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Burke Ó, Zeden MS, O'Gara JP. The pathogenicity and virulence of the opportunistic pathogen Staphylococcus epidermidis. Virulence 2024; 15:2359483. [PMID: 38868991 DOI: 10.1080/21505594.2024.2359483] [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: 02/02/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024] Open
Abstract
The pervasive presence of Staphylococcus epidermidis and other coagulase-negative staphylococci on the skin and mucous membranes has long underpinned a casual disregard for the infection risk that these organisms pose to vulnerable patients in healthcare settings. Prior to the recognition of biofilm as an important virulence determinant in S. epidermidis, isolation of this microorganism in diagnostic specimens was often overlooked as clinically insignificant with potential delays in diagnosis and onset of appropriate treatment, contributing to the establishment of chronic infection and increased morbidity or mortality. While impressive progress has been made in our understanding of biofilm mechanisms in this important opportunistic pathogen, research into other virulence determinants has lagged S. aureus. In this review, the broader virulence potential of S. epidermidis including biofilm, toxins, proteases, immune evasion strategies and antibiotic resistance mechanisms is surveyed, together with current and future approaches for improved therapeutic interventions.
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Affiliation(s)
- Órla Burke
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | | | - James P O'Gara
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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2
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Qiao W, Jia C, Yang J, Gao G, Guo D, Xu X, Wu Z, Saris PEJ, Xu H, Qiao M. Production of bacterial cellulose-based peptidopolysaccharide BC-L with anti-listerial properties using a co-cultivation strategy. Int J Biol Macromol 2024; 274:133047. [PMID: 38857722 DOI: 10.1016/j.ijbiomac.2024.133047] [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: 01/02/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Bacterial cellulose (BC) has been found extensive applications in diverse domains for its exceptional attributes. However, the lack of antibacterial properties hampers its utilization in food and biomedical sectors. Leucocin, a bacteriocin belonging to class IIa, is synthesized by Leuconostoc that demonstrates potent efficacy against the foodborne pathogen, Listeria monocytogenes. In the current study, co-culturing strategy involving Kosakonia oryzendophytica FY-07 and Leuconostoc carnosum 4010 was used to confer anti-listerial activity to BC, which resulted in the generation of leucocin-containing BC (BC-L). The physical characteristics of BC-L, as determined by X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA), were similar to the physical characteristics of BC. Notably, the experimental results of disc diffusion and growth curve indicated that the BC-L film exhibited a potent inhibitory effect against L. monocytogenes. Scanning electron microscopy (SEM) showed that BC-L exerts its bactericidal activity by forming pores on the bacterial cell wall. Despite the BC-L antibacterial mechanism, which involves pore formation, the mammalian cell viability remained unaffected by the BC-L film. The measurement results of zeta potential indicated that the properties of BC changed after being loaded with leucocin. Based on these findings, the anti-listerial BC-L generated through this co-culture system holds promise as a novel effective antimicrobial agent for applications in meat product preservation and packaging.
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Affiliation(s)
- Wanjin Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki 00940, Finland
| | - Chunhui Jia
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiyuan Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dingyi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xian Xu
- School of Life Science, Shanxi University, Taiyuan 030000, China
| | - Zhenzhou Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki 00940, Finland
| | - Haijin Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Mingqiang Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; School of Life Science, Shanxi University, Taiyuan 030000, China.
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3
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Yi L, Qi T, Li X, Zeng K. Controlling soft rot of green pepper by bacteriocin paracin wx3 and its effect on storage quality of green pepper. Food Chem 2024; 447:138962. [PMID: 38518614 DOI: 10.1016/j.foodchem.2024.138962] [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: 01/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024]
Abstract
A bacteriocin paracin wx3 was investigated as a candidate of natural preservative to control green pepper soft rot. Firstly, paracin wx3 was heterologously expressed in Pichia pastoris X33 with an improved yield of 0.537 g/L. Its size and amino acid sequence were confirmed by Tricine-SDS-PAGE and LC-MS/MS. Then, result of antibacterial activity showed that its MIC value against Pectobacterium carotovorum was 16 μg/mL. In vitro, paracin wx3 completely killed the pathogen at high concentrations ≥8 × MIC. In vivo, disease incidence of green pepper soft rot was decreased from 90% (control) to <2% (8 × MIC). Subsequently, results of action mode showed that paracin wx3 inhibited the growth of pathogen by pore-formation on cell membrane. Last, paracin wx3 treatment reduced losses of weight, firmness, total soluble solid, Vc of green pepper during storage. It also inhibited the production of soft rot volatile p-xylene, 1-butanol, 2-methyl-2-propanol, 3-hydroxybutan-2-one-D, 2-pentyl furan, butanal, etc.
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Affiliation(s)
- Lanhua Yi
- College of Food Science, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China
| | - Teng Qi
- College of Food Science, Southwest University, Chongqing 400715, PR China; Chongqing Tianyou Dairy Co.,Ltd., Chongqing 401120, PR China
| | - Xiaofen Li
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China.
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4
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Rutter JW, Dekker L, Clare C, Slendebroek ZF, Owen KA, McDonald JAK, Nair SP, Fedorec AJH, Barnes CP. A bacteriocin expression platform for targeting pathogenic bacterial species. Nat Commun 2024; 15:6332. [PMID: 39068147 PMCID: PMC11283563 DOI: 10.1038/s41467-024-50591-8] [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: 11/21/2023] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Bacteriocins are antimicrobial peptides that are naturally produced by many bacteria. They hold great potential in the fight against antibiotic resistant bacteria, including ESKAPE pathogens. Engineered live biotherapeutic products (eLBPs) that secrete bacteriocins can be created to deliver targeted bacteriocin production. Here we develop a modular bacteriocin secretion platform that can be used to express and secrete multiple bacteriocins from non-pathogenic Escherichia coli host strains. As a proof of concept we create Enterocin A (EntA) and Enterocin B (EntB) secreting strains that show strong antimicrobial activity against Enterococcus faecalis and Enterococcus faecium in vitro, and characterise this activity in both solid culture and liquid co-culture. We then develop a Lotka-Volterra model that can be used to capture the interactions of these competitor strains. We show that simultaneous exposure to EntA and EntB can delay Enterococcus growth. Our system has the potential to be used as an eLBP to secrete additional bacteriocins for the targeted killing of pathogenic bacteria.
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Affiliation(s)
- Jack W Rutter
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Linda Dekker
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Chania Clare
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Zoe F Slendebroek
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Kimberley A Owen
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Julie A K McDonald
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, UK
| | - Sean P Nair
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
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5
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Ahlawat S, Shukla BN, Singh V, Sharma Y, Choudhary P, Rao A. GLYCOCINS: The sugar peppered antimicrobials. Biotechnol Adv 2024:108415. [PMID: 39033836 DOI: 10.1016/j.biotechadv.2024.108415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Glycosylated bacteriocins, known as glycocins, were first discovered in 2011. These bioactive peptides are produced by bacteria to gain survival advantages. They exhibit diverse types of glycans and demonstrate varied antimicrobial activity. Currently, there are 13 experimentally known glycocins, with over 250 identified in silico across different bacterial phyla. Notably, glycocins are recognized for their glycan-mediated antimicrobial activity, proving effective against drug-resistant and foodborne pathogens. Many glycocins contain rare S-linked glycans. Glycosyltransferases (GTs), responsible for transferring sugar to glycocins and involved in glycocin biosynthesis, often cluster together in the producer's genome. This clustering makes them valuable for custom glycoengineering with diverse substrate specificities. Heterologous expression of glycocins has paved the way for the establishment of microbial factories for glycopeptide and glycoconjugate production across various industries. In this review, we emphasize the primary roles of fully and partially characterized glycocins and their glycosylating enzymes. Additionally, we explore how specific glycan structures facilitate these functions in antibacterial activities. Furthermore, we discuss newer approaches and increasing efforts aimed at exploiting bacterial glycobiology for the development of food preservatives and as replacements or complements to traditional antibiotics, particularly in the face of antibiotic-resistant pathogenic bacteria.
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Affiliation(s)
- Shimona Ahlawat
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
| | | | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yogita Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | | | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India; Food Safety and Standards Authority of India ( FSSAI), New Delhi 110002, India.
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6
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Contessa CR, Moreira EC, Moraes CC, de Medeiros Burkert JF. Production and SERS characterization of bacteriocin-like inhibitory substances by latilactobacillus sakei in whey permeate powder: exploring natural antibacterial potential. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03065-6. [PMID: 39014172 DOI: 10.1007/s00449-024-03065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
Bacteriocins are antimicrobial compounds that have awakened interest across several industries due to their effectiveness. However, their large-scale production often becomes unfeasible on an industrial scale, primarily because of high process costs. Addressing this challenge, this work analyzes the potential of using low-cost whey permeate powder, without any supplementation, to produce bacteriocin-like inhibitory substances (BLIS) through the fermentation of Latilactobacillus sakei. For this purpose, different concentrations of whey permeate powder (55.15 gL-1, 41.3 gL-1 and 27.5 gL-1) were used. The ability of L. sakei to produce BLIS was evaluated, as well as the potential of crude cell-free supernatant to act as a preservative. Raman spectroscopy and surface-enhanced Raman scattering (SERS) provided detailed insights into the composition and changes occurring during fermentation. SERS, in particular, enhanced peak definition significantly, allowing for the identification of key components, such as lactose, proteins, and phenylalanine, which are crucial in understanding the fermentation process and BLIS characteristics. The results revealed that the concentration of 55.15 gL-1 of whey permeate powder, in flasks without agitation and a culture temperature of 32.5 °C, presented the highest biological activity of BLIS, reaching 99% of inhibition of Escherichia coli and Staphylococcus aureus with minimum inhibitory concentration of 36-45%, respectively. BLIS production began within 60 h of cultivation and was associated with class II bacteriocins. The results demonstrate a promising approach for producing BLIS in an economical and environmentally sustainable manner, with potential implications for various industries.
