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Wang KKA, Singh J, Albin JS, Pentelute BL, Nolan EM. Class IIb Microcin MccM Interferes with Oxidative Phosphorylation in Escherichia coli. ACS Chem Biol 2024. [PMID: 39172990 DOI: 10.1021/acschembio.4c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Dysbiosis of the human gut microbiota is linked to numerous diseases. Understanding the molecular mechanisms by which microbes interact and compete with one another is required for developing successful strategies to modulate the microbiome. The natural product Microcin M (MccM) consists of a 77-residue bioactive peptide conjugated to a siderophore and is a class II microcin involved in microbial competition with an enigmatic mode-of-action. In this work, we investigated the basis for MccM activity and leveraged bioinformatics to expand the known chemical diversity of class II microcins. We applied automated fast-flow solid phase peptide synthesis coupled with chemoenzymatic chemistry to acquire MccM and demonstrated that its activity was bacteriostatic. We then used our synthetic molecule to ascertain that catecholate siderophore transporters in Escherichia coli K-12 are necessary for MccM import. Once inside the cell, we found that MccM treatment decreased the levels of intracellular ATP and interfered with gene expression. These effects were ameliorated in genetic mutants lacking ATP synthase or in conditions that support substrate-level phosphorylation. Further, we showed that MccM elevated the levels of reactive oxygen species within the target cell. We propose that MccM effects its bacteriostatic activity by decreasing the total energy level of the cell through inhibition of oxidative phosphorylation. Lastly, using genome mining, we bioinformatically identified 171 novel putative class II microcins. Our investigation sheds light on the natural processes involved in microbial competition and provides inspiration, in the form of new molecules, for future therapeutic endeavors.
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Affiliation(s)
- Kwo-Kwang Abraham Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jupneet Singh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - John S Albin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Jandl B, Dighe S, Gasche C, Makristathis A, Muttenthaler M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin Microbiol Rev 2024:e0013323. [PMID: 38995034 DOI: 10.1128/cmr.00133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.
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Affiliation(s)
- Bernhard Jandl
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Christoph Gasche
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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3
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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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4
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. Turbidimetric bioassays: A solution to antimicrobial activity detection in asymptomatic bacteriuria isolates against uropathogenic Escherichia coli. Microbiologyopen 2024; 13:e1411. [PMID: 38706434 PMCID: PMC11070844 DOI: 10.1002/mbo3.1411] [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: 02/15/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and SK-106-1). The inhibition of the CFS by proteinase K suggested that the antimicrobial activity was proteinaceous in nature, potentially bacteriocins. The activity of E. coli PUTS 58 and SK-106-1 was enhanced in an artificial urine medium, with both inhibiting all eight UPECs. A putative microcin H47 operon was identified in E. coli SK-106-1, along with a previously identified microcin V and colicin E7 in E. coli PUTS 37 and PUTS 58, respectively. These findings indicate that ABU bacteriocin-producers could serve as viable prophylactics and therapeutics in the face of increasing antibiotic resistance among uropathogens.
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Affiliation(s)
- Ciara Kenneally
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Craig P. Murphy
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Roy D. Sleator
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Eamonn P. Culligan
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
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5
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Cherrak Y, Salazar MA, Yilmaz K, Kreuzer M, Hardt WD. Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner. PLoS Biol 2024; 22:e3002616. [PMID: 38865418 PMCID: PMC11168627 DOI: 10.1371/journal.pbio.3002616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
The gastrointestinal tract is densely colonized by a polymicrobial community known as the microbiota which serves as primary line of defence against pathogen invasion. The microbiota can limit gut-luminal pathogen growth at different stages of infection. This can be traced to specific commensal strains exhibiting direct or indirect protective functions. Although these mechanisms hold the potential to develop new approaches to combat enteric pathogens, they remain far from being completely described. In this study, we investigated how a mouse commensal Escherichia coli can outcompete Salmonella enterica serovar Typhimurium (S. Tm). Using a salmonellosis mouse model, we found that the commensal E. coli 8178 strain relies on a trojan horse trap strategy to limit S. Tm expansion in the inflamed gut. Combining mutants and reporter tools, we demonstrated that inflammation triggers the expression of the E. coli 8178 antimicrobial microcin H47 toxin which, when fused to salmochelin siderophores, can specifically alter S. Tm growth. This protective function was compromised upon disruption of the E. coli 8178 tonB-dependent catecholate siderophore uptake system, highlighting a previously unappreciated crosstalk between iron intake and microcin H47 activity. By identifying the genetic determinants mediating S. Tm competition, our work not only provides a better mechanistic understanding of the protective function displayed by members of the gut microbiota but also further expands the general contribution of microcins in bacterial antagonistic relationships. Ultimately, such insights can open new avenues for developing microbiota-based approaches to better control intestinal infections.
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Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Koray Yilmaz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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6
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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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7
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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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8
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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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Zafar H, Saier MHH. An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes. Microb Physiol 2024; 34:133-141. [PMID: 38636461 PMCID: PMC11283328 DOI: 10.1159/000538779] [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: 01/08/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community. SUMMARY This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut. KEY MESSAGES Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Milton H. Herman Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, La Jolla, California, 92093-0116, USA
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10
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Kastrat E, Cheng HP. Escherichia coli has an undiscovered ability to inhibit the growth of both Gram-negative and Gram-positive bacteria. Sci Rep 2024; 14:7420. [PMID: 38548840 PMCID: PMC10978900 DOI: 10.1038/s41598-024-57996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
The ability for bacteria to form boundaries between neighboring colonies as the result of intra-species inhibition has been described for a limited number of species. Here, we report that intra-species inhibition is more common than previously recognized. We demonstrated that swimming colonies of four Escherichia coli strains and six other bacteria form inhibitory zones between colonies, which is not caused by nutrient depletion. This phenomenon was similarly observed with non-flagellated bacteria. We developed a square-streaking pattern assay which revealed that Escherichia coli BW25113 inhibits the growth of other E. coli, and surprisingly, other Gram-positive and negative bacteria, including multi-drug resistant clinical isolates. Altogether, our findings demonstrate intra-species inhibition is common and might be used by E. coli to inhibit other bacteria. Our findings raise the possibility for a common mechanism shared across bacteria for intra-species inhibition. This can be further explored for a potential new class of antibiotics.
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Affiliation(s)
- Ertan Kastrat
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA
- The Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Hai-Ping Cheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA.
- The Graduate Center, City University of New York, New York, NY, 10016, USA.
