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Pereira AP, Antunes P, Peixe L, Freitas AR, Novais C. Current insights into the effects of cationic biocides exposure on Enterococcus spp. Front Microbiol 2024; 15:1392018. [PMID: 39006755 PMCID: PMC11242571 DOI: 10.3389/fmicb.2024.1392018] [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: 02/26/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Cationic biocides (CBs), such as quaternary ammonium compounds and biguanides, are critical for controlling the spread of bacterial pathogens like Enterococcus spp., a leading cause of multidrug-resistant healthcare-associated infections. The widespread use of CBs in recent decades has prompted concerns about the potential emergence of Enterococcus spp. populations exhibiting resistance to both biocides and antibiotics. Such concerns arise from their frequent exposure to subinhibitory concentrations of CBs in clinical, food chain and diverse environmental settings. This comprehensive narrative review aimed to explore the complexity of the Enterococcus' response to CBs and of their possible evolution toward resistance. To that end, CBs' activity against diverse Enterococcus spp. collections, the prevalence and roles of genes associated with decreased susceptibility to CBs, and the potential for co- and cross-resistance between CBs and antibiotics are reviewed. Significant methodological and knowledge gaps are identified, highlighting areas that future studies should address to enhance our comprehension of the impact of exposure to CBs on Enterococcus spp. populations' epidemiology. This knowledge is essential for developing effective One Health strategies that ensure the continued efficacy of these critical agents in safeguarding Public Health.
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Affiliation(s)
- Ana P Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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Tadesse BT, Svetlicic E, Zhao S, Berhane N, Jers C, Solem C, Mijakovic I. Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms. Microbiol Res 2024; 283:127702. [PMID: 38552381 DOI: 10.1016/j.micres.2024.127702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark; Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark
| | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Ethiopia
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark.
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark; Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Takahashi K, Tsuji M, Nakagawasai O, Miyagawa K, Kurokawa K, Mochida-Saito A, Iwasa M, Iwasa H, Suzuki S, Takeda H, Tadano T. Anxiolytic effects of Enterococcus faecalis 2001 on a mouse model of colitis. Sci Rep 2024; 14:11519. [PMID: 38769131 PMCID: PMC11106339 DOI: 10.1038/s41598-024-62309-3] [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: 03/05/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
Ulcerative colitis (UC) is a refractory inflammatory bowel disease, which is known to cause psychiatric disorders such as anxiety and depression at a high rate in addition to peripheral inflammatory symptoms. However, the pathogenesis of these psychiatric disorders remains mostly unknown. While prior research revealed that the Enterococcus faecalis 2001 (EF-2001) suppressed UC-like symptoms and accompanying depressive-like behaviors, observed in a UC model using dextran sulfate sodium (DSS), whether it has an anxiolytic effect remains unclear. Therefore, we examined whether EF-2001 attenuates DSS-induced anxiety-like behaviors. Treatment with 2% DSS for seven days induced UC-like symptoms and anxiety-like behavior through the hole-board test, increased serum lipopolysaccharide (LPS) and corticosterone concentration, and p-glucocorticoid receptor (GR) in the prefrontal cortex (PFC), and decreased N-methyl-D-aspartate receptor subunit (NR) 2A and NR2B expression levels in the PFC. Interestingly, these changes were reversed by EF-2001 administration. Further, EF-2001 administration enhanced CAMKII/CREB/BDNF-Drebrin pathways in the PFC of DSS-treated mice, and labeling of p-GR, p-CAMKII, and p-CREB showed colocalization with neurons. EF-2001 attenuated anxiety-like behavior by reducing serum LPS and corticosterone levels linked to the improvement of UC symptoms and by facilitating the CAMKII/CREB/BDNF-Drebrin pathways in the PFC. Our findings suggest a close relationship between UC and anxiety.
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Affiliation(s)
- Kohei Takahashi
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi, 324-8501, Japan
| | - Minoru Tsuji
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi, 324-8501, Japan.