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Affiliation(s)
- Camila Ramão Contessa
- Engineering and Science of Food Graduate Program, College of Chemistry and Food Engineering, Laboratory Bioprocess Engineering, Federal University of Rio Grande, PO Box 474, Rio Grande, RS, 96203-900, Brazil.
| | - Eduardo Ceretta Moreira
- Science and Engineering of Materials Graduate Program, Spectroscopy Laboratory, Federal University of Pampa, PO Box 1650, Bagé, RS, 96413170, Brazil
| | - Caroline Costa Moraes
- Science and Engineering of Materials Graduate Program, Laboratory of Microbiology and Food Toxicology, Federal University of Pampa, PO Box 1650, Bagé, RS, 96413170, Brazil
| | - Janaína Fernandes de Medeiros Burkert
- Engineering and Science of Food Graduate Program, College of Chemistry and Food Engineering, Laboratory Bioprocess Engineering, Federal University of Rio Grande, PO Box 474, Rio Grande, RS, 96203-900, Brazil
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7
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Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 2024; 187:3761-3778.e16. [PMID: 38843834 DOI: 10.1016/j.cell.2024.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Laboratory of Microbial Processes & Biodiversity - LMPB, Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; APC Microbiome & School of Medicine, University College Cork, Cork, Ireland
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chengkai Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China; State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia.
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Jakaria Al-Mujahidy SM, Kryukov K, Ikeo K, Saito K, Uddin ME, Ibn Sina AA. Functional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains. Microbiol Spectr 2024; 12:e0347023. [PMID: 38771133 PMCID: PMC11218508 DOI: 10.1128/spectrum.03470-23] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subsp. bulgaricus. During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against Escherichia coli ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus. IMPORTANCE This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic Lactobacillus delbrueckii subsp. indicus TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.
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Affiliation(s)
- Sk. Md. Jakaria Al-Mujahidy
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kei Saito
- Laboratory of Physics and Cell Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Md. Ekhlas Uddin
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka, Bangladesh
| | - Abu Ali Ibn Sina
- Australian Institute for Bioengineering & Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
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9
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Uniacke-Lowe S, Stanton C, Hill C, Ross RP. The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins. Microorganisms 2024; 12:1346. [PMID: 39065114 PMCID: PMC11278639 DOI: 10.3390/microorganisms12071346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.
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Affiliation(s)
- Shona Uniacke-Lowe
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
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10
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Wang Y, Wang X, Liu X, Lin B. Research Progress on Strategies for Improving the Enzyme Properties of Bacteriophage Endolysins. J Microbiol Biotechnol 2024; 34:1189-1196. [PMID: 38693045 PMCID: PMC11239441 DOI: 10.4014/jmb.2312.12050] [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: 01/02/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 05/03/2024]
Abstract
Bacterial resistance to commonly used antibiotics is one of the major challenges to be solved today. Bacteriophage endolysins (Lysins) have become a hot research topic as a new class of antibacterial agents. They have promising applications in bacterial infection prevention and control in multiple fields, such as livestock and poultry farming, food safety, clinical medicine and pathogen detection. However, many phage endolysins display low bactericidal activities, short half-life and narrow lytic spectrums. Therefore, some methods have been used to improve the enzyme properties (bactericidal activity, lysis spectrum, stability and targeting the substrate, etc) of bacteriophage endolysins, including deletion or addition of domains, DNA mutagenesis, chimerization of domains, fusion to the membrane-penetrating peptides, fusion with domains targeting outer membrane transport systems, encapsulation, the usage of outer membrane permeabilizers. In this review, research progress on the strategies for improving their enzyme properties are systematically presented, with a view to provide references for the development of lysins with excellent performances.
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Affiliation(s)
- Yulu Wang
- Shunde Women and Children's Hospital, Guangdong Medical University, Foshan 528300, P.R. China
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xue Wang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xin Liu
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Bokun Lin
- Shunde Women and Children's Hospital, Guangdong Medical University, Foshan 528300, P.R. China
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, P.R. China
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11
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Wang C, Le MNT, Kawada-Matsuo M, Hisatsune J, Sugawara Y, Arai C, Nakanishi J, Takeda K, Shiba H, Sugai M, Komatsuzawa H. Ursoricin, a bacteriocin of Streptococcus ursoris, has potent activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci. Appl Environ Microbiol 2024; 90:e0016224. [PMID: 38775468 PMCID: PMC11218630 DOI: 10.1128/aem.00162-24] [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: 01/30/2024] [Accepted: 04/19/2024] [Indexed: 06/19/2024] Open
Abstract
The emergence of drug-resistant bacteria, particularly methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), has increased the need to discover novel antimicrobial agents that are effective against these species. Here, we describe the identification and purification of the mutacin BHT-B-like gene locus and bacteriocin peptide from Streptococcus ursoris, which is closely related to Streptococcus ratti; hence, we named this bacteriocin ursoricin. Ursoricin is a cationic, chromosome-encoded peptide that has potent antimicrobial effects against Gram-positive pathogens, including MRSA and VRE, with minimum inhibitory concentrations in the micromolar range. Ursoricin also inhibits the biofilm formation of high biofilm-forming S. aureus. Antibacterial activity was retained after treatment at 100°C for 60 min at a pH range of 3-9 and was partially reduced by treatment with proteinase K for 2 h (63% residual activity). The potent anti-MRSA, anti-VRE, and antibiofilm effects of ursoricin suggest that it is a possible candidate for the treatment of MRSA, VRE, and biofilm-associated infections. IMPORTANCE The emergence of multidrug-resistant bacteria worldwide has posed a significant public health threat and economic burdens that make the identification and development of novel antimicrobial agents urgent. Bacteriocins are promising new agents that exhibit antibacterial activity against a wide range of human pathogens. In this study, we report that the bacteriocin produced by Streptococcus ursoris showed good antibacterial activity against a wide range of Staphylococcus aureus and enterococcus strains, particularly methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and high biofilm-forming S. aureus. Interestingly, this bacteriocin had a stronger effect on S. aureus than on Staphylococcus epidermidis, which is a major commensal bacterium in human skin; this result is important when considering the disturbance of bacterial flora, especially on the skin, mediated by the application of antibacterial agents.
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Affiliation(s)
- Chutian Wang
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Mi Nguyen-Tra Le
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Junzo Hisatsune
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yo Sugawara
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chika Arai
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jun Nakanishi
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Katsuhiro Takeda
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Motoyuki Sugai
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Centre for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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12
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Fijan S, Kürti P, Rozman U, Šostar Turk S. A critical assessment of microbial-based antimicrobial sanitizing of inanimate surfaces in healthcare settings. Front Microbiol 2024; 15:1412269. [PMID: 38933019 PMCID: PMC11199901 DOI: 10.3389/fmicb.2024.1412269] [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: 04/04/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The global rise in antimicrobial resistance (AMR) poses a significant public health threat, especially in healthcare settings, where controlling the spread of antimicrobial genes is crucial. While person-to-person transmission remains the primary route for healthcare-associated infections (HAIs), hospital surfaces serve as key reservoirs for antimicrobial-resistant microorganisms. Regular cleaning and disinfection of these surfaces are essential. Microbial-based products for sanitizing hospital surfaces have emerged as promising tools to combat HAIs and AMR. However, a review of 32 publications found inconsistencies and potential risks. A total of 15 publications included hospital-based trials, while the rest were either in vitro or in situ assays, reviews, book chapters, or commentaries. In most of the hospital-based studies, specific strains of applied microorganisms were not identified, and the term "probiotic" was inaccurately used. These products mainly featured spores from Bacillus and Priestia genera, which was mainly hypothesized to work through competitive exclusion. Most hospital-based studies have shown that the application of microbial-based products resulted in a significant reduction in pathogens on surfaces, thereby contributing to a decrease in the incidence of healthcare-associated infections (HAIs). Further research is however needed to understand the effectiveness, mechanisms of action, and safety of microbial-based sanitizing agents. Strain-level identification is crucial for safety assessments, yet many reviewed products lacked this information. Consequently, there is a need for rigorous safety evaluations within existing regulatory frameworks to ensure the efficacy and safety of microbial-based cleaning products in healthcare settings.
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Affiliation(s)
- Sabina Fijan
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
| | | | - Urška Rozman
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
| | - Sonja Šostar Turk
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
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13
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Kennedy NW, Comstock LE. Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare. Cell Host Microbe 2024; 32:794-803. [PMID: 38870897 PMCID: PMC11216714 DOI: 10.1016/j.chom.2024.05.006] [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: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.
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Affiliation(s)
- Nolan W Kennedy
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
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14
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Morandini L, Caulier S, Bragard C, Mahillon J. Bacillus cereus sensu lato antimicrobial arsenal: An overview. Microbiol Res 2024; 283:127697. [PMID: 38522411 DOI: 10.1016/j.micres.2024.127697] [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: 12/17/2023] [Revised: 02/25/2024] [Accepted: 03/16/2024] [Indexed: 03/26/2024]
Abstract
The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.
