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Acero-Pimentel D, Romero-Sánchez DI, Fuentes-Curiel SN, Quirasco M. Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression. Antonie Van Leeuwenhoek 2024; 117:40. [PMID: 38393447 PMCID: PMC10891205 DOI: 10.1007/s10482-024-01938-0] [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: 07/28/2023] [Accepted: 01/28/2024] [Indexed: 02/25/2024]
Abstract
Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.
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Affiliation(s)
- Daniel Acero-Pimentel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Diana I Romero-Sánchez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sac Nicté Fuentes-Curiel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Maricarmen Quirasco
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico.
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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.
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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
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Liu W, Cheng M, Li J, Zhang P, Fan H, Hu Q, Han M, Su L, He H, Tong Y, Ning K, Long Y. Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 18:696-707. [PMID: 33607294 PMCID: PMC8377022 DOI: 10.1016/j.gpb.2020.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
The gut microbiota of intensive care unit (ICU) patients displays extreme dysbiosis associated with increased susceptibility to organ failure, sepsis, and septic shock. However, such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota. We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis. We collected 131 fecal samples from 64 ICU patients diagnosed with sepsis or septic shock and performed 16S rRNA gene sequencing to dissect their gut microbiota compositions. During the development of sepsis or septic shock and during various medical treatments, the ICU patients always exhibited two dysbiotic microbiota patterns, or ICU-enterotypes, which could not be explained by host properties such as age, sex, and body mass index, or external stressors such as infection site and antibiotic use. ICU-enterotype I (ICU E1) comprised predominantly Bacteroides and an unclassified genus of Enterobacteriaceae, while ICU-enterotype II (ICU E2) comprised predominantly Enterococcus. Among more critically ill patients with Acute Physiology and Chronic Health Evaluation II (APACHE II) scores > 18, septic shock was more likely to occur with ICU E1 (P = 0.041). Additionally, ICU E1 was correlated with high serum lactate levels (P = 0.007). Therefore, different patterns of dysbiosis were correlated with different clinical outcomes, suggesting that ICU-enterotypes should be diagnosed as independent clinical indices. Thus, the microbial-based human index classifier we propose is precise and effective for timely monitoring of ICU-enterotypes of individual patients. This work is a first step toward precision medicine for septic patients based on their gut microbiota profiles.
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Affiliation(s)
- Wanglin Liu
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinman Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Peng Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qinghe Hu
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Longxiang Su
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Huaiwu He
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yun Long
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China.
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Belguesmia Y, Bendjeddou K, Kempf I, Boukherroub R, Drider D. Heterologous Biosynthesis of Five New Class II Bacteriocins From Lactobacillus paracasei CNCM I-5369 With Antagonistic Activity Against Pathogenic Escherichia coli Strains. Front Microbiol 2020; 11:1198. [PMID: 32636812 PMCID: PMC7318550 DOI: 10.3389/fmicb.2020.01198] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus paracasei CNCM I-5369 isolated from a traditional Algerian dairy product produces extracellular inhibitory substances, namely, bacteriocins, which are active against a panel of pathogenic Escherichia coli strains. This activity was observed only at a narrow pH 4.5–5, and resulted to be heat stable and sensitive to the action of proteolytic enzymes, which indicate a proteinaceous nature. This new strain has a genome of 2,752,975 bp, with a 46.6% G + C ratio and contains at least 2664 coding sequences. The Bagel software analysis identified five open reading frames (ORFs) that are translated to new class II bacteriocin. Each ORF was cloned in frame with a His-tag tail and expressed in E. coli BL21 (DE3) (pLysS) strain. Of note, each fusion protein carrying any of these ORFs at the C- or N-terminal position resulted to be active against E. coli 184 strain used as target organism. This manuscript reports the first multi-bacteriocinogenic strain producing five new class II bacteriocins with activity against Gram-negative bacilli (GNB), namely, E. coli. Heterologous expression and activity of each new class II bacteriocin were demonstrated.
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Affiliation(s)
- Yanath Belguesmia
- UMR Transfrontalière BioEcoAgro N° 1158, Université de Lille, INRAE, Université de Liège, UPJV, YNCREA, Université d'Artois, Universite du Littoral Côte d'Opale, ICV - Institut Charles Viollette, Lille, France
| | - Kamel Bendjeddou
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Béjaïa, Algeria
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie Bactériologie Antibiorésistance, Ploufragan, France.,Université Bretagne Loire, Rennes, France
| | - Rabah Boukherroub
- Université de Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520 - IEMN, Lille, France
| | - Djamel Drider
- UMR Transfrontalière BioEcoAgro N° 1158, Université de Lille, INRAE, Université de Liège, UPJV, YNCREA, Université d'Artois, Universite du Littoral Côte d'Opale, ICV - Institut Charles Viollette, Lille, France
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Salomskiene J, Jonkuviene D, Macioniene I, Abraitiene A, Zeime J, Repeckiene J, Vaiciulyte-Funk L. Differences in the occurence and efficiency of antimicrobial compounds produced by lactic acid bacteria. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-018-03227-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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