1
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BMC Biol 2024; 22:148. [PMID: 38965531 PMCID: PMC11225191 DOI: 10.1186/s12915-024-01937-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. RESULTS To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. CONCLUSIONS The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.
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Affiliation(s)
- Sanasar G Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
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2
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Martiny HM, Munk P, Brinch C, Aarestrup FM, Calle ML, Petersen TN. Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome. Microbiol Spectr 2024; 12:e0410823. [PMID: 38832899 PMCID: PMC11218503 DOI: 10.1128/spectrum.04108-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets. Using more than 6.76∙108 read fragments aligned to acquired ARGs to infer pairwise correlation coefficients, we found that more ARGs correlated with each other in human and animal sampling origins than in soil and water environments. Furthermore, we argued that the correlations could serve as risk profiles of resistance co-occurring to critically important antimicrobials (CIAs). Using these profiles, we found evidence of several ARGs conferring resistance for CIAs being co-abundant, such as tetracycline ARGs correlating with most other forms of resistance. In conclusion, this study highlights the important ARG players indirectly involved in shaping the resistomes of various environments that can serve as monitoring targets in AMR surveillance programs. IMPORTANCE Understanding the collateral effects happening in a resistome can reveal previously unknown links between antimicrobial resistance genes (ARGs). Through the analysis of pairwise ARG abundances in 214K metagenomic samples, we observed that the co-abundance is highly dependent on the environmental context and argue that these correlations can be used to show the risk of co-selection occurring in different settings.
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Affiliation(s)
- Hannah-Marie Martiny
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - M. Luz Calle
- Biosciences Department, Faculty of Sciences and Technology, University of Vic - Central University of Catalonia, Vic, Spain
| | - Thomas N. Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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Mancuso CP, Baker JS, Qu E, Tripp AD, Balogun IO, Lieberman TD. Intraspecies warfare restricts strain coexistence in human skin microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592803. [PMID: 38765968 PMCID: PMC11100718 DOI: 10.1101/2024.05.07.592803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization success in vivo2-4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
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Affiliation(s)
- Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Ishaq O. Balogun
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02142, USA
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Zamudio R, Boerlin P, Mulvey MR, Haenni M, Beyrouthy R, Madec JY, Schwarz S, Cormier A, Chalmers G, Bonnet R, Zhanel GG, Kaspar H, Mather AE. Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids. EBioMedicine 2024; 103:105097. [PMID: 38608515 PMCID: PMC11024496 DOI: 10.1016/j.ebiom.2024.105097] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood. METHODS In this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n = 192 ESC-R E. coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences. FINDINGS We identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E. coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E. coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents. INTERPRETATION We provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR. FUNDING This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food ChainBB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin 12277, Germany
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom; University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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5
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Zhu S, Hong J, Wang T. Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 2024; 15:800. [PMID: 38280843 PMCID: PMC10821886 DOI: 10.1038/s41467-024-45154-w] [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: 07/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.
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Affiliation(s)
- Shiben Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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6
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576128. [PMID: 38313259 PMCID: PMC10836074 DOI: 10.1101/2024.01.17.576128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.
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Affiliation(s)
- Sanasar G. Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sofya K. Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Kerkvliet JJ, Bossers A, Kers JG, Meneses R, Willems R, Schürch AC. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements. PeerJ 2024; 12:e16695. [PMID: 38188174 PMCID: PMC10771768 DOI: 10.7717/peerj.16695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.
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Affiliation(s)
- Jesse J. Kerkvliet
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Alex Bossers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
- Wageningen University, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jannigje G. Kers
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Rob Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
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8
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Alonso-del Valle A, Toribio-Celestino L, Quirant A, Pi CT, DelaFuente J, Canton R, Rocha EPC, Ubeda C, Peña-Miller R, San Millan A. Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria. Proc Natl Acad Sci U S A 2023; 120:e2314135120. [PMID: 38096417 PMCID: PMC10741383 DOI: 10.1073/pnas.2314135120] [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: 08/27/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild-type enterobacterial strains isolated from hospitalized patients. Our results revealed significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.
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Affiliation(s)
- Aida Alonso-del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Anna Quirant
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
| | - Carles Tardio Pi
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica Yucatán, Universidad Nacional Autónoma de México, Yucatán04510, México
| | - Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramon y Cajal de Investigacion Sanitaria, Madrid28034, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris75015, France
| | - Carles Ubeda
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Rafael Peña-Miller
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
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9
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Irby I, Brown SP. The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023. J Evol Biol 2023; 36:1582-1586. [PMID: 37975503 PMCID: PMC10805371 DOI: 10.1111/jeb.14239] [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: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023]
Abstract
Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).
