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Guimarães LC, Garcia GD, Cavalcante FS, Dias GM, de Farias FM, Saintive S, Abad EDD, Ferreira DDC, dos Santos KRN. Methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus produce antimicrobial substances against members of the skin microbiota in children with atopic dermatitis. FEMS Microbiol Ecol 2024; 100:fiae070. [PMID: 38806244 PMCID: PMC11141783 DOI: 10.1093/femsec/fiae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/09/2024] [Accepted: 05/04/2024] [Indexed: 05/30/2024] Open
Abstract
Coagulase-negative Staphylococcus (CoNS) species inhibiting Staphylococcus aureus has been described in the skin of atopic dermatitis (AD) patients. This study evaluated whether Staphylococcus spp. from the skin and nares of AD and non-AD children produced antimicrobial substances (AMS). AMS production was screened by an overlay method and tested against NaOH, proteases and 30 indicator strains. Clonality was assessed by pulsed-field gel electrophoresis. Proteinaceous AMS-producers were investigated for autoimmunity by the overlay method and presence of bacteriocin genes by polymerase chain reaction. Two AMS-producers had their genome screened for AMS genes. A methicillin-resistant S. aureus (MRSA) produced proteinaceous AMS that inhibited 51.7% of the staphylococcal indicator strains, and it was active against 60% of the colonies selected from the AD child where it was isolated. On the other hand, 57 (8.8%) CoNS from the nares and skin of AD and non-AD children, most of them S. epidermidis (45.6%), reduced the growth of S. aureus and other CoNS species. Bacteriocin-related genes were detected in the genomes of AMS-producers. AMS production by CoNS inhibited S. aureus and other skin microbiota species from children with AD. Furthermore, an MRSA colonizing a child with AD produced AMS, reinforcing its contribution to dysbiosis and disease severity.
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Affiliation(s)
- Lorrayne Cardoso Guimarães
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gizele Duarte Garcia
- Departamento de Clínica Médica, Instituto de Ciências Médicas, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Fernanda Sampaio Cavalcante
- Departamento de Clínica Médica, Instituto de Ciências Médicas, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Graciela Maria Dias
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Simone Saintive
- Ambulatório de Dermatologia Pediátrica, Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eliane de Dios Abad
- Ambulatório de Dermatologia Pediátrica, Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis de Carvalho Ferreira
- Faculdade de Odontologia, Universidade Estácio de Sá, Rio de Janeiro, Brazil
- Faculdade de Odontologia, Universidade Veiga de Almeida, Rio de Janeiro, Brazil
- Faculdade de Enfermagem, Departamento de Fundamentos de Enfermagem, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kátia Regina Netto dos Santos
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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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.
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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
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
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Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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Success of microbial genes based transgenic crops: Bt and beyond Bt. Mol Biol Rep 2021; 48:8111-8122. [PMID: 34716867 DOI: 10.1007/s11033-021-06760-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/09/2021] [Indexed: 10/19/2022]
Abstract
Transgenic technology could hold the key to help farmers to fulfill the ever increasing fast-paced global demand for food. Microbes have always wondered us by their potentials and thriving abilities in the extreme conditions. The use of microorganisms as a gene source in transgenic development is a promising option for crop improvement. The aforesaid approach has already for improving the characteristics of food, industrial, horticulture, and floriculture crops. Many transgenic crops containing microbial genes have been accepted by the farmers and consumers worldwide over the last few decades. The acceptance has brought remarkable changes in the status of society by providing food safety, economic, and health benefits. Among transgenic plants harboring microbial genes, Bacillus thuringiensis (Bt) based transgenic were more focused and documented owing to its significant performance in controlling insects. However, other microbial gene-based transgenic plants have also reserved their places in the farmer's field globally. Therefore, in this review, we have thrown some light on successful transgenic plants harboring microbial genes other than Bt, having application in agriculture. Also, we presented the role of microbial genetic element and product thereof in the inception of biotechnology and discussed the potential of microbial genes in crop improvement.