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Affiliation(s)
| | - Simon Caulier
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Claude Bragard
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
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15
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Landa G, Aguerri L, Irusta S, Mendoza G, Arruebo M. PLGA nanoparticle-encapsulated lysostaphin for the treatment of Staphylococcus aureus infections. Int J Biol Macromol 2024; 271:132563. [PMID: 38782313 DOI: 10.1016/j.ijbiomac.2024.132563] [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: 04/07/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Staphylococcus aureus possesses the ability to become pathogenic, leading to severe and life-threatening infections. Its methicillin-resistant variant MRSA has garnered high-priority status due to its increased morbidity and associated mortality. This emphasizes the urgency for novel anti-staphylococcal agents. The bacteriocin lysostaphin stands out for its remarkable bactericidal activity against S. aureus, including MRSA, outperforming conventional antibiotics. However, the clinical application of lysostaphin faces challenges, including enzymatic activity loss under physiological conditions and potential immunogenicity. This study introduces a novel approach by encapsulating lysostaphin within polylactic-co-glycolic acid (PLGA) nanoparticles, a biodegradable copolymer known for its biocompatibility and sustained drug release ability. The study assesses the antimicrobial activity of lysostaphin-loaded PLGA nanoparticles against different S. aureus strains, and we also used GFP-expressing S. aureus for facilitating its traceability in planktonic, biofilm, and intracellular infection models. The results showed the significant reduction in bacteria viability both in planktonic and biofilm states. The in vitro intracellular infection model demonstrated the significantly enhanced efficiency of the developed nanoparticles compared to the treatment with the free bacteriocin. This research presents lysostaphin encapsulation within PLGA nanoparticles and offers promising avenues for enhancing lysostaphin's therapeutic efficacy against S. aureus infections.
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Affiliation(s)
- Guillermo Landa
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; Department of Chemical and Environmental Engineering, University of Zaragoza, Campus Río Ebro-Edificio I+D, C/Poeta Mariano Esquillor S/N, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragon), 50009 Zaragoza, Spain.
| | - Laura Aguerri
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; Department of Chemical and Environmental Engineering, University of Zaragoza, Campus Río Ebro-Edificio I+D, C/Poeta Mariano Esquillor S/N, 50018 Zaragoza, Spain
| | - Silvia Irusta
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; Department of Chemical and Environmental Engineering, University of Zaragoza, Campus Río Ebro-Edificio I+D, C/Poeta Mariano Esquillor S/N, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragon), 50009 Zaragoza, Spain
| | - Gracia Mendoza
- Aragon Health Research Institute (IIS Aragon), 50009 Zaragoza, Spain; Department of Pharmacology and Physiology, Forensic and Legal Medicine, University of Zaragoza, 50009 Zaragoza, Spain.
| | - Manuel Arruebo
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; Department of Chemical and Environmental Engineering, University of Zaragoza, Campus Río Ebro-Edificio I+D, C/Poeta Mariano Esquillor S/N, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragon), 50009 Zaragoza, Spain
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16
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Oliveira FS, da Silva Rodrigues R, Cavicchioli VQ, de Carvalho AF, Nero LA. Influence of different culture media on the antimicrobial activity of Pediococcus pentosaceus ST65ACC against Listeria monocytogenes. Braz J Microbiol 2024:10.1007/s42770-024-01391-1. [PMID: 38789904 DOI: 10.1007/s42770-024-01391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Pediococcus pentosaceus ST65ACC is a bacteriocinogenic lactic acid bacteria (LAB) isolated from Brazilian artisanal cheese that is capable of inhibiting different food pathogens, mainly Listeria monocytogenes. The production of bacteriocins can be influenced by several growth conditions, such as temperature, pH, and medium composition. This study aimed to evaluate the effect of different culture media on the production of bacteriocins and antimicrobial activity of P. pentosaceus ST65ACC on L. monocytogenes Scott A. The strains were inoculated alone and in coculture in four different media: BHI broth, MRS broth, meat broth, and reconstituted skim milk (RSM) 10% (w/v). The culture media were then incubated at 37 °C for 96 h, and count analysis, pH measurement, and bacteriocin production were performed at 0, 24, 48, 72 and 96 h. L. monocytogenes was inhibited to nondetectable levels in coculture with P. pentosaceus ST65ACC in MRS broth within 96 h, consistent with the high production of bacteriocin throughout the analysis period (3,200-12,800 AU/mL). However, lower inhibitory activities of P. pentosaceus ST65ACC on L. monocytogenes Scott A were recorded in BHI, RSM, and meat broth, with low or no production of bacteriocins at the analyzed times. The composition of these culture media may have repressed the production and activity of bacteriocins and, consequently, the antagonist activity of P. pentosaceus ST65ACC on L. monocytogenes Scott A. The results showed that the antimicrobial activity was more effective in MRS broth, presenting greater production of bacteriocins and less variability when compared to the other media analyzed.
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Affiliation(s)
- Francielly Soares Oliveira
- Departamento de Veterinária, InsPOA- Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil
- InovaLeite - Laboratório de Pesquisa em Leites e Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil
| | - Rafaela da Silva Rodrigues
- Departamento de Veterinária, InsPOA- Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil
- InovaLeite - Laboratório de Pesquisa em Leites e Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil
| | - Valéria Quintana Cavicchioli
- Centro de Pesquisa em Alimentos, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás, Goiânia, 74690 900, GO, Brazil
| | - Antônio Fernandes de Carvalho
- InovaLeite - Laboratório de Pesquisa em Leites e Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil
| | - Luís Augusto Nero
- Departamento de Veterinária, InsPOA- Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Viçosa, 36570 900, MG, Brazil.
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17
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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [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: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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18
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Li W, Zeng Z, Zhou D, Wang G, Wang Z, Li Y, Han Y, Qin M, Luo C, Feng S, Cao W. Effect of oral administration of microcin Y on growth performance, intestinal barrier function and gut microbiota of chicks challenged with Salmonella Pullorum. Vet Res 2024; 55:66. [PMID: 38778424 PMCID: PMC11112776 DOI: 10.1186/s13567-024-01321-x] [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: 12/05/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
The lasso peptide microcin Y (MccY) effectively inhibits various serotypes of Salmonella in vitro, but the antibacterial effect against S. Pullorum in poultry is still unclear. This study was the first to evaluate the safety and anti-S. Pullorum infection of MccY in specific pathogen-free (SPF) chicks. The safety test showed that the body weight, IgA and IgM levels of serum, and cecal microbiota structure of 3 groups of chicks orally administrated with different doses of MccY (5 mg/kg, 10 mg/kg, 20 mg/kg) for 14 days were not significantly different from those of the control group. Then, the chicks were randomized into 3 groups for the experiment of anti-S. Pullorum infection: (I) negative control group (NC), (II) S. Pullorum-challenged group (SP, 5 × 108 CFU/bird), (III) MccY-treated group (MccY, 20 mg/kg). The results indicated that compared to the SP group, treatment of MccY increased body weight and average daily gain (P < 0.05), reduced S. Pullorum burden in feces, liver, and cecum (P < 0.05), enhanced the thymus, and decreased the spleen and liver index (P < 0.05). Additionally, MccY increased the jejunal villus height, lowered the jejunal and ileal crypt depth (P < 0.05), and upregulated the expression of IL-4, IL-10, ZO-1 in the jejunum and ileum, as well as CLDN-1 in the jejunum (P < 0.05) compared to the SP group. Furthermore, MccY increased probiotic flora (Barnesiella, etc.), while decreasing (P < 0.05) the relative abundance of pathogenic flora (Escherichia and Salmonella, etc.) compared to the SP group.
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Affiliation(s)
- Wenjing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhiwei Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Di Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guyao Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zepeng Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yu Han
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Changqi Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.
| | - Weisheng Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.
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19
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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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20
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Upoma N, Akter N, Ferdousi FK, Sultan MZ, Rahman S, Alodhayb A, Alibrahim KA, Habib A. Interactions of Co(II)- and Zn(II)porphyrin of 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin with DNA in Aqueous Solution and Their Antimicrobial Activities. ACS OMEGA 2024; 9:22325-22335. [PMID: 38799349 PMCID: PMC11112571 DOI: 10.1021/acsomega.4c01708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/31/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024]
Abstract
Antibiotics are frequently used to treat, prevent, or control bacterial infections, but in recent years, infections resistant to all known classes of conventional antibiotics have significantly grown. The development of novel, nontoxic, and nonincursive antimicrobial methods that work more quickly and efficiently than the present antibiotics is required to combat this growing public health issue. Here, Co(II) and Zn(II) derivatives of tetrakis(1-methylpyridinium-4yl)porphyrin [H2TMPyP]4+ as a tetra(ρ-toluenesulfonate) were synthesized and purified to investigate their interactions with DNA (pH 7.40, 25 °C) using UV-vis, fluorescence techniques, and antimicrobial activity. UV-vis results showed that [H2TMPyP]4+ had a high hypochromicity (∼64%) and a substantial bathochromic shift (Δλ, 14 nm), while [Co(II)TMPyP]4+ and [Zn(II)TMPyP]4+ showed little hypochromicity (∼37%) and a small bathochromic shift (Δλ, 3-6 nm). Results reveal that [H2TMPyP]4+ interacts with DNA via intercalation, while Co(II)- and [Zn(II)TMPyP]4+ interact with DNA via outside self-stacking. Fluorescence results also confirmed the interaction of [H2TMPyP]4+ and the metalloporphyrins with DNA. Results of the antimicrobial activity assay revealed that the metalloporphyrins showed inhibitory effects on Gram-positive and Gram-negative bacteria and fungi, but that neither the counterions nor [H2TMPyP]4+ exhibited any inhibitory effects. Mechanism of antimicrobial activities of metalloporphyrins are discussed.
