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Kogay R, Wolf YI, Koonin EV. Defence systems and horizontal gene transfer in bacteria. Environ Microbiol 2024; 26:e16630. [PMID: 38643972 PMCID: PMC11034907 DOI: 10.1111/1462-2920.16630] [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: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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Kogay R, Wolf YI, Koonin EV. Defense systems and horizontal gene transfer in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579689. [PMID: 38410456 PMCID: PMC10896350 DOI: 10.1101/2024.02.09.579689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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Sisk-Hackworth L, Brown J, Sau L, Levine AA, Tam LYI, Ramesh A, Shah RS, Kelley-Thackray ET, Wang S, Nguyen A, Kelley ST, Thackray VG. Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities. Biol Sex Differ 2023; 14:79. [PMID: 37932822 PMCID: PMC10626657 DOI: 10.1186/s13293-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine. METHODS We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice. RESULTS Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the Bacteroidaceae, Eggerthellaceae, Muribaculaceae, and Rikenellaceae families, which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (Escherichia Shigella, Lachnoclostridium, and Eggerthellaceae genus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine. CONCLUSIONS Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
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Affiliation(s)
- Laura Sisk-Hackworth
- University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Jada Brown
- University of California San Diego, La Jolla, CA, USA
| | - Lillian Sau
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Reeya S Shah
- University of California San Diego, La Jolla, CA, USA
| | | | - Sophia Wang
- University of California San Diego, La Jolla, CA, USA
| | - Anita Nguyen
- University of California San Diego, La Jolla, CA, USA
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de Oliveira Vieira KC, da Silva ABB, Felício SA, Lira FS, de Figueiredo C, Bezirtzoglou E, Pereira VC, Nakagaki WR, Nai GA, Winkelströter LK. Orange juice containing Pediococcus acidilactici CE51 modulates the intestinal microbiota and reduces induced inflammation in a murine model of colitis. Sci Rep 2023; 13:18513. [PMID: 37898635 PMCID: PMC10613252 DOI: 10.1038/s41598-023-45819-4] [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: 01/28/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023] Open
Abstract
The management of inflammatory bowel diseases has been widely investigated, especially ulcerative colitis. Thus, studies with the application of new probiotic products are needed in the prevention/treatment of these clinical conditions. The objective of this work was to evaluate the effects of probiotic orange juice containing Pediococcus acidilactici CE51 in a murine model of colitis. 45 male Swiss lineage mice were used, divided into five groups (n = 9): control, colitis, colitis + probiotic (probiotic orange juice containing CE51), colitis + placebo (orange juice) and colitis + sulfasalazine (10 mg/kg/Weight). The induction of colitis was performed with dextran sodium sulfate (3%). The treatment time was 5 and 15 days after induction. Histopathological analysis, serum measurements of TNF-α and C-reactive protein and metagenomic analysis of feces were performed after euthanasia. Probiotic treatment reduced inflammation in the small intestine, large intestine and spleen. The probiotic did not alter the serum dosages of TNF-α and C-reactive protein. Their use maintained the quantitative ratio of the phylum Firmicutes/Bacteroidetes and increased Lactobacillus helveticus with 15 days of treatment (p < 0.05). The probiotic orange juice containing P. acidilactici CE51 positively modulated the gut microbiota composition and attenuated the inflammation induced in colitis.
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Affiliation(s)
- Karolinny Cristiny de Oliveira Vieira
- Health Sciences Faculty, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Cidade Universitária, Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Ana Beatriz Batista da Silva
- Master in Health Science, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Suelen Aparecida Felício
- Master in Health Science, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Fábio Santos Lira
- Department of Physical Education, Faculdade de Ciências e Tecnologia, Universidade Estadual Paulista, UNESP, Rua Roberto Simonsen, 305, Presidente Prudente, Sao Paulo, 19060-900, Brazil
| | - Caíque de Figueiredo
- Department of Physical Education, Faculdade de Ciências e Tecnologia, Universidade Estadual Paulista, UNESP, Rua Roberto Simonsen, 305, Presidente Prudente, Sao Paulo, 19060-900, Brazil
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Dragana, 68100, Alexandroupolis, Greece
| | - Valéria Cataneli Pereira
- Health Sciences Faculty, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Cidade Universitária, Presidente Prudente, Sao Paulo, 19050-920, Brazil
- Master in Health Science, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Wilson Romero Nakagaki
- Health Sciences Faculty, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Cidade Universitária, Presidente Prudente, Sao Paulo, 19050-920, Brazil
- Master in Health Science, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Gisele Alborghetti Nai
- Health Sciences Faculty, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Cidade Universitária, Presidente Prudente, Sao Paulo, 19050-920, Brazil
| | - Lizziane Kretli Winkelströter
- Health Sciences Faculty, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Cidade Universitária, Presidente Prudente, Sao Paulo, 19050-920, Brazil.