| | - Osamu Nakagawasai
- Division of Pharmacology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-Ku, Sendai, Miyagi, 981-8558, Japan
| | - Kazuya Miyagawa
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi, 324-8501, Japan
| | - Kazuhiro Kurokawa
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi, 324-8501, Japan
| | - Atsumi Mochida-Saito
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi, 324-8501, Japan
| | - Masahiro Iwasa
- Nihon Berm Co., Ltd., 16-12, Nihonbashi-Kodenmacho, Chuo-Ku, Tokyo, 103-0001, Japan
| | - Hiroyuki Iwasa
- Nihon Berm Co., Ltd., 16-12, Nihonbashi-Kodenmacho, Chuo-Ku, Tokyo, 103-0001, Japan
| | - Shigeo Suzuki
- Nihon Berm Co., Ltd., 16-12, Nihonbashi-Kodenmacho, Chuo-Ku, Tokyo, 103-0001, Japan
| | - Hiroshi Takeda
- Department of Pharmacology, School of Pharmacy at Fukuoka, International University of Health and Welfare, 137-1 Enokizu, Okawa, Fukuoka, 831-8501, Japan
| | - Takeshi Tadano
- Division of Pharmacology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-Ku, Sendai, Miyagi, 981-8558, Japan
- Department of Environment and Preventive Medicine, Graduate School of Medicine Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa, 920-8640, Japan
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4
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Zheng Y, Duan Z, Wu Y, Luo Y, Peng X, Wu J. Analysis of the Cadmium Removal Mechanism of Human Gut Bacteria Enterococcus faecalis Strain ATCC19433 from a Genomic Perspective. Biol Trace Elem Res 2024:10.1007/s12011-024-04169-6. [PMID: 38602649 DOI: 10.1007/s12011-024-04169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Cadmium (Cd) is one of the most well-known toxic metals capable of entering the human body via the food chain, leading to serious health problems. Human gut microbes play a pivotal role in controlling Cd bioavailability and toxicity within the human gastrointestinal tract, primarily due to their capacity for Cd adsorption and metabolism. In this work, a Cd-resistant bacterial strain, Enterococcus faecalis strain ATCC19433 was isolated from human gut microbiota. Cd binding assays and comprehensive characterization analyses were performed, revealing the ability of strain ATCC19433 to remove Cd from the solution. Cd adsorption primarily occurred on the bacterial cell walls, which was ascribed to the exciting of functional groups on the bacterial surfaces, containing alkyl, amide II, and phosphate groups; meanwhile, Cd could enter cells, probably through transport channels or via diffusion. These results indicated that Cd removal by the strain was predominantly dependent on biosorption and bioaccumulation. Whole-genome sequencing analyses further suggested the probable mechanisms of biosorption and bioaccumulation, including Cd transport by transporter proteins, active efflux of Cd by cadmium efflux pumps, and mitigating oxidative stress-induced cell damage by DNA repair proteases. This study evaluated the Cd removal capability and mechanism of Enterococcus faecalis strain ATCC19433 while annotating the genetic functions related to Cd removal, which may facilitate the development of potential human gut strains for the removal of Cd.
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Affiliation(s)
- Yu Zheng
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
- Guizhou Ecological Environment Resources Management Co., LTD, Guiyang, 550009, China
| | - Zhibin Duan
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
- School of Public Health, Zunyi Medical University, Zunyi, 563006, China
| | - Yonggui Wu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.
- Guizhou Hostile Environment Ecological Restoration Technology Engineering Research Centre, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystem Observation and Research Station, Ministry of Education, Guiyang, 550025, China.
| | - Yang Luo
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Xiaoyu Peng
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Jianye Wu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
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Dreyer A, Lenz C, Groß U, Bohne W, Zautner AE. Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure. BMC Microbiol 2024; 24:110. [PMID: 38570789 PMCID: PMC10988882 DOI: 10.1186/s12866-024-03253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND All gastrointestinal pathogens, including Enterococcus faecalis and Enterococcus faecium, undergo adaptation processes during colonization and infection. In this study, we investigated by data-independent acquisition mass spectrometry (DIA-MS) two crucial adaptations of these two Enterococcus species at the proteome level. Firstly, we examined the adjustments to cope with bile acid concentrations at 0.05% that the pathogens encounter during a potential gallbladder infection. Therefore, we chose the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) as well as the secondary bile acid deoxycholic acid (DCA), as these are the most prominent bile acids. Secondly, we investigated the adaptations from an aerobic to a microaerophilic environment, as encountered after oral-fecal infection, in the absence and presence of deoxycholic acid (DCA). RESULTS Our findings showed similarities, but also species-specific variations in the response to the different bile acids. Both Enterococcus species showed an IC50 in the range of 0.01- 0.023% for DCA and CDCA in growth experiments and both species were resistant towards 0.05% CA. DCA and CDCA had a strong effect on down-expression of proteins involved in translation, transcription and replication in E. faecalis (424 down-expressed proteins with DCA, 376 down-expressed proteins with CDCA) and in E. faecium (362 down-expressed proteins with DCA, 391 down-expressed proteins with CDCA). Proteins commonly significantly altered in their expression in all bile acid treated samples were identified for both species and represent a "general bile acid response". Among these, various subunits of a V-type ATPase, different ABC-transporters, multi-drug transporters and proteins related to cell wall biogenesis were up-expressed in both species and thus seem to play an essential role in bile acid resistance. Most of the differentially expressed proteins were also identified when E. faecalis was incubated with low levels of DCA at microaerophilic conditions instead of aerobic conditions, indicating that adaptations to bile acids and to a microaerophilic atmosphere can occur simultaneously. CONCLUSIONS Overall, these findings provide a detailed insight into the proteomic stress response of two Enterococcus species and help to understand the resistance potential and the stress-coping mechanisms of these important gastrointestinal bacteria.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
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Daca A, Jarzembowski T. From the Friend to the Foe- Enterococcus faecalis Diverse Impact on the Human Immune System. Int J Mol Sci 2024; 25:2422. [PMID: 38397099 PMCID: PMC10888668 DOI: 10.3390/ijms25042422] [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: 01/30/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Enterococcus faecalis is a bacterium which accompanies us from the first days of our life. As a commensal it produces vitamins, metabolizes nutrients, and maintains intestinal pH. All of that happens in exchange for a niche to inhabit. It is not surprising then, that the bacterium was and is used as an element of many probiotics and its positive impact on the human immune system and the body in general is hard to ignore. This bacterium has also a dark side though. The plasticity and relative ease with which one acquires virulence traits, and the ability to hide from or even deceive and use the immune system to spread throughout the body make E. faecalis a more and more dangerous opponent. The statistics clearly show its increasing role, especially in the case of nosocomial infections. Here we present the summarization of current knowledge about E. faecalis, especially in the context of its relations with the human immune system.