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Affiliation(s)
| | - Nazmin Akter
- Department
of Chemistry, University of Dhaka, Dhaka 1000, Bangladesh
| | | | - Md. Zakir Sultan
- Centre
for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka 1000, Bangladesh
| | - Shofiur Rahman
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alodhayb
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department
of Chemistry, College of Science, Princess
Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ahsan Habib
- Department
of Chemistry, University of Dhaka, Dhaka 1000, Bangladesh
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21
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NODA M, DANSHIITSOODOL N, KANNO K, SUGIYAMA M. Silk-derived sericin/fibroin mixture drink fermented with plant-derived Lactococcus lactis BM32-1 improves constipation and related microbiota: a randomized, double-blind, and placebo-controlled clinical trial. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2024; 43:282-292. [PMID: 38966048 PMCID: PMC11220338 DOI: 10.12938/bmfh.2023-102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/18/2024] [Indexed: 07/06/2024]
Abstract
We previously showed through clinical trials that one plant-derived lactic acid bacteria (LAB) can improve constipation. We preliminarily found that the plant-derived LAB Lactococcus lactis BM32-1 can grow in a mixture of sericin and fibroin, which are extracted from silk and have been reported to help promote health. Thus, in the present study, we evaluated the favorable effect of a sericin/fibroin mixture (S/F-M), which was extracted from silk prepared from cocoons reared in an aseptic rearing system using an artificial diet, fermented with the BM32-1 strain through a clinical trial. The trial was conducted at Hiroshima University from June to October 2022 as a double-blind, placebo-controlled, randomized parallel-group comparative study with 50 eligible subjects (aged 23-71) who had an average defecation frequency of less than 5 times per week. The subjects were instructed to drink 100 mL of fermented S/F-M or placebo every day. After the 12 weeks of the clinical trial period, the average defecation frequency increased significantly-1.4 times higher than that at baseline in the test group-as compared with the placebo group. Furthermore, the fecal microbiota was also compared before and after treatment, revealing that intake of the fermented S/F-M significantly multiplied the relative abundance of the genera Enterococcus and Clostridium, which have been reported to contribute to the amelioration of constipation by improving the gut microbiota and producing butyric acid, respectively. In conclusion, the S/F-M fermented using the BM32-1 strain improves defecation frequency through alteration of the gut microbiota.
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Affiliation(s)
- Masafumi NODA
- Department of Probiotic Science for Preventive Medicine,
Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi,
Minami-ku, Hiroshima 734-8551, Japan
| | - Narandalai DANSHIITSOODOL
- Department of Probiotic Science for Preventive Medicine,
Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi,
Minami-ku, Hiroshima 734-8551, Japan
| | - Keishi KANNO
- Department of General Internal Medicine, Hiroshima University
Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan
| | - Masanori SUGIYAMA
- Department of Probiotic Science for Preventive Medicine,
Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi,
Minami-ku, Hiroshima 734-8551, Japan
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22
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Oftedal TF, Diep DB, Kjos M. Design of Novel Saposin-like Bacteriocins Using a Hybrid Approach. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10264-w. [PMID: 38713419 DOI: 10.1007/s12602-024-10264-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
A multitude of approaches will be required to respond to the threat posed by the emergence and spread of antibiotic resistant pathogens. Bacteriocins have gained increasing attention as a possible alternative to antibiotics, as such peptide antimicrobials have mechanisms of action different from antibiotics and are therefore equally potent against antibiotic resistant bacteria as their susceptible counterparts. A group of bacteriocins known as saposin-like bacteriocins is believed to act directly on the bacterial membrane. Based on seven saposin-like leaderless bacteriocins, we have constructed a library of hybrid peptides containing all combinations of the N- and C-terminal halves of the native bacteriocins. All hybrid peptides were synthesized using in vitro protein expression and assayed for antimicrobial activity towards several pathogens. Of the 42 hybrid peptides, antimicrobial activity was confirmed for 11 novel hybrid peptides. Furthermore, several of the hybrid peptides exhibited altered antimicrobial spectra and apparent increase in potency compared to the peptides from which they were derived. The most promising hybrid, termed ISP26, was then obtained synthetically and shown to inhibit most of the Gram-positive species tested, including opportunistic pathogens and food spoilage bacteria. Additionally, ISP26 was shown to inhibit Acinetobacter, a species of Gram-negative bacteria frequently isolated from nosocomial infections. The activity of the hybrid library provides valuable insights into the design and screening of new active bacteriocins.
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Affiliation(s)
- Thomas F Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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23
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Wang Y, Gao C, Niu W, Han S, Qin M, Tian Z, Zuo W, Xia X, Wang H, Li Y. Polystyrene microplastics promote intestinal colonization of Aeromonas veronii through inducing intestinal microbiota dysbiosis. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133976. [PMID: 38461664 DOI: 10.1016/j.jhazmat.2024.133976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
Abstract
The premise that pathogen colonized microplastics (MPs) can promote the spread of pathogens has been widely recognized, however, their role in the colonization of pathogens in a host intestine has not been fully elucidated. Here, we investigated the effect of polystyrene MPs (PS-MPs) on the colonization levels of Aeromonas veronii, a typical aquatic pathogen, in the loach (Misgurnus anguillicaudatus) intestine. Multiple types of MPs were observed to promote the intestinal colonization of A. veronii, among which PS-MPs exhibited the most significant stimulating effect (67.18% increase in A. veronii colonization). PS-MPs inflicted serious damage to the intestinal tracts of loaches and induced intestinal microbiota dysbiosis. The abundance of certain intestinal bacteria with resistance against A. veronii colonization decreased, with Lactococcus sp. showing the strongest colonization resistance (73.64% decline in A. veronii colonization). Fecal microbiota transplantation was performed, which revealed that PS-MPs induced intestinal microbiota dysbiosis was responsible for the increased colonization of A. veronii in the intestine. It was determined that PS-MPs reshaped the intestinal microbiota community to attenuate the colonization resistance against A. veronii colonization, resulting in an elevated intestinal colonization levels of A. veronii.
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Affiliation(s)
- Yuqi Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Chao Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Wenfang Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Shuo Han
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Mengyuan Qin
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Zhuo Tian
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wenjing Zuo
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaohua Xia
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hailei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China; Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Yi Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China.
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24
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Khoso A, Hussain A, Rehman M, Akram S, Ahmad D, Bin-Asif H, Zahid S, Hasan KA, Ali SA. Molecular Assessments of Antimicrobial Protein Enterocins and Quorum Sensing Genes and Their Role in Virulence of the Genus Enterococcus. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10278-4. [PMID: 38703322 DOI: 10.1007/s12602-024-10278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
Enterococcus has emerged as an opportunistic pathogen because of its antibiotic resistance and virulence profile, which makes it a causative agent of several diseases like endocarditis, surgical site, and urinary tract infections. Currently, species of this genus are the 2nd most frequently isolated microorganisms from hospital-acquired infections. Significant association with hospitals and unhygienic conditions of the environments has made them resistant to a wide range of antibiotics. On the brighter side, enterococci have the ability to produce antimicrobial proteins (i.e., enterocins) that exhibit wide antagonistic activity, thus making them useful microbes in the food and pharmaceutical industries. Enterocins are also involved in niche control in gut microbiota which is regulated by the quorum sensing (QS) system. A bacterial communication system that is controlled by the fsr operon in enterococci consists of FsrABDC, ef1097, and GelE/SprE genes. Hence, the present study was conducted for molecular assessment of enterocins and quorum sensing genes, inter-environmental correlation, and species prevalence of enterococci isolated from different environmental niches of Karachi, Pakistan. Obtained results revealed the highest prevalence of E. faecium and E. faecalis in all environments. Bacterial antagonism and enterocin genes were observed significantly high in poultry environments. The inter-environmental correlation indicated a strong positive correlation of freshwater with sewage and soil environments. Similarly, the fsr regulatory system was mostly identified in poultry-related environments, and a significant correlation between QS system and biofilm formation was established. In conclusion, this study confirmed the high prevalence of E. faecium in all tested sources, high enterocin production in non-clinical environments, and more fsr regulatory genes in poultry-related environments.
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Affiliation(s)
- Arisha Khoso
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Abrar Hussain
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Marium Rehman
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Saira Akram
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Diyar Ahmad
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Hassan Bin-Asif
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Sindhu Zahid
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Khwaja Ali Hasan
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
- Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Syed Abid Ali
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, at International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
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25
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Su L, Yang R, Sheng Y, Ullah S, Zhao Y, Shunjiayi H, Zhao Z, Wang Q. Insights into the oral microbiota in human systemic cancers. Front Microbiol 2024; 15:1369834. [PMID: 38756728 PMCID: PMC11098135 DOI: 10.3389/fmicb.2024.1369834] [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: 01/13/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
The oral cavity stands as one of the pivotal interfaces facilitating the intricate interaction between the human body and the external environment. The impact of diverse oral microorganisms on the emergence and progression of various systemic cancers, typified by oral cancer, has garnered increasing attention. The potential pathogenicity of oral bacteria, notably the anaerobic Porphyromonas gingivalis and Fusobacterium nucleatum, has been extensively studied and exhibits obvious correlation with different carcinoma types. Furthermore, oral fungi and viruses are closely linked to oropharyngeal carcinoma. Multiple potential mechanisms of oral microbiota-induced carcinogenesis have been investigated, including heightened inflammatory responses, suppression of the host immune system, influence on the tumor microenvironment, anti-apoptotic activity, and promotion of malignant transformation. The disturbance of microbial equilibrium and the migration of oral microbiota play a pivotal role in facilitating oncogenic functions. This review aims to comprehensively outline the pathogenic mechanisms by which oral microbiota participate in carcinogenesis. Additionally, this review delves into their potential applications in cancer prevention, screening, and treatment. It proves to be a valuable resource for researchers investigating the intricate connection between oral microbiota and systemic cancers.