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11
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [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: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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12
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Telhig S, Pham NP, Ben Said L, Rebuffat S, Ouellette M, Zirah S, Fliss I. Exploring the genetic basis of natural resistance to microcins. Microb Genom 2024; 10:001156. [PMID: 38407259 PMCID: PMC10926693 DOI: 10.1099/mgen.0.001156] [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: 03/29/2023] [Accepted: 11/28/2023] [Indexed: 02/27/2024] Open
Abstract
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Ismaïl Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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13
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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14
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Baquero F, Rodríguez-Beltrán J, Coque TM, del Campo R. Boosting Fitness Costs Associated with Antibiotic Resistance in the Gut: On the Way to Biorestoration of Susceptible Populations. Biomolecules 2024; 14:76. [PMID: 38254676 PMCID: PMC10812938 DOI: 10.3390/biom14010076] [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: 11/25/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The acquisition and expression of antibiotic resistance implies changes in bacterial cell physiology, imposing fitness costs. Many human opportunistic pathogenic bacteria, such as those causing urinary tract or bloodstream infections, colonize the gut. In this opinionated review, we will examine the various types of stress that these bacteria might suffer during their intestinal stay. These stresses, and their compensatory responses, probably have a fitness cost, which might be additive to the cost of expressing antibiotic resistance. Such an effect could result in a disadvantage relative to antibiotic susceptible populations that might replace the resistant ones. The opinion proposed in this paper is that the effect of these combinations of fitness costs should be tested in antibiotic resistant bacteria with susceptible ones as controls. This testing might provide opportunities to increase the bacterial gut stress boosting physiological biomolecules or using dietary interventions. This approach to reduce the burden of antibiotic-resistant populations certainly must be answered empirically. In the end, the battle against antibiotic resistance should be won by antibiotic-susceptible organisms. Let us help them prevail.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
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15
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Tan YH, Arros P, Berríos-Pastén C, Wijaya I, Chu WHW, Chen Y, Cheam G, Mohamed Naim AN, Marcoleta AE, Ravikrishnan A, Nagarajan N, Lagos R, Gan YH. Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut. THE ISME JOURNAL 2024; 18:wrae054. [PMID: 38547398 PMCID: PMC11020217 DOI: 10.1093/ismejo/wrae054] [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: 01/11/2024] [Revised: 02/24/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
The hypervirulent lineages of Klebsiella pneumoniae (HvKp) cause invasive infections such as Klebsiella-liver abscess. Invasive infection often occurs after initial colonization of the host gastrointestinal tract by HvKp. Over 80% of HvKp isolates belong to the clonal group 23 sublineage I that has acquired genomic islands (GIs) GIE492 and ICEKp10. Our analysis of 12 361 K. pneumoniae genomes revealed that GIs GIE492 and ICEKp10 are co-associated with the CG23-I and CG10118 HvKp lineages. GIE492 and ICEKp10 enable HvKp to make a functional bacteriocin microcin E492 (mccE492) and the genotoxin colibactin, respectively. We discovered that GIE492 and ICEKp10 play cooperative roles and enhance gastrointestinal colonization by HvKp. Colibactin is the primary driver of this effect, modifying gut microbiome diversity. Our in vitro assays demonstrate that colibactin and mccE492 kill or inhibit a range of Gram-negative Klebsiella species and Escherichia coli strains, including Gram-positive bacteria, sometimes cooperatively. Moreover, mccE492 and colibactin kill human anaerobic gut commensals that are similar to the taxa found altered by colibactin in the mouse intestines. Our findings suggest that GIs GIE492 and ICEKp10 enable HvKp to kill several commensal bacterial taxa during interspecies interactions in the gut. Thus, acquisition of GIE492 and ICEKp10 could enable better carriage in host populations and explain the dominance of the CG23-I HvKp lineage.
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Affiliation(s)
- Yi Han Tan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Indrik Wijaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Wilson H W Chu
- National Public Health Laboratory, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442, Republic of Singapore
| | - Yahua Chen
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
| | - Guoxiang Cheam
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
| | - Ahmad Nazri Mohamed Naim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Niranjan Nagarajan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
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16
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Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol 2024; 9:200-213. [PMID: 38110697 PMCID: PMC11310079 DOI: 10.1038/s41564-023-01544-2] [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: 02/22/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
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Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Daniela Janek
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Jan Bornikoel
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Berscheid
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sophia Krauss
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon J Jaag
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Norah Alqahtani
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José Manuel Beltrán-Beleña
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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17
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Gu Q, Yan J, Lou Y, Zhang Z, Li Y, Zhu Z, Liu M, Wu D, Liang Y, Pu J, Zhao X, Xiao H, Li P. Bacteriocins: Curial guardians of gastrointestinal tract. Compr Rev Food Sci Food Saf 2024; 23:e13292. [PMID: 38284593 DOI: 10.1111/1541-4337.13292] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
The human gastrointestinal (GI) tract microbiome secretes various metabolites that play pivotal roles in maintaining host physiological balance and influencing disease progression. Among these metabolites, bacteriocins-small, heat-stable peptides synthesized by ribosomes-are notably prevalent in the GI region. Their multifaceted benefits have garnered significant interest in the scientific community. This review comprehensively explores the methods for mining bacteriocins (traditional separation and purification, bioinformatics, and artificial intelligence), their effects on the stomach and intestines, and their complex bioactive mechanisms. These mechanisms include flora regulation, biological barrier restoration, and intervention in epithelial cell pathways. By detailing each well-documented bacteriocin, we reveal the diverse ways in which bacteriocins interact with the GI environment. Moreover, the future research direction is prospected. By further studying the function and interaction of intestinal bacteriocins, we can discover new pharmacological targets and develop drugs targeting intestinal bacteriocins to regulate and improve human health. It provides innovative ideas and infinite possibilities for further exploration, development, and utilization of bacteriocins. The inevitable fact is that the continuously exploration of bacteriocins is sure to bring the promising future for demic GI health understanding and interference strategy.
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Affiliation(s)
- Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Yan
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yeqing Lou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zihao Zhang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yonglu Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zichun Zhu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Manman Liu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Danli Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Liang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Pu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaodan Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
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18
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Ha EJ, Hong SM, Kim SJ, Ahn SM, Kim HW, Choi KS, Kwon HJ. Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli. Antibiotics (Basel) 2023; 12:1714. [PMID: 38136748 PMCID: PMC10740950 DOI: 10.3390/antibiotics12121714] [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: 09/27/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.
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Affiliation(s)
- Eun-Jin Ha
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Sun-Min Ahn
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Ho-Won Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Republic of Korea
- GeNiner Inc., Seoul 08826, Republic of Korea
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19
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Ríos Colombo NS, Perez-Ibarreche M, Draper LA, O’Connor PM, Field D, Ross RP, Hill C. Impact of bacteriocin-producing strains on bacterial community composition in a simplified human intestinal microbiota. Front Microbiol 2023; 14:1290697. [PMID: 38143858 PMCID: PMC10748383 DOI: 10.3389/fmicb.2023.1290697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Bacteriocins are antimicrobial peptides that have been studied for decades as food bio-preservatives or as alternatives to antibiotics. They also have potential as modulators of the gut microbiome, which has been linked to human health. However, it is difficult to predict a priori how bacteriocins will impact complex microbial communities through direct and indirect effects. Here we assess the effect of different bacteriocin-producing strains on a Simplified Human Intestinal Microbiota (SIHUMI) model, using a set of bacteriocin-producing strains (Bac+) and otherwise isogenic non-producers (Bac-). Bacteriocins from different classes and with different activity spectra were selected, including lantibiotics such as lacticin 3147 and nisin A, and pediocin-like bacteriocins such as pediocin PA-1 among other peptides. SIHUMI is a bacterial consortium of seven diverse human gut species that assembles to a predictable final composition in a particular growth medium. Each member can be individually tracked by qPCR. Bac+ and Bac- strains were superimposed on the SIHUMI system, and samples were taken at intervals up to 48 h. The genome copy number of each SIHUMI member was evaluated using specific primers. We establish that the composition of the community changes in response to the presence of either broad- or narrow-spectrum bacteriocin producers and confirm that there are significant off-target effects. These effects were analyzed considering antagonistic inter-species interactions within the SIHUMI community, providing a comprehensive insight into the possible mechanisms by which complex communities can be shaped by bacteriocins.
