Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens
All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as <i>Lactobacillus plantarum</i>. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel d...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-01-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/28/2/491 |
| _version_ | 1797438395006320640 |
|---|---|
| author | Tariq Aziz Muhammad Naveed Syeda Izma Makhdoom Urooj Ali Muhammad Saad Mughal Abid Sarwar Ayaz Ali Khan Yang Zhennai Manal Y. Sameeh Anas S. Dablool Amnah A. Alharbi Muhammad Shahzad Abdulhakeem S. Alamri Majid Alhomrani |
| author_facet | Tariq Aziz Muhammad Naveed Syeda Izma Makhdoom Urooj Ali Muhammad Saad Mughal Abid Sarwar Ayaz Ali Khan Yang Zhennai Manal Y. Sameeh Anas S. Dablool Amnah A. Alharbi Muhammad Shahzad Abdulhakeem S. Alamri Majid Alhomrani |
| author_sort | Tariq Aziz |
| collection | DOAJ |
| description | All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as <i>Lactobacillus plantarum</i>. 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 <i>YW11</i>. Whole genome sequencing of Lp <i>YW11</i> 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 <i>YW11</i> 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 <i>Salmonella</i>, <i>Shigella</i>, <i>Campylobacter</i>, and <i>Yersinia</i>, 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. |
| first_indexed | 2024-03-09T11:37:17Z |
| format | Article |
| id | doaj.art-8e329d32c1b54123ae5febee0f609e27 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T11:37:17Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-8e329d32c1b54123ae5febee0f609e272023-11-30T23:40:37ZengMDPI AGMolecules1420-30492023-01-0128249110.3390/molecules28020491Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic PathogensTariq Aziz0Muhammad Naveed1Syeda Izma Makhdoom2Urooj Ali3Muhammad Saad Mughal4Abid Sarwar5Ayaz Ali Khan6Yang Zhennai7Manal Y. Sameeh8Anas S. Dablool9Amnah A. Alharbi10Muhammad Shahzad11Abdulhakeem S. Alamri12Majid Alhomrani13Beijing 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, ChinaDepartment of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, PakistanDepartment of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, PakistanDepartment of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, PakistanDepartment of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, PakistanBeijing 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, ChinaDepartment of Biotechnology, University of Malakand, Chakdara 18800, PakistanBeijing 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, ChinaChemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi ArabiaDepartment of Public Health, Health Sciences College Al-Leith, Umm Al-Qura University, Makkah al-Mukarramah 24382, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi ArabiaInstitute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, PakistanDepartment of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaDepartment of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaAll nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as <i>Lactobacillus plantarum</i>. 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 <i>YW11</i>. Whole genome sequencing of Lp <i>YW11</i> 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 <i>YW11</i> 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 <i>Salmonella</i>, <i>Shigella</i>, <i>Campylobacter</i>, and <i>Yersinia</i>, 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.https://www.mdpi.com/1420-3049/28/2/491<i>LP</i> YW11whole genomestreptinruminococcinnutritive bacteriocingut microbiota |
| spellingShingle | Tariq Aziz Muhammad Naveed Syeda Izma Makhdoom Urooj Ali Muhammad Saad Mughal Abid Sarwar Ayaz Ali Khan Yang Zhennai Manal Y. Sameeh Anas S. Dablool Amnah A. Alharbi Muhammad Shahzad Abdulhakeem S. Alamri Majid Alhomrani Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens Molecules <i>LP</i> YW11 whole genome streptin ruminococcin nutritive bacteriocin gut microbiota |
| title | Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens |
| title_full | Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens |
| title_fullStr | Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens |
| title_full_unstemmed | Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens |
| title_short | Genome Investigation and Functional Annotation of <i>Lactiplantibacillus plantarum</i> YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens |
| title_sort | genome investigation and functional annotation of i lactiplantibacillus plantarum i yw11 revealing streptin and ruminococcin a as potent nutritive bacteriocins against gut symbiotic pathogens |
| topic | <i>LP</i> YW11 whole genome streptin ruminococcin nutritive bacteriocin gut microbiota |
| url | https://www.mdpi.com/1420-3049/28/2/491 |
| work_keys_str_mv | AT tariqaziz genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT muhammadnaveed genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT syedaizmamakhdoom genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT uroojali genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT muhammadsaadmughal genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT abidsarwar genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT ayazalikhan genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT yangzhennai genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT manalysameeh genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT anassdablool genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT amnahaalharbi genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT muhammadshahzad genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT abdulhakeemsalamri genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens AT majidalhomrani genomeinvestigationandfunctionalannotationofilactiplantibacillusplantarumiyw11revealingstreptinandruminococcinaaspotentnutritivebacteriocinsagainstgutsymbioticpathogens |