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7
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Benjdia A, Berteau O. Radical SAM Enzymes and Ribosomally-Synthesized and Post-translationally Modified Peptides: A Growing Importance in the Microbiomes. Front Chem 2021; 9:678068. [PMID: 34350157 PMCID: PMC8326336 DOI: 10.3389/fchem.2021.678068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
To face the current antibiotic resistance crisis, novel strategies are urgently required. Indeed, in the last 30 years, despite considerable efforts involving notably high-throughput screening and combinatorial libraries, only few antibiotics have been launched to the market. Natural products have markedly contributed to the discovery of novel antibiotics, chemistry and drug leads, with more than half anti-infective and anticancer drugs approved by the FDA being of natural origin or inspired by natural products. Among them, thanks to their modular structure and simple biosynthetic logic, ribosomally synthesized and posttranslationally modified peptides (RiPPs) are promising scaffolds. In addition, recent studies have highlighted the pivotal role of RiPPs in the human microbiota which remains an untapped source of natural products. In this review, we report on recent developments in radical SAM enzymology and how these unique biocatalysts have been shown to install complex and sometimes unprecedented posttranslational modifications in RiPPs with a special focus on microbiome derived enzymes.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
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8
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Blake KS, Choi J, Dantas G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell Mol Life Sci 2021; 78:2585-2606. [PMID: 33582841 PMCID: PMC8005480 DOI: 10.1007/s00018-020-03717-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022]
Abstract
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.
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Affiliation(s)
- Kevin S Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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Balty C, Guillot A, Fradale L, Brewee C, Lefranc B, Herrero C, Sandström C, Leprince J, Berteau O, Benjdia A. Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes. J Biol Chem 2020; 295:16665-16677. [PMID: 32972973 PMCID: PMC8188230 DOI: 10.1074/jbc.ra120.015371] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | | | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
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Bosák J, Hrala M, Micenková L, Šmajs D. Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins. Expert Rev Anti Infect Ther 2020; 19:309-322. [PMID: 32856960 DOI: 10.1080/14787210.2020.1816824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized. AREAS COVERED We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect. EXPERT OPINION The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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11
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Sukhum KV, Diorio-Toth L, Dantas G. Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance. Clin Pharmacol Ther 2019; 106:512-524. [PMID: 31172511 PMCID: PMC6692204 DOI: 10.1002/cpt.1535] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
Antibiotic-resistant organisms (AROs) are a major concern to public health worldwide. While antibiotics have been naturally produced by environmental bacteria for millions of years, modern widespread use of antibiotics has enriched resistance mechanisms in human-impacted bacterial environments. Antibiotic resistance genes (ARGs) continue to emerge and spread rapidly. To combat the global threat of antibiotic resistance, researchers must develop methods to rapidly characterize AROs and ARGs, monitor their spread across space and time, and identify novel ARGs and resistance pathways. We review how high-throughput sequencing-based methods can be combined with classic culture-based assays to characterize, monitor, and track AROs and ARGs. Then, we evaluate genomic and metagenomic methods for identifying ARGs and biosynthetic pathways for novel antibiotics from genomic data sets. Together, these genomic analyses can improve surveillance and prediction of emerging resistance threats and accelerate the development of new antibiotic therapies to combat resistance.
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Affiliation(s)
- Kimberley V. Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Luke Diorio-Toth
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- To whom correspondence should be addressed during review: LD-T ()
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA
- Corresponding author: GD ()
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Abstract
The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.