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Affiliation(s)
| | | | | | - Paula M. O’Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
| | - Des Field
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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20
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Bartram E, Asai M, Gabant P, Wigneshweraraj S. Enhancing the antibacterial function of probiotic Escherichia coli Nissle: when less is more. Appl Environ Microbiol 2023; 89:e0097523. [PMID: 37930328 PMCID: PMC10686094 DOI: 10.1128/aem.00975-23] [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: 06/13/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
Probiotic bacteria confer multiple health benefits, including preventing the growth, colonization, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria, and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probiotic Escherichia coli strain Nissle (EcN) the ability to produce microcin C (McC) from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon while ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in a Galleria mellonella infection model of enterohemorrhagic E. coli, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little-to-none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic, or diagnostic applications. Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial "probiotic" bacteria to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side effects on the performance of such bacteria, thereby compromising their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic, or diagnostic applications.
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Affiliation(s)
- Emma Bartram
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Masanori Asai
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
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21
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Caradec T, Anoz-Carbonell E, Petrov R, Billamboz M, Antraygues K, Cantrelle FX, Boll E, Beury D, Hot D, Drobecq H, Trivelli X, Hartkoorn RC. A Novel Natural Siderophore Antibiotic Conjugate Reveals a Chemical Approach to Macromolecule Coupling. ACS CENTRAL SCIENCE 2023; 9:2138-2149. [PMID: 38033789 PMCID: PMC10683483 DOI: 10.1021/acscentsci.3c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Inspired by natural sideromycins, the conjugation of antibiotics to siderophores is an attractive strategy to facilitate "Trojan horse" delivery of antibiotics into bacteria. Genome analysis of a soil bacterium, Dactylosporangium fulvum, found a "hybrid" biosynthetic gene cluster responsible for the production of both an antibiotic, pyridomycin, and a novel chlorocatechol-containing siderophore named chlorodactyloferrin. While both of these natural products were synthesized independently, analysis of the culture supernatant also identified a conjugate of both molecules. We then found that the addition of ferric iron to purified chlorodactyloferrin and pyridomycin instigated their conjugation, leading to the formation of a covalent bond between the siderophore-catechol and the pyridomycin-pyridine groups. Using model reactants, this iron-based reaction was found to proceed through a Michael-type addition reaction, where ferric iron oxidizes the siderophore-catechol group into its quinone form, which is then attacked by the antibiotic pyridyl-nitrogen to form the catechol-pyridinium linkage. These findings prompted us to explore if other "cargo" molecules could be attached to chlorodactyloferrin in a similar manner, and this was indeed confirmed with a pyridine-substituted TAMRA fluorophore as well as with pyridine-substituted penicillin, rifampicin, and norfloxacin antibiotic analogues. The resultant biomimetic conjugates were demonstrated to effectively enter a number of bacteria, with TAMRA-chlorodactyloferrin conjugates causing fluorescent labeling of the bacteria, and with penicillin and rifampicin conjugates eliciting antibiotic activity. These findings open up new opportunities for the design and facile synthesis of a novel class of biomimetic siderophore conjugates with antibiotic activity.
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Affiliation(s)
- Thibault Caradec
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Ernesto Anoz-Carbonell
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Ravil Petrov
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Muriel Billamboz
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- JUNIA,
Health and Environment, Laboratory of Sustainable
Chemistry and Health, F-59000 Lille, France
| | - Kevin Antraygues
- Université
Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Francois-Xavier Cantrelle
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- CNRS, EMR9002
BSI Integrative Structural Biology, 59000 Lille, France
| | - Emmanuelle Boll
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- CNRS, EMR9002
BSI Integrative Structural Biology, 59000 Lille, France
| | - Delphine Beury
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie
& Santé, F-59000 Lille, France
| | - David Hot
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie
& Santé, F-59000 Lille, France
| | - Herve Drobecq
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Xavier Trivelli
- Université
Lille, CNRS, INRAE, Centrale Lille, Université d’Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, 59000 Lille, France
| | - Ruben C. Hartkoorn
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
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22
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Sanz-García F, Gil-Gil T, Laborda P, Blanco P, Ochoa-Sánchez LE, Baquero F, Martínez JL, Hernando-Amado S. Translating eco-evolutionary biology into therapy to tackle antibiotic resistance. Nat Rev Microbiol 2023; 21:671-685. [PMID: 37208461 DOI: 10.1038/s41579-023-00902-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are urgently needed. Therefore, preserving the efficacy of the antibiotics currently in use and developing compounds and strategies that specifically target antibiotic-resistant pathogens is critical. The identification of robust trends of antibiotic resistance evolution and of its associated trade-offs, such as collateral sensitivity or fitness costs, is invaluable for the design of rational evolution-based, ecology-based treatment approaches. In this Review, we discuss these evolutionary trade-offs and how such knowledge can aid in informing combination or alternating antibiotic therapies against bacterial infections. In addition, we discuss how targeting bacterial metabolism can enhance drug activity and impair antibiotic resistance evolution. Finally, we explore how an improved understanding of the original physiological function of antibiotic resistance determinants, which have evolved to reach clinical resistance after a process of historical contingency, may help to tackle antibiotic resistance.
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Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Clinical Microbiology, 9301, Rigshospitalet, Copenhagen, Denmark
| | - Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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23
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Martínez JL, Baquero F. What are the missing pieces needed to stop antibiotic resistance? Microb Biotechnol 2023; 16:1900-1923. [PMID: 37417823 PMCID: PMC10527211 DOI: 10.1111/1751-7915.14310] [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] [Received: 04/19/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023] Open
Abstract
As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.