- Master in Health Science, UNOESTE (University of Western Sao Paulo), 700, Jose Bongiovani St., Presidente Prudente, Sao Paulo, 19050-920, Brazil.
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Wang Y, He Y, Liang Y, Liu H, Chen X, Kulyar MFEA, Shahzad A, Wei K, Li K. Fecal microbiota transplantation attenuates Escherichia coli infected outgrowth by modulating the intestinal microbiome. Microb Cell Fact 2023; 22:30. [PMID: 36803386 PMCID: PMC9936653 DOI: 10.1186/s12934-023-02027-z] [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: 10/23/2022] [Accepted: 01/21/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Given the crucial role of gut microbiota in animal and human health, studies on modulating the intestinal microbiome for therapeutic purposes have grasped a significant attention, of which the role of fecal microbiota transplantation (FMT) has been emphasized. METHODS In the current study, we evaluated the effect of FMT on gut functions in Escherichia coli (E. coli) infection by using mice model. Moreover, we also investigated the subsequently dependent variables of infection, i.e., body weight, mortality, intestinal histopathology, and the expression changes in tight junction proteins (TJPs). RESULTS The FMT effectively decreased weight loss and mortality to a certain extent with the restoration of intestinal villi that resulted in high histological scores for jejunum tissue damage (p < 0.05). The effect of FMT on alleviating the reduction of intestinal TJPs was also proved by immunohistochemistry analysis and mRNA expression levels. Moreover, the abundance of health-threatening bacteria, belonging to phylum Proteobacteria, family Enterobacteriaceae and Tannerellaceae, genus Escherichia-Shigella, Sphingomonas, Collinsella, etc., were significantly increased, whereas beneficial bacteria, belonging to phylum Firmicutes, family Lactobacillaceae, genus Lactobacillus were decreased in the gut of infected mice. Furthermore, we sought to investigate the association of clinical symptoms with FMT treatment with modulation in gut microbiota. According to beta diversity, the microbial community of gut microbiota results reflected the similarities between non-infected and FMT groups. The improvement of the intestinal microbiota in FMT group was characterized by the significant high level of beneficial microorganisms with the synergistic decrease of Escherichia-Shigella, Acinetobacter, and other taxa. CONCLUSION The findings suggest a beneficial host-microbiome correlation following fecal microbiota transplanatation for controlling gut infections and pathogens-associated diseases.
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Affiliation(s)
- Yaping Wang
- grid.27871.3b0000 0000 9750 7019Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yuanyuan He
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Han Liu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Xiushuang Chen
- grid.27871.3b0000 0000 9750 7019Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China ,grid.27871.3b0000 0000 9750 7019MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Muhammad Fakhar-e-Alam Kulyar
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Asim Shahzad
- grid.412496.c0000 0004 0636 6599Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100 Pakistan
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Davray D, Bawane H, Kulkarni R. Non-redundant nature of Lactiplantibacillus plantarum plasmidome revealed by comparative genomic analysis of 105 strains. Food Microbiol 2023; 109:104153. [DOI: 10.1016/j.fm.2022.104153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
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Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes. mSystems 2022; 7:e0019122. [PMID: 36069451 PMCID: PMC9600348 DOI: 10.1128/msystems.00191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Sewage water from around the world contains an abundance of short plasmids, several of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions are only starting to be unveiled. Here, we utilized a previously created data set of 159,332 assumed small plasmids from 24 different global sewage samples. The detailed phylogeny, as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera, were investigated to understand sewage plasmidome dynamics globally. A total of 58,429 circular elements carried genes encoding plasmid-related features, and MASH distance analyses showed a high degree of diversity. A single (yet diverse) cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Our results suggested a prevalence of plasmid-backbone gene combinations over others. This could be related to selected bacterial genera that act as bacterial hosts. These combinations also mirrored the geographical locations of the sewage samples. Our functional domain network analysis identified three groups of plasmids. However, these backbone domains were not exclusive to any given group, and Acinetobacter was the dominant host genus among the theta-replicating plasmids, which contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common in the sewage plasmidomes and were found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotic resistance for these pathogens from around the globe. IMPORTANCE Antimicrobial resistance is a global threat to human health, as it inhibits our ability to treat infectious diseases. This study utilizes sewage water plasmidomes to identify plasmid-derived features and highlights antimicrobial resistance genes, particularly macrolide resistance genes, as abundant in sewage water plasmidomes in Firmicutes and Acinetobacter hosts. The emergence of macrolide resistance in these bacteria suggests that macrolide selective pressure exists in sewage water and that the resident bacteria can readily acquire macrolide resistance via small plasmids.
