101
|
Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness. Microbiol Spectr 2023; 11:e0317622. [PMID: 36472430 PMCID: PMC9927498 DOI: 10.1128/spectrum.03176-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. IMPORTANCE Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.
Collapse
|
102
|
Hussain A, Patwekar U, Mongad DS, Shouche YS. Strategizing the human microbiome for small molecules: Approaches and perspectives. Drug Discov Today 2023; 28:103459. [PMID: 36435302 DOI: 10.1016/j.drudis.2022.103459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/03/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
Studies of the human microbiome are providing a deeper understanding of its significance to human health, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human-microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize distinct molecules outmatches its known chemical space, and small-molecule discovery in this context remains in its infancy. The profiling of microbiome-derived small molecules and their contextualization through cause-effect mechanistic studies may provide a better understanding of host-microbe interactions, guide new therapeutic interventions, and modulate microbiome-based therapies. This review describes the advances, approaches, and allied challenges in mining new microbial scaffolds from the human microbiome using genomic, microbe cultivation, and chemical analytic platforms. In the future, the complete biological characterization of a single microbe-derived molecule that has a specific therapeutic application could resolve the current limitations of microbiota-modulating therapies.
Collapse
Affiliation(s)
- Aehtesham Hussain
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India.
| | - Umera Patwekar
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Dattatray S Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| |
Collapse
|
103
|
Zhao JX, Yue JM. Frontier studies on natural products: moving toward paradigm shifts. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
104
|
Huang H, Su Y, Wang C, Lei B, Song X, Wang W, Wu P, Liu X, Dong X, Zhong L. Injectable Tissue-Adhesive Hydrogel for Photothermal/Chemodynamic Synergistic Antibacterial and Wound Healing Promotion. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2714-2724. [PMID: 36602415 DOI: 10.1021/acsami.2c19566] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
It is an exigent need for the development of hydrogel dressings with desirable injectability, good adhesive, antibacterial, and wound healing promotion properties. Herein, the multifunctional injectable hydrogels with good tissue adhesion are designed based on Ag-doped Mo2C-derived polyoxometalate (AgPOM) nanoparticles, urea, gelatin, and tea polyphenols (TPs) for antibacterial and wound healing acceleration. After being injected into the tissue, urea diffuses out under the concentration gradient, and TPs and gelatin chains recombine to trigger the in situ formation of hydrogel with excellent adhesiveness. AgPOM fixed in the hydrogel could not only react with hydrogen peroxide in the infection site to generate singlet oxygen to kill the bacteria but also convert near-infrared light into heat under 1060 nm laser irradiation to realize sterilization. In vitro studies display the high bactericidal ability of the hydrogel against drug-resistant Staphylococcus aureus and also exhibit a prominent therapeutic effect on infected wounds through synergistic photothermal/chemodynamic therapy and accelerate wound healing. Hence, the injectable hydrogel with AgPOM as the antimicrobial agent can be a novel therapeutic agent for drug-resistant bacteria-infected wounds and wound healing promotion.
Collapse
Affiliation(s)
- Han Huang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing211816, China
| | - Yan Su
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing211816, China
| | - Chenxi Wang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing211816, China
| | - Bing Lei
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng252059, China
| | - Xuejiao Song
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing211816, China
| | - Wenjun Wang
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng252059, China
| | - Pan Wu
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Pharmaceutical College Guangxi Medical University, Guangxi Medical University, Guangxi530021, China
| | - Xiyu Liu
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Pharmaceutical College Guangxi Medical University, Guangxi Medical University, Guangxi530021, China
| | - Xiaochen Dong
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing211816, China
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou221116, China
| | - Liping Zhong
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Pharmaceutical College Guangxi Medical University, Guangxi Medical University, Guangxi530021, China
| |
Collapse
|
105
|
Shim H. Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity. Antibiotics (Basel) 2023; 12:antibiotics12020204. [PMID: 36830114 PMCID: PMC9952447 DOI: 10.3390/antibiotics12020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies.
Collapse
Affiliation(s)
- Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea
| |
Collapse
|
106
|
Ongwae GM, Lepori I, Chordia MD, Dalesandro BE, Apostolos AJ, Siegrist MS, Pires MM. Measurement of Small Molecule Accumulation into Diderm Bacteria. ACS Infect Dis 2023; 9:97-110. [PMID: 36530146 DOI: 10.1021/acsinfecdis.2c00435] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some of the most dangerous bacterial pathogens (Gram-negative and mycobacterial) deploy a formidable secondary membrane barrier to reduce the influx of exogenous molecules. For Gram-negative bacteria, this second exterior membrane is known as the outer membrane (OM), while for the Gram-indeterminate Mycobacteria, it is known as the "myco" membrane. Although different in composition, both the OM and mycomembrane are key structures that restrict the passive permeation of small molecules into bacterial cells. Although it is well-appreciated that such structures are principal determinants of small molecule permeation, it has proven to be challenging to assess this feature in a robust and quantitative way or in complex, infection-relevant settings. Herein, we describe the development of the bacterial chloro-alkane penetration assay (BaCAPA), which employs the use of a genetically encoded protein called HaloTag, to measure the uptake and accumulation of molecules into model Gram-negative and mycobacterial species, Escherichia coli and Mycobacterium smegmatis, respectively, and into the human pathogen Mycobacterium tuberculosis. The HaloTag protein can be directed to either the cytoplasm or the periplasm of bacteria. This offers the possibility of compartmental analysis of permeation across individual cell membranes. Significantly, we also showed that BaCAPA can be used to analyze the permeation of molecules into host cell-internalized E. coli and M. tuberculosis, a critical capability for analyzing intracellular pathogens. Together, our results show that BaCAPA affords facile measurement of permeability across four barriers: the host plasma and phagosomal membranes and the diderm bacterial cell envelope.
Collapse
Affiliation(s)
- George M Ongwae
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Irene Lepori
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brianna E Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
107
|
Wang Y, Xu B, Chen H, Yang F, Huang J, Jiao X, Zhang Y. Environmental factors and gut microbiota: Toward better conservation of deer species. Front Microbiol 2023; 14:1136413. [PMID: 36960286 PMCID: PMC10027939 DOI: 10.3389/fmicb.2023.1136413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
Thousands of microbial species inhabiting the animal gut, collectively known as the gut microbiota, play many specific roles related to host nutrient metabolism and absorption, immune regulation, and protection from pathogenic bacteria. Gut microbiota composition is affected by several internal and external factors, such as the host genotype, dietary intake, breeding environment, and antibiotic exposure. As deer species are important members for maintaining ecosystem balance, understanding the effects of multiple factors on the gut microbiota of deer species, particularly endangered ones, is crucial. In this review, we summarize and discuss the factors that significantly affect the gut microbiota of deer and present the impacts of these factors on microbial composition. In particular, we focused on the changes in gut microbiota due to dietary differences under different conditions, including seasonal changes, different geographical locations, and captivity, as well as weaning and pathogen disturbance. Understanding the correlations between gut microbiota composition and its driving factors is important for evaluating and improving the captive breeding environment for better conservation of endangered deer species, and reintroducing wild deer populations in the future.
Collapse
Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Xin’an Jiao,
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- *Correspondence: Yunzeng Zhang,
| |
Collapse
|
108
|
Tamai M, Yamazaki Y, Ito T, Nakagawa S, Nakamura Y. Pathogenic role of the staphylococcal accessory gene regulator quorum sensing system in atopic dermatitis. Front Cell Infect Microbiol 2023; 13:1178650. [PMID: 37124047 PMCID: PMC10140505 DOI: 10.3389/fcimb.2023.1178650] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
The skin is home to various bacteria, archaea, fungi, and viruses, collectively referred to as the skin microbiota. Patients with certain skin diseases reportedly have unique skin "dysbiosis," a condition involving imbalanced microbiota, suggesting that dysbiosis in the skin may be either causal or a consequence of specific skin diseases. Atopic dermatitis (AD) is the most common allergic skin disease that affects 15-20% of children and 2-10% of adults worldwide. Both intrinsic genetic factors, such as susceptibility to type 2 inflammation or skin barrier dysfunction, and extrinsic environmental factors, such as air pollen and skin microbiota, contribute to AD. Staphylococcus aureus, which does not often colonize the skin of healthy individuals, is commonly identified in the lesional skin of patients with AD and is correlated with the disease flare. However, the role of S. aureus in the pathogenesis of AD has not been elucidated. Here, we discuss the pathological behavior of S. aureus, focusing on accessory gene regulator (Agr) quorum sensing, which is a fundamental bacterial cell-to-cell interaction mechanism that affects the behavior of S. aureus and other members of the microbial community. Importantly, beyond bacteria-bacteria interactions, the Agr quorum sensing system also regulates various virulence factors, which induce type 2 and IL-17-dependent skin inflammation in the host. Furthermore, the colonization of Agr-positive S. aureus in early life accelerates the development of pediatric AD. Finally, we aim to highlight the current efforts to establish novel therapeutic methods to ameliorate or prevent AD through Agr-targeted intervention.