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Affiliation(s)
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Department of MicrobiologyRamón y Cajal University Hospital, CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
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24
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Santos-Júnior CD, Der Torossian Torres M, Duan Y, del Río ÁR, Schmidt TS, 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. Computational exploration of the global microbiome for antibiotic discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555663. [PMID: 37693522 PMCID: PMC10491242 DOI: 10.1101/2023.08.31.555663] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Marcelo Der Torossian 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, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, 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, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Thomas S.B. Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, 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, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, 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
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- International Human Phenome Institute, 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, 28223 Pozuelo de Alarcón, 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, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
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25
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Le MNT, Nguyen THH, Trinh VM, Nguyen TPB, Kawada-Matsuo M, Kayama S, Sugai M, Komatsuzawa H. Comprehensive Analysis of Bacteriocins Produced by the Hypermucoviscous Klebsiella pneumoniae Species Complex. Microbiol Spectr 2023; 11:e0086323. [PMID: 37154746 PMCID: PMC10269471 DOI: 10.1128/spectrum.00863-23] [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: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/10/2023] Open
Abstract
Klebsiella pneumoniae produces several kinds of bacteriocins that have antimicrobial effects against closely related species, but few studies have comprehensively reported bacteriocin distribution among the Klebsiella population. In this study, we identified bacteriocin genes in 180 K. pneumoniae species complex genomes, including 170 hypermucoviscous isolates, and investigated the antibacterial activity against 50 strains, including antimicrobial-resistant organisms, belonging to multiple species, namely, Klebsiella spp., Escherichia coli, Pseudomonas spp., Acinetobacter spp., Enterobacter cloacae, Stenotrophomonas maltophilia, Chryseobacterium indologenes, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus mutans. Our study determined that 32.8% (59/180) of isolates carried at least one bacteriocin type. Different types of bacteriocin were usually present in different specific sequence types (STs); meanwhile, bacteriocins were not detected in certain STs. Microcin E492 was the most prevalent bacteriocin (14.4%), mostly in ST23 isolates, and displayed a wide spectrum of activity, including against Klebsiella spp., E. coli, Pseudomonas spp., and Acinetobacter spp. Cloacin-like bacteriocin was detected in 7.2% of strains, all of which were non-ST23 isolates, and exhibited inhibitory activity against closely related species, mainly Klebsiella spp. Klebicin B-like bacteriocin was detected at a rate of 9.4%, although 82.4% of these strains carried a disrupted bacteriocin gene, and an inhibitory effect could not be observed from the intact-gene-carrying isolates. Other bacteriocins, such as microcin S-like, microcin B17, and klebicin C-like, were detected at lower rates and had limited inhibitory activity. Our findings suggested that Klebsiella strains that carry different bacteriocin types may affect the composition of the surrounding bacterial community. IMPORTANCE Klebsiella pneumoniae is a Gram-negative commensal bacterium that asymptomatically colonizes human mucosal membranes, such as the intestinal tract, but it is also a leading cause of health care- and community-associated infections. Additionally, multidrug-resistant K. pneumoniae has been continuously evolving, which significantly challenges the available chemotherapeutic treatment for its infections. K. pneumoniae produces several kinds of antimicrobial peptides known as bacteriocins, which have antibacterial activity against closely related species. This work was the first comprehensive report of bacteriocin distribution among the hypermucoviscous K. pneumoniae species complex population and the inhibitory activity of each bacteriocin type against various species, including multidrug-resistant strains. Our findings provide a foundation for future studies on the K. pneumoniae species complex, including studies on the competition within the microflora and the potential applications of bacteriocins in treating multidrug-resistant bacteria.
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Affiliation(s)
- Mi Nguyen-Tra Le
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Thao Huu-Huong Nguyen
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Van Minh Trinh
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tam Phuc-Bao Nguyen
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Shizuo Kayama
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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26
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Cesaro A, Lin S, Pardi N, de la Fuente-Nunez C. Advanced delivery systems for peptide antibiotics. Adv Drug Deliv Rev 2023; 196:114733. [PMID: 36804008 PMCID: PMC10771258 DOI: 10.1016/j.addr.2023.114733] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Antimicrobial peptides (AMPs) hold promise as alternatives to traditional antibiotics for preventing and treating multidrug-resistant infections. Although they have potent antimicrobial efficacy, AMPs are mainly limited by their susceptibility to proteases and potential off-site cytotoxicity. Designing the right delivery system for peptides can help to overcome such limitations, thus improving the pharmacokinetic and pharmacodynamic profiles of these drugs. The versatility of peptides and their genetically encodable structure make them suitable for both conventional and nucleoside-based formulations. In this review, we describe the main drug delivery procedures developed so far for peptide antibiotics: lipid nanoparticles, polymeric nanoparticles, hydrogels, functionalized surfaces, and DNA- and RNA-based delivery systems.
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Affiliation(s)
- Angela Cesaro
- 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, United States; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Shuangzhe Lin
- 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, United States; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - 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, United States; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States.
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Kirundi J, Moghadamrad S, Urbaniak C. Microbiome-liver crosstalk: A multihit therapeutic target for liver disease. World J Gastroenterol 2023; 29:1651-1668. [PMID: 37077519 PMCID: PMC10107210 DOI: 10.3748/wjg.v29.i11.1651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/05/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023] Open
Abstract
Liver disease has become a leading cause of death, particularly in the West, where it is attributed to more than two million deaths annually. The correlation between gut microbiota and liver disease is still not fully understood. However, it is well known that gut dysbiosis accompanied by a leaky gut causes an increase in lipopolysaccharides in circulation, which in turn evoke massive hepatic inflammation promoting liver cirrhosis. Microbial dysbiosis also leads to poor bile acid metabolism and low short-chain fatty acids, all of which exacerbate the inflammatory response of liver cells. Gut microbial homeostasis is maintained through intricate processes that ensure that commensal microbes adapt to the low oxygen potential of the gut and that they rapidly occupy all the intestinal niches, thus outcompeting any potential pathogens for available nutrients. The crosstalk between the gut microbiota and its metabolites also guarantee an intact gut barrier. These processes that protect against destabilization of gut microbes by potential entry of pathogenic bacteria are collectively called colonization resistance and are equally essential for liver health. In this review, we shall investigate how the mechanisms of colonization resistance influence the liver in health and disease and the microbial-liver crosstalk potential as therapeutic target areas.
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Affiliation(s)
- Jorum Kirundi
- Department of Biomedical Research, University of Bern, Bern 3014, Switzerland
| | - Sheida Moghadamrad
- Department of Gastroenterology/Hepatology, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona and Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano 6900, Switzerland
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Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers. Eur J Clin Microbiol Infect Dis 2023; 42:229-254. [PMID: 36680641 PMCID: PMC9899200 DOI: 10.1007/s10096-023-04548-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.
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29
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Almeida MC, da Costa PM, Sousa E, Resende DISP. Emerging Target-Directed Approaches for the Treatment and Diagnosis of Microbial Infections. J Med Chem 2023; 66:32-70. [PMID: 36586133 DOI: 10.1021/acs.jmedchem.2c01212] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
With the rising levels of drug resistance, developing efficient antimicrobial therapies has become a priority. A promising strategy is the conjugation of antibiotics with relevant moieties that can potentiate their activity by target-directing. The conjugation of siderophores with antibiotics allows them to act as Trojan horses by hijacking the microorganisms' highly developed iron transport systems and using them to carry the antibiotic into the cell. Through the analysis of relevant examples of the past decade, this Perspective aims to reveal the potential of siderophore-antibiotic Trojan horses for the treatment of infections and the role of siderophores in diagnostic techniques. Other conjugated molecules will be the subject of discussion, namely those involving vitamin B12, carbohydrates, and amino acids, as well as conjugated compounds targeting protein degradation and β-lactamase activated prodrugs.
