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Allen B, Gonzalez-Cabaleiro R, Ofiteru ID, Øvreås L, Sloan WT, Swan D, Curtis T. Diversity and metabolic energy in bacteria. FEMS Microbiol Lett 2023; 370:fnad043. [PMID: 37193662 PMCID: PMC10214464 DOI: 10.1093/femsle/fnad043] [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: 11/02/2022] [Revised: 04/03/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023] Open
Abstract
Why are some groups of bacteria more diverse than others? We hypothesize that the metabolic energy available to a bacterial functional group (a biogeochemical group or 'guild') has a role in such a group's taxonomic diversity. We tested this hypothesis by looking at the metacommunity diversity of functional groups in multiple biomes. We observed a positive correlation between estimates of a functional group's diversity and their metabolic energy yield. Moreover, the slope of that relationship was similar in all biomes. These findings could imply the existence of a universal mechanism controlling the diversity of all functional groups in all biomes in the same way. We consider a variety of possible explanations from the classical (environmental variation) to the 'non-Darwinian' (a drift barrier effect). Unfortunately, these explanations are not mutually exclusive, and a deeper understanding of the ultimate cause(s) of bacterial diversity will require us to determine if and how the key parameters in population genetics (effective population size, mutation rate, and selective gradients) vary between functional groups and with environmental conditions: this is a difficult task.
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Affiliation(s)
- Ben Allen
- School of Engineering Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Irina Dana Ofiteru
- School of Engineering Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Postboks 7803 5020 Bergen, Norway
| | - William T Sloan
- Department of Civil Engineering, Glasgow University, Glasgow G12 8QQ, UK
| | - Donna Swan
- School of Engineering Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas Curtis
- School of Engineering Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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2
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Abstract
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
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3
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Genotyping and multivariate regression trees reveal ecological diversification within the Microcystis aeruginosa complex along a wide environmental gradient. Appl Environ Microbiol 2021; 88:e0147521. [PMID: 34818109 DOI: 10.1128/aem.01475-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Addressing the ecological and evolutionary processes underlying biodiversity patterns is essential to identify the mechanisms shaping community structure and function. In bacteria, the formation of new ecologically distinct populations (ecotypes) is proposed as one of the main drivers of diversification. New ecotypes arise when mutations in key functional genes or acquisition of new metabolic pathways by horizontal gene transfer allow the population to exploit new resources, permitting their coexistence with the parental population. We previously reported the presence of microcystin-producing organisms of the Microcystis aeruginosa complex (toxic MAC) through an 800 km environmental gradient ranging from freshwater to estuarine-marine waters in South America. We hypothesize that the success of toxic MAC in such a gradient is due to the existence of very closely related populations that are ecologically distinct (ecotypes), each specialized to a specific arrangement of environmental variables. Here, we analyzed toxic MAC genetic diversity through qPCR and high-resolution melting analysis (HRMA) of a functional gene (mcyJ, microcystin synthetase cluster). We explored the variability of the mcyJ gene along the environmental gradient by multivariate classification and regression trees (mCART). Six groups of mcyJ genotypes were distinguished and associated with different combinations of water temperature, conductivity and turbidity. We propose that each mcyJ variant associated to a defined environmental condition is an ecotype (or species) whose relative abundances vary according to their fitness in the local environment. This mechanism would explain the success of toxic MAC in such a wide array of environmental conditions. Importance Organisms of the Microcystis aeruginosa Complex form harmful algal blooms (HABs) in nutrient-rich water bodies worldwide. MAC HABs are difficult to manage owing to the production of potent toxins (microcystins) that resist water treatment. Besides, the role of microcystins in the ecology of MAC organisms is still elusive, meaning that the environmental conditions driving the toxicity of the bloom are not clear. Furthermore, the lack of coherence between morphology-based and genomic-based species classification makes it difficult to draw sound conclusions about when and where each member species of the MAC will dominate the bloom. Here, we propose that the diversification process and success of toxic MAC in a wide range of waterbodies involves the generation of ecotypes, each specialized in a particular niche, whose relative abundance varies according to its fitness in the local environment. This knowledge can improve the generation of accurate prediction models of MAC growth and toxicity, helping to prevent human and animal intoxication.