Collapse
Affiliation(s)
- Masakazu Tamai
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuriko Yamazaki
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, Japan
- Cutaneous Allergy and Host Defense, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- *Correspondence: Yuumi Nakamura, ; Yuriko Yamazaki,
| | - Tomoka Ito
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seitaro Nakagawa
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Yuumi Nakamura
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, Japan
- Cutaneous Allergy and Host Defense, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- *Correspondence: Yuumi Nakamura, ; Yuriko Yamazaki,
| |
Collapse
|
109
|
Heinemann AS, Stalp JL, Bonifacio JPP, Silva F, Willers M, Heckmann J, Fehlhaber B, Völlger L, Raafat D, Normann N, Klos A, Hansen G, Schmolke M, Viemann D. Silent neonatal influenza A virus infection primes systemic antimicrobial immunity. Front Immunol 2023; 14:1072142. [PMID: 36761727 PMCID: PMC9902881 DOI: 10.3389/fimmu.2023.1072142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Infections with influenza A viruses (IAV) cause seasonal epidemics and global pandemics. The majority of these infections remain asymptomatic, especially among children below five years of age. Importantly, this is a time, when immunological imprinting takes place. Whether early-life infections with IAV affect the development of antimicrobial immunity is unknown. Using a preclinical mouse model, we demonstrate here that silent neonatal influenza infections have a remote beneficial impact on the later control of systemic juvenile-onset and adult-onset infections with an unrelated pathogen, Staphylococcus aureus, due to improved pathogen clearance and clinical resolution. Strategic vaccination with a live attenuated IAV vaccine elicited a similar protection phenotype. Mechanistically, the IAV priming effect primarily targets antimicrobial functions of the developing innate immune system including increased antimicrobial plasma activity and enhanced phagocyte functions and antigen-presenting properties at mucosal sites. Our results suggest a long-term benefit from an exposure to IAV during the neonatal phase, which might be exploited by strategic vaccination against influenza early in life to enforce the host's resistance to later bacterial infections.
Collapse
Affiliation(s)
- Anna Sophie Heinemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Jan Lennart Stalp
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | | | - Filo Silva
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Maike Willers
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Julia Heckmann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Beate Fehlhaber
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Lena Völlger
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Dina Raafat
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany.,Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Nicole Normann
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Klos
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Center for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dorothee Viemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.,Center for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Translational Pediatrics, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany.,Center for Infection Research, University Würzburg, Würzburg, Germany
| |
Collapse
|
110
|
Fernández-Fernández R, Abdullahi IN, González-Azcona C, Ulloa A, Martínez A, García-Vela S, Höfle U, Zarazaga M, Lozano C, Torres C. Detection of antimicrobial producing Staphylococcus from migratory birds: Potential role in nasotracheal microbiota modulation. Front Microbiol 2023; 14:1144975. [PMID: 37113241 PMCID: PMC10126283 DOI: 10.3389/fmicb.2023.1144975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/06/2023] [Indexed: 04/29/2023] Open
Abstract
A collection of 259 staphylococci of 13 different species [212 coagulase-negative (CoNS) and 47 coagulase-positive (CoPS)] recovered from nasotracheal samples of 87 healthy nestling white storks was tested by the spot-on-lawn method for antimicrobial-activity (AA) against 14 indicator bacteria. Moreover, extracts of AP isolates were obtained [cell-free-supernatants (CFS) both crude and concentrated and butanol extracts] and tested against the 14 indicator bacteria. The microbiota modulation capacity of AP isolates was tested considering: (a) intra-sample AA, against all Gram-positive bacteria recovered in the same stork nasotracheal sample; (b) inter-sample AA against a selection of representative Gram-positive bacteria of the nasotracheal microbiota of all the storks (30 isolates of 29 different species and nine genera). In addition, enzymatic susceptibility test was carried out in selected AP isolates and bacteriocin encoding genes was studied by PCR/sequencing. In this respect, nine isolates (3.5%; seven CoNS and two CoPS) showed AA against at least one indicator bacteria and were considered antimicrobial-producing (AP) isolates. The AP isolates showed AA only for Gram-positive bacteria. Three of these AP isolates (S. hominis X3764, S. sciuri X4000, and S. chromogenes X4620) revealed AA on all extract conditions; other four AP isolates only showed activity in extracts after concentration; the remaining two AP isolates did not show AA in any of extract conditions. As for the microbiota modulation evaluation, three of the nine AP-isolates revealed intra-sample AA. It is to highlight the potent inter-sample AA of the X3764 isolate inhibiting 73% of the 29 representative Gram-positive species of the nasotracheal stork microbiota population. On the other hand, enzymatic analysis carried out in the two highest AP isolates (X3764 and X4000) verified the proteinaceous nature of the antimicrobial compound and PCR analysis revealed the presence of lantibiotic-like encoding genes in the nine AP isolates. In conclusion, these results show that nasotracheal staphylococci of healthy storks, and especially CoNS, produce antimicrobial substances that could be important in the modulations of their nasal microbiota.
Collapse
Affiliation(s)
- Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen González-Azcona
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Adriana Ulloa
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Agustí Martínez
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Sara García-Vela
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
- Department of Food Science, University of Laval, Québec City, QC, Canada
| | - Ursula Höfle
- SaBio (Health and Biotechnology) Research Group, Game and Wildlife Research Institute, Spanish National Research Council/University of Castilla–La Mancha, Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
- *Correspondence: Carmen Torres,
| |
Collapse
|
111
|
Torres Salazar B, Lange A, Camus L, Heilbronner S. Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals. Methods Mol Biol 2023; 2601:39-54. [PMID: 36445578 DOI: 10.1007/978-1-0716-2855-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Soil-derived microorganisms have been sampled intensively throughout the last decades in order to discover bacterial strains that produce new antibiotics. The increasing emergence of multidrug-resistant bacteria and the constant high demand for new antibiotic classes are leading to the sampling and investigation of new microbiomes that contain antimicrobial producers. Human-associated microbiomes are therefore gaining more and more attention. This chapter presents a detailed description of how human microbiomes can be sampled and how microbiota members from skin and nasal samples can be isolated. Different methods for antimicrobial compound screening are presented.
Collapse
Affiliation(s)
- Benjamin Torres Salazar
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
| | - Anna Lange
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Laura Camus
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany.
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
| |
Collapse
|
112
|
Thirupathi K, Raorane CJ, Ramkumar V, Ulagesan S, Santhamoorthy M, Raj V, Krishnakumar GS, Phan TTV, Kim SC. Update on Chitosan-Based Hydrogels: Preparation, Characterization, and Its Antimicrobial and Antibiofilm Applications. Gels 2022; 9:gels9010035. [PMID: 36661802 PMCID: PMC9858335 DOI: 10.3390/gels9010035] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Chitosan is a prominent biopolymer in research for of its physicochemical properties and uses. Each year, the number of publications based on chitosan and its derivatives increases. Because of its comprehensive biological properties, including antibacterial, antioxidant, and tissue regeneration activities, chitosan and its derivatives can be used to prevent and treat soft tissue diseases. Furthermore, chitosan can be employed as a nanocarrier for therapeutic drug delivery. In this review, we will first discuss chitosan and chitosan-based hydrogel polymers. The structure, functionality, and physicochemical characteristics of chitosan-based hydrogels are addressed. Second, a variety of characterization approaches were used to analyze and validate the physicochemical characteristics of chitosan-based hydrogel materials. Finally, we discuss the antibacterial, antibiofilm, and antifungal uses of supramolecular chitosan-based hydrogels. This review study can be used as a base for future research into the production of various types of chitosan-based hydrogels in the antibacterial and antifungal fields.