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Affiliation(s)
- Agnieszka Daca
- Department of Physiopathology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Tomasz Jarzembowski
- Department of Microbiology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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Yegin Z, Mamatova Z, Yurt MNZ, Tasbasi BB, Acar EE, Ucak S, Süleymanoğlu AA, Aydin A, Ozalp VC, Sudagidan M. A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan. Chem Biodivers 2024; 21:e202301374. [PMID: 38230544 DOI: 10.1002/cbdv.202301374] [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: 09/06/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.
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Affiliation(s)
- Zeynep Yegin
- Medical Laboratory Techniques Program, Vocational School of Health Services, Sinop University, 57000, Sinop, Türkiye
| | - Zhanylbubu Mamatova
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Mediha Nur Zafer Yurt
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Behiye Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Elif Esma Acar
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Samet Ucak
- Department of Medical Biology and Genetics, School of Medicine, Istanbul Aydin University, Kucukcekmece, 34295, Istanbul, Türkiye
| | - Ali Anıl Süleymanoğlu
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Ali Aydin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Faculty of Medicine, Atilim University, 06830, Ankara, Türkiye
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
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Maitreya A, Qureshi A. Genomic and phenotypic characterisation of Enterococcus mundtii AM_AQ_BC8 for its anti-biofilm, antimicrobial and probiotic potential. Arch Microbiol 2024; 206:84. [PMID: 38296886 DOI: 10.1007/s00203-023-03816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Enterococcus mundtii AM_AQ_BC8 isolated from biofouled filtration membrane was characterised as a potential probiotic bacterium showing strong L-lactic acid-producing capability. Experimental studies revealed that E. mundtii AM_AQ_BC8 possess antibiofilm and antimicrobial ability too, as tested against strong biofilm-forming bacteria like Pseudomonas spp. The present study has evaluated the genetic potential of E. mundtii AM_AQ_BC8 through genome sequencing. Whole genome analysis revealed the presence of key genes like ldh_1 and ldh_2 responsible for lactic acid production along with genes encoding probiotic features such as acid and bile salt resistance (dnaK, dnaJ, argS), fatty acid synthesis (fabD, fabE) and lactose utilisation (lacG, lacD). The phylogenomic analysis based on OrthoANI (99.85%) and dDDH (96.8%) values revealed that the strain AM_AQ_BC8 shared the highest homology with E. mundtii. The genome sequence of strain AM_AQ_BC8 has been deposited to NCBI and released with GenBank accession no. SAMN32531201. The study primarily demonstrated the probiotic potential of E. mundtii AM_AQ_BC8 isolate, for L-lactate synthesis in high concentration (8.98 g/L/day), which also showed anti-biofilm and antimicrobial activities.