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Affiliation(s)
- Lan Su
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Rui Yang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Yanan Sheng
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Saif Ullah
- Department of Microbiology School of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Yuheng Zhao
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Hu Shunjiayi
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhuo Zhao
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Qingjing Wang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
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26
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [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: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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27
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Li X, Li W, Zhao L, Li Y, He W, Ding K, Cao P. Characterization and Assessment of Native Lactic Acid Bacteria from Broiler Intestines for Potential Probiotic Properties. Microorganisms 2024; 12:749. [PMID: 38674693 PMCID: PMC11052334 DOI: 10.3390/microorganisms12040749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Probiotics are the most promising alternative to antibiotics for improving animal production and controlling pathogenic infections, while strains derived from natural hosts are considered highly desirable due to their good adaptation to the gastrointestinal tract. The aim of this study was to screen Lactobacillus with broad-spectrum antibacterial activity from broilers fed an antibiotic-free diet and evaluate their potential as poultry probiotics. A total of 44 lactic acid bacteria (LAB) strains were isolated from the intestines of healthy broilers, among which 3 strains exhibited outstanding antimicrobial activity and were subsequently identified through 16S rRNA sequencing as Enterococcus faecium L8, Lactiplantibacillus plantarum L10, and Limosilactobacillus reuteri H11. These three isolates demonstrated potent bacteriostatic activity against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, and Salmonella cholerae, with inhibition zones ranging from 15.67 ± 1.53 to 21.33 ± 0.58 mm. The selected LAB strains exhibited high tolerance to acid and bile salts, with L. reuteri H11 displaying the highest survival rate (ranging from 34.68% to 110.28%) after exposure to 0.3% (w/v) bile salts for 6 h or a low pH environment (pH 2, 2.5, and 3) for 3 h. Notably, L. reuteri H11 outperformed other strains in terms of hydrophobicity (84.31%), auto-aggregation (53.12%), and co-aggregation with E. coli ATCC 25922 (36.81%) and S. aureus ATCC 6538 (40.20%). In addition, the three LAB isolates were either fully or moderately susceptible to the tested antibiotics, except for strain L8, which resisted gentamycin and vancomycin. Consequently, these three LAB strains, especially L. reuteri H11, isolated from the intestines of broiler chickens, represent promising probiotic candidates that can be employed as feed additives to enhance production performance and control poultry pathogens.
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Affiliation(s)
| | | | | | | | | | | | - Pinghua Cao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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28
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Tathode MS, Bonomo MG, Zappavigna S, Mang SM, Bocchetti M, Camele I, Caraglia M, Salzano G. Whole-genome analysis suggesting probiotic potential and safety properties of Pediococcus pentosaceus DSPZPP1, a promising LAB strain isolated from traditional fermented sausages of the Basilicata region (Southern Italy). Front Microbiol 2024; 15:1268216. [PMID: 38638895 PMCID: PMC11024341 DOI: 10.3389/fmicb.2024.1268216] [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: 07/27/2023] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Many lactic acid bacteria (LAB) strains are currently gaining attention in the food industry and various biological applications because of their harmless and functional properties. Given the growing consumer demand for safe food, further research into potential probiotic bacteria is beneficial. Therefore, we aimed to characterize Pediococcus pentosaceus DSPZPP1, a LAB strain isolated from traditional fermented sausages from the Basilicata region of Southern Italy. Methods In this study, we analyzed the whole genome of the P. pentosaceus DSPZPP1 strain and performed in silico characterization to evaluate its applicability for probiotics and use in the food industry. Results and Discussion The whole-genome assembly and functional annotations revealed many interesting characteristics of the DSPZPP1 strain. Sequencing raw reads were assembled into a draft genome of size 1,891,398 bp, with a G + C content of 37.3%. Functional annotation identified 1930 protein-encoding genes and 58 RNAs including tRNA, tmRNA, and 16S, 23S, and 5S rRNAs. The analysis shows the presence of genes that encode water-soluble B-group vitamins such as biotin, folate, coenzyme A, and riboflavin. Furthermore, the analysis revealed that the DSPZPP1 strain can synthesize class II bacteriocin, penocin A, adding importance to the food industry for bio-enriched food. The DSPZPP1 genome does not show the presence of plasmids, and no genes associated with antimicrobial resistance and virulence were found. In addition, two intact bacteriophages were identified. Importantly, the lowest probability value in pathogenicity analysis indicates that this strain is non-pathogenic to humans. 16 s rRNA-based phylogenetic analysis and comparative analysis based on ANI and Tetra reveal that the DSPZPP1 strain shares the closest evolutionary relationship with P. pentosaceus DSM 20336 and other Pediococcus strains. Analysis of carbohydrate active enzymes (CAZymes) identified glycosyl transferases (GT) as a main class of enzymes followed by glycoside hydrolases (GH). Our study shows several interesting characteristics of the isolated DSPZPP1 strain from fermented Italian sausages, suggesting its potential use as a promising probiotic candidate and making it more appropriate for selection as a future additive in biopreservation.
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Affiliation(s)
- Madhura S. Tathode
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Maria Grazia Bonomo
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
| | - Silvia Zappavigna
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Stefania Mirela Mang
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Giovanni Salzano
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
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29
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Caffrey EB, Sonnenburg JL, Devkota S. Our extended microbiome: The human-relevant metabolites and biology of fermented foods. Cell Metab 2024; 36:684-701. [PMID: 38569469 DOI: 10.1016/j.cmet.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.
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Affiliation(s)
- Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA.
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel Diseases Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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30
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Goult JD, Van DCL, Taylor YV, Inns PG, Kaminska R, Vesely M, Kleanthous C, Paci E. Structural constraints of pyocin S2 import through the ferripyoverdine receptor FpvAI. PNAS NEXUS 2024; 3:pgae124. [PMID: 38577260 PMCID: PMC10994204 DOI: 10.1093/pnasnexus/pgae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
TonB-dependent transporters (TBDTs) mediate energized transport of essential nutrients into gram-negative bacteria. TBDTs are increasingly being exploited for the delivery of antibiotics to drug-resistant bacteria. While much is known about ground state complexes of TBDTs, few details have emerged about the transport process itself. In this study, we exploit bacteriocin parasitization of a TBDT to probe the mechanics of transport. Previous work has shown that the N-terminal domain of Pseudomonas aeruginosa-specific bacteriocin pyocin S2 (PyoS2NTD) is imported through the pyoverdine receptor FpvAI. PyoS2NTD transport follows the opening of a proton-motive force-dependent pore through FpvAI and the delivery of its own TonB box that engages TonB. We use molecular models and simulations to formulate a complete translocation pathway for PyoS2NTD that we validate using protein engineering and cytotoxicity measurements. We show that following partial removal of the FpvAI plug domain which occludes the channel, the pyocin's N-terminus enters the channel by electrostatic steering and ratchets to the periplasm. Application of force, mimicking that exerted by TonB, leads to unraveling of PyoS2NTD as it squeezes through the channel. Remarkably, while some parts of PyoS2NTD must unfold, complete unfolding is not required for transport, a result we confirmed by disulfide bond engineering. Moreover, the section of the FpvAI plug that remains embedded in the channel appears to serve as a buttress against which PyoS2NTD is pushed to destabilize the domain. Our study reveals the limits of structural deformation that accompanies import through a TBDT and the role the TBDT itself plays in accommodating transport.
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Affiliation(s)
- Jonathan D Goult
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Daniel C L Van
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Yasmin V Taylor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Patrick G Inns
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Martin Vesely
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna 40127, Italy
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Xu J, Xu X, Jiang Y, Fu Y, Shen C. Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning. ENVIRONMENT INTERNATIONAL 2024; 186:108574. [PMID: 38507933 DOI: 10.1016/j.envint.2024.108574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.
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Affiliation(s)
- Jiaqi Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Xin Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yunhan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China.
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32
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Vijayakumar S, G V, Krishnapura PR, Iyyaswami R. Production of nisin from Lactococcus lactis in acid-whey with nutrient supplementation. Prep Biochem Biotechnol 2024; 54:494-502. [PMID: 37607210 DOI: 10.1080/10826068.2023.2249091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The production of Nisin, an FDA-approved food preservative, was attempted by Lactococcus lactis subsp. lactis ATCC® 11454 using the underutilized milk industry effluent, acid-whey, as a substrate. Nisin production was further improved by studying the effect of supplementation of nutrients and non-nutritional parameters. The addition of yeast extract (6% w/v) as nitrogen source and sucrose (4% w/v) as carbon source were found to be suitable nutrients for the maximum nisin production. The changes in the medium pH due to lactic acid accumulation during batch fermentation and its influence on the production of nisin were analyzed in the optimized whey medium (OWM). The production characteristics in OWM were further compared with the nisin production in MRS media. The influence of nisin as an inducer for its own production was also studied and found that the addition of nisin at 0.22 mg/ml promote the nisin production. The analysis of consumption of various metal ions present in the OWM during the nisin production was also analyzed, and found that the copper ions are the most consumed ion. The highest nisin yield of 2.6 × 105 AU/mL was obtained with OWM.
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Affiliation(s)
- Sahana Vijayakumar
- Department of Chemical Engineering, National Institute of Technology Karnataka, Mangaluru, Karnataka, India
| | - Vishnu G
- Department of Chemical Engineering, National Institute of Technology Karnataka, Mangaluru, Karnataka, India
| | - Prajna Rao Krishnapura
- Department of Chemical Engineering, National Institute of Technology Karnataka, Mangaluru, Karnataka, India
| | - Regupathi Iyyaswami
- Department of Chemical Engineering, National Institute of Technology Karnataka, Mangaluru, Karnataka, India
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33
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Jones J, Murphy CP, Sleator RD, Culligan EP. An exploratory in silico analysis of bacteriocin gene clusters in the urobiome. MICROBIOME RESEARCH REPORTS 2024; 3:24. [PMID: 38846023 PMCID: PMC11153084 DOI: 10.20517/mrr.2023.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 06/09/2024]
Abstract
Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production. Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7. Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins. Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.