Collapse
Affiliation(s)
- Kokila Thirupathi
- Department of Physics, Sri Moogambigai College of Arts and Science for Women, Palacode 636808, India
| | | | - Vanaraj Ramkumar
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Selvakumari Ulagesan
- Division of Fisheries Life Sciences, Pukyong National University, Nam-gu, Busan 48513, Republic of Korea
| | | | - Vinit Raj
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Correspondence: (V.R.); (T.T.V.P.); (S.-C.K.)
| | - Gopal Shankar Krishnakumar
- Department of Biotechnology, Applied Biomaterials Laboratory, PSG Institute of Advanced Studies, Coimbatore 641004, India
| | - Thi Tuong Vy Phan
- Center for Advanced Chemistry, Institute of Research and Development, Duy Tan University, 03 Quang Trung, Hai Chau, Danang 550000, Vietnam
- Faculty of Environmental and Chemical Engineering, Duy Tan University, 03 Quang Trung, Hai Chau, Danang 550000, Vietnam
- Correspondence: (V.R.); (T.T.V.P.); (S.-C.K.)
| | - Seong-Cheol Kim
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Correspondence: (V.R.); (T.T.V.P.); (S.-C.K.)
| |
Collapse
|
113
|
Ye J, Chen X. Current Promising Strategies against Antibiotic-Resistant Bacterial Infections. Antibiotics (Basel) 2022; 12:antibiotics12010067. [PMID: 36671268 PMCID: PMC9854991 DOI: 10.3390/antibiotics12010067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Infections caused by antibiotic-resistant bacteria (ARB) are one of the major global health challenges of our time. In addition to developing new antibiotics to combat ARB, sensitizing ARB, or pursuing alternatives to existing antibiotics are promising options to counter antibiotic resistance. This review compiles the most promising anti-ARB strategies currently under development. These strategies include the following: (i) discovery of novel antibiotics by modification of existing antibiotics, screening of small-molecule libraries, or exploration of peculiar places; (ii) improvement in the efficacy of existing antibiotics through metabolic stimulation or by loading a novel, more efficient delivery systems; (iii) development of alternatives to conventional antibiotics such as bacteriophages and their encoded endolysins, anti-biofilm drugs, probiotics, nanomaterials, vaccines, and antibody therapies. Clinical or preclinical studies show that these treatments possess great potential against ARB. Some anti-ARB products are expected to become commercially available in the near future.
Collapse
|
114
|
Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
Collapse
Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| |
Collapse
|
115
|
The Discovery of Oropharyngeal Microbiota with Inhibitory Activity against Pathogenic Neisseria gonorrhoeae and Neisseria meningitidis: An In Vitro Study of Clinical Isolates. Microorganisms 2022; 10:microorganisms10122497. [PMID: 36557750 PMCID: PMC9787740 DOI: 10.3390/microorganisms10122497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the essential oil-based mouthwash Listerine Cool Mint® (Listerine). Oropharyngeal swabs from 64 men who have sex with men (n = 118) from a previous study (PReGo study) were analysed (ClinicalTrials.gov, NCT03881007). These included 64 baseline and 54 samples following three months of daily use of Listerine. Inhibition was confirmed by agar overlay assay, and inhibitory bacteria isolated using replica plating and identified using MALDI-TOF. The number of inhibitory isolates were compared before and after Listerine use. Thirty-one pharyngeal samples (26%) showed inhibitory activity against N. gonorrhoeae and/or N. meningitidis, and 62 inhibitory isolates were characterised. Fourteen species belonging to the genera Streptococci and Rothia were identified. More inhibitory isolates were observed following Listerine use compared to baseline, although this effect was not statistically significant (p = 0.073). This study isolated and identified inhibitory bacteria against pathogenic Neisseria spp. and established that daily Listerine use did not decrease their prevalence. These findings could provide a new approach for the prevention and treatment of pharyngeal Neisseria infections.
Collapse
|
116
|
Hammond EN, Kates AE, Putman-Buehler N, Watson L, Godfrey JJ, Brys N, Deblois C, Steinberger AJ, Cox MS, Skarlupka JH, Haleem A, Bentz ML, Suen G, Safdar N. A quality improvement study on the relationship between intranasal povidone-iodine and anesthesia and the nasal microbiota of surgery patients. PLoS One 2022; 17:e0278699. [PMID: 36490265 PMCID: PMC9733847 DOI: 10.1371/journal.pone.0278699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The composition of the nasal microbiota in surgical patients in the context of general anesthesia and nasal povidone-iodine decolonization is unknown. The purpose of this quality improvement study was to determine: (i) if general anesthesia is associated with changes in the nasal microbiota of surgery patients and (ii) if preoperative intranasal povidone-iodine decolonization is associated with changes in the nasal microbiota of surgery patients. MATERIALS AND METHODS One hundred and fifty-one ambulatory patients presenting for surgery were enrolled in a quality improvement study by convenience sampling. Pre- and post-surgery nasal samples were collected from patients in the no intranasal decolonization group (control group, n = 54). Pre-decolonization nasal samples were collected from the preoperative intranasal povidone-iodine decolonization group (povidone-iodine group, n = 97). Intranasal povidone-iodine was administered immediately prior to surgery and continued for 20 minutes before patients proceeded for surgery. Post-nasal samples were then collected. General anesthesia was administered to both groups. DNA from the samples was extracted for 16S rRNA sequencing on an Illumina MiSeq. RESULTS In the control group, there was no evidence of change in bacterial diversity between pre- and post-surgery samples. In the povidone-iodine group, nasal bacterial diversity was greater in post-surgery, relative to pre-surgery (Shannon's Diversity Index (P = 0.038), Chao's richness estimate (P = 0.02) and Inverse Simpson index (P = 0.027). Among all the genera, only the relative abundance of the genus Staphylococcus trended towards a decrease in patients after application (FDR adjusted P = 0.06). Abundant genera common to both povidone-iodine and control groups included Staphylococcus, Bradyrhizobium, Corynebacterium, Dolosigranulum, Lactobacillus, and Moraxella. CONCLUSIONS We found general anesthesia was not associated with changes in the nasal microbiota. Povidone-iodine treatment was associated with nasal microbial diversity and decreased abundance of Staphylococcus. Future studies should examine the nasal microbiota structure and function longitudinally in surgical patients receiving intranasal povidone-iodine.
Collapse
Affiliation(s)
- Eric N. Hammond
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, WI, United States of America
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Ashley E. Kates
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
| | - Nathan Putman-Buehler
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Lauren Watson
- SSM Health, St. Mary’s Hospital, Madison, WI, United States of America
| | - Jared J. Godfrey
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
| | - Nicole Brys
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Courtney Deblois
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andrew J. Steinberger
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Madison S. Cox
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Joseph H. Skarlupka
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ambar Haleem
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Michael L. Bentz
- Division of Plastic and Reconstructive Surgery and Urology, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nasia Safdar
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
- * E-mail:
| |
Collapse
|
117
|
Chen H, Zhao Q, Zhong Q, Duan C, Krutmann J, Wang J, Xia J. Skin Microbiome, Metabolome and Skin Phenome, from the Perspectives of Skin as an Ecosystem. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:363-382. [PMID: 36939800 PMCID: PMC9712873 DOI: 10.1007/s43657-022-00073-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/11/2022] [Indexed: 11/07/2022]
Abstract
Skin is a complex ecosystem colonized by millions of microorganisms, including bacteria, fungi, and viruses. Skin microbiota is believed to exert critical functions in maintaining host skin health. Profiling the structure of skin microbial community is the first step to overview the ecosystem. However, the community composition is highly individualized and extremely complex. To explore the fundamental factors driving the complexity of the ecosystem, namely the selection pressures, we review the present studies on skin microbiome from the perspectives of ecology. This review summarizes the following: (1) the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment, highlighting their proposed function on skin microbiota; (2) the features of dominant skin commensals to occupy ecological niches, through self-adaptation and microbe-microbe interactions; (3) how skin microbes, by their structures or bioactive molecules, reshape host skin phenotypes, including skin immunity, maintenance of skin physiology such as pH and hydration, ultraviolet (UV) protection, odor production, and wound healing. This review aims to re-examine the host-microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.
Collapse
Affiliation(s)
- Huizhen Chen
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Qi Zhao
- grid.27255.370000 0004 1761 1174Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
- grid.435557.50000 0004 0518 6318IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, D-40225 Germany
| | - Qian Zhong
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Cheng Duan
- grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, 511458 China
| | - Jean Krutmann
- grid.435557.50000 0004 0518 6318IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, D-40225 Germany
| | - Jiucun Wang
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
- grid.506261.60000 0001 0706 7839Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, 200438 China
| | - Jingjing Xia
- grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, 511458 China
| |
Collapse
|
118
|
Bernal FA, Hammann P, Kloss F. Natural products in antibiotic development: is the success story over? Curr Opin Biotechnol 2022; 78:102783. [PMID: 36088735 DOI: 10.1016/j.copbio.2022.102783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022]
Abstract
Natural product (NP)-based antibiotics have been exploited for more than eighty years and continue saving uncountable lives every year. However, antimicrobial R&D is inadequate to counteract antimicrobial resistance. The majority of marketed antibiotics are inspired by NP classes that were discovered more than 50 years ago. With the advent of advanced genomic approaches, cultivation methods, and modern analytical techniques, NP discovery holds promise that there are way more powerful antibiotic scaffolds to be discovered. However, the currently lean antibiotic R&D pipeline shows a clear trend away from NP-based programs and innovative compounds are also rare in early stages. Within this review, we give an overview of the current NP antibiotic development pipeline, elaborate constraints the field is facing, and suggest measures to streamline NP-based antibiotic discovery. It is unlikely that NPs have lost significance, but reinforcement of discovery will require more targeted efforts and support to revitalize this established source.