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Affiliation(s)
- Mariana C Almeida
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Paulo M da Costa
- CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Diana I S P Resende
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
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Lee SM, Keum HL, Sul WJ. Bacterial Crosstalk via Antimicrobial Peptides on the Human Skin: Therapeutics from a Sustainable Perspective. J Microbiol 2023; 61:1-11. [PMID: 36719618 DOI: 10.1007/s12275-022-00002-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 02/01/2023]
Abstract
The skin's epidermis is an essential barrier as the first guard against invading pathogens, and physical protector from external injury. The skin microbiome, which consists of numerous bacteria, fungi, viruses, and archaea on the epidermis, play a key role in skin homeostasis. Antibiotics are a fast-acting and effective treatment method, however, antibiotic use is a nuisance that can disrupt skin homeostasis by eradicating beneficial bacteria along with the intended pathogens and cause antibiotic-resistant bacteria spread. Increased numbers of antimicrobial peptides (AMPs) derived from humans and bacteria have been reported, and their roles have been well defined. Recently, modulation of the skin microbiome with AMPs rather than artificially synthesized antibiotics has attracted the attention of researchers as many antibiotic-resistant strains make treatment mediation difficult in the context of ecological problems. Herein, we discuss the overall insights into the skin microbiome, including its regulation by different AMPs, as well as their composition and role in health and disease.
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Affiliation(s)
- Seon Mi Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hye Lim Keum
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Functional Fermented Milk with Fruit Pulp Modulates the In Vitro Intestinal Microbiota. Foods 2022; 11:foods11244113. [PMID: 36553855 PMCID: PMC9778618 DOI: 10.3390/foods11244113] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The effect of putative probiotic fermented milk (FM) with buriti pulp (FMB) or passion fruit pulp (FMPF) or without fruit pulp (FMC) on the microbiota of healthy humans was evaluated. FM formulations were administered into a simulator of the human intestinal microbial ecosystem (SHIME®) to evaluate the viability of lactic acid bacteria (LAB), microbiota composition, presence of short-chain fatty acids (SCFA), and ammonium ions. The probiotic LAB viability in FM was affected by the addition of the fruit pulp. Phocaeicola was dominant in the FMPF and FMB samples; Bifidobacterium was related to FM formulations, while Alistipes was associated with FMPF and FMB, and Lactobacillus and Lacticaseibacillus were predominant in FMC. Trabulsiella was the central element in the FMC, while Mediterraneibacter was the central one in the FMPF and FMB networks. The FM formulations increased the acetic acid, and a remarkably high amount of propionic and butyric acids were detected in the FMB treatment. All FM formulations decreased the ammonium ions compared to the control; FMPF samples stood out for having lower amounts of ammonia. The probiotic FM with fruit pulp boosted the beneficial effects on the intestinal microbiota of healthy humans in addition to increasing SCFA in SHIME® and decreasing ammonium ions, which could be related to the presence of bioactive compounds.
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Abstract
Microcins are a class of antimicrobial peptides produced by certain Gram-negative bacterial species to kill or inhibit the growth of competing bacteria. Only 10 unique, experimentally validated class II microcins have been identified, and the majority of these come from Escherichia coli. Although the current representation of microcins is sparse, they exhibit a diverse array of molecular functionalities, uptake mechanisms, and target specificities. This broad diversity from such a small representation suggests that microcins may have untapped potential for bioprospecting peptide antibiotics from genomic data sets. We used a systematic bioinformatics approach to search for verified and novel class II microcins in E. coli and other species within its family, Enterobacteriaceae. Nearly one-quarter of the E. coli genome assemblies contained one or more microcins, where the prevalence of hits to specific microcins varied by isolate phylogroup. E. coli isolates from human extraintestinal and poultry meat sources were enriched for microcins, while those from freshwater were depleted. Putative microcins were found in various abundances across all five distinct phylogenetic lineages of Enterobacteriaceae, with a particularly high prevalence in the "Klebsiella" clade. Representative genome assemblies from species across the Enterobacterales order, as well as a few outgroup species, also contained putative microcin sequences. This study suggests that microcins have a complicated evolutionary history, spanning far beyond our limited knowledge of the currently validated microcins. Efforts to functionally characterize these newly identified microcins have great potential to open a new field of peptide antibiotics and microbiome modulators and elucidate the ways in which bacteria compete with each other. IMPORTANCE Class II microcins are small bacteriocins produced by strains of Gram-negative bacteria in the Enterobacteriaceae. They are generally understood to play a role in interbacterial competition, although direct evidence of this is limited, and they could prove informative in developing new peptide antibiotics. However, few examples of verified class II microcins exist, and novel microcins are difficult to identify due to their sequence diversity, making it complicated to study them as a group. Here, we overcome this limitation by developing a bioinformatics pipeline to detect microcins in silico. Using this pipeline, we demonstrate that both verified and novel class II microcins are widespread within and outside the Enterobacteriaceae, which has not been systematically shown previously. The observed prevalence of class II microcins suggests that they are ecologically important, and the elucidation of novel microcins provides a resource that can be used to expand our knowledge of the structure and function of microcins as antibacterials.
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Huo Y, Jiang Q, Zhao W. Meta-analysis of metagenomics reveals the signatures of vaginal microbiome in preterm birth. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Mortzfeld BM, Palmer JD, Bhattarai SK, Dupre HL, Mercado-Lubio R, Silby MW, Bang C, McCormick BA, Bucci V. Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic. Gut Microbes 2022; 14:2127633. [PMID: 36175830 PMCID: PMC9542533 DOI: 10.1080/19490976.2022.2127633] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gastrointestinal (GI) tract is the reservoir for multidrug resistant (MDR) pathogens, specifically carbapenem-resistant (CR) Klebsiella pneumoniae and other Enterobacteriaceae, which often lead to the spread of antimicrobial resistance genes, severe extraintestinal infections, and lethal outcomes. Selective GI decolonization has been proposed as a new strategy for preventing transmission to other body sites and minimizing spreading to susceptible individuals. Here, we purify the to-date uncharacterized class IIb microcin I47 (MccI47) and demonstrate potent inhibition of numerous Enterobacteriaceae, including multidrug-resistant clinical isolates, in vitro at concentrations resembling those of commonly prescribed antibiotics. We then genetically modify the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to produce MccI47 from a stable multicopy plasmid by using MccI47 toxin production in a counterselection mechanism to engineer one of the native EcN plasmids, which renders provisions for inducible expression and plasmid selection unnecessary. We then test the clinical relevance of the MccI47-producing engineered EcN in a murine CR K. pneumoniae colonization model and demonstrate significant MccI47-dependent reduction of CR K. pneumoniae abundance after seven days of daily oral live biotherapeutic administration without disruption of the resident microbiota. This study provides the first demonstration of MccI47 as a potent antimicrobial against certain Enterobacteriaceae, and its ability to significantly reduce the abundance of CR K. pneumoniae in a preclinical animal model, when delivered from an engineered live biotherapeutic product. This study serves as the foundational step toward the use of engineered live biotherapeutic products aimed at the selective removal of MDR pathogens from the GI tract.