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Affiliation(s)
- Anuja Maitreya
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute Nehru Marg, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Jin X, Cai R, Wang R, Cao Y, Dai Z, Hu Z, Ge X, Tao L, Zhang L. Antibiotic Resistance Characterization and Molecular Characteristics of Enterococcus Species Isolated from Combination Probiotic Preparations in China. Foodborne Pathog Dis 2024; 21:36-43. [PMID: 37824752 DOI: 10.1089/fpd.2023.0025] [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] [Indexed: 10/14/2023] Open
Abstract
Enterococci can act as reservoirs for antibiotic-resistant genes that are potentially at risk of being transferred to other bacteria that inhabit in the gastrointestinal tract. The aim of this study was to determine the phenotypic and molecular characteristics of antibiotic-resistant enterococci isolated from probiotic preparations. In total, we isolated 15 suspected Enterococcus species from 5 compound probiotics, which were identified by 16S rDNA as 12 Enterococcus faecium and 3 Enterococcus faecalis. Determination of antimicrobial susceptibility by the microdilution broth method showed widespread resistance to sulfamethoxazole (100%), norfloxacin (99.3%), azithromycin (99.3%), gentamicin (86.7%), and chloramphenicol (20%). Whole genome sequencing of five resistant strains revealed that all had circular DNA chromosomes and that E. faecium J-1-A to J-4-A contained a plasmid, while E. faecalis J-5-A did not. The results of the resistance gene analysis revealed that each strain contained approximately 30 resistance genes, with the antibiotic resistance genes and the multidrug resistance efflux pump genes mdtG, lmrC, and lmrD detected in all strains. The chloramphenicol resistance genes ykkC and ykkD were first identified in E. faecalis. And there were 21, 19, 21, 21, and 29 virulence factors involved in strains, respectively. Further analysis of the gene islands (GIs) revealed that each strain contained more than 10 GIs. The above results confirm the existence of hidden dangers in the safety of probiotics and remind us to carefully select probiotic preparations containing enterococcal strains to avoid the potential spread of resistance and pathogenicity.
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Affiliation(s)
- Xin Jin
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Rui Cai
- Emergency Department, Jiangsu Province Hospital of Chinese Medicine, Jiangsu, Nanjing, China
| | - Ruirong Wang
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Yu Cao
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Zhen Dai
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Ziyan Hu
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Xiaoming Ge
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Lei Tao
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Ling Zhang
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
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10
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Matle I, Atanda AC, Pierneef R, Magwedere K, Mafuna T. Resistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africa. Genomics 2023; 115:110742. [PMID: 37967685 DOI: 10.1016/j.ygeno.2023.110742] [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: 05/18/2023] [Revised: 10/18/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
Enterococcus faecalis is a ubiquitous bacterium found in various environments, including processed beef meat, and is known for its importance in both food safety and public health. This pivotal significance stems not solely from its virulence but also from its adeptness in eliciting multidrug-resistant infections in humans. The aim of this study was to investigate the population structure, resistome, mobilome, and virulome of E. faecalis obtained from processed beef meat sources in South Africa. A total of eight genomes sequenced in this study were examined, alongside 78 publicly available, high-quality genomes of E. faecalis, with a comprehensive analysis conducted to identify antimicrobial resistance (AMR) determinants, virulence factors, and mobile genetic elements (MGE). Six distinct sequence types (STs) (ST79, ST860, ST40, ST238, ST21, and ST700) and 41 core virulence factors were found across all the genomes. The virulence factors included genes encoding adherence (ace, asa1, Ef0485, ebpA, ebpB, ebpC, srtC); exoenzyme (Ef3023, Ef0818, gelE, sprE); immunomodulation (cpsA, cpsB, cpsC, cpsD, cpsE, cpsF, cpsG, cpsH, cpsI, cpsK), and biofilm formation (bopD, fsrA, fsrB, fsrC). In addition, AMR genes were identified across all genomes, which include aminoglycoside resistance (ant(6)-Ia), trimethoprim resistance (dfrA), drug and biocide resistance (efrA and efrB), multidrug efflux pump (emeA), clindamycin quinupristin-dalfopristin, dalfopristin resistance (lsaA), and tetracycline resistance (tetM). The genomes of E. faecalis sequenced here contained a variety of MGEs, including Insertion Sequences (ISs), transposons, prophages, and plasmids, which may have facilitated genetic exchange within and between these species. The results highlight that beef meat products act as a reservoir for virulent E. faecalis strains possessing antibiotic-resistance traits. This study provides insight into the genomic characteristics, antimicrobial resistance genes, virulence factors, and genetic mobile elements associated with eight E. faecalis isolates from processed beef meat in the Gauteng province of South Africa.
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Affiliation(s)
- Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Abimbola Comfort Atanda
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa; Department of Life Sciences, University of South Africa, Florida Campus, South Africa
| | - Rian Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa; Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria 0001, South Africa; Microbiome@UP, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - Thendo Mafuna
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa.