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Sieow BFL, Nurminen TJ, Ling H, Chang MW. Meta-Omics- and Metabolic Modeling-Assisted Deciphering of Human Microbiota Metabolism. Biotechnol J 2019; 14:e1800445. [PMID: 31144773 DOI: 10.1002/biot.201800445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Indexed: 12/15/2022]
Abstract
The human microbiota is a complex community of commensal, symbiotic, and pathogenic microbes that play a crucial role in maintaining the homeostasis of human health. Such a homeostasis is maintained through the collective functioning of enzymatic genes responsible for the production of metabolites, enabling the interaction and signaling within microbiota as well as between microbes and the human host. Understanding microbial genes, their associated chemistries and functions would be valuable for engineering systemic metabolic pathways within the microbiota to manage human health and diseases. Given that there are many unknown gene metabolic functions and interactions, increasing efforts have been made to gain insights into the underlying functions of microbiota metabolism. This can be achieved through culture-independent metagenomic approaches and metabolic modeling to simulate the microenvironment of human microbiota. In this article, the recent advances in metagenome mining and functional profiling for the discovery of the genetic and biochemical links in human microbiota metabolism as well as metabolic modeling for simulation and prediction of metabolic fluxes in the human microbiota are reviewed. This review provides useful insights into the understanding, reconstruction, and modulation of the human microbiota guided by the knowledge acquired from the basic understanding of the human microbiota metabolism.
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Affiliation(s)
- Brendan Fu-Long Sieow
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
| | - Toni Juhani Nurminen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
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14
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Maldonado-Carmona N, Vázquez-Hernández M, Patiño Chávez OJ, Rodríguez-Luna SD, Jiménez Rodríguez O, Sanchez S, Ceapă CD. Impact of ∼omics in the detection and validation of potential anti-infective drugs. Curr Opin Pharmacol 2019; 48:1-7. [PMID: 30921690 DOI: 10.1016/j.coph.2019.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/25/2022]
Abstract
New anti-infective drugs are an unmet necessity of modern medicine. The use of ∼omics technologies has exponentially increased the knowledge on active anti-infective structures, where to search for them and their mechanisms of action. Research involving extreme and unique environments (such as endophytes) revealed their potential for many yet unknown active molecules. This work intends to review a recent research involving discovery of secondary metabolites with an established anti-infective action which was mediated by one of the ∼omics sciences: genomics, proteomics, transcriptomics, metabolomics, glycomics or their combinations, as well as the software at the base of these discoveries.
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Affiliation(s)
- Nidia Maldonado-Carmona
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Melissa Vázquez-Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Osiris Jair Patiño Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Stefany Daniela Rodríguez-Luna
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Omar Jiménez Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Sergio Sanchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico.
| | - Corina Diana Ceapă
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico.
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15
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Abstract
Natural products have long played a pivotal role in the development of therapeutics for a variety of diseases. Traditionally, soil and marine environments have provided a rich reservoir from which diverse chemical scaffolds could be discovered. Recently, the human microbiome has been recognized as a promising niche from which secondary metabolites with therapeutic potential have begun to be isolated. In this Review, we address how the expansive history of identifying bacterial natural products in other environments is informing the approaches being brought to bear on the study of the human microbiota. We also touch on how these tools can lead to insights about microbe-microbe and host-microbe interactions and help generate biological hypotheses that may lead to developments of new therapeutic modalities.
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16
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Complete Genome Sequence of Acinetobacter radioresistens Strain LH6, a Multidrug-Resistant Bacteriophage-Propagating Strain. Microbiol Resour Announc 2018; 7:MRA00929-18. [PMID: 30533885 PMCID: PMC6256452 DOI: 10.1128/mra.00929-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/15/2018] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance is a major problem worldwide. Understanding the interplay between drug-resistant pathogens, such as Acinetobacter baumannii and related species, potentially acting as environmental reservoirs is critical for preventing the spread of resistance determinants. Here we report the complete genome sequence of a multidrug-resistant bacteriophage-propagating strain of Acinetobacter radioresistens.
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17
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Mousa WK, Athar B, Merwin NJ, Magarvey NA. Antibiotics and specialized metabolites from the human microbiota. Nat Prod Rep 2017; 34:1302-1331. [DOI: 10.1039/c7np00021a] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human microbiota associated with each body site produce specialized molecules to kill human pathogens. Advanced bioinformatics tools will help to discover unique microbiome chemistry.
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Affiliation(s)
- Walaa K. Mousa
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Bilal Athar
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nishanth J. Merwin
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nathan A. Magarvey
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
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