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Affiliation(s)
- Benedikt M. Mortzfeld
- Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,CONTACT Benedikt M. Mortzfeld Program in Microbiome Dynamics Universty of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jacob D. Palmer
- Department of Zoology, University of Oxford, Oxford, UK,Department of Biochemistry, University of Oxford, Oxford, UK
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, Universty of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Haley L. Dupre
- Department of Bioengineering, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Regino Mercado-Lubio
- Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Mark W. Silby
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Zu Kiel, Kiel, Germany
| | - Beth A. McCormick
- Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, Universty of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Program in Systems Biology, Universty of Massachusetts Chan Medical School, Worcester, MA, USA,Vanni Bucci Department of Microbiology and Physiological Systems, Universty of Massachusetts Chan Medical School, Worcester, MA, USA
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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Seukep AJ, Mbuntcha HG, Kuete V, Chu Y, Fan E, Guo MQ. What Approaches to Thwart Bacterial Efflux Pumps-Mediated Resistance? Antibiotics (Basel) 2022; 11:antibiotics11101287. [PMID: 36289945 PMCID: PMC9598416 DOI: 10.3390/antibiotics11101287] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
An effective response that combines prevention and treatment is still the most anticipated solution to the increasing incidence of antimicrobial resistance (AMR). As the phenomenon continues to evolve, AMR is driving an escalation of hard-to-treat infections and mortality rates. Over the years, bacteria have devised a variety of survival tactics to outwit the antibiotic’s effects, yet given their great adaptability, unexpected mechanisms are still to be discovered. Over-expression of efflux pumps (EPs) constitutes the leading strategy of bacterial resistance, and it is also a primary driver in the establishment of multidrug resistance (MDR). Extensive efforts are being made to develop antibiotic resistance breakers (ARBs) with the ultimate goal of re-sensitizing bacteria to medications to which they have become unresponsive. EP inhibitors (EPIs) appear to be the principal group of ARBs used to impair the efflux system machinery. Due to the high toxicity of synthetic EPIs, there is a growing interest in natural, safe, and innocuous ones, whereby plant extracts emerge to be excellent candidates. Besides EPIs, further alternatives are being explored including the development of nanoparticle carriers, biologics, and phage therapy, among others. What roles do EPs play in the occurrence of MDR? What weapons do we have to thwart EP-mediated resistance? What are the obstacles to their development? These are some of the core questions addressed in the present review.
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Affiliation(s)
- Armel Jackson Seukep
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea P.O. Box 63, Cameroon
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
| | - Helene Gueaba Mbuntcha
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Victor Kuete
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Yindi Chu
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Enguo Fan
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- College of Life Sciences, Linyi University, Linyi 276005, China
- Correspondence: (E.F.); (M.-Q.G.)
| | - Ming-Quan Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: (E.F.); (M.-Q.G.)
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Marković KG, Grujović MŽ, Koraćević MG, Nikodijević DD, Milutinović MG, Semedo-Lemsaddek T, Djilas MD. Colicins and Microcins Produced by Enterobacteriaceae: Characterization, Mode of Action, and Putative Applications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11825. [PMID: 36142096 PMCID: PMC9517006 DOI: 10.3390/ijerph191811825] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Enterobacteriaceae are widely present in many environments related to humans, including the human body and the food that they consume, from both plant or animal origin. Hence, they are considered relevant members of the gastrointestinal tract microbiota. On the other hand, these bacteria are also recognized as putative pathogens, able to impair human health and, in food, they are considered indicators for the microbiological quality and hygiene status of a production process. Nevertheless, beneficial properties have also been associated with Enterobacteriaceae, such as the ability to synthesize peptides and proteins, which can have a role in the structure of microbial communities. Among these antimicrobial molecules, those with higher molecular mass are called colicins, while those with lower molecular mass are named microcins. In recent years, some studies show an emphasis on molecules that can help control the development of pathogens. However, not enough data are available on this subject, especially related to microcins. Hence, this review gathers and summarizes current knowledge on colicins and microcins, potential usage in the treatment of pathogen-associated diseases and cancer, as well as putative applications in food biotechnology.
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Affiliation(s)
- Katarina G. Marković
- Institute for Information Technologies, Department of Science, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Mirjana Ž. Grujović
- Institute for Information Technologies, Department of Science, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Maja G. Koraćević
- Innovation Center, University of Niš, 18000 Niš, Serbia
- Faculty of Medicine, Department of Pharmacy, University of Niš, 18000 Niš, Serbia
| | - Danijela D. Nikodijević
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Milena G. Milutinović
- Faculty of Science, Department of Biology and Ecology, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Teresa Semedo-Lemsaddek
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Milan D. Djilas
- Institute for Public Health of Vojvodina, Futoška 121, 21000 Novi Sad, Serbia
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Lynch JP, Goers L, Lesser CF. Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. Trends Pharmacol Sci 2022; 43:772-786. [PMID: 35232591 PMCID: PMC9378478 DOI: 10.1016/j.tips.2022.02.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
Abstract
Engineered microbes are rapidly being developed for the delivery of therapeutic modalities to sites of disease. Escherichia coli Nissle 1917 (EcN), a genetically tractable probiotic with a well-established human safety record, is emerging as a favored chassis. Here, we summarize the latest progress in rationally engineered variants of EcN for the treatment of infectious diseases, metabolic disorders, and inflammatory bowel diseases (IBDs) when administered orally, as well as cancers when injected directly into tumors or the systemic circulation. We also discuss emerging studies that raise potential safety concerns regarding these EcN-based strains as therapeutics due to their secretion of a genotoxic colibactin that can promote the formation of DNA double-stranded breaks in mammalian DNA.
