. BMC Microbiol 2020; 20:322. [PMID: 33096980 PMCID: PMC7584074 DOI: 10.1186/s12866-020-01980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. RESULTS The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. CONCLUSION Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.
Collapse
Affiliation(s)
- Rim El Jeni
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Kais Ghedira
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Monia El Bour
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Alia Benkahla
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
- Medical School of Tunis, University of Tunis El Manar, 1007 Tunis, Tunisia
| |
Collapse
|
12
|
Min B, Kim K, Li V, Cho S, Kim H. Changes in Cell Membrane Fatty Acid Composition of Streptococcus thermophilus in Response to Gradually Increasing Heat Temperature. J Microbiol Biotechnol 2020; 30:739-748. [PMID: 32482940 PMCID: PMC9745660 DOI: 10.4014/jmb.1912.12053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
In this study, a method of heat adaptation was implemented in an attempt to increase the upper thermal threshold of two Streptococcus thermophilus found in South Korea and identified the alterations in membrane fatty acid composition to adaptive response to heat. In order to develop heat tolerant lactic acid bacteria, heat treatment was continuously applied to bacteria by increasing temperature from 60°C until the point that no surviving cell was detected. Our results indicated significant increase in heat tolerance of heat-adapted strains compared to the wild type (WT) strains. In particular, the survival ratio of basically low heat-tolerant strain increased even more. In addition, the strains with improved heat tolerance acquired cross protection, which improved their survival ratio in acid, bile salts and osmotic conditions. A relation between heat tolerance and membrane fatty acid composition was identified. As a result of heat adaptation, the ratio of unsaturated to saturated fatty acids (UFA/SFA) and C18:1 relative concentration were decreased. C6:0 in only heatadapted strains and C22:0 in only the naturally high heat tolerant strain were detected. These results support the hypothesis, that the consequent increase of SFA ratio is a cellular response to environmental stresses such as high temperatures, and it is able to protect the cells from acid, bile salts and osmotic conditions via cross protection. This study demonstrated that the increase in heat tolerance can be utilized as a mean to improve bacterial tolerance against various environmental stresses.
Collapse
Affiliation(s)
- Bonggyu Min
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kkotnim Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Vladimir Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 0886, Republic of Korea
| | - Seoae Cho
- C&K genomics Inc., C-1008, H businesspark, Seoul 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 0886, Republic of Korea
- C&K genomics Inc., C-1008, H businesspark, Seoul 08826, Republic of Korea
| |
Collapse
|
13
|
Comparison of Antimicrobial Resistance and Pan-Genome of Clinical and Non-Clinical Enterococcus cecorum from Poultry Using Whole-Genome Sequencing. Foods 2020; 9:foods9060686. [PMID: 32466367 PMCID: PMC7353540 DOI: 10.3390/foods9060686] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 02/07/2023] Open
Abstract
Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol, suggesting possible new mechanisms of resistance to these drugs. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.
Collapse
|
14
|
Presence of Different Bacterial Species in Thermal Sources and Novelty in Their Industrial Enzyme Productions. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.3.08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
15
|
Koringa PG, Thakkar JR, Pandit RJ, Hinsu AT, Parekh MJ, Shah RK, Jakhesara SJ, Joshi CG. Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing. Funct Integr Genomics 2018; 19:237-247. [DOI: 10.1007/s10142-018-0640-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/25/2018] [Accepted: 10/12/2018] [Indexed: 01/14/2023]
|
16
|
Ghattargi VC, Gaikwad MA, Meti BS, Nimonkar YS, Dixit K, Prakash O, Shouche YS, Pawar SP, Dhotre DP. Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains. BMC Genomics 2018; 19:652. [PMID: 30180794 PMCID: PMC6122445 DOI: 10.1186/s12864-018-5043-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/27/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. RESULTS E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains. CONCLUSIONS Beyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.
Collapse
Affiliation(s)
- Vikas C. Ghattargi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
- Department of Biotechnology, Basaveshwar Engineering College, Bagalkot, Karnataka 587102 India
| | - Meghana A. Gaikwad
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Bharati S. Meti
- Department of Biotechnology, Basaveshwar Engineering College, Bagalkot, Karnataka 587102 India
| | - Yogesh S. Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Kunal Dixit
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Yogesh S. Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Shrikant P. Pawar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Dhiraj P. Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| |
Collapse
|