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Baqer Almayali EJ, Al-Kraety IAA, Maki Naji A, Abd almunaam LH. Bacteriological study and its antibiotics susceptibility pattern of Otitis Media in Iraqi patients. BIONATURA 2023; 8:1-7. [DOI: 10.21931/rb/2023.08.01.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Otitis media is an acute upper respiratory tract infection-related inflammation of the middle ear and tympanic membrane, frequently affecting children. Typically, a subsequent bacterial infection complicates a viral infection, which ultimately causes the condition. The study aims to study the function of bacterial ear infections and its causes, as well as their resistance to medications, which was the focus of this investigation. The first axis of the research was the identification of bacterial isolates using recognized diagnostic tools, and the second axis was determining the antibiotic's resistance and sensitivity. Patients with otitis media were gathered from Al-Hakim General Hospital and Al-Sadr city hospital in Al-Najaf city between November 2020 and April 2021 for 100 clinical samples. More than 80 samples were found to be infected with bacteria. Bacterial strains found in this investigation are ( 30 ) isolates of Pseudomonas aeruginosa, (20) isolates of Klebsiella spp, (20) isolates of Proteus spp, ( 15 ) isolates of Staphylococcus aureus, (8) isolates Escherichia coli and (7) isolates Enterococcus fecalies. As part of this research, the disk diffusion method was used to assess how sensitive the test was. The results showed that Pseudomonas aeruginosa was resistant to most antibiotics, particularly the penicillin family, cephalosporin, and trimethoprim, with the existence of isolates resistant to meropenem. The investigation results varied for the quinolone, aminoglycoside, and macrolide families. Klebsiella spp. were tested for antibiotic sensitivity and found to be resistant to most antibiotics, particularly those in the penicillin family, cephalosporins, and trimethoprim. Some quinolones, aminoglycosides, and macrolides are also resistant. Proteus spp were resistant to most antibiotics, particularly the penicillin family (except for augmentin, which had some sensitive isolates) and cephalosporin (except for cefdinir and cefepime) had some susceptible isolates) and trimethoprim, in addition to the presence of isolates resistant to meropenem. There is a discrepancy in the examination results for the quinolone family. The aminoglycoside family is also highly resistant. S. aureus isolates were resistant to penicillin (except for augmentin, which some isolates were responsive to), trimethoprim, and quinolones, with the presence of isolates resistant to vancomycin. The macrolide class ( azithromycin) also has a significant resistance level. Escherichia coli is susceptible to meropenem, imipenem, and certain cephalosporin generations. Augmentin, cefepime, cephalothin, meropenem, imipenem, and azithromycin were ineffective against Enterococcus fecal. The conclusion is that Pseudomonas spp has a role in ear infections and the germs Klebsiella spp., Proteus spp., Staphylococcus aureus, Escherichia coli, and Enterococcus fecalies. Penicillin and cephalosporin resistance was seen in the majority of the identified isolates. The existence of isolates of Proteus and Pseudomonas species resistant to meropenem. Vancomycin-resistant strains of Staphylococcus aureus isolates are present.
Keywords: Otitis media, Resistance antibiotic, S.aureus, P.aerginosa
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Affiliation(s)
- Enas Jalil Baqer Almayali
- Department of Medical Laboratory Technique, Faculty of Medical and Health Technique, University of Alkafeel. Najaf, Iraq
| | - Israa Abdul Ameer Al-Kraety
- Department of Medical Laboratory Technique, Faculty of Medical and Health Technique, University of Alkafeel. Najaf, Iraq
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Baliyan N, Maurya AK, Kumar A, Agnihotri VK, Kumar R. Probiotics from the bovine raw milk of Lahaul valley showed cis-9, trans-11 conjugated linoleic acid isomer and antioxidant activity with food formulation ability. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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13
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Kavitake D, Devi PB, Delattre C, Reddy GB, Shetty PH. Exopolysaccharides produced by Enterococcus genus - An overview. Int J Biol Macromol 2023; 226:111-120. [PMID: 36493920 DOI: 10.1016/j.ijbiomac.2022.12.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Exopolysaccharide (EPS) biomolecules produced by lactic acid bacteria (LAB) are of prodigious interest due to their unique structural, physico-chemical, and functional characteristics. Several genera of LAB including Enterococcus spp. have been studied for EPS production by various research groups worldwide. EPS produced by various strains from Enterococcus spp. have shown a wide range of functional and technological properties with potential commercial applications. Numerous techniques are used in the characterization of Enterococcus EPS to reveal their structure, linkage, monosaccharide units, functional groups, morphology, and thermal properties. Bioactive potentials of Enterococcus EPS include antioxidant, antibacterial, antibiofilm, anticancer, immunological, prebiotic, and antidiabetic potentials which have been widely reported. These functional and biological properties make Enterococcus EPS a candidate of great importance for multiple applications in the area of food, pharmaceuticals, biomedical and environmental. This review is focused on EPS produced by various strains of the Enterococcus genus isolated from different sources. Several procedures and parameters involved in the production and purification of Enterococcus EPS are also deliberated along with the functional aspects and potential applications.
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Affiliation(s)
- Digambar Kavitake
- Department of Biochemistry, ICMR - National Institute of Nutrition, Hyderabad, 500007, India
| | - Palanisamy Bruntha Devi
- Department of Food Science and Technology, Pondicherry University, Pondicherry 605014, India
| | - Cedric Delattre
- Clermont Auvergne INP, Institut Pascal, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
| | - G Bhanuprakash Reddy
- Department of Biochemistry, ICMR - National Institute of Nutrition, Hyderabad, 500007, India.
