1
|
Shah AB, Cho H, Shim SH. Exploring the bioactive landscape: peptides and non-peptides from the human microbiota. NPJ Biofilms Microbiomes 2025; 11:76. [PMID: 40341751 PMCID: PMC12062242 DOI: 10.1038/s41522-025-00713-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 04/28/2025] [Indexed: 05/11/2025] Open
Abstract
The human microbiota, consisting of trillions of bacteria from six main phyla, produces peptide and non-peptide secondary metabolites which have antibacterial properties vital to medicine and biotechnology. These metabolites influence biological processes linked to diseases, yet much remains unknown. This review explores their structures and functions, aiming to spur novel metabolite discovery and advance drug development.
Collapse
Affiliation(s)
- Abdul Bari Shah
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Hyeonjae Cho
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
2
|
Hasnat S, Rahman MM, Yeasmin F, Jubair M, Helmy YA, Islam T, Hoque MN. Genomic and Computational Analysis Unveils Bacteriocin Based Therapeutics against Clinical Mastitis Pathogens in Dairy Cows. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10563-w. [PMID: 40295467 DOI: 10.1007/s12602-025-10563-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: 04/24/2025] [Indexed: 04/30/2025]
Abstract
Clinical mastitis (CM) remains a critical challenge in dairy production, exacerbated by the global rise of antibiotic-resistant pathogens, which threatens herd health and productivity. This study pioneers a dual genomic-computational strategy to develop bacteriocin-based therapeutics-a promising alternative to conventional antibiotics-by targeting conserved virulence mechanisms in CM-causing pathogens. We aimed to (i) identify essential core proteins in CM-causing pathogens of dairy cows using the genomic approach; and (ii) assess the efficacy of bacteriocin peptides (BPs) as novel therapeutic agents targeting the selected core proteins for sustainable management of mastitis. Through pan-genomic analysis of 16 clinically relevant pathogens, including Staphylococcus aureus, S. warneri, Streptococcus agalactiae, S. uberis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, P. putida, and P. asiatica, we identified 65 evolutionarily conserved core proteins. Prioritization based on essentiality, virulence, and resistance potential revealed Rho (transcription termination factor) and HupB (nucleoid-associated protein) as high-value therapeutic targets due to their critical roles in bacterial survival and pathogenicity. A computational screen of 70 BPs identified 14 candidates with high binding affinity for both Rho and HupB proteins. Molecular dynamics simulations demonstrated that BP8, a novel dual-action bacteriocin, competitively inhibits Rho-mediated transcription termination and disrupts HupB-DNA interactions, effectively crippling bacterial replication and virulence. BP8 exhibited superior structural stability and binding efficacy compared to other candidates, positioning it as a potent broad-spectrum agent against diverse CM pathogens, including multidrug-resistant strains. Our study underscores the untapped potential of bacteriocins in veterinary medicine, offering a sustainable solution to mitigate antibiotic overuse and resistance. The computational validation of BP8 provides a foundational framework for developing targeted therapies, with implications for reducing dairy industry losses and improving animal welfare. Further in vitro and in vivo studies are warranted to translate these insights into practical therapeutics.
Collapse
Affiliation(s)
- Soharth Hasnat
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Gazipur Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Morshedur Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Gazipur Agricultural University, Gazipur, 1706, Bangladesh
| | - Farzana Yeasmin
- Institute of Biotechnology and Genetic Engineering, Gazipur Agricultural University, Gazipur, 1706, Bangladesh
| | - Mohammad Jubair
- iccdr'b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, 1212, Bangladesh
| | - Yosra A Helmy
- Department of Veterinary Science, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY, 40546-0099, USA
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Gazipur Agricultural University, Gazipur, 1706, Bangladesh.
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Gazipur Agricultural University, Gazipur, 1706, Bangladesh.
| |
Collapse
|
3
|
Nicholas-Haizelden K, Chong CE, Alqahtani N, Alsaadi SE, Horsburgh MJ. Complete genome sequence of Staphylococcus epidermidis B273 and its epidermicin NI01 biosynthesis plasmid. Microbiol Resour Announc 2025; 14:e0096124. [PMID: 39791916 PMCID: PMC11812387 DOI: 10.1128/mra.00961-24] [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: 09/03/2024] [Accepted: 12/11/2024] [Indexed: 01/12/2025] Open
Abstract
The human skin commensal Staphylococcus epidermidis produces diverse, therapeutically relevant bacteriocins. We report the complete whole-genome sequence of the nasal isolate S. epidermidis B273, which contains a plasmid with the biosynthetic gene cluster for epidermicin NI01, a broad-spectrum type II antimicrobial peptide.