Collapse
Affiliation(s)
- Freddy A Bernal
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) and Department of Pharmacy Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.
| |
Collapse
|
119
|
Zhao N, Cheng D, Yang Z, Liu Y, Wang Y, Jian Y, Wang H, Li M, Bae T, Liu Q. Virulence adaption to environment promotes the age-dependent nasal colonization of Staphylococcus aureus. Emerg Microbes Infect 2022; 11:1402-1415. [PMID: 35508433 PMCID: PMC9132443 DOI: 10.1080/22221751.2022.2074316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus is an important human commensal bacteria colonizing the human body, especially the nasal cavity. The nasal carriage can be a source of S. aureus bacteremia. However, the bacterial factors contributing to nasal colonization are not completely understood. By analysing S. aureus strains from the nasal cavity of the children, young adults, and seniors, we found that the low activity of the SaeRS two-component system (TCS) is an important determinant for S. aureus to colonize in seniors. The senior group isolates of S. aureus showed a rather distinct sequence type composition as compared with other age group isolates. The senior group isolates showed not only a lower gene carriage of enterotoxins a, c, and q but also lower hemolytic activity against human red blood cells. Of regulators affecting hemolysin production (i.e. agr, saeRS, rot, rsp, and sarS), only the SaeRS TCS showed an age-dependent decrease of activity. The decreased virulence and better colonization ability of the senior group isolates of S. aureus were confirmed in the mouse model. The senior group isolates showed the lowest survival and the best adhesion and colonizing ability. Also, the senior nasal secretions supported S. aureus survival better than the child and young adult nasal secretions. These results indicated that the senior nasal cavity favours colonization of S. aureus with higher adhesion and lower virulence, to which the reduced SaeRS TCS activity contributes. Taken together, our results illustrate an example of bacterial adaptation to the changing host environment.
Collapse
Affiliation(s)
- Na Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Danhong Cheng
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ziyu Yang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanan Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ying Jian
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hua Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, USA
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| |
Collapse
|
120
|
Chong AC, Visitsunthorn K, Ong PY. Genetic/Environmental Contributions and Immune Dysregulation in Children with Atopic Dermatitis. J Asthma Allergy 2022; 15:1681-1700. [PMID: 36447957 PMCID: PMC9701514 DOI: 10.2147/jaa.s293900] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/11/2022] [Indexed: 08/01/2023] Open
Abstract
Atopic dermatitis (AD) is one of the most common skin conditions in humans. AD affects up to 20% of children worldwide and results in morbidity for both patients and their caregivers. The basis of AD is an interplay between genetics and the environment characterized by immune dysregulation. A myriad of mutations that compromise the skin barrier and/or immune function have been linked to AD. Of these, filaggrin gene (FLG) mutations are the most evidenced. Many other mutations have been implicated in isolated studies that are often unreplicated, creating an archive of genes with potential but unconfirmed relevance to AD. Harnessing big data, polygenic risk scores (PRSs) and genome-wide association studies (GWAS) may provide a more practical strategy for identifying the genetic signatures of AD. Epigenetics may also play a role. Staphylococcus aureus is the most evidenced microbial contributor to AD. Cutaneous dysbiosis may result in over-colonization by pathogenic strains and aberrant skin immunity and inflammation. Aeroallergens, air pollution, and climate are other key environmental contributors to AD. The right climate and/or commensals may improve AD for some patients.
Collapse
Affiliation(s)
- Albert C Chong
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Peck Y Ong
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
121
|
Montecillo JAV, Bae H. In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity. Sci Rep 2022; 12:18883. [PMID: 36344604 PMCID: PMC9640594 DOI: 10.1038/s41598-022-20461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.
Collapse
Affiliation(s)
- Jake Adolf V. Montecillo
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
| | - Hanhong Bae
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
| |
Collapse
|
122
|
The microbiota and aging microenvironment in pancreatic cancer: Cell origin and fate. Biochim Biophys Acta Rev Cancer 2022; 1877:188826. [DOI: 10.1016/j.bbcan.2022.188826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/30/2022]
|
123
|
Rimoli CV, de Oliveira Pedro R, Miranda PB. Interaction mechanism of chitosan oligomers in pure water with cell membrane models studied by SFG vibrational spectroscopy. Colloids Surf B Biointerfaces 2022; 219:112782. [PMID: 36063719 DOI: 10.1016/j.colsurfb.2022.112782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 11/20/2022]
Abstract
Chitosan is a versatile and biocompatible cationic antimicrobial polymer obtained from sustainable sources that is effective against a wide range of microorganisms. Although it is soluble only at low pH, chitosan oligomers (ChitO) are soluble in pure water and thus more appropriate for antibacterial applications. Although there is a vast literature on chitosan's antimicrobial activity, the molecular details of its interaction with biomembranes remain unclear. Here we investigate these molecular interactions by resorting to phospholipid Langmuir films (zwitterionic DPPC and anionic DPPG) as simplified membrane models (for mammalian and bacterial membranes, respectively), and using SFG vibrational spectroscopy to probe lipid tail conformation, headgroup dynamics and interfacial water orientation. For comparison, we also investigate the interactions of another simple cationic antimicrobial polyelectrolyte, poly(allylamine) hydrochloride - PAH. By forming the lipid films over the polyelectrolyte solutions, we found that both have only a very small interaction with DPPC, but PAH adsorption is able to invert the interfacial water orientation (membrane potential). This might explain why ChitO is compatible with mammalian cells, while PAH is toxic. In contrast, their interaction with DPPG films is much stronger, even more so for ChitO, with both insertion within the lipid film and interaction with the oppositely charged headgroups. Again, PAH adsorption inverts the membrane potential, while ChitO does not. Finally, ChitO interaction with DPPG is weaker if the antimicrobial is injected underneath a pre-assembled Langmuir film, and its interaction mode depends on the time interval between end of film compression and ChitO injection. These differences between ChitO and PAH effects on the model membranes highlight the importance of molecular structure and intermolecular interactions for their bioactivity, and therefore this study may provide insights for the rational design of more effective antimicrobial molecules.
Collapse
Affiliation(s)
- Caio Vaz Rimoli
- Sao Carlos Physics Institute, University of Sao Paulo, CP 369, Sao Carlos CEP 13560-970, SP, Brazil; Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, College de France, 24 Rue Lhomond, F-75005 Paris, France
| | - Rafael de Oliveira Pedro
- Sao Carlos Physics Institute, University of Sao Paulo, CP 369, Sao Carlos CEP 13560-970, SP, Brazil; Department of exact and earth sciences, Minas Gerais State University (UEMG), Ituiutaba CEP 38302-192, MG, Brazil
| | - Paulo B Miranda
- Sao Carlos Physics Institute, University of Sao Paulo, CP 369, Sao Carlos CEP 13560-970, SP, Brazil.
| |
Collapse
|
124
|
Lee HJ, Kim M. Skin Barrier Function and the Microbiome. Int J Mol Sci 2022; 23:13071. [PMID: 36361857 PMCID: PMC9654002 DOI: 10.3390/ijms232113071] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023] Open
Abstract
Human skin is the largest organ and serves as the first line of defense against environmental factors. The human microbiota is defined as the total microbial community that coexists in the human body, while the microbiome refers to the collective genome of these microorganisms. Skin microbes do not simply reside on the skin but interact with the skin in a variety of ways, significantly affecting the skin barrier function. Here, we discuss recent insights into the symbiotic relationships between the microbiome and the skin barrier in physical, chemical, and innate/adaptive immunological ways. We discuss the gut-skin axis that affects skin barrier function. Finally, we examine the effects of microbiome dysbiosis on skin barrier function and the role of these effects in inflammatory skin diseases, such as acne, atopic dermatitis, and psoriasis. Microbiome cosmetics can help restore skin barrier function and improve these diseases.
Collapse
Affiliation(s)
| | - Miri Kim
- Department of Dermatology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, #10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea
| |
Collapse
|
125
|
Zeng Y, Liang JQ. Nasal Microbiome and Its Interaction with the Host in Childhood Asthma. Cells 2022; 11:cells11193155. [PMID: 36231116 PMCID: PMC9563732 DOI: 10.3390/cells11193155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host–microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.