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Wang Q, Zhang L, Zhang Y, Chen H, Song J, Lyu M, Chen R, Zhang L. Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7. Front Microbiol 2022; 13:1008648. [PMID: 36419435 PMCID: PMC9677121 DOI: 10.3389/fmicb.2022.1008648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.
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Affiliation(s)
- Qian Wang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lei Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yiju Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianghua Song
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lixin Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lixin Zhang,
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Panthee S, Hamamoto H, Paudel A, Kaito C, Suzuki Y, Sekimizu K. Hybrid assembly using long reads resolves repeats and completes the genome sequence of a laboratory strain of Staphylococcus aureus subsp. Aureus RN4220. Heliyon 2022; 8:e11376. [PMID: 36387480 PMCID: PMC9660545 DOI: 10.1016/j.heliyon.2022.e11376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/30/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus aureus RN4220 has been extensively used by staphylococcal researchers as an intermediate strain for genetic manipulation due to its ability to accept foreign DNA. Despite its wide use in laboratories, its complete genome is not available. In this study, we used a hybrid genome assembly approach using minION long reads and Illumina short reads to sequence the complete genome of S. aureus RN4220. The comparative analysis of the annotated complete genome showed the presence of 39 genes fragmented in the previous assembly, many of which were located near the repeat regions. Using RNA-Seq reads, we showed that a higher number of reads could be mapped to the complete genome than the draft genome and the gene expression profile obtained using the complete genome also differs from that obtained from the draft genome. Furthermore, by comparative transcriptomic analysis, we showed the correlation between expression levels of staphyloxanthin biosynthetic genes and the production of yellow pigment. This study highlighted the importance of long reads in completing microbial genomes, especially those possessing repetitive elements. S. aureus RN4220 is used as an intermediate strain for genetic manipulation. We completed its genome and found 39 fragmented genes in previous genome assembly. RNA-Seq analysis improved mapping of the reads with the use of complete genome. Expression of staphyloxanthin biosynthetic genes was correlated with its production.
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Colicins of Escherichia coli Lead to Resistance against the Diarrhea-Causing Pathogen Enterotoxigenic E. coli in Pigs. Microbiol Spectr 2022; 10:e0139622. [PMID: 36190425 PMCID: PMC9603048 DOI: 10.1128/spectrum.01396-22] [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: 12/30/2022] Open
Abstract
Gut microbes can affect host adaptation to various environment conditions. Escherichia coli is a common gut species, including pathogenic strains and nonpathogenic strains. This study was conducted to investigate the effects of different E. coli strains in the gut on the health of pigs. In this study, the complete genomes of two E. coli strains isolated from pigs were sequenced. The whole genomes of Y18J and the enterotoxigenic E. coli strain W25K were compared to determine their roles in pig adaptation to disease. Y18J was isolated from feces of healthy piglets and showed strong antimicrobial activity against W25K in vitro. Gene knockout experiments and complementation analysis followed by modeling the microbe-microbe interactions demonstrated that the antagonistic mechanism of Y18J against W25K relied on the bacteriocins colicin B and colicin M. Compared to W25K, Y18J is devoid of exotoxin-coding genes and has more secondary-metabolite-biosynthetic gene clusters. W25K carries more genes involved in genome replication, in accordance with a shorter cell cycle observed during a growth experiment. The analysis of gut metagenomes in different pig breeds showed that colicins B and M were enriched in Laiwu pigs, a Chinese local breed, but were scarce in boars and Duroc pigs. IMPORTANCE This study revealed the heterogeneity of E. coli strains from pigs, including two strains studied by both in silico and wet experiments in detail and 14 strains studied by bioinformatics analysis. E. coli Y18J may improve the adaptability of pigs toward disease resistance through the production of colicins B and M. Our findings could shed light on the pathogenic and harmless roles of E. coli in modern animal husbandry, leading to a better understanding of intestinal-microbe-pathogen interactions in the course of evolution.
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Hamamoto H, Ogasawara AA, Iwasa M, Sekimizu K. Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences. Front Microbiol 2022; 13:959063. [PMID: 36033901 PMCID: PMC9411961 DOI: 10.3389/fmicb.2022.959063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
In the development and manufacture of fermented foods, it is crucial to control and manage the bacterial species used in the products. We previously reported a complete genome sequence analysis of the Enterococcus faecalis EF-2001 strain that was used for supplements. By comparing this sequence to the publicly available complete genome sequence of E. faecalis strains, we were able to identify specific sequences of the EF-2001 strain. We designed primer sets to amplify these specific regions and performed a polymerase chain reaction (PCR). We confirmed that the DNA fragments were specifically amplified in the genome of the EF-2001 strain, but not those of other lactic acid bacteria (LABs) or strains of the same genus. Furthermore, these primers amplified DNA fragments even in genomic DNA extracted from heat-treated bacteria at 121°C and foods containing the EF-2001 strain. These results suggest that this method allows for simple and highly accurate identification of specific fermentation strains, such as LABs at the strain level, which will be useful for controlling the quality of fermented foods.