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Affiliation(s)
| | | | | | - Eamonn P. Culligan
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork T12 P928, Ireland
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Liu H, Wei X, Wang Z, Huang X, Li M, Hu Z, Zhang K, Hu Q, Peng H, Shang W, Yang Y, Wang Y, Lu S, Rao X. LysSYL: a broad-spectrum phage endolysin targeting Staphylococcus species and eradicating S. aureus biofilms. Microb Cell Fact 2024; 23:89. [PMID: 38528536 DOI: 10.1186/s12934-024-02359-4] [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: 01/20/2024] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Staphylococcus aureus and its single or mixed biofilm infections seriously threaten global public health. Phage therapy, which uses active phage particles or phage-derived endolysins, has emerged as a promising alternative strategy to antibiotic treatment. However, high-efficient phage therapeutic regimens have yet to be established. RESULTS In this study, we used an enrichment procedure to isolate phages against methicillin-resistant S. aureus (MRSA) XN108. We characterized phage SYL, a new member of the Kayvirus genus, Herelleviridae family. The phage endolysin LysSYL was expressed. LysSYL demonstrated stability under various conditions and exhibited a broader range of efficacy against staphylococcal strains than its parent phage (100% vs. 41.7%). Moreover, dynamic live/dead bacterial observation demonstrated that LysSYL could completely lyse MRSA USA300 within 10 min. Scan and transmission electron microscopy revealed evident bacterial cell perforation and deformation. In addition, LysSYL displayed strong eradication activity against single- and mixed-species biofilms associated with S. aureus. It also had the ability to kill bacterial persisters, and proved highly effective in eliminating persistent S. aureus when combined with vancomycin. Furthermore, LysSYL protected BALB/c mice from lethal S. aureus infections. A single-dose treatment with 50 mg/kg of LysSYL resulted in a dramatic reduction in bacterial loads in the blood, liver, spleen, lungs, and kidneys of a peritonitis mouse model, which resulted in rescuing 100% of mice challenged with 108 colony forming units of S. aureus USA300. CONCLUSIONS Overall, the data provided in this study highlight the strong therapeutic potential of endolysin LysSYL in combating staphylococcal infections, including mono- and mixed-species biofilms related to S. aureus.
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Affiliation(s)
- He Liu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Xuemei Wei
- Medical Research Institute, Southwest University, Chongqing, 400700, China
| | - Zhefen Wang
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan Province, China
| | - Xiaonan Huang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Mengyang Li
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing, 400044, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Kexin Zhang
- Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, 400700, China
| | - Qiwen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Yuting Wang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China.
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China.
- Medical Research Institute, Southwest University, Chongqing, 400700, China.
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35
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Chiang BH, Vega G, Dunwoody SC, Patnode ML. Bacterial interactions on nutrient-rich surfaces in the gut lumen. Infect Immun 2024:e0048023. [PMID: 38506518 DOI: 10.1128/iai.00480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.
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Affiliation(s)
- Bo Huey Chiang
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Giovanni Vega
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Sarah C Dunwoody
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Michael L Patnode
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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36
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Sadaoka N, Le MNT, Kawada-Matsuo M, Eng S, Zendo T, Nakanishi J, Takeda K, Shiba H, Komatsuzawa H. Opposing genetic polymorphisms of two ABC transporters contribute to the variation of nukacin resistance in Streptococcus mutans. Appl Environ Microbiol 2024; 90:e0208423. [PMID: 38411065 PMCID: PMC10952377 DOI: 10.1128/aem.02084-23] [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: 11/19/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Streptococcus mutans is a cariogenic bacterium that produces a variety of bacteriocins and retains resistance to these bacteriocins. In this study, we investigated the susceptibility of 127 S. mutans strains to nukacins produced by Staphylococcus spp., which are commensal bacteria in humans. We detected diverse susceptibilities among strains. Nineteen strains had a disrupted LctF (type I), which is responsible for nukacin susceptibility, whereas the remaining 108 strains had an intact LctF (type II) and displayed resistance to nukacins. However, the type I strains still showed resistance to nukacins to some extent. Interestingly, 18/19 (94.7%) type I strains carried a mukA-T locus, which is related to the synthesis of mutacin K8, and mukFEG, an ABC transporter. In contrast, among type II strains, only 6/108 strains (5.6%) had both the mukA-T locus and mukFEG, 19/108 strains (17.6%) carried only mukFEG, and 83/108 strains (76.9%) harbored neither mukA-T nor mukFEG. We also found that MukF had two variants: 305 amino acids (type α) and 302 amino acids (type β). All type I strains showed a type α (MukFα), whereas most type II strains with mukFEG (22/25 strains) had a type β (MukFβ). Then, we constructed a mukFEG-deletion mutant complemented with MukFαEG or MukFβEG and found that only MukFαEG was involved in nukacin resistance. The nukacin resistance capability of type II-LctFEG was stronger than that of MukFαEG. In conclusion, we identified a novel nukacin resistance factor, MukFEG, and either LctFEG or MukFEG was active in most strains via genetic polymorphisms depending on mukA-T genes. IMPORTANCE Streptococcus mutans is an important pathogenic bacterium not only for dental caries but also for systemic diseases. S. mutans is known to produce a variety of bacteriocins and to retain resistance these bacteriocins. In this study, two ABC transporters, LctFEG and MukFEG, were implicated in nukacin resistance and each ABC transporter has two subtypes, active and inactive. Of the two ABC transporters, only one ABC transporter was always resistant, while the other ABC transporter was inactivated by genetic mutation. Interestingly, this phenomenon was defined by the presence or absence of the mutacin K8 synthesis gene region, one of the bacteriocins of S. mutans. This suggests that the resistance acquisition is tightly controlled in each strain. This study provides important evidence that the insertion of bacteriocin synthesis genes is involved in the induction of genetic polymorphisms and suggests that bacteriocin synthesis genes may play an important role in bacterial evolution.
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Affiliation(s)
- Naoki Sadaoka
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Mi Nguyen-Tra Le
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Sopongselamuny Eng
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Jun Nakanishi
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Katsuhiro Takeda
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
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Chen P, Ye T, Li C, Praveen P, Hu Z, Li W, Shang C. Embracing the era of antimicrobial peptides with marine organisms. Nat Prod Rep 2024; 41:331-346. [PMID: 37743806 DOI: 10.1039/d3np00031a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Covering: 2018 to Jun of 2023The efficiency of traditional antibiotics has been undermined by the proliferation of antibiotic-resistant pathogenic microorganisms, necessitating the pursuit of innovative therapeutic agents. Antimicrobial peptides (AMPs), which are part of host defence peptides found ubiquitously in nature, exhibiting a wide range of activity towards bacteria, fungi, and viruses, offer a highly promising candidate solution. The efficacy of AMPs can frequently be augmented via alterations to their amino acid sequences or structural adjustments. Given the vast reservoir of marine life forms and their distinctive ecosystems, marine AMPs stand as a burgeoning focal point in the quest for alternative peptide templates extracted from natural sources. Advances in identification and characterization techniques have accelerated the discoveries of marine AMPs, thereby stimulating AMP customization, optimization, and synthesis research endeavours. This review presents an overview of recent discoveries related to the intriguing qualities of marine AMPs. Emphasis will be placed upon post-translational modifications (PTMs) of marine AMPs and how they may impact functionality and potency. Additionally, this review considers ways in which marine PTM might support larger-scale, heterologous AMP manufacturing initiatives, providing insights into translational applications of these important biomolecules.
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Affiliation(s)
- Pengyu Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ting Ye
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Chunyuan Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Praveen Praveen
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Chenjing Shang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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38
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Thuy TTD, Lu HF, Bregente CJB, Huang FCA, Tu PC, Kao CY. Characterization of the broad-spectrum antibacterial activity of bacteriocin-like inhibitory substance-producing probiotics isolated from fermented foods. BMC Microbiol 2024; 24:85. [PMID: 38468236 PMCID: PMC10926564 DOI: 10.1186/s12866-024-03245-0] [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: 06/30/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
Antimicrobial peptides, such as bacteriocin, produced by probiotics have become a promising novel class of therapeutic agents for treating infectious diseases. Selected lactic acid bacteria (LAB) isolated from fermented foods with probiotic potential were evaluated for various tests, including exopolysaccharide production, antibiotic susceptibility, acid and bile tolerance, antibacterial activity, and cell adhesion and cytotoxicity to gastric cell lines. Six selected LAB strains maintained their high viability under gastrointestinal conditions, produced high exopolysaccharides, showed no or less cytotoxicity, and adhered successfully to gastric cells. Furthermore, three strains, Weissella confusa CYLB30, Lactiplantibacillus plantarum CYLB47, and Limosilactobacillus fermentum CYLB55, demonstrated a strong antibacterial effect against drug-resistant Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica serovar Choleraesuis, Enterococcus faecium, and Staphylococcus aureus. Whole genome sequencing was performed on these three strains using the Nanopore platform; then, the results showed that all three strains did not harbor genes related to toxins, superantigens, and acquired antimicrobial resistance, in their genome. The bacteriocin gene cluster was found in CYLB47 genome, but not in CYLB30 and CYLB55 genomes. In SDS-PAGE, the extract of CYLB30 and CYLB47 bacteriocin-like inhibitory substance (BLIS) yielded a single band with a size of less than 10 kDa. These BLIS inhibited the growth and biofilm formation of drug-resistant P. aeruginosa and methicillin-resistant S. aureus (MRSA), causing membrane disruption and inhibiting adhesion ability to human skin HaCaT cells. Moreover, CYLB30 and CYLB47 BLIS rescued the larvae after being infected with P. aeruginosa and MRSA infections. In conclusion, CYLB30 and CYLB47 BLIS may be potential alternative treatment for multidrug-resistant bacteria infections.
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Affiliation(s)
- Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street, Taipei, 112, Taiwan
| | - Hsu-Feng Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Carl Jay Ballena Bregente
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street, Taipei, 112, Taiwan
- College of Medical Technology, Southwestern University PHINMA, Cebu, Philippines
| | | | - Pei-Chun Tu
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street, Taipei, 112, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street, Taipei, 112, Taiwan.