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Moradi J, Fathollahi M, Halimi S, Alvandi A, Abiri R, Vaziri S, Rezaei A. Characterization of resistome in Lactobacillus genomic sequences from the human gut. J Glob Antimicrob Resist 2022; 30:451-458. [DOI: 10.1016/j.jgar.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/20/2022] [Indexed: 10/18/2022] Open
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Zhang C, Xu Y, Wu S, Zheng W, Song S, Ai C. Fabrication of astaxanthin-enriched colon-targeted alginate microspheres and its beneficial effect on dextran sulfate sodium-induced ulcerative colitis in mice. Int J Biol Macromol 2022; 205:396-409. [PMID: 35176325 DOI: 10.1016/j.ijbiomac.2022.02.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/22/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023]
Abstract
Astaxanthin (Ax) with a strong antioxidant activity is beneficial to human health, but its application is limited by its highly unsaturated structure and poor water-solubility. Ax-enriched colon targeted alginate particles (Ax-Alg) was prepared by high-pressure spraying and ionic gelation, and most of particles was in the range of 0.5-3.2 μm in a diameter. The in vitro models showed that Ax-Alg can maintain the structural integrity in the different conditions (pH, heat and ion). In addition, Ax-Alg can well tolerate the conditions in the mouth, stomach and small intestine and reach the colon where Ax was released due to fermentation of gut microbiota. Mice experiment showed that Ax-Alg reduced dextran sulfate sodium-induced colitis, involving weight loss, disease activity index, colonic mucosal integrity and inflammation, and oxidative damage. On the other hand, Ax-Alg regulated the gut microbiota composition and reduced the abundances of Bacteroidetes members that had positive correlation with ulcerative colitis. Ax-Alg had better effect on the treatment of ulcerative colitis than oil-in-water emulsion, which can be attributed to the synergistic effect of Ax and alginate. This study can be helpful for the application of colon-targeted delivery system in the foods and treatment of colon diseases.
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Affiliation(s)
- Chenxi Zhang
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China
| | - Yuxin Xu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China
| | - Shuang Wu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China
| | - Weiyun Zheng
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China
| | - Shuang Song
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China
| | - Chunqing Ai
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China.
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Surve S, Shinde DB, Kulkarni R. Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods. Sci Rep 2022; 12:1940. [PMID: 35121802 PMCID: PMC8816928 DOI: 10.1038/s41598-022-05850-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/18/2022] [Indexed: 01/11/2023] Open
Abstract
Lactiplantibacillus plantarum is one of the most diverse species of lactic acid bacteria found in various habitats. The aim of this work was to perform preliminary phenotypic and genomic characterization of two novel and potentially probiotic L. plantarum strains isolated from Indian foods, viz., dhokla batter and jaggery. Both the strains were bile and acid tolerant, utilized various sugars, adhered to intestinal epithelial cells, produced exopolysaccharides and folate, were susceptible for tetracycline, erythromycin, and chloramphenicol, did not cause hemolysis, and exhibited antimicrobial and plant phenolics metabolizing activities. The genetic determinants of bile tolerance, cell-adhesion, bacteriocins production, riboflavin and folate biosynthesis, plant polyphenols utilization, and exopolysaccharide production were found in both the strains. One of the strains contained a large number of unique genes while the other had a simultaneous presence of glucansucrase and fructansucrase genes which is a rare trait in L. plantarum. Comparative genome analysis of 149 L. plantarum strains highlighted high variation in the cell-adhesion and sugar metabolism genes while the genomic regions for some other properties were relatively conserved. This work highlights the unique properties of our strains along with the probiotic and technically important genomic features of a large number of L. plantarum strains.
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Affiliation(s)
- Sarvesh Surve
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, 412115, India.,Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH, 03755, USA
| | - Dasharath B Shinde
- 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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Levante A, Lazzi C, Vatsellas G, Chatzopoulos D, Dionellis VS, Makrythanasis P, Neviani E, Folli C. Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution. Microorganisms 2021; 9:microorganisms9030648. [PMID: 33800997 PMCID: PMC8003834 DOI: 10.3390/microorganisms9030648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022] Open
Abstract
The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in lactic acid bacteria. In this work, genome sequences of Lacticaseibacillus strains of dairy origin were compared, focusing on the distribution of type I TA systems homologous to Lpt/RNAII and of the most common type II TA systems. A high number of TA systems have been identified spread in all the analyzed strains, with type I TA systems mainly located on plasmid DNA. The type II TA systems identified in these strains highlight the diversity of encoded toxins and antitoxins and their organization. This study opens future perspectives on the use of genomic data as a resource for the study of TA systems distribution and prevalence in microorganisms of industrial relevance.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Giannis Vatsellas
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Dimitris Chatzopoulos
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Vasilis S. Dionellis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Periklis Makrythanasis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
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