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Affiliation(s)
- Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Hachio-ji shi, Tokyo, Japan
| | | | | | - Kazuhisa Sekimizu
- Drug Discoveries by Silkworm Models, Faculty of Pharma-Science, Teikyo University, Hachio-ji shi, Tokyo, Japan
- Genome Pharmaceuticals Institute, Ltd., Bunkyo-ku, Tokyo, Japan
- *Correspondence: Kazuhisa Sekimizu,
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Fu X, Lyu L, Wang Y, Zhang Y, Guo X, Chen Q, Liu C. Safety assessment and probiotic characteristics of Enterococcus lactis JDM1. Microb Pathog 2022; 163:105380. [PMID: 34979271 DOI: 10.1016/j.micpath.2021.105380] [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: 09/01/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1. METHODS Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability. RESULTS E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect. CONCLUSION E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.
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Affiliation(s)
- Xiaomei Fu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Lyu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Wang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Chen
- Institute of Intestinal Diseases, Shanghai Tenth People's Hospital Affiliated to Tongji University, Shanghai, 200072, China.
| | - Chang Liu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Novel Pathogenic Mucorales Identified Using the Silkworm Infection Model. J Fungi (Basel) 2021; 7:jof7110995. [PMID: 34829282 PMCID: PMC8621750 DOI: 10.3390/jof7110995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/20/2021] [Indexed: 02/06/2023] Open
Abstract
Mucormycosis, a rare but highly fatal infection, is caused by fungi of the order Mucorales. Due to their ubiquitous nature, reduced susceptibility to antifungals, acid tolerance, and ability to infect immunocompromised patients through rapid dissemination, these fungi have been frequently reported to infect the COVID-19 patients. In order to develop strategies to overcome mucormycosis, it is essential to understand and identify novel Mucorales present in the environment. In this study, we report the identification of four novel pathogenic Mucorales using the silkworm (Bombyx mori) model. The strains’ phylogeny was analyzed using the genome sequence of the large subunit ribosomal ribonucleic acid (LSU rRNA) and the internal transcribed spacer (ITS) region, where strains 1-3, 5-3, and S286-1101 claded with Mucor orantomantidis, and strain 827-14 claded with Backusella lamprospora. All the strains had a cold-sensitive phenotype with their inability to grow prominently at 4 °C. Mucor sp. 1-3 and 5-3 were characterized by their filamentous and yeast-like growth under aerobic and anaerobic conditions, respectively. The yeast colonies of Mucor sp. 5-3 had multipolar budding cells often observed with cleaved cell surfaces under a scanning electron microscope. We further found that these strains were able to kill immunocompromised mice suggesting their pathogenicity to mammals. Our study established an invertebrate model-based screening system to identify novel pathogenic Mucorales from the natural environment and provided a clue towards the rapid increase in COVID-19 related mucormycosis.
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Tóth AG, Csabai I, Judge MF, Maróti G, Becsei Á, Spisák S, Solymosi N. Mobile Antimicrobial Resistance Genes in Probiotics. Antibiotics (Basel) 2021; 10:antibiotics10111287. [PMID: 34827225 PMCID: PMC8614787 DOI: 10.3390/antibiotics10111287] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.
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Affiliation(s)
- Adrienn Gréta Tóth
- Health Services Management Training Centre, Semmelweis University, 1125 Budapest, Hungary;
| | - István Csabai
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Maura Fiona Judge
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, 6726 Szeged, Hungary;
- Faculty of Water Sciences, University of Public Service, 6500 Baja, Hungary
| | - Ágnes Becsei
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA;
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
- Correspondence: ; Tel.: +36-30-9347-069
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R M, S I, Kv S, Kp S, T R, G S, K R. Genomic characterization of Enterobacter xiangfangensis STP-3: Application to real time petroleum oil sludge bioremediation. Microbiol Res 2021; 253:126882. [PMID: 34619415 DOI: 10.1016/j.micres.2021.126882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Sustainable treatment of petroleum oil sludge still remains as a major challenge to petroleum refineries. Bioremediation is the promising technology involving bacteria for simultaneous production of biosurfactant and followed by degradation of petroleum compounds. Complete genomic knowledge on such potential microbes could accentuate its successful exploitation. The present study discusses the genomic characteristics of novel biosurfactant producing petrophilic/ petroleum hydrocarbon degrading strain, Enterobacter xiangfangensis STP-3, isolated from petroleum refinery oil sludge contaminated soil. The genome has 4,584,462 bp and 4372 protein coding sequences. Functional analysis using the RAST and KEGG databases revealed the presence of biosynthetic gene clusters linked to glycolipid and lipopeptide production and multiple key candidate genes linked with the degradation pathway of petroleum hydrocarbons. Orthology study revealed diversity in gene clusters associated to membrane transport, carbohydrate, amino acid metabolism, virulence and defence mechanisms, and nucleoside and nucleotide synthesis. The comparative analysis with 27 other genomes predicted that the core genome contributes to its inherent bioremediation potential, whereas the accessory genome influences its environmental adaptability in unconventional environmental conditions. Further, experimental results showed that E. xiangfangensis STP-3 was able to degrade PHCs by 82 % in 14 days during the bioremediation of real time petroleum oil sludge with the concomitant production of biosurfactant and metabolic enzymes, To the best of our knowledge, no comprehensive genomic study has been previously reported on the biotechnological prospective of this species.