Collapse
Affiliation(s)
- Yao Zeng
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jessie Qiaoyi Liang
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence: ; Tel.: +852-37636124
| |
Collapse
|
126
|
Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
Collapse
|
127
|
Olunoiki E, Rehner J, Bischoff M, Koshel E, Vogt T, Reichrath J, Becker SL. Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review. Life (Basel) 2022; 12:life12091420. [PMID: 36143456 PMCID: PMC9503882 DOI: 10.3390/life12091420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future.
Collapse
Affiliation(s)
- Esther Olunoiki
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
- “Solution Chemistry of Advanced Materials and Technologies” (SCAMT) Institute, ITMO University, 191002 St. Petersburg, Russia
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Elena Koshel
- “Solution Chemistry of Advanced Materials and Technologies” (SCAMT) Institute, ITMO University, 191002 St. Petersburg, Russia
| | - Thomas Vogt
- Department of Dermatology, Venereology, Allergology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Jörg Reichrath
- Department of Dermatology, Venereology, Allergology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Sören L. Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
- Correspondence: ; Tel.: +49-6841-16-23900
| |
Collapse
|
128
|
Prat M, Guenezan J, Drugeon B, Burucoa C, Mimoz O, Pichon M. Impact of Skin Disinfection on Cutaneous Microbiota, before and after Peripheral Venous Catheter Insertion. Antibiotics (Basel) 2022; 11:antibiotics11091209. [PMID: 36139988 PMCID: PMC9495181 DOI: 10.3390/antibiotics11091209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction. Patients with invasive medical devices are at high risk for infection. Skin colonization is the initial stage of these infections, leading to the recommendation of practices requiring disinfection using antiseptics. Microbial communities playing a major role in skin health could be impacted by antiseptic procedures. Aim. To characterize and compare the bacterial communities of skin samples from patients before an antisepsis procedure, and after removal of the medical device itself, according to the nature of the antiseptic molecule (povidone iodine or chlorhexidine). Methods. The study focused on alterations in bacterial communities depending on the nature of the antiseptic procedure and type of intravascular device. After amplification of 16S rDNA, libraries (n = 498 samples) were sequenced using MiSeq platform. Results. Using an in-house pipeline (QIIME2 modules), while no alteration in skin microbiota diversity was associated with antiseptic procedure or PVC type, according to culture results (p < 0.05), alterations were at times associated with restricted diversity and higher dissimilarity (p < 0.05). Antiseptic procedures and PVC types were associated with the modification of specific bacterial representations with modulation of the Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio (modulation of C. acnes, Prevotella, Lagierella, and Actinomyces spp.) (p < 0.05). At baseline, the microbiota shows certain bacteria that are significantly associated with future PVC colonization and/or bacteremia (p < 0.05). All of these modulations were associated with altered expression of metabolic pathways (p < 0.05). Discussion. Finally, this work highlights the need to optimize the management of patients requiring intravascular devices, possibly by modulating the skin microbiota.
Collapse
Affiliation(s)
- Manon Prat
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Jeremy Guenezan
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Bertrand Drugeon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Christophe Burucoa
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Olivier Mimoz
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Maxime Pichon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
- Correspondence: ; Tel.: +33-(0)5-4944-4143
| |
Collapse
|
129
|
Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
Collapse
Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| |
Collapse
|
130
|
Ito Y, Amagai M. Controlling skin microbiome as a new bacteriotherapy for inflammatory skin diseases. Inflamm Regen 2022; 42:26. [PMID: 36045395 PMCID: PMC9434865 DOI: 10.1186/s41232-022-00212-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
The skin serves as the interface between the human body and the environment and interacts with the microbial community. The skin microbiota consists of microorganisms, such as bacteria, fungi, mites, and viruses, and they fluctuate depending on the microenvironment defined by anatomical location and physiological function. The balance of interactions between the host and microbiota plays a pivotal role in the orchestration of skin homeostasis; however, the disturbance of the balance due to an alteration in the microbial communities, namely, dysbiosis, leads to various skin disorders. Recent developments in sequencing technology have provided new insights into the structure and function of skin microbial communities. Based on high-throughput sequencing analysis, a growing body of evidence indicates that a new treatment using live bacteria, termed bacteriotherapy, is a feasible therapeutic option for cutaneous diseases caused by dysbiosis. In particular, the administration of specific bacterial strains has been investigated as an exclusionary treatment strategy against pathogens associated with chronic skin disorders, whereas the safety, efficacy, and sustainability of this therapeutic approach using isolated live bacteria need to be further explored. In this review, we summarize our current understanding of the skin microbiota, as well as therapeutic strategies using characterized strains of live bacteria for skin inflammatory diseases. The ecosystem formed by interactions between the host and skin microbial consortium is still largely unexplored; however, advances in our understanding of the function of the skin microbiota at the strain level will lead to the development of new therapeutic methods.
Collapse
Affiliation(s)
- Yoshihiro Ito
- Department of Dermatology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.,RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| |
Collapse
|
131
|
Affiliation(s)
- Rustam Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| |
Collapse
|
132
|
Liu J, Jiang W, Xu Q, Zheng Y. Progress in Antibacterial Hydrogel Dressing. Gels 2022; 8:503. [PMID: 36005104 PMCID: PMC9407327 DOI: 10.3390/gels8080503] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/10/2023] Open
Abstract
Antibacterial hydrogel has excellent antibacterial property and good biocompatibility, water absorption and water retention, swelling, high oxygen permeability, etc.; therefore, it widely applied in biomedicine, intelligent textiles, cosmetics, and other fields, especially for medical dressing. As a wound dressing, the antibacterial hydrogel has the characteristics of absorbing wound liquid, controlling drug release, being non-toxic, being without side effects, and not causing secondary injury to the wound. Its preparation method is simple, and can crosslink via covalent or non-covalent bond, such as γ-radiation croFsslinking, free radical polymerization, graft copolymerization, etc. The raw materials are easy to obtain; usually these include chondroitin sulfate, sodium alginate, polyvinyl alcohol, etc., with different raw materials being used for different antibacterial modes. According to the hydrogel matrix and antibacterial mode, the preparation method, performance, antibacterial mechanism, and classification of antibacterial hydrogels are summarized in this paper, and the future development direction of the antibacterial hydrogel as wound dressing is proposed.
Collapse
Affiliation(s)
- Jie Liu
- College of Light Industry and Textile, Qiqihar University, Qiqihar 161006, China
- Engineering Research Center for Hemp and Product in Cold Region of Ministry of Education, Qiqihar 161006, China
| | - Wenqi Jiang
- College of Light Industry and Textile, Qiqihar University, Qiqihar 161006, China
| | - Qianyue Xu
- College of Light Industry and Textile, Qiqihar University, Qiqihar 161006, China
| | - Yongjie Zheng
- College of Light Industry and Textile, Qiqihar University, Qiqihar 161006, China
- Engineering Research Center for Hemp and Product in Cold Region of Ministry of Education, Qiqihar 161006, China
| |
Collapse
|
133
|
Mutagonda RF, Bwire G, Sangeda RZ, Kilonzi M, Mlyuka H, Ndunguru J, Jonathan A, Makani J, Minja IK, Ruggajo P, Balandya E, Kamuhabwa AAR. Nasopharyngeal Carriage and Antibiogram of Pneumococcal and Other Bacterial Pathogens from Children with Sickle Cell Disease in Tanzania. Infect Drug Resist 2022; 15:4407-4418. [PMID: 35992757 PMCID: PMC9390788 DOI: 10.2147/idr.s367873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/03/2022] [Indexed: 01/30/2023] Open
Abstract
Background Bacterial infections contribute significantly to morbidity and mortality in sickle cell disease (SCD) patients, particularly children under five years of age. In Tanzania, prophylaxis against pneumococcal infection among children with SCD advocates the use of both oral penicillin V (PV) and pneumococcal vaccines (PNV). Therefore, this study aimed to investigate nasopharyngeal carriage and antibiogram of Streptococcal pneumoniae (S. pneumoniae) and Staphylococcus aureus (S. aureus) in children with SCD in Tanzania. Methods This cross-sectional study was undertaken at the two Sickle Pan-African Research Consortium (SPARCO) study sites in Dar es salaam, Tanzania. The study was conducted for six months and enrolled children with SCD between the ages of 6 to 59-months. A semi-structured questionnaire was used to collect patient data. Nasopharyngeal swabs were collected from all participants and cultured for Streptococcal pneumoniae and other bacterial isolates. Antimicrobial susceptibility tests of the isolates were done using the disc diffusion method. Results Out of 204 participants, the overall prevalence of bacterial carriage was 53.4%, with S. aureus (23.5%), coagulase-negative Staphylococci (CoNS) (23%) and S. pneumoniae (7.8%) being commonly isolated. In antibiotic susceptibility testing, S. aureus isolates were most resistant to penicillin (81.8%), whereas 81.3% of S. pneumoniae isolates were resistant to co-trimoxazole. The least antimicrobial resistance was observed for chloramphenicol for both S. aureus and S. pneumoniae isolates (6.3% versus 0%). The proportion of multi-drug resistance (MDR) was 66.7% for S. aureus isolates and 25% for S. pneumoniae isolates. Conclusion There are substantially high nasopharyngeal carriage pathogenic bacteria in children with SCD in Dar es Salaam, Tanzania. The presence of MDR strains to the commonly used antibiotics suggests the need to reconsider optimizing antimicrobial prophylaxis in children with SCD and advocacy on pneumococcal vaccines.