Collapse
Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Charlotte E. Chong
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Norah Alqahtani
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Biology, College of Science, Qassim University, Buradyah, Saudi Arabia
| | - Samah E. Alsaadi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
4
|
Shah AB, Shim SH. Human microbiota peptides: important roles in human health. Nat Prod Rep 2025; 42:151-194. [PMID: 39545326 DOI: 10.1039/d4np00042k] [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: 11/17/2024]
Abstract
Covering: 1974 to 2024Human microbiota consist of a diverse array of microorganisms, such as bacteria, Eukarya, archaea, and viruses, which populate various parts of the human body and live in a cooperatively beneficial relationship with the host. They play a crucial role in supporting the functional balance of the microbiome. The coevolutionary progression has led to the development of specialized metabolites that have the potential to substitute traditional antibiotics in combating global health challenges. Although there has been a lot of research on the human microbiota, there is a considerable lack of understanding regarding the wide range of peptides that these microbial populations produce. Particularly noteworthy are the antibiotics that are uniquely produced by the human microbiome, especially by bacteria, to protect against invasive infections. This review seeks to fill this knowledge gap by providing a thorough understanding of various peptides, along with their in-depth biological importance in terms of human disorders. Advancements in genomics and the understanding of molecular mechanisms that control the interactions between microbiota and hosts have made it easier to find peptides that come from the human microbiome. We hope that this review will serve as a basis for developing new therapeutic approaches and personalized healthcare strategies. Additionally, it emphasizes the significance of these microbiota in the field of natural product discovery and development.
Collapse
Affiliation(s)
- Abdul Bari Shah
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Zhao Y, Bitzer A, Power JJ, Belikova D, Torres Salazar BO, Adolf LA, Gerlach D, Krismer B, Heilbronner S. Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability. THE ISME JOURNAL 2024; 18:wrae123. [PMID: 38987933 PMCID: PMC11296517 DOI: 10.1093/ismejo/wrae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens, such as methicillin-resistant Staphylococcus aureus, can reside within the nasal microbiota, which increases the risk of infection. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic species and S. aureus, but the underlying molecular mechanisms remain poorly understood. The nasal cavity is iron-limited, and bacteria are known to produce iron-scavenging siderophores to proliferate in such environments. Siderophores are public goods that can be consumed by all members of a bacterial community. Accordingly, siderophores are known to mediate bacterial competition and collaboration, but their role in the nasal microbiome is unknown. Here, we show that siderophore acquisition is crucial for S. aureus nasal colonization in vivo. We screened 94 nasal bacterial strains from seven genera for their capacity to produce siderophores as well as to consume the siderophores produced by S. aureus. We found that 80% of the strains engaged in siderophore-mediated interactions with S. aureus. Non-pathogenic corynebacterial species were found to be prominent consumers of S. aureus siderophores. In co-culture experiments, consumption of siderophores by competitors reduced S. aureus growth in an iron-dependent fashion. Our data show a wide network of siderophore-mediated interactions between the species of the human nasal microbiome and provide mechanistic evidence for inter-species competition and collaboration impacting pathogen proliferation. This opens avenues for designing nasal probiotics to displace S. aureus from the nasal cavity of humans.
Collapse
Affiliation(s)
- Yanfeng Zhao
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Laboratory Medicine Center, The Second Affiliated Hospital, Nanjing Medical University, 210011 Nanjing, P. R. China
| | - Alina Bitzer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Jeffrey John Power
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Darya Belikova
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
| | - Benjamin Orlando Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Lea Antje Adolf
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
| | - David Gerlach
- Ludwig-Maximilians-Universität München, Faculty of Biology, Microbiology, 82152 Martinsried, Germany
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Simon Heilbronner
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
- Ludwig-Maximilians-Universität München, Faculty of Biology, Microbiology, 82152 Martinsried, Germany
- German Center for Infection Research “DZIF” partnersite Tübingen, Germany
| |
Collapse
|