- Health Innovation Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Microbiota Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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39
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Balcha ES, Macey MC, Gemeda MT, Cavalazzi B, Woldesemayat AA. Mining the microbiome of Lake Afdera to gain insights into microbial diversity and biosynthetic potential. FEMS MICROBES 2024; 5:xtae008. [PMID: 38560625 PMCID: PMC10979467 DOI: 10.1093/femsmc/xtae008] [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: 09/02/2023] [Revised: 01/24/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with Acinetobacter (18.6%) and Pseudomonas (11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles.
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Affiliation(s)
- Ermias Sissay Balcha
- School of Medical Laboratory Science, College of Health Sciences, Hawassa University, 16417, Hawassa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
| | - Michael C Macey
- Astrobiology OU, School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mesfin Tafesse Gemeda
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
| | - Barbara Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - Adugna Abdi Woldesemayat
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
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40
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Raphel S, Halami PM. Genome mining of Bacillus licheniformis MCC2514 for the identification of lasso peptide biosynthetic gene cluster and its characterization. Arch Microbiol 2024; 206:143. [PMID: 38443732 DOI: 10.1007/s00203-024-03877-w] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/28/2024] [Indexed: 03/07/2024]
Abstract
The probiotic strain Bacillus licheniformis MCC2514 has been shown to produce a strong antibacterial peptide and the whole genome sequence of this strain is also reported in our previous study. The present study is focused on the genome level investigation of this peptide antibiotic and its characterization. Genome mining of the culture revealed the presence of three putative bacteriocin clusters, viz. lichenicidin, sonorensin and lasso peptide. Hence, the mode of action of the peptide was investigated by reporter assay, scanning electron microscopy, and Fourier Transform Infrared spectroscopy. Additionally, the peptide treated groups of Kocuria rhizophila showed a reduction in the fold expression for transcription-related genes. The gene expression studies, quantitative β-galactosidase induction assay using the RNA stress reporter strain, yvgS along with the homology studies concluded that lasso peptide is responsible for the antibacterial activity of the peptide which acts as an inhibitor of RNA biosynthesis. Gene expression analysis showed a considerable increase in fold expression of lasso peptide genes at various fermentation hours. Also, the peptide was isolated, and its time-kill kinetics and minimum inhibitory concentration against the indicator pathogen K. rhizophila were examined. The peptide was also purified and the molecular weight was determined to be ~ 2 kDa. Our study suggests that this bacteriocin can function as an effective antibacterial agent in food products as well as in therapeutics as it contains lasso peptide, which inhibits the RNA biosynthesis.
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Affiliation(s)
- Steji Raphel
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - Prakash M Halami
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India.
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India.
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41
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Álvarez-Martínez FJ, Díaz-Puertas R, Barrajón-Catalán E, Micol V. Plant-Derived Natural Products for the Treatment of Bacterial Infections. Handb Exp Pharmacol 2024. [PMID: 38418668 DOI: 10.1007/164_2024_706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Bacterial infections are a significant public health concern, and the emergence of antibiotic-resistant bacteria (ARB) has become a major challenge for modern medicine. The overuse and misuse of antibiotics have contributed to the development of ARB, which has led to the need for alternative therapies. Plant-derived natural products (PNPs) have been extensively studied for their potential as alternative therapies for the treatment of bacterial infections. The diverse chemical compounds found in plants have shown significant antibacterial properties, making them a promising source of novel antibacterial agents. The use of PNPs as antibacterial agents is particularly appealing because they offer a relatively safe and cost-effective approach to the treatment of bacterial infections. This chapter aims to provide an overview of the current state of research on PNPs as antibacterial agents. It will cover the mechanisms of action of the main PNPs against bacterial pathogens and discuss their potential to be used as complementary therapies to combat ARB. This chapter will also highlight the most common screening methodologies to discover new PNPs and the challenges and future prospects in the development of these compounds as antibacterial agents.
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Affiliation(s)
- Francisco Javier Álvarez-Martínez
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
- Institute of Sanitary and Biomedical Research of Alicante (ISABIAL), Alicante, Spain
| | - Rocío Díaz-Puertas
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
| | - Enrique Barrajón-Catalán
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain.
- Department of Pharmacy, Elche University Hospital-FISABIO, Elche, Spain.
| | - Vicente Micol
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
- CIBER, Pathophysiology of Obesity and Nutrition, CIBERobn, Carlos III Health Institute (CB12/03/30038), Madrid, Spain
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42
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Liu Y, Bu Y, Cao J, Liu Y, Zhang T, Hao L, Yi H. Effect of Fermented Milk Supplemented with Nisin or Plantaricin Q7 on Inflammatory Factors and Gut Microbiota in Mice. Nutrients 2024; 16:680. [PMID: 38474811 DOI: 10.3390/nu16050680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Lactic-acid-bacteria-derived bacteriocins are used as food biological preservatives widely. Little information is available on the impact of bacteriocin intake with food on gut microbiota in vivo. In this study, the effects of fermented milk supplemented with nisin (FM-nisin) or plantaricin Q7 (FM-Q7) from Lactiplantibacillus plantarum Q7 on inflammatory factors and the gut microbiota of mice were investigated. The results showed that FM-nisin or FM-Q7 up-regulated IFN-γ and down-regulated IL-17 and IL-12 in serum significantly. FM-nisin down-regulated TNF-α and IL-10 while FM-Q7 up-regulated them. The results of 16S rRNA gene sequence analysis suggested that the gut microbiome in mice was changed by FM-nisin or FM-Q7. The Firmicutes/Bacteroides ratio was reduced significantly in both groups. It was observed that the volume of Akkermansia_Muciniphila was significantly reduced whereas those of Lachnospiraceae and Ruminococcaceae were increased. The total number of short-chain fatty acids (SCFAs) in the mouse feces of the FM-nisin group and FM-Q7 group was increased. The content of acetic acid was increased while the butyric acid content was decreased significantly. These findings indicated that FM-nisin or FM-Q7 could stimulate the inflammation response and alter gut microbiota and metabolic components in mice. Further in-depth study is needed to determine the impact of FM-nisin or FM-Q7 on the host's health.
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Affiliation(s)
- Yisuo Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
| | - Yushan Bu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
| | - Jiayuan Cao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
| | - Yinxue Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
| | - Tai Zhang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
| | - Linlin Hao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
| | - Huaxi Yi
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
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43
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Nooij S, Vendrik KEW, Zwittink RD, Ducarmon QR, Keller JJ, Kuijper EJ, Terveer EM. Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Med 2024; 16:37. [PMID: 38419010 PMCID: PMC10902993 DOI: 10.1186/s13073-024-01306-7] [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: 08/23/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases. METHODS We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics. RESULTS Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years. CONCLUSIONS Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.
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Affiliation(s)
- Sam Nooij
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands.
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands.
| | - Karuna E W Vendrik
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Quinten R Ducarmon
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Ed J Kuijper
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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Landete JM, Montiel R, Rodríguez-Mínguez E, Arqués JL. Enterocins Produced by Enterococci Isolated from Breast-Fed Infants: Antilisterial Potential. CHILDREN (BASEL, SWITZERLAND) 2024; 11:261. [PMID: 38397373 PMCID: PMC10887673 DOI: 10.3390/children11020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Enterocins are bacteriocins synthesized by Enterococcus strains that show an interesting antimicrobial effectiveness against foodborne pathogens such as Listeria monocytogenes. The objectives of this study were to identify and analyze the expression of enterocin genes of Enterococcus isolated from breast-fed infants and evaluate their ability to inhibit three human isolates of virulent L. monocytogenes, as well as some probiotic bacteria. The susceptibility of the strains of L. monocytogenes to fifteen antibiotics was tested, detecting their resistance to cefoxitin (constitutively resistant), oxacillin, and clindamycin. The production of enterocins A, B, and P was observed in Enterococcus faecium isolates, while enterocin AS-48 was detected in an Enterococcus faecalis isolate. AS-48 showed antilisterial activity by itself, while the joint action of enterocins A and B or B and P was necessary for inhibiting L. monocytogenes, demonstrating the synergistic effect of those combinations. The presence of multiple enterocin genes does not assure the inhibition of L. monocytogenes strains. However, the expression of multiple enterocin genes showed a good correlation with the inhibition capacity of these strains. Furthermore, the potential beneficial strains of lactobacilli and bifidobacteria examined were not inhibited by any of the enterocins produced individually or in combination, with the exception of Bifidobacterium longum BB536, which was inhibited by enterocin AS-48 and the joint production of enterocins A and B or B and P. The enterocins studied here could be candidates for developing alternative treatments against antibiotic-resistant bacterial infections. Moreover, these selected enterocin-producing E. faecium strains isolated from breast-fed infants could be used as probiotic strains due to their antilisterial effect, as well as the absence of virulence factors.
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Affiliation(s)
| | | | | | - Juan L. Arqués
- Department of Food Technology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, INIA-CSIC, Carretera de La Coruña Km 7, 28040 Madrid, Spain; (J.M.L.); (R.M.); (E.R.-M.)