Collapse
Affiliation(s)
- Ritah F Mutagonda
- Department of Clinical Pharmacy and Pharmacology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Correspondence: Ritah F Mutagonda, Department of Clinical Pharmacy and Pharmacology, Muhimbili University of Health and Allied Sciences, P.O BOX 65013, Dar es salaam, Tanzania, Tel +255 713 816481, Email ;
| | - George Bwire
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Raphael Zozimus Sangeda
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Manase Kilonzi
- Department of Clinical Pharmacy and Pharmacology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Hamu Mlyuka
- Department of Clinical Pharmacy and Pharmacology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Joyce Ndunguru
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Agnes Jonathan
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Julie Makani
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Irene Kida Minja
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Restorative Dentistry, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Paschal Ruggajo
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Internal Medicine, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Emmanuel Balandya
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania,Department of Physiology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - Appolinary A R Kamuhabwa
- Department of Clinical Pharmacy and Pharmacology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| |
Collapse
|
134
|
Microbial Interplay in Skin and Chronic Wounds. CURRENT CLINICAL MICROBIOLOGY REPORTS 2022. [DOI: 10.1007/s40588-022-00180-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Purpose of Review
Microbial infections in chronic wounds can often lead to lower-limb amputation, decrease in quality of life, and increase in mortality rate, and there is an unmet need to distinguish between pathogens and colonisers in these chronic wounds. Hence, identifying the composition of healthy skin microbiota, microbes associated with chronic wound and healing processes, and microbial interactions and host response in healing wounds vs. non-healing wounds can help us in formulating innovative individual-centric treatment protocols.
Recent Findings
This review highlights various metabolites and biomarkers produced by microbes that have been identified to modulate these interactions, particularly those involved in host–microbe and microbe–microbe communication. Further, considering that many skin commensals demonstrate contextual pathogenicity, we provide insights into promising initiatives in the wound microbiome research.
Summary
The skin microbiome is highly diverse and variable, and considering its importance remains to be a hotspot of medical investigations and research to enable us to prevent and treat skin disorders and chronic wound infections. This is especially relevant now considering that non-healing and chronic wounds are highly prevalent, generally affecting lower extremities as seen in diabetic foot ulcers, venous leg ulcers, and pressure ulcers. Pathogenic bacteria are purported to have a key role in deferring healing of wounds. However, the role of skin microflora in wound progression has been a subject of debate. In this review, we discuss biomarkers associated with chronic wound microenvironment along with the relevance of skin microflora and their metabolites in determining the chronicity of wounds.
Collapse
|
135
|
Ide K, Saeki T, Arikawa K, Yoda T, Endoh T, Matsuhashi A, Takeyama H, Hosokawa M. Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing. Front Microbiol 2022; 13:955404. [PMID: 35992707 PMCID: PMC9389210 DOI: 10.3389/fmicb.2022.955404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the bacterial strains corresponding to human individuals. A culture-independent genomics approach is an effective tool for obtaining massive high-quality bacterial genomes. Here we present a single-cell genome sequencing to obtain comprehensive whole-genome sequences of uncultured skin bacteria from skin swabs. We recovered 281 high-quality (HQ) and 244 medium-quality single-amplified genomes (SAGs) of multiple skin bacterial species from eight individuals, including cohabiting group. Single-cell sequencing outperformed in the genome recovery from the same skin swabs, showing 10-fold non-redundant strain genomes compared to the shotgun metagenomic sequencing and binning approach. We then focused on the abundant skin bacteria and identified intra-species diversity, especially in 47 Moraxella osloensis derived HQ SAGs, characterizing the strain-level heterogeneity at mobile genetic element profiles, including plasmids and prophages. Even between the cohabiting individual hosts, they have unique skin bacterial strains in the same species, which shows microdiversity in each host. Genetic and functional differences between skin bacterial strains are predictive of in vivo competition to adapt bacterial genome to utilize the sparse nutrients available on the skin or produce molecules that inhibit the colonization of other microbes or alter their behavior. Thus, single-cell sequencing provides a large number of genomes of higher resolution and quality than conventional metagenomic analysis and helps explore the skin commensal bacteria at the strain level, linking taxonomic and functional information.
Collapse
Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- bitBiome, Inc., Tokyo, Japan
| | | | | | | | | | | | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- bitBiome, Inc., Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
- *Correspondence: Masahito Hosokawa,
| |
Collapse
|
136
|
A balanced gut microbiota is essential to maintain health in captive sika deer. Appl Microbiol Biotechnol 2022; 106:5659-5674. [PMID: 35922588 DOI: 10.1007/s00253-022-12111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
Abstract
Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.
Collapse
|
137
|
Zhang Y, Li P, Ma Y, Wang J, Chen Y. Artificial intelligence accelerates the mining of bioactive small molecules from human microbiome. Clin Transl Med 2022; 12:e1011. [PMID: 35968909 PMCID: PMC9377150 DOI: 10.1002/ctm2.1011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yue Ma
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jun Wang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
138
|
Durand BARN, Pouget C, Magnan C, Molle V, Lavigne JP, Dunyach-Remy C. Bacterial Interactions in the Context of Chronic Wound Biofilm: A Review. Microorganisms 2022; 10:microorganisms10081500. [PMID: 35893558 PMCID: PMC9332326 DOI: 10.3390/microorganisms10081500] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic wounds, defined by their resistance to care after four weeks, are a major concern, affecting millions of patients every year. They can be divided into three types of lesions: diabetic foot ulcers (DFU), pressure ulcers (PU), and venous/arterial ulcers. Once established, the classical treatment for chronic wounds includes tissue debridement at regular intervals to decrease biofilm mass constituted by microorganisms physiologically colonizing the wound. This particular niche hosts a dynamic bacterial population constituting the bed of interaction between the various microorganisms. The temporal reshuffle of biofilm relies on an organized architecture. Microbial community turnover is mainly associated with debridement (allowing transitioning from one major representant to another), but also with microbial competition and/or collaboration within wounds. This complex network of species and interactions has the potential, through diversity in antagonist and/or synergistic crosstalk, to accelerate, delay, or worsen wound healing. Understanding these interactions between microorganisms encountered in this clinical situation is essential to improve the management of chronic wounds.
Collapse
Affiliation(s)
- Benjamin A. R. N. Durand
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Cassandra Pouget
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Chloé Magnan
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Virginie Molle
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, 34000 Montpellier, France;
| | - Jean-Philippe Lavigne
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Catherine Dunyach-Remy
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
- Correspondence: ; Tel.: +33-466-683-202
| |
Collapse
|
139
|
Fernández-Fernández R, Lozano C, Ruiz-Ripa L, Robredo B, Azcona-Gutiérrez JM, Alonso CA, Aspiroz C, Zarazaga M, Torres C. Antimicrobial Resistance and Antimicrobial Activity of Staphylococcus lugdunensis Obtained from Two Spanish Hospitals. Microorganisms 2022; 10:microorganisms10081480. [PMID: 35893538 PMCID: PMC9332302 DOI: 10.3390/microorganisms10081480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 12/05/2022] Open
Abstract
Staphylococcus lugdunensis is a coagulase-negative-staphylococci (CoNS) that lately has gained special attention in public health as a human pathogen and also as a bacteriocin-producer bacteria. In this study, we characterized 56 S. lugdunensis isolates recovered from human samples in two Spanish hospitals. Antimicrobial susceptibility testing was performed and antimicrobial resistance and virulence genotypes were determined. Antimicrobial activity (AA) production was evaluated by the spot-on-lawn method against 37 indicator bacteria, including multidrug-resistant (MDR) isolates, and the presence of the lugD gene coding for lugdunin bacteriocin was analyzed by PCR. The antibiotic resistance detected was as follows (% resistance/genes detected): penicillin (44.6%/blaZ), oxacillin (1.8%/mecA on SCCmec-V), erythromycin-clindamycin inducible (7.1%/erm(C), msrA), tetracycline (5.3%/tetK), gentamicin and/or tobramycin (3.6%/ant(4′)-Ia, acc(6′)-aph(2″)), and fosfomycin (21.4%). A MDR phenotype was detected in 5% of isolates. Twenty-one of the S. lugdunensis isolates showed susceptibility to all 20 antibiotics tested (37.5%). The screening for AA revealed 23 antimicrobial producer (AP) isolates with relevant inhibition against coagulase-positive-staphylococci (CoPS), including both methicillin-susceptible and –resistant S. aureus. The lugD gene was detected in 84% of the 56 S. lugdunensis isolates. All of the AP S. lugdunensis isolates (n = 23) carried the lugD gene and it was also detected in 24 of the non-AP isolates, suggesting different gene expression levels. One of the AP isolates stood out due to its high antimicrobial activity against more than 70% of the indicator bacteria tested, so it will be further characterized at genomic and proteomic level.