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Vico P, Iriarte A, Bonilla S, Piccini C. Metagenomic analysis of Raphidiopsisraciborskii microbiome: beyond the individual. Biodivers Data J 2021; 9:e72514. [PMID: 34754266 PMCID: PMC8553701 DOI: 10.3897/bdj.9.e72514] [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: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Raphidiopsisraciborskii is a toxic, invasive bacteria with a defined biogeographic pattern attributed to the generation of ecotypes subjected to local environmental filters and to phenotypic plasticity. The interactions taking place between the cyanobacterium and the other bacteria inhabiting the external polysaccharide-rich matrix surrounding the cells, or phycosphere, may be ecotype-specific and would have different influence on the carbon and nutrient cycling in the ecosystem. Here, we describe the bacterial community or microbiome (assessed by 16S rRNA metagenomics) associated to two R.raciborskii strains that have been described as different ecotypes: the saxitoxin-producer MVCC19 and the non-toxic LB2897. Our results showed that both ecotypes share 50% of their microbiomes and differ in their dominant taxa. The taxon having the highest abundance in the microbiome of MVCC19 was Neorhizobium (22.5% relative abundance), while the dominant taxon in LB2897 was the PlanctomycetesSM1A02 (26.2% relative abundance). These groups exhibit different metabolic capabilities regarding nitrogen acquisition (symbiotic nitrogen-fixing in Neorhizobium vs. anammox in SM1A02), suggesting the existence of ecotype-specific microbiomes that play a relevant role in cyanobacterial niche-adaptation. In addition, as saxitoxin and analogues are nitrogen-rich (7 atoms per molecule), we hypothesise that saxitoxin-producing R.raciborskii benefits from external sources of nitrogen provided by the microbiome bacteria. Based on these findings, we propose that the mechanisms involved in the assembly of the cyanobacterial microbiome community are ecotype-dependent.
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Affiliation(s)
- Paula Vico
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
| | - Andrés Iriarte
- Instituto de Higiene, Facultad de Medicina, UDELAR, Montevideo, Uruguay Instituto de Higiene, Facultad de Medicina, UDELAR Montevideo Uruguay
| | - Sylvia Bonilla
- Sección Limnología. Facultad de Ciencias, UDELAR, Montevideo, Uruguay Sección Limnología. Facultad de Ciencias, UDELAR Montevideo Uruguay
| | - Claudia Piccini
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
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5
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Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK. ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ 2021; 9:e11376. [PMID: 34055480 PMCID: PMC8142932 DOI: 10.7717/peerj.11376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance.
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Affiliation(s)
- Natasha Pavlovikj
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Joao Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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6
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Thaler DS. Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same? Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.565649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.
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7
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Becraft ED, Moya A. Editorial: Searching for the Boundaries of Microbial Speciation in a Rapidly Evolving World. Front Microbiol 2021; 12:808595. [PMID: 35003040 PMCID: PMC8733662 DOI: 10.3389/fmicb.2021.808595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/29/2021] [Indexed: 02/05/2023] Open
Affiliation(s)
- Eric Daniel Becraft
- Department of Biology, University of North Alabama, Florence, AL, United States
- *Correspondence: Eric Daniel Becraft
| | - Andrés Moya
- Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
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8
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Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Syst Appl Microbiol 2020; 44:126165. [PMID: 33360413 DOI: 10.1016/j.syapm.2020.126165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/21/2022]
Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (=DSM 106348T=CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments.
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9
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 PMCID: PMC7610499 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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10
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Hall RJ, Whelan FJ, McInerney JO, Ou Y, Domingo-Sananes MR. Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes. Front Microbiol 2020; 11:1569. [PMID: 32849327 PMCID: PMC7396663 DOI: 10.3389/fmicb.2020.01569] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/17/2020] [Indexed: 02/01/2023] Open
Abstract
Horizontal gene transfer (HGT) is one of the most important processes in prokaryote evolution. The sharing of DNA can spread neutral or beneficial genes, as well as genetic parasites across populations and communities, creating a large proportion of the variability acted on by natural selection. Here, we highlight the role of HGT in enhancing the opportunities for conflict and cooperation within and between prokaryote genomes. We discuss how horizontally acquired genes can cooperate or conflict both with each other and with a recipient genome, resulting in signature patterns of gene co-occurrence, avoidance, and dependence. We then describe how interactions involving horizontally transferred genes may influence cooperation and conflict at higher levels (populations, communities, and symbioses). Finally, we consider the benefits and drawbacks of HGT for prokaryotes and its fundamental role in understanding conflict and cooperation from the gene-gene to the microbiome level.