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46
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Liu F, van Heel AJ, Kuipers OP. Engineering circular bacteriocins: structural and functional effects of α-helix exchanges and disulfide introductions in circularin A. Front Microbiol 2024; 15:1337647. [PMID: 38435696 PMCID: PMC10905743 DOI: 10.3389/fmicb.2024.1337647] [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: 11/13/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Circular bacteriocins form a distinct group of antimicrobial peptides (AMPs) characterized by their unique head-to-tail ligated circular structure and functional properties. They belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) family. The ribosomal origin of these peptides facilitates rapid diversification through mutations in the precursor genes combined with specific modification enzymes. In this study, we primarily explored the bacteriocin engineering potential of circularin A, a circular bacteriocin produced by Clostridium beijerinckii ATCC 25752. Specifically, we employed strategies involving α-helix replacements and disulfide bond introductions to investigate their effects on both biosynthesis and bioactivity of the bacteriocin. The results show the feasibility of peptide engineering to introduce certain structural properties into circularin A through carefully designed approaches. The introduction of cysteines for potential disulfide bonds resulted in a substantial reduction in bacteriocin biosynthesis and/or bioactivity, indicating the importance of maintaining dynamic flexibility of α-helices in circularin A, while reduction of the potential disulfide in one case increased the activity. The 5 α-helices of circularin A were respectively replaced by corresponding helices from another circular peptide, enterocin AS-48, and modestly active peptides were obtained in a few cases. Overall, this study provides valuable insights into the engineering potential of circular bacteriocins as antimicrobial agents, including their structural and functional restrictions and their suitability as peptide engineering scaffolds. This helps to pave the way for the development of novel antimicrobial peptides with tailored properties based on circular bacteriocins.
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Affiliation(s)
- Fangfang Liu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
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Lafuente I, Sevillano E, Peña N, Cuartero A, Hernández PE, Cintas LM, Muñoz-Atienza E, Borrero J. Production of Pumilarin and a Novel Circular Bacteriocin, Altitudin A, by Bacillus altitudinis ECC22, a Soil-Derived Bacteriocin Producer. Int J Mol Sci 2024; 25:2020. [PMID: 38396696 PMCID: PMC10888436 DOI: 10.3390/ijms25042020] [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: 01/09/2024] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The rise of antimicrobial resistance poses a significant global health threat, necessitating urgent efforts to identify novel antimicrobial agents. In this study, we undertook a thorough screening of soil-derived bacterial isolates to identify candidates showing antimicrobial activity against Gram-positive bacteria. A highly active antagonistic isolate was initially identified as Bacillus altitudinis ECC22, being further subjected to whole genome sequencing. A bioinformatic analysis of the B. altitudinis ECC22 genome revealed the presence of two gene clusters responsible for synthesizing two circular bacteriocins: pumilarin and a novel circular bacteriocin named altitudin A, alongside a closticin 574-like bacteriocin (CLB) structural gene. The synthesis and antimicrobial activity of the bacteriocins, pumilarin and altitudin A, were evaluated and validated using an in vitro cell-free protein synthesis (IV-CFPS) protocol coupled to a split-intein-mediated ligation procedure, as well as through their in vivo production by recombinant E. coli cells. However, the IV-CFPS of CLB showed no antimicrobial activity against the bacterial indicators tested. The purification of the bacteriocins produced by B. altitudinis ECC22, and their evaluation by MALDI-TOF MS analysis and LC-MS/MS-derived targeted proteomics identification combined with massive peptide analysis, confirmed the production and circular conformation of pumilarin and altitudin A. Both bacteriocins exhibited a spectrum of activity primarily directed against other Bacillus spp. strains. Structural three-dimensional predictions revealed that pumilarin and altitudin A may adopt a circular conformation with five- and four-α-helices, respectively.
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Affiliation(s)
- Irene Lafuente
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Ester Sevillano
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Nuria Peña
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Alicia Cuartero
- Centro de Educación Infantil, Primaria y Secundaria Obligatoria (CEIPSO) El Cantizal, Avenida Atenas s/n, 28232 Las Rozas, Madrid, Spain;
| | - Pablo E. Hernández
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Luis M. Cintas
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
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48
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Peng Z, Wang D, He Y, Wei Z, Xie M, Xiong T. Gut Distribution, Impact Factor, and Action Mechanism of Bacteriocin-Producing Beneficial Microbes as Promising Antimicrobial Agents in Gastrointestinal Infection. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10222-6. [PMID: 38319538 DOI: 10.1007/s12602-024-10222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Gastrointestinal (GI) infection by intestinal pathogens poses great threats to human health, and the therapeutic use of antibiotics has reached a bottleneck due to drug resistance. The developments of antimicrobial peptides produced by beneficial bacteria have drawn attention by virtue of effective, safe, and not prone to developing resistance. Though bacteriocin as antimicrobial agent in gut infection has been intensively investigated and reviewed, reviews on that of bacteriocin-producing beneficial microbes are very rare. It is important to explicitly state the prospect of bacteriocin-producing microbes in prevention of gastrointestinal infection towards their application in host. This review discusses the potential of gut as an appropriate resource for mining targeted bacteriocin-producing microbes. Then, host-related factors affecting the bacteriocin production and activity of bacteriocin-producing microbes in the gut are summarized. Accordingly, the multiple mechanisms (direct inhibition and indirect inhibition) behind the preventive effects of bacteriocin-producing microbes on gut infection are discussed. Finally, we propose several targeted strategies for the manipulation of bacteriocin-producing beneficial microbes to improve their performance in antimicrobial outcomes. We anticipate an upcoming emergence of developments and applications of bacteriocin-producing beneficial microbes as antimicrobial agent in gut infection induced by pathogenic bacteria.
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Affiliation(s)
- Zhen Peng
- School of Food Science and Technology, Nanchang University, Nanchang, China
- International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, Jiangxi, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Donglin Wang
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yuyan He
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ziqi Wei
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Mingyong Xie
- School of Food Science and Technology, Nanchang University, Nanchang, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Tao Xiong
- School of Food Science and Technology, Nanchang University, Nanchang, China.
- International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, Jiangxi, China.
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China.
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49
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Jirillo E, Palmirotta R, Colella M, Santacroce L. A Bird's-Eye View of the Pathophysiologic Role of the Human Urobiota in Health and Disease: Can We Modulate It? PATHOPHYSIOLOGY 2024; 31:52-67. [PMID: 38390942 PMCID: PMC10885084 DOI: 10.3390/pathophysiology31010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
For a long time, urine has been considered sterile in physiological conditions, thanks to the particular structure of the urinary tract and the production of uromodulin or Tamm-Horsfall protein (THP) by it. More recently, thanks to the development and use of new technologies, i.e., next-generation sequencing and expanded urine culture, the identification of a microbial community in the urine, the so-called urobiota, became possible. Major phyla detected in the urine are represented by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Particularly, the female urobiota is largely represented by Lactobacillus spp., which are very active against urinary pathogenic Escherichia (E.) coli (UPEC) strains via the generation of lactic acid and hydrogen peroxide. Gut dysbiosis accounts for recurrent urinary tract infections (UTIs), so-called gut-bladder axis syndrome with the formation of intracellular bacterial communities in the course of acute cystitis. However, other chronic urinary tract infections are caused by bacterial strains of intestinal derivation. Monomicrobial and polymicrobial infections account for the outcome of acute and chronic UTIs, even including prostatitis and chronic pelvic pain. E. coli isolates have been shown to be more invasive and resistant to antibiotics. Probiotics, fecal microbial transplantation, phage therapy, antimicrobial peptides, and immune-mediated therapies, even including vaccines for the treatment of UTIs, will be described.
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Affiliation(s)
- Emilio Jirillo
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Raffaele Palmirotta
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Marica Colella
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
- Doctoral School, eCampus University, 22060 Novedrate, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
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Trintinaglia M, de Brito KCT, Kobayashi RKT, Otutumi LK, Nakazato G, de Souza Gazal LE, Cruz VD, de Brito BG. Phenotypic and genotypic characterizations of bacteria isolated from the respiratory microbiota of healthy turkeys with potential for probiotic composition. Vet Res Commun 2024; 48:381-390. [PMID: 37707656 DOI: 10.1007/s11259-023-10217-8] [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: 01/25/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Desirable characteristics of Staphylococcus sp., Streptococcus sp., Bacillus sp., Klebsiella sp., Escherichia coli, and Pseudomonas pseudoalcaligenes isolated from the trachea of healthy turkeys were evaluated as probiotic candidates in the search for new alternatives to solve antimicrobial resistance issues in poultry. In current study phenotypic and genotypic capacity to produce bacteriocin-like substances, efficacy to inhibit the growth of avian pathogens, susceptibility to antimicrobials of bacteria isolated from the respiratory microbiota of healthy turkeys, and the presence of virulence-associated genes (VAGs) predictors of Avian Pathogenic Escherichia coli (APEC) were evaluated. Nine E. coli and one Klebsiella sp. strains produced bacteriocin-like substances, and all harbored the cvaA gene. Some strains also showed antagonistic activity against APEC. Multidrug-resistant profile was found in 54% of the strains. Six strains of bacteriocin-like substances producing E. coli also harbored 3-5 VAGs. The study showed that two bacterial genuses (Klebsiella sp. and E. coli) present desirable probiotic characteristics. Our results identified strains with potential for poultry's respiratory probiotic.
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Affiliation(s)
- Michele Trintinaglia
- Secretariat of Agriculture, Department of Agricultural Diagnosis and Research - Postgraduate Program in Animal Health of the Institute for Veterinary Research Desidério Finamor, Livestock and Rural Development of Rio Grande do Sul, Eldorado do Sul, (RS), Brazil
| | - Kelly Cristina Tagliari de Brito
- Secretariat of Agriculture, Department of Agricultural Diagnosis and Research - Postgraduate Program in Animal Health of the Institute for Veterinary Research Desidério Finamor, Livestock and Rural Development of Rio Grande do Sul, Eldorado do Sul, (RS), Brazil.
| | | | - Luciana Kazue Otutumi
- Postgraduate Program in Animal Science with Emphasis on Bioactive Products), Universidade Paranaense, Umuarama, Brazil
| | - Gerson Nakazato
- Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | | | - Benito Guimarães de Brito
- Secretariat of Agriculture, Department of Agricultural Diagnosis and Research - Postgraduate Program in Animal Health of the Institute for Veterinary Research Desidério Finamor, Livestock and Rural Development of Rio Grande do Sul, Eldorado do Sul, (RS), Brazil
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