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Schwarzerova J, Zeman M, Babak V, Jureckova K, Nykrynova M, Varga M, Weckwerth W, Dolejska M, Provaznik V, Rychlik I, Cejkova D. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Microbiol Spectr 2024; 12:e0196423. [PMID: 38099617 PMCID: PMC10782964 DOI: 10.1128/spectrum.01964-23] [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: 05/09/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.
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Affiliation(s)
- Jana Schwarzerova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Zeman
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Margaret Varga
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Valentine Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | - Darina Cejkova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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Dineen RL, Bottacini F, O'Connell‐Motherway M, van Sinderen D. Transcriptional landscape of the pMP7017 megaplasmid and its impact on the Bifidobacterium breve UCC2003 transcriptome. Microb Biotechnol 2024; 17:e14405. [PMID: 38206097 PMCID: PMC10832533 DOI: 10.1111/1751-7915.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/02/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
The 190 kb megaplasmid pMP7017 of Bifidobacterium breve JCM7017 represents the first conjugative and largest plasmid characterised within this genus to date. In the current study, we adopted an integrated approach combining transcriptomics, whole genome comparative analysis and metagenomic data mining to understand the biology of pMP7017 and related megaplasmids, and to assess the impact of plasmid-carriage on the host strain. The data generated revealed variations within basic features of promoter elements which correlate with a high level of transcription on the plasmid and highlight the transcriptional activity of genes encoding both offensive and defensive adaptations, including a Type IIL restriction-modification system, an anti-restriction system and four Type II toxin-antitoxin systems. Furthermore, a highly transcribed tmRNA, which likely provides translational support to the host strain, was identified, making pMP7017 the first plasmid of the Bifidobacterium genus and the smallest plasmid known to express a tmRNA. Analyses of synteny and variability among pMP7017 and related plasmids indicate substantial diversity in gene organisation and accessory gene cargo highlighting diverse (co-)evolution and potential host-specific rearrangements and adaptations. Systematic analysis of the codon usage profile of transcriptionally active pMP7017-encoded genes suggests that pMP7017 originated from (sub)species of Bifidobacterium longum. Furthermore, mining of metagenomic data suggests the presence of pMP7017-homologues in ~10% of microbiome samples, mostly infants and/or mothers from various geographical locations. Comparative transcriptome analysis of the B. breve UCC2003 chromosome in the presence or absence of pMP7017 revealed differential expression of genes representing 8% of the total gene pool. Genes involved in genetic information processing were exclusively upregulated, while altered expression of genes involved in biofilm production and polysaccharide biosynthesis was also observed.
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Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
| | - Francesca Bottacini
- School of MicrobiologyUniversity College CorkCorkIreland
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [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: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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Rodríguez-Beltrán J, León-Sampedro R, Ramiro-Martínez P, de la Vega C, Baquero F, Levin BR, San Millán Á. Translational demand is not a major source of plasmid-associated fitness costs. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200463. [PMID: 34839712 PMCID: PMC8628068 DOI: 10.1098/rstb.2020.0463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Plasmids are key drivers of bacterial evolution because they are crucial agents for the horizontal transfer of adaptive traits, such as antibiotic resistance. Most plasmids entail a metabolic burden that reduces the fitness of their host if there is no selection for plasmid-encoded genes. It has been hypothesized that the translational demand imposed by plasmid-encoded genes is a major mechanism driving the fitness cost of plasmids. Plasmid-encoded genes typically present a different codon usage from host chromosomal genes. As a consequence, the translation of plasmid-encoded genes might sequestrate ribosomes on plasmid transcripts, overwhelming the translation machinery of the cell. However, the pervasiveness and origins of the translation-derived costs of plasmids are yet to be assessed. Here, we systematically altered translation efficiency in the host cell to disentangle the fitness effects produced by six natural antibiotic resistance plasmids. We show that limiting translation efficiency either by reducing the number of available ribosomes or their processivity does not increase plasmid costs. Overall, our results suggest that ribosomal paucity is not a major contributor to plasmid fitness costs. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Ricardo León-Sampedro
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Paula Ramiro-Martínez
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Carmen de la Vega
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
- Centro de Investigación Biológica en Red, Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Bruce R. Levin
- Department of Biology, Emory University, Atlanta, GA, USA
- Antibiotic Resistance Center, Emory University, Atlanta, GA, USA
| | - Álvaro San Millán
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
- Centro de Investigación Biológica en Red, Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología–CSIC, 28049 Madrid, Spain
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