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Affiliation(s)
- Rebecca J Hall
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fiona J Whelan
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Yaqing Ou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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Drewnowska JM, Stefanska N, Czerniecka M, Zambrowski G, Swiecicka I. Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations. Appl Environ Microbiol 2020; 86:e03032-19. [PMID: 32220844 PMCID: PMC7237779 DOI: 10.1128/aem.03032-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacillus cereus sensu lato comprises Gram-positive spore-forming bacteria producing toxins associated with foodborne diseases. Three pore-forming enterotoxins, nonhemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK), are considered the primary factors in B. cereus sensu lato diarrhea. The aim of this study was to determine the potential risk of enterotoxicity among soil B. cereus sensu lato isolates representing diverse phylogroups and originated from different geographic locations with various climates (Burkina Faso, Kenya, Argentina, Kazakhstan, and Poland). While nheA- and hblA-positive isolates were present among all B. cereus sensu lato populations and distributed across all phylogenetic groups, cytK-2-positive strains predominated in geographic regions with an arid hot climate (Africa) and clustered together on a phylogenetic tree mainly within mesophilic groups III and IV. The highest in vitro cytotoxicity to Caco-2 and HeLa cells was demonstrated by the strains clustered within phylogroups II and IV. Overall, our results suggest that B. cereus sensu lato pathogenicity is a comprehensive process conditioned by many intracellular factors and diverse environmental conditions.IMPORTANCE This research offers a new route for a wider understanding of the dependency between pathogenicity and phylogeny of a natural bacterial population, specifically within Bacillus cereus sensu lato, that is widely distributed around the world and easily transferred into food products. Our study indicates differences in the phylogenetic and geographical distributions of potential enterotoxigenic B. cereus sensu lato strains. Hence, these bacilli possess a risk for human health, and rapid testing methods for their identification are greatly needed. In particular, the detection of the CytK enterotoxin should be a supporting strategy for the identification of pathogenic B. cereus sensu lato.
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Affiliation(s)
| | - Natalia Stefanska
- Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland
| | - Magdalena Czerniecka
- Department of Cytobiochemistry, Faculty of Biology, University of Bialystok, Bialystok, Poland
- Laboratory of Tissue Culture, Faculty of Biology, University of Bialystok, Bialystok, Poland
| | - Grzegorz Zambrowski
- Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland
- Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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12
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Chibani CM, Roth O, Liesegang H, Wendling CC. Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements. BMC Genomics 2020; 21:354. [PMID: 32393168 PMCID: PMC7216594 DOI: 10.1186/s12864-020-6735-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate [1] those genomic signatures that characterize a habitat-specific ecotype and [2] the source of genomic variation within this ecotype. RESULTS We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~ 90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. CONCLUSION We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.
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Affiliation(s)
- Cynthia Maria Chibani
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University, 37077, Göttingen, Germany
- Institute for Microbiology and Genetics, Georg-August University Goettingen, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Olivia Roth
- GEOMAR, Helmholtz Centre for Ocean Research, Marine Evolutionary Ecology, Duesternbrooker Weg 20, 24105, Kiel, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University, 37077, Göttingen, Germany
| | - Carolin Charlotte Wendling
- GEOMAR, Helmholtz Centre for Ocean Research, Marine Evolutionary Ecology, Duesternbrooker Weg 20, 24105, Kiel, Germany.
- Department of Environmental Systems Science, ETH Zürich, Universitätsstraße 16, 8092, Zürich, Switzerland.
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13
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Drewnowska J, Fiodor A, Barboza-Corona J, Swiecicka I. Chitinolytic activity of phylogenetically diverse Bacillus cereus sensu lato from natural environments. Syst Appl Microbiol 2020; 43:126075. [DOI: 10.1016/j.syapm.2020.126075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/29/2023]
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14
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Yang DD, Alexander A, Kinnersley M, Cook E, Caudy A, Rosebrock A, Rosenzweig F. Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment. Appl Environ Microbiol 2020; 86:e00051-20. [PMID: 32060029 PMCID: PMC7117940 DOI: 10.1128/aem.00051-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.
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Affiliation(s)
- Dong-Dong Yang
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ashley Alexander
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Margie Kinnersley
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Emily Cook
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amy Caudy
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adam Rosebrock
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
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15
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Koch H, Germscheid N, Freese HM, Noriega-Ortega B, Lücking D, Berger M, Qiu G, Marzinelli EM, Campbell AH, Steinberg PD, Overmann J, Dittmar T, Simon M, Wietz M. Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Sci Rep 2020; 10:809. [PMID: 31964928 PMCID: PMC6972757 DOI: 10.1038/s41598-020-57526-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/23/2019] [Indexed: 01/28/2023] Open
Abstract
Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nora Germscheid
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dominik Lücking
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Galaxy Qiu
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Western Sydney University, Hawkesbury, Australia
| | - Ezequiel M Marzinelli
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
- University of Sydney, Camperdown, Australia
| | - Alexandra H Campbell
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- University of Sunshine Coast, Sunshine Coast, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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16
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MacKenzie KD, Wang Y, Musicha P, Hansen EG, Palmer MB, Herman DJ, Feasey NA, White AP. Parallel evolution leading to impaired biofilm formation in invasive Salmonella strains. PLoS Genet 2019; 15:e1008233. [PMID: 31233504 PMCID: PMC6611641 DOI: 10.1371/journal.pgen.1008233] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/05/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
Pathogenic Salmonella strains that cause gastroenteritis are able to colonize and replicate within the intestines of multiple host species. In general, these strains have retained an ability to form the rdar morphotype, a resistant biofilm physiology hypothesized to be important for Salmonella transmission. In contrast, Salmonella strains that are host-adapted or even host-restricted like Salmonella enterica serovar Typhi, tend to cause systemic infections and have lost the ability to form the rdar morphotype. Here, we investigated the rdar morphotype and CsgD-regulated biofilm formation in two non-typhoidal Salmonella (NTS) strains that caused invasive disease in Malawian children, S. Typhimurium D23580 and S. Enteritidis D7795, and compared them to a panel of NTS strains associated with gastroenteritis, as well as S. Typhi strains. Sequence comparisons combined with luciferase reporter technology identified key SNPs in the promoter region of csgD that either shut off biofilm formation completely (D7795) or reduced transcription of this key biofilm regulator (D23580). Phylogenetic analysis showed that these SNPs are conserved throughout the African clades of invasive isolates, dating as far back as 80 years ago. S. Typhi isolates were negative for the rdar morphotype due to truncation of eight amino acids from the C-terminus of CsgD. We present new evidence in support of parallel evolution between lineages of nontyphoidal Salmonella associated with invasive disease in Africa and the archetypal host-restricted invasive serovar; S. Typhi. We hypothesize that the African invasive isolates are becoming human-adapted and 'niche specialized' with less reliance on environmental survival, as compared to gastroenteritis-causing isolates.