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Affiliation(s)
- Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa Goers
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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40
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Dicks LMT, Vermeulen W. Do Bacteria Provide an Alternative to Cancer Treatment and What Role Does Lactic Acid Bacteria Play? Microorganisms 2022; 10:microorganisms10091733. [PMID: 36144335 PMCID: PMC9501580 DOI: 10.3390/microorganisms10091733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is one of the leading causes of mortality and morbidity worldwide. According to 2022 statistics from the World Health Organization (WHO), close to 10 million deaths have been reported in 2020 and it is estimated that the number of cancer cases world-wide could increase to 21.6 million by 2030. Breast, lung, thyroid, pancreatic, liver, prostate, bladder, kidney, pelvis, colon, and rectum cancers are the most prevalent. Each year, approximately 400,000 children develop cancer. Treatment between countries vary, but usually includes either surgery, radiotherapy, or chemotherapy. Modern treatments such as hormone-, immuno- and antibody-based therapies are becoming increasingly popular. Several recent reports have been published on toxins, antibiotics, bacteriocins, non-ribosomal peptides, polyketides, phenylpropanoids, phenylflavonoids, purine nucleosides, short chain fatty acids (SCFAs) and enzymes with anticancer properties. Most of these molecules target cancer cells in a selective manner, either directly or indirectly through specific pathways. This review discusses the role of bacteria, including lactic acid bacteria, and their metabolites in the treatment of cancer.
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Bacteriocin-Producing Escherichia coli Isolated from the Gastrointestinal Tract of Farm Animals: Prevalence, Molecular Characterization and Potential for Application. Microorganisms 2022; 10:microorganisms10081558. [PMID: 36013976 PMCID: PMC9413453 DOI: 10.3390/microorganisms10081558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Due to the spread of antibiotic-resistant bacteria, new alternatives to antibiotics and ways to prevent infections are being sought. Bacteriocin-producing bacteria are therefore attracting attention due to their probiotic potential as a safe alternative to antimicrobial drugs. The aim of this work was to determine the prevalence of bacteriocin-encoded genes among Escherichia coli strains from healthy farm animals and to characterize the presence of virulence-associated genes, the possibility of prophage induction, and hemolytic and bacterial antagonistic activity of the bacteriocin-producing E. coli in order to reveal their potential for application. It was found that 17 of 72 E. coli strains (23.6%) produced bacteriocins. Among them, 18 out of 30 bacteriocin genes were detected: the most prevalent genes were those for microcin M (58.8%), colicin E1 (52.9%), and colicin M (35.3%). Colicin Ia (29.4%), colicin E9, colicin Ib, colicin B (23.5%), and colicin E9 (17.7%) genes were also frequent, while the prevalence of genes encoding microcins V, B17, and H47 and colicins E3, K, N, U, Y, 5, and 10 did not exceed 11.8%. At least two different bacteriocin genes were detected in all 17 bacteriocinogenic strains; the highest number of different bacteriocin genes detected in one strain was seven genes. E. coli strains with combinations of colicin E1 and E or microcin M and colicin E1 genes were more prevalent than others (17.7%). Among the 17 bacteriocin-producing E. coli strains, 5.9% were hemolytic, 47.1% contained prophages, and 58.8% carried genes encoding toxins. Cell-free supernatants of bacteriocin-producing strains were shown to inhibit the growth of pathogenic E. coli strains belonging to the APEC, STEC, and ETEC pathotypes. Thus, among the studied bacteriocin-producing E. coli isolated from the gastrointestinal tract of farm animals, three strains with high antagonistic bacterial activity and the absence of pathogenicity genes, prophages, and hemolytic activity were identified and therefore have potential for application.
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Novel approaches for the treatment of infections due to multidrug-resistant bacterial pathogens. Future Med Chem 2022; 14:1133-1148. [PMID: 35861021 DOI: 10.4155/fmc-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial resistance (AMR), which is a major challenge for global healthcare, emerging because of several reasons including overpopulation, increased global migration and selection pressure due to enhanced use of antibiotics. Antibiotics are the widely used therapeutic options to combat infectious diseases; however, unfortunately, inadequate and irregular antibiotic courses are also major contributing factors in the emergence of AMR. Additionally, persistent failure to develop and commercialize new antibiotics has created the scarcity of effective anti-infective drugs. Thus, there is an urgent need for a new class of antimicrobials and other novel approaches to curb the menace of AMR. Besides the conventional approaches, some novel approaches such as the use of antimicrobial peptides, bacteriophages, immunomodulation, host-directed therapy and antibodies have shown really promising potentials.
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43
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In pursuit of next-generation therapeutics: Antimicrobial peptides against superbugs, their sources, mechanism of action, nanotechnology-based delivery, and clinical applications. Int J Biol Macromol 2022; 218:135-156. [PMID: 35868409 DOI: 10.1016/j.ijbiomac.2022.07.103] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) attracted attention as potential source of novel antimicrobials. Multi-drug resistant (MDR) infections have emerged as a global threat to public health in recent years. Furthermore, due to rapid emergence of new diseases, there is pressing need for development of efficient antimicrobials. AMPs are essential part of the innate immunity in most living organisms, acting as the primary line of defense against foreign invasions. AMPs kill a wide range of microorganisms by primarily targeting cell membranes or intracellular components through a variety of ways. AMPs can be broadly categorized based on their physico-chemical properties, structure, function, target and source of origin. The synthetic analogues produced either with suitable chemical modifications or with the use of suitable delivery systems are projected to eliminate the constraints of toxicity and poor stability commonly linked with natural AMPs. The concept of peptidomimetics is gaining ground around the world nowadays. Among the delivery systems, nanoparticles are emerging as potential delivery tools for AMPs, amplifying their utility against a variety of pathogens. In the present review, the broad classification of various AMPs, their mechanism of action (MOA), challenges associated with AMPs, current applications, and novel strategies to overcome the limitations have been discussed.