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Affiliation(s)
- Muneeswari R
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Iyappan S
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Kancheepuram District, Tamil Nadu, India
| | - Swathi Kv
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Sudheesh Kp
- Nutrition, Genetics and Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, 600028, Tamil Nadu, India
| | - Rajesh T
- CSIR-National Environmental Engineering Research Institute, Chennai Zonal Lab, Tamil Nadu, India
| | - Sekaran G
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Ramani K
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India.
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22
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Barbinta-Patrascu ME, Gorshkova Y, Ungureanu C, Badea N, Bokuchava G, Lazea-Stoyanova A, Bacalum M, Zhigunov A, Petrovic S. Characterization and Antitumoral Activity of Biohybrids Based on Turmeric and Silver/Silver Chloride Nanoparticles. MATERIALS (BASEL, SWITZERLAND) 2021; 14:4726. [PMID: 34443248 PMCID: PMC8401137 DOI: 10.3390/ma14164726] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
The phyto-development of nanomaterials is one of the main challenges for scientists today, as it offers unusual properties and multifunctionality. The originality of our paper lies in the study of new materials based on biomimicking lipid bilayers loaded with chlorophyll, chitosan, and turmeric-generated nano-silver/silver chloride particles. These materials showed a good free radical scavenging capacity between 76.25 and 93.26% (in vitro tested through chemiluminescence method) and a good antimicrobial activity against Enterococcus faecalis bacterium (IZ > 10 mm). The anticancer activity of our developed bio-based materials was investigated against two cancer cell lines (human colorectal adenocarcinoma cells HT-29, and human liver carcinoma cells HepG2) and compared to one healthy cell line (human fibroblast BJ cell line). Cell viability was evaluated for all prepared materials after a 24 h treatment and was used to select the biohybrid with the highest therapeutic index (TI); additionally, the hemolytic activity of the samples was also evaluated. Finally, we investigated the morphological changes induced by the developed materials against the cell lines studied. Biophysical studies on these materials were done by correlating UV-Vis and FTIR absorption spectroscopy, with XRD, SANS, and SAXS methods, and with information provided by microscopic techniques (AFM, SEM/EDS). In conclusion, these "green" developed hybrid systems are an important alternative in cancer treatment, and against health problems associated with drug-resistant infections.
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Affiliation(s)
- Marcela-Elisabeta Barbinta-Patrascu
- Department of Electricity, Solid-State Physics and Biophysics, Faculty of Physics, University of Bucharest, 405 Atomistilor Street, P.O. Box MG-11, 077125 Bucharest-Măgurele, Romania;
| | - Yulia Gorshkova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie, 6 Dubna, 141980 Moscow, Russia;
- Institute of Physics, Kazan Federal University, 16a Kremlyovskaya Street, 420008 Kazan, Russia
| | - Camelia Ungureanu
- General Chemistry Department, Faculty of Applied Chemistry and Materials Science, University “Politehnica” of Bucharest, 1-7, Polizu Street, 011061 Bucharest, Romania;
| | - Nicoleta Badea
- General Chemistry Department, Faculty of Applied Chemistry and Materials Science, University “Politehnica” of Bucharest, 1-7, Polizu Street, 011061 Bucharest, Romania;
| | - Gizo Bokuchava
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie, 6 Dubna, 141980 Moscow, Russia;
| | - Andrada Lazea-Stoyanova
- Low Temperature Plasma Department, National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, Magurele, 077125 Ilfov, Romania;
| | - Mihaela Bacalum
- Department of Life and Environmental Physics, “Horia Hulubei” National Institute of Physics and Nuclear Engineering, 077125 Măgurele, Romania;
| | - Alexander Zhigunov
- Institute of Macromolecular Chemistry AS CR, Heyrovskeho nam. 2, 162 06 Prague 6, Czech Republic;
| | - Sanja Petrovic
- Department of Chemical Technology, Faculty of Technology, University of Nis, Bulevar Oslobodjenja 124, 16000 Leskovac, Serbia;
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