Collapse
Affiliation(s)
- Rosa Fernández-Fernández
- Área Bioquímica y Biología Molecular, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain; (R.F.-F.); (L.R.-R.); (M.Z.)
| | - Carmen Lozano
- Área Bioquímica y Biología Molecular, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain; (R.F.-F.); (L.R.-R.); (M.Z.)
- Correspondence: (C.L.); (C.T.)
| | - Laura Ruiz-Ripa
- Área Bioquímica y Biología Molecular, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain; (R.F.-F.); (L.R.-R.); (M.Z.)
| | - Beatriz Robredo
- Área Didáctica de las Ciencias Experimentales, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain;
| | | | - Carla Andrea Alonso
- Servicio de Microbiología, Hospital San Pedro, 26006 Logroño, Spain; (J.M.A.-G.); (C.A.A.)
| | - Carmen Aspiroz
- Servicio de Microbiología, Hospital Royo Villanova, 50015 Zaragoza, Spain;
| | - Myriam Zarazaga
- Área Bioquímica y Biología Molecular, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain; (R.F.-F.); (L.R.-R.); (M.Z.)
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, OneHealth-UR Research Group, Universidad de La Rioja, 26006 Logroño, Spain; (R.F.-F.); (L.R.-R.); (M.Z.)
- Correspondence: (C.L.); (C.T.)
| |
Collapse
|
140
|
Wei G, He Y. Antibacterial and Antibiofilm Activities of Novel Cyclic Peptides against Methicillin-Resistant Staphylococcus aureus. Int J Mol Sci 2022; 23:8029. [PMID: 35887376 PMCID: PMC9321466 DOI: 10.3390/ijms23148029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has led to serious infections, especially in hospitals and clinics, where treatment and prevention have become more difficult due to the formation of biofilms. Owing to biofilm-derived antibiotic tolerance, the currently available traditional antibiotics have failed to treat MRSA infections. Hence, there is a urgent need to develop novel antibiotics for treating life-threatening MRSA infections. Lugdunin (cyclic peptide-1), a nonribosomal cyclic peptide produced by Staphylococcus lugdunensis, exhibits potent antimicrobial activity against MRSA. Amazingly, cyclic peptide-1 and its analogues cyclic peptide-11 and cyclic peptide-14 have the ability to disperse mature MRSA biofilms and show anti-clinical MRSA activity, including MRSA persister cells. In addition, these three cyclic peptide compounds have non-toxicity, lower hemolytic activity and lack of resistance development. Our results indicate that cyclic peptide-1, cyclic peptide-11, and cyclic peptide-14 have great potential as new antimicrobial drug candidates for the treatment of clinical MRSA infections.
Collapse
Affiliation(s)
- Guoxing Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| |
Collapse
|
141
|
Hu T, Gu Z, Williams GR, Strimaite M, Zha J, Zhou Z, Zhang X, Tan C, Liang R. Layered double hydroxide-based nanomaterials for biomedical applications. Chem Soc Rev 2022; 51:6126-6176. [PMID: 35792076 DOI: 10.1039/d2cs00236a] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Against the backdrop of increased public health awareness, inorganic nanomaterials have been widely explored as promising nanoagents for various kinds of biomedical applications. Layered double hydroxides (LDHs), with versatile physicochemical advantages including excellent biocompatibility, pH-sensitive biodegradability, highly tunable chemical composition and structure, and ease of composite formation with other materials, have shown great promise in biomedical applications. In this review, we comprehensively summarize the recent advances in LDH-based nanomaterials for biomedical applications. Firstly, the material categories and advantages of LDH-based nanomaterials are discussed. The preparation and surface modification of LDH-based nanomaterials, including pristine LDHs, LDH-based nanocomposites and LDH-derived nanomaterials, are then described. Thereafter, we systematically describe the great potential of LDHs in biomedical applications including drug/gene delivery, bioimaging diagnosis, cancer therapy, biosensing, tissue engineering, and anti-bacteria. Finally, on the basis of the current state of the art, we conclude with insights on the remaining challenges and future prospects in this rapidly emerging field.
Collapse
Affiliation(s)
- Tingting Hu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine (ACN), University of New South Wales, Sydney, NSW 2052, Australia
| | - Gareth R Williams
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Margarita Strimaite
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiajia Zha
- Department of Electrical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong.
| | - Zhan Zhou
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Xingcai Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,School of Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Chaoliang Tan
- Department of Electrical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong. .,Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Kowloon, Hong Kong.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Ruizheng Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| |
Collapse
|
142
|
Wang L, Peng C, Gong B, Yang Z, Song J, Li L, Xu L, Yue T, Wang X, Yang M, Xu H, Liu X. Actinobacteria Community and Their Antibacterial and Cytotoxic Activity on the Weizhou and Xieyang Volcanic Islands in the Beibu Gulf of China. Front Microbiol 2022; 13:911408. [PMID: 35903476 PMCID: PMC9317746 DOI: 10.3389/fmicb.2022.911408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/13/2022] [Indexed: 12/05/2022] Open
Abstract
Weizhou Island and Xieyang Island are two large and young volcanic sea islands in the northern part of the South China Sea. In this study, high-throughput sequencing (HTS) of 16S rRNA genes was used to explore the diversity of Actinobacteria in the Weizhou and Xieyang Islands. Moreover, a traditional culture-dependent method was utilized to isolate Actinobacteria, and their antibacterial and cytotoxic activities were detected. The alpha diversity indices (ACE metric) of the overall bacterial communities for the larger island (Weizhou) were higher than those for the smaller island (Xieyang). A beta diversity analysis showed a more dispersive pattern of overall bacterial and actinobacterial communities on a larger island (Weizhou). At the order level, Frankiales, Propionibacteriales, Streptomycetales, Micrococcales, Pseudonocardiales, Micromonosporales, Glycomycetales, Corynebacteriales, and Streptosporangiales were the predominant Actinobacteria. A total of 22.7% of the OTUs shared 88%-95% similarity with some known groups. More interestingly, 15 OTUs formed a distinct and most predominant clade, and shared identities of less than 95% with any known families. This is the first report about this unknown group and their 16S rRNA sequences obtained from volcanic soils. A total of 268 actinobacterial strains were isolated by the culture-dependent method. Among them, 55 Streptomyces species were isolated, representing that 76.6% of the total. S. variabilis and S. flavogriseus were the most abundant. Moreover, some rare Actinobacteria were isolated. These included Micromonospora spp., Nocardia spp., Amycolatopsis spp., Tsukamurella spp., Mycobacterium spp., and Nonomuraea spp. Among them, eight Streptomyces spp. exhibited antibacterial activity against Bacillus cereus. Only three strains inhibited the growth of Escherichia coli. Four strains showed good activity against aquatic pathogenic bacterial strains of Streptococcus iniae. The cytotoxicity assay results showed that 27 strains (10.07%) exhibited cytotoxic activity against HeLa and A549 cell lines. Many actinobacterial strains with cytotoxic activity were identified as rare Actinobacteria, which illustrated that volcanic islands are vast reservoirs for Actinobacteria with promising antibacterial and cytotoxic activity. This study may significantly improve our understanding of actinobacterial communities on volcanic islands. The isolated Actinobacteria showed promising prospects for future use.