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Affiliation(s)
- Iris Irby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
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10
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Salloum PM, Jorge F, Poulin R. Different trematode parasites in the same snail host: Species-specific or shared microbiota? Mol Ecol 2023; 32:5414-5428. [PMID: 37615348 DOI: 10.1111/mec.17111] [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: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such as imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals of the same population. Here, we tested several predictions regarding the microbiota of four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. and Maritrema novaezealandense) that parasitize the same snail host population. We predicted that each parasite species would harbour a distinct microbiota, with microbial composition similarity decreasing with increasing phylogenetic distance among parasite species. We also predicted that trematode species co-infecting the same individual host would influence each other's microbiota. We detected significant differences in alpha and beta diversity, as well as differential abundance, in the microbiota of the four trematode species. We found no evidence that phylogenetically closely related trematodes had more similar microbiota. We also uncovered indicator bacterial taxa that were significantly associated with each trematode species. Trematode species sharing the same snail host showed evidence of mostly one-sided bacterial exchanges, with the microbial community of one species approaching that of the other. We hypothesize that natural selection acting on specific microbial lineages may be important to maintain differences in horizontally acquired microbes, with vertical transmission also playing a role. In particular, one trematode species had a more consistent and diverse bacteriota than the others, potentially a result of stronger stabilizing pressures. We conclude that species-specific processes shape microbial community assembly in different trematodes exploiting the same host population.
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Affiliation(s)
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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Deng Y, Mou T, Wang J, Su J, Yan Y, Zhang YQ. Characterization of three rapidly growing novel Mycobacterium species with significant polycyclic aromatic hydrocarbon bioremediation potential. Front Microbiol 2023; 14:1225746. [PMID: 37744919 PMCID: PMC10517868 DOI: 10.3389/fmicb.2023.1225746] [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: 05/30/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
Mycobacterium species exhibit high bioremediation potential for the degradation of polycyclic aromatic hydrocarbons (PAHs) that are significant environmental pollutants. In this study, three Gram-positive, rapidly growing strains (YC-RL4T, MB418T, and HX176T) were isolated from petroleum-contaminated soils and were classified as Mycobacterium within the family Mycobacteriaceae. Genomic average nucleotide identity (ANI; < 95%) and digital DNA-DNA hybridization (dDDH; < 70%) values relative to other Mycobacterium spp. indicated that the strains represented novel species. The morphological, physiological, and chemotaxonomic characteristics of the isolates also supported their affiliation with Mycobacterium and their delineation as novel species. The strains were identified as Mycobacterium adipatum sp. nov. (type strain YC-RL4T = CPCC 205684T = CGMCC 1.62027T), Mycobacterium deserti sp. nov. (type strain MB418T = CPCC 205710T = KCTC 49782T), and Mycobacterium hippophais sp. nov. (type strain HX176T = CPCC 205372T = KCTC 49413T). Genes encoding enzymes involved in PAH degradation and metal resistance were present in the genomes of all three strains. Specifically, genes encoding alpha subunits of aromatic ring-hydroxylating dioxygenases were encoded by the genomes. The genes were also identified as core genes in a pangenomic analysis of the three strains along with 70 phylogenetically related mycobacterial strains that were previously classified as Mycolicibacterium. Notably, strain YC-RL4T could not only utilize phthalates as their sole carbon source for growth, but also convert di-(2-ethylhexyl) phthalate into phthalic acid. These results indicated that strains YC-RL4T, MB418T, and HX176T were important resources with significant bioremediation potential in soils contaminated by PAHs and heavy metals.
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Affiliation(s)
- Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herbs, Beijing, China
| | - Tong Mou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herbs, Beijing, China
| | - Junhuan Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Dao-di Herbs, Beijing, China
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12
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Kim M, Cha IT, Lee KE, Li M, Park SJ. Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium. Microbiol Spectr 2023; 11:e0100323. [PMID: 37594286 PMCID: PMC10655711 DOI: 10.1128/spectrum.01003-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, Jeju, South Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, South Korea
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13
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Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA. Profiling novel lateral gene transfer events in the human microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552500. [PMID: 37609252 PMCID: PMC10441418 DOI: 10.1101/2023.08.08.552500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.
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Affiliation(s)
- Tiffany Y Hsu
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Etienne Nzabarushimana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis Wong
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chengwei Luo
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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14
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Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
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Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
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Shade A. Microbiome rescue: directing resilience of environmental microbial communities. Curr Opin Microbiol 2023; 72:102263. [PMID: 36657335 DOI: 10.1016/j.mib.2022.102263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/30/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023]
Abstract
Earth's climate crisis threatens to disrupt ecosystem services and destabilize food security. Microbiome management will be a crucial component of a comprehensive strategy to maintain stable microbinal functions for ecosystems and plants in the face of climate change. Microbiome rescue is the directed, community-level recovery of microbial populations and functions lost after an environmental disturbance. Microbiome rescue aims to propel a resilience trajectory for community functions. Rescue can be achieved via demographic, functional, adaptive, or evolutionary recovery of disturbance-sensitive populations. Various ecological mechanisms support rescue, including dispersal, reactivation from dormancy, functional redundancy, plasticity, and diversification, and these mechanisms can interact. Notably, controlling microbial reactivation from dormancy is a potentially fruitful but underexplored target for rescue.
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Affiliation(s)
- Ashley Shade
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, École Centrale de Lyon, Ampère, UMR5005, 69134 Ecully cedex, France; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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