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Telhig S, Ben Said L, Torres C, Rebuffat S, Zirah S, Fliss I. Evaluating the Potential and Synergetic Effects of Microcins against Multidrug-Resistant Enterobacteriaceae. Microbiol Spectr 2022; 10:e0275221. [PMID: 35543514 PMCID: PMC9241698 DOI: 10.1128/spectrum.02752-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/12/2022] [Indexed: 11/20/2022] Open
Abstract
The advent of multidrug-resistant bacteria has hampered the development of new antibiotics, exacerbating their morbidity and mortality. In this context, the gastrointestinal tract reveals a valuable source of novel antimicrobials. Microcins are bacteriocins produced by members of the family Enterobacteriaceae, which are endowed with a wide diversity of structures and mechanisms of action, and exert potent antibacterial activity against closely related bacteria. In this study, we investigated the antibacterial activities of four microcins against 54 Enterobacteriaceae isolates from three species (Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica). The selected microcins, microcin C (McC, nucleotide peptide), microcin J25 (MccJ25, lasso peptide), microcin B17 (MccB17, linear azol(in)e-containing peptide), and microcin E492 (MccE492, siderophore peptide) carry different post-translational modifications and have distinct mechanisms of action. MICs and minimal bactericidal concentrations (MBC) of the microcins were measured and the efficacy of combinations of the microcins together or with antibiotics was assessed to identify potential synergies. Every isolate showed sensitivity to at least one microcin with MIC values ranging between 0.02 μM and 42.5 μM. Among the microcins tested, McC exhibited the broadest spectrum of inhibition with 46 strains inhibited, closely followed by MccE492 with 38 strains inhibited, while MccJ25 showed the highest activity. In general, microcin activity was observed to be independent of antibiotic resistance profile and strain genus. Of the 42 tested combinations, 20 provided enhanced activity (18 out of 20 being microcin-antibiotic combinations), with two being synergetic. IMPORTANCE With their wide range of structures and mechanisms of action, microcins are shown to exert antibacterial activities against Enterobacteriaceae resistant to antibiotics together with synergies with antibiotics and in particular colistin.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
| | - Carmen Torres
- Department of Food and Agriculture, University of La Rioja, Logrono, Spain
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Québec, Canada
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45
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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46
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Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
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Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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47
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Baquero F, del Campo R, Martínez JL. Interventions in Nicotinamide Adenine Dinucleotide Metabolism, the Intestinal Microbiota and Microcin Peptide Antimicrobials. Front Mol Biosci 2022; 9:861603. [PMID: 35372517 PMCID: PMC8967132 DOI: 10.3389/fmolb.2022.861603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
A proper NADH/NAD + balance allows for the flow of metabolic and catabolic activities determining cellular growth. In Escherichia coli, more than 80 NAD + dependent enzymes are involved in all major metabolic pathways, including the post-transcriptional build-up of thiazole and oxazole rings from small linear peptides, which is a critical step for the antibiotic activity of some microcins. In recent years, NAD metabolism boosting drugs have been explored, mostly precursors of NAD + synthesis in human cells, with beneficial effects on the aging process and in preventing oncological and neurological diseases. These compounds also enhance NAD + metabolism in the human microbiota, which contributes to these beneficial effects. On the other hand, inhibition of NAD + metabolism has been proposed as a therapeutic approach to reduce the growth and propagation of tumor cells and mitigating inflammatory bowel diseases; in this case, the activity of the microbiota might mitigate therapeutic efficacy. Antibiotics, which reduce the effect of microbiota, should synergize with NAD + metabolism inhibitors, but these drugs might increase the proportion of antibiotic persistent populations. Conversely, antibiotics might have a stronger killing effect on bacteria with active NAD + production and reduce the cooperation of NAD + producing bacteria with tumoral cells. The use of NADH/NAD + modulators should take into consideration the use of antibiotics and the population structure of the microbiota.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Infectious Diseases (CIBER-INFEC), Madrid, Spain
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48
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Hashem I, Van Impe JFM. A Game Theoretic Analysis of the Dual Function of Antibiotics. Front Microbiol 2022; 12:812788. [PMID: 35250912 PMCID: PMC8889009 DOI: 10.3389/fmicb.2021.812788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
There are two major views toward the role of antibiotics in microbial social interactions. The classical view is that antibiotics serve as weapons, produced by a bacterial species, at a significant cost, to inhibit the growth of its competitors. This view is supported by observations that antibiotics are usually upregulated by stress responses that infer the intensity of ecological competition, such as nutrient limitation and cellular damage, which point out to a competitive role for antibiotics. The other ecological function frequently assigned to antibiotics is that they serve as signaling molecules which regulate the collective behavior of a microbial community. Here, we investigate the conditions at which a weapon can serve as a signal in the context of microbial competition. We propose that an antibiotic will serve as a signal whenever a potential alteration of the growth behavior of the signal receiver, in response to a subinhibitory concentration (SIC) of the antibiotic, reduces the competitive pressure on the signal producer. This in turn would lead to avoiding triggering the stress mechanisms of the signal producer responsible for further antibiotics production. We show using individual-based modeling that this reduction of competitive pressure on the signal producer can happen through two main classes of responses by the signal recipient: competition tolerance, where the recipient reduces its competitive impact on the signal producer by switching to a low growth rate/ high yield strategy, and niche segregation, where the recipient reduces the competitive pressure on the signal producer by reducing their niche overlap. Our hypothesis proposes that antibiotics serve as signals out of their original function as weapons in order to reduce the chances of engaging in fights that would be costly to both the antibiotic producer as well as to its competitors.
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Affiliation(s)
- Ihab Hashem
- Department of Chemical Engineering, BioTeC+ & OPTEC, KU Leuven, Ghent, Belgium
| | - Jan F M Van Impe
- Department of Chemical Engineering, BioTeC+ & OPTEC, KU Leuven, Ghent, Belgium
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49
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Suissa R, Oved R, Jankelowitz G, Turjeman S, Koren O, Kolodkin-Gal I. Molecular genetics for probiotic engineering: dissecting lactic acid bacteria. Trends Microbiol 2022; 30:293-306. [PMID: 34446338 DOI: 10.1016/j.tim.2021.07.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
The composition of the gut microbiome is greatly influenced by nutrition and dietary alterations which can also induce large temporary microbial shifts. However, the molecular mechanisms that promote these changes remain to be determined. Species of the family Lactobacillaceae and Bacillus species are genetically manipulatable bacteria that are naturally found in the human gastrointestinal (GI) tract and are often considered models of beneficial microbiota. Here, we identify specific conserved molecular pathways that play a key role in host colonization by beneficial members of the microbiota. In particular, we highlight three pathways important to the success of lactic acid bacteria (LAB) in the GI tract: glycolysis and fermentation, microbial communication via membrane vesicles, and condition-dependent antibiotic production. We elaborate on how the understanding of these circuits can lead to the development of novel therapeutic approaches to combat GI tract infections.
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Affiliation(s)
- Ronit Suissa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefad, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefad, Israel.
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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50
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Chen H(D, Ma Z(S. Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis. Evol Bioinform Online 2022; 18:11769343221128540. [DOI: 10.1177/11769343221128540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/28/2022] [Indexed: 11/24/2022] Open
Abstract
It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats along the DT could be distinguished as 4 types (niches) including (i) stool; (ii) sub-gingival plaques (SubP) and supra-gingival plaques (SupP); (iii) tongue dorsum (TD), throat (TH), palatine tonsils (PT), and saliva (Sal); and (iv) hard palate (HP) and buccal mucosa (BM), and keratinized gingiva (KG). These niches are different not only in composition, but also in metabolic potentials. In a previous study, we applied Harris et al’s multi-site neutral and Tang and Zhou’s niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan’s near-neural model and Ning et al’s stochasticity analysis framework to quantify the niche-neutral continuum of the DT microbiome distribution to shed light on the possible ecological/evolutionary mechanism that shapes the continuum. Overall but excluding the stool site, the proportion of neutral OTUs (46%) is slightly higher than that of the positive selection (38%), but significantly higher than negative selection (15%). The gut (stool) exhibited 3 to 12 times lower neutrality than other DT sites. The analysis also cross-verified our previous hypothesis that the KG ( keratinized gingiva) is of distinct assembly dynamics in the DT microbiome, should be treated as a fifth niche. Our findings offer new insight on the long-standing debate concerning whether a minimum of 2-mm of KG width is necessary for marginal periodontal health.
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Affiliation(s)
- Hongju (Daisy) Chen
- Department of Mathematics and Statistics, Honghe University, Yunnan, China
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, Yunnan, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
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