Collapse
Affiliation(s)
- Lin Wang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Chunyan Peng
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Bin Gong
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Zicong Yang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Jingjing Song
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Lu Li
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Lili Xu
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Tao Yue
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, China
| | - Xiaolin Wang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Mengping Yang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
| | - Huimin Xu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, China
| | - Xiong Liu
- Sea Area Use Dynamic Supervising and Managing Center of Fangchenggang City, Fangchenggang, China
| |
Collapse
|
143
|
Alterations in the nasopharyngeal microbiota associated with active and latent tuberculosis. Tuberculosis (Edinb) 2022; 136:102231. [DOI: 10.1016/j.tube.2022.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/24/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022]
|
144
|
The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. Nat Ecol Evol 2022; 6:1132-1144. [PMID: 35773344 DOI: 10.1038/s41559-022-01795-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/11/2022] [Indexed: 01/04/2023]
Abstract
The coral reef microbiome is central to reef health and resilience. Competitive interactions between opportunistic coral pathogens and other commensal microbes affect the health of coral. Despite great advances over the years in sequencing-based microbial profiling of healthy and diseased coral, the molecular mechanism underlying colonization competition has been much less explored. In this study, by examining the culturable bacteria inhabiting the gastric cavity of healthy Galaxea fascicularis, a scleractinian coral, we found that temperate phages played a major role in mediating colonization competition in the coral microbiota. Specifically, the non-toxigenic Vibrio sp. inhabiting the healthy coral had a much higher colonization capacity than the coral pathogen Vibrio coralliilyticus, yet this advantage was diminished by the latter killing the former. Pathogen-encoded LodAB, which produces hydrogen peroxide, triggers the lytic cycle of prophage in the non-toxicogenic Vibrio sp. Importantly, V. coralliilyticus could outcompete other coral symbiotic bacteria (for example, Endozoicomonas sp.) through LodAB-dependent prophage induction. Overall, we reveal that LodAB can be used by pathogens as an important weapon to gain a competitive advantage over lysogenic competitors when colonizing corals.
Collapse
|
145
|
Walker M. Human skin through the ages. Int J Pharm 2022; 622:121850. [PMID: 35623487 DOI: 10.1016/j.ijpharm.2022.121850] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022]
Abstract
As the largest organ of the human body the skin offers a protective role, providing a tough but pliable covering that provides the major barrier between the internal organs and the environment. It actively regulates water loss and is both oxygen and carbon dioxide permeable, and influences temperature regulation and immunological functions through its sensory properties. Both intrinsic and enhanced environmental factors contribute to the progressive deterioration of the skin with increasing age. Cutaneous problems are therefore an unavoidable and inevitable consequence of aging skin, which can prove to be both cosmetically unacceptable to those who succumb to these problems, as well as even life threatening if skin breakdown becomes chronic as is case with leg ulceration. This in turn has major implications for long-term impact on those looking after them (e.g., family, carers, etc.) and a huge burden on the health care system.
Collapse
|
146
|
Kosecka-Strojek M, Wolska-Gębarzewska M, Podbielska-Kubera A, Samet A, Krawczyk B, Międzobrodzki J, Michalik M. May Staphylococcus lugdunensis Be an Etiological Factor of Chronic Maxillary Sinuses Infection? Int J Mol Sci 2022; 23:ijms23126450. [PMID: 35742895 PMCID: PMC9224237 DOI: 10.3390/ijms23126450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
Staphylococcus lugdunensis is an opportunistic pathogen found in the healthy human skin microbiome bacterial community that is able to cause infections of diverse localization, manifestation, and course, including laryngological infections, such as necrotizing sinusitis. Chronic maxillary sinusitis is a disease present in up to one third of European and American populations, and its etiology is not fully described. Within this study, we aimed to characterize 18 S. lugdunensis strains recovered from maxillary sinuses and evaluate them as etiological agents of chronic disease. We performed MLST analysis, the complex analysis of both phenotypic and genetic virulence factors, antibiotic susceptibility profiles, and biofilm formation assay for the detection of biofilm-associated genes. Altogether, S. lugdunensis strains were clustered into eight different STs, and we demonstrated several virulence factors associated with the chronic disease. All tested strains were able to produce biofilm in vitro with numerous strains with a very strong ability, and overall, they were mostly susceptible to antibiotics, although we found resistance to fosfomycin, erythromycin, and clindamycin in several strains. We believe that further in-depth analysis of S. lugdunensis strains from different niches, including the nasal one, should be performed in the future in order to reduce infection rate and broaden the knowledge about this opportunistic pathogen that is gaining attention.
Collapse
Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland; (M.W.-G.); (J.M.)
- Correspondence:
| | - Mariola Wolska-Gębarzewska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland; (M.W.-G.); (J.M.)
| | | | - Alfred Samet
- MML Centre, Bagno 2, 00-112 Warsaw, Poland; (A.P.-K.); (A.S.); (M.M.)
| | - Beata Krawczyk
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland;
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland; (M.W.-G.); (J.M.)
| | - Michał Michalik
- MML Centre, Bagno 2, 00-112 Warsaw, Poland; (A.P.-K.); (A.S.); (M.M.)
| |
Collapse
|
147
|
Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature 2022; 606:754-760. [PMID: 35614211 PMCID: PMC9913614 DOI: 10.1038/s41586-022-04648-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2022] [Indexed: 01/26/2023]
Abstract
Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.
Collapse
Affiliation(s)
- Yancong Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J. McIver
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gleb Pishchany
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey N. Thompson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ayshwarya Subramanian
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - April Pawluk
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R. Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Afrah Shafquat
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ramnik J. Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S. Garrett
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andy Krueger
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,These authors jointly supervised this work: Curtis Huttenhower & Eric A. Franzosa
| |
Collapse
|
148
|
Shaaban MT, Abdelhamid RM, Zayed M, Ali SM. Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota. BIOTECHNOLOGY REPORTS 2022; 34:e00706. [PMID: 35686002 PMCID: PMC9171440 DOI: 10.1016/j.btre.2022.e00706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/24/2022]
Abstract
Metagenomics technique has the ability for production of novel antimicrobial agents. Marine sediment samples from Alexandria used as a source for production of novel antimicrobial agents. Activity of the RSMM C3 antimicrobial agent was a wide spectrum towards different microorganisms. Molecular analysis and characterization of RSMM C3 antimicrobial agent ensure novelty.
Diseases and epidemics in the current days need new types of antibiotics in order to be able to eliminate them. The goal of this research is to use metagenomics to identify isolated utilitarian gene (s) as antimicrobial specialists. Collection of diverse locations from sea sediment samples from Alexandria and extraction of total DNA, restriction enzyme fragmentation, cloning into pUC19 vector, and expression of the isolated gene(s) in E. coli DH5α were all part of the process. Characterization of Antimicrobial agent was done for the best clone for antimicrobial agent's production to detect efficiency, optimum pH, thermal stability, pH stability, effect of different compounds on antimicrobial activity, and residual activity of product after preservation in room temperature. Amino acid sequence of RSMM C3 gene (1250 bp) was 72% identity with Herbaspirillum sp. The ideal temperature level of the RSMM C3 antimicrobial agent production was 36 °C. The antimicrobial agent RSMM C3′s stability was stable at -20 °Celsius for up to two months without thawing. The antibacterial agent RSMM C3 was stable at 4 °C for 14 days without loss in activity. The ideal pH level of the RSMM C3 antimicrobial agent was 6. Remain activity was gradually decreased at pH 5, 6, 6.5 and 7 (86.1, 96.9, 97.2 and 94.9%, respectively). On the other hand, residual activity was (92 and 84%) at (pH 7.5 and 8) for 8 days. The tested antimicrobial RSMM C3 was stable against 1 mM of different compounds (DMSO, Glycerol, NaCl, CaCl2, MgCl2, ZnCl2, FeSO4, MnSO4 and CuSO4). The research provides for the Metagenomics technique that has the ability for the production of novel antimicrobial agents produced by clone RSMM C3 which has a wide spectrum activity towards different microorganisms comparing to other antibiotics as Ampicillin and Tetracycline.
Collapse
Affiliation(s)
- Mohamed T Shaaban
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
| | - Reham M Abdelhamid
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
- Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Muhammad Zayed
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
| | - Safaa M Ali
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt
| |
Collapse
|
149
|
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.
Collapse
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
| |
Collapse
|
150
|
MDR Pumps as Crossroads of Resistance: Antibiotics and Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11060734. [PMID: 35740141 PMCID: PMC9220107 DOI: 10.3390/antibiotics11060734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
At present, antibiotic resistance represents a global problem in modern medicine. In the near future, humanity may face a situation where medicine will be powerless against resistant bacteria and a post-antibiotic era will come. The development of new antibiotics is either very expensive or ineffective due to rapidly developing bacterial resistance. The need to develop alternative approaches to the treatment of bacterial infections, such as phage therapy, is beyond doubt. The cornerstone of bacterial defense against antibiotics are multidrug resistance (MDR) pumps, which are involved in antibiotic resistance, toxin export, biofilm, and persister cell formation. MDR pumps are the primary non-specific defense of bacteria against antibiotics, while drug target modification, drug inactivation, target switching, and target sequestration are the second, specific line of their defense. All bacteria have MDR pumps, and bacteriophages have evolved along with them and use the bacteria’s need for MDR pumps to bind and penetrate into bacterial cells. The study and understanding of the mechanisms of the pumps and their contribution to the overall resistance and to the sensitivity to bacteriophages will allow us to either seriously delay the onset of the post-antibiotic era or even prevent it altogether due to phage-antibiotic synergy.
Collapse
|