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Affiliation(s)
- Keith D. MacKenzie
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Yejun Wang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Guangdong, China
| | - Patrick Musicha
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Elizabeth G. Hansen
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Melissa B. Palmer
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Dakoda J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Nicholas A. Feasey
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
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17
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González V, Santamaría RI, Bustos P, Pérez-Carrascal OM, Vinuesa P, Juárez S, Martínez-Flores I, Cevallos MÁ, Brom S, Martínez-Romero E, Romero D. Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters. Front Microbiol 2019; 10:910. [PMID: 31114559 PMCID: PMC6503217 DOI: 10.3389/fmicb.2019.00910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 01/07/2023] Open
Abstract
The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.
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Affiliation(s)
- Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rosa Isela Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Susana Brom
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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18
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Abstract
Our intestine is a melting pot of interactions between microbial and human cells. This gene-rich ecosystem modulates our health, but questions remain unanswered regarding its genetic structure, such as, “How rapid is evolutionary change in the human gut microbiome? How can its function be maintained?” Much research on the microbiome has characterized the species it contains. Yet the high growth rate and large population sizes of many species, and the mutation rate of most microbes (approximately 10−3 per genome per generation), could imply that evolution might be happening in our gut along our lifetime. In support of this view, Garud and colleagues present an analysis that begins to unravel the pattern of short- and long-term evolution of dozens of gut species. Even with limited longitudinal short-read sequence data, significant evolutionary dynamics—shaped by both positive and negative selection—can be detected on human microbiomes. This may only be the tip of the iceberg, as recent work on mice suggests, and its full extent should be revealed with dense time series long-read sequence data and new eco-evolutionary theory. Trillions of bacteria inhabiting our intestinal tract contribute to our wellbeing. This Primer explores how the known capacity of bacteria to rapidly adapt in the lab plays out in our own bodies; evolutionary changes are detected within months, allowing commensal bacteria to evolve through our lifetime.
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Affiliation(s)
- Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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19
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Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol 2019; 17:e3000102. [PMID: 30673701 PMCID: PMC6361464 DOI: 10.1371/journal.pbio.3000102] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.
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Affiliation(s)
- Nandita R. Garud
- Gladstone Institutes, San Francisco, California, United States of America
| | - Benjamin H. Good
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
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20
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Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V. Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis. PLoS One 2018; 13:e0207304. [PMID: 30419061 PMCID: PMC6231662 DOI: 10.1371/journal.pone.0207304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/28/2018] [Indexed: 02/01/2023] Open
Abstract
Phylogenomics and genome scale positive selection analyses were performed on 29 Corynebacterium pseudotuberculosis genomes that were isolated from different hosts, including representatives of the Ovis and Equi biovars. A total of 27 genes were identified as undergoing adaptive changes. An analysis of the clades within this species and these biovars, the genes specific to each branch, and the genes responding to selective pressure show clear differences, indicating that adaptation and specialization is occurring in different clades. These changes are often correlated with the isolation host but could indicate responses to some undetermined factor in the respective niches. The fact that some of these more-rapidly evolving genes have homology to known virulence factors, antimicrobial resistance genes and drug targets shows that this type of analysis could be used to identify novel targets, and that these could be used as a way to control this pathogen.
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Affiliation(s)
| | - Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Aristóteles Góes Neto
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Cesar Pereira Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Vasco Azevedo
- Department of General Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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