1
|
Ide-Pérez MR, Sánchez-Reyes A, Folch-Mallol JL, Sánchez-Carbente MDR. Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLoS One 2024; 19:e0297232. [PMID: 38354109 PMCID: PMC10866521 DOI: 10.1371/journal.pone.0297232] [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: 08/25/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024] Open
Abstract
Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.
Collapse
Affiliation(s)
- Martín R. Ide-Pérez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ayixon Sánchez-Reyes
- Investigador por México-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | |
Collapse
|
2
|
Huang Y, Song MH, Li SG, Yu Shen H, Qu PH, Zhang DF. Preliminary comparative genomics analysis among Corynebacterium kroppenstedtii complex necessitates a reassessment of precise species associated with mastitis. J Appl Microbiol 2024; 135:lxad314. [PMID: 38130215 DOI: 10.1093/jambio/lxad314] [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: 09/01/2023] [Revised: 12/09/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
AIMS This study aimed to characterize the first complete genome of Corynebacterium parakroppenstedtii and clarify the evolutionary relationship in the Corynebacterium kroppenstedtii complex (CKC) by using comparative genomics analysis. METHODS AND RESULTS The genome of isolate yu01 from a breast specimen was sequenced, and 35 CKC genomes were collected. Analysis of 16S rRNA, rpoB, and fusA suggested ambiguous identification, whereas ANI analysis assigned isolate yu01 as Coryne. parakroppenstedtii. The fourth genospecies "Corynebacterium aliikroppenstedtii" was identified in CKC. Comparative genomics analysis suggested that the genomic arrangement in CKC was highly conserved. A total of 43 potential virulence genes and 79 species-specific genes were detected. Most genome-based phylogenetic analysis were incapable of resolving the interspecific evolutionary relationships among CKCs. A total of 20 core genes were found to be distinguishable in CKC. CONCLUSIONS This study suggested the limited divergence and unavailability of normal single gene-based identification in CKC and questioned the precise species of strains associated with mastitis, identified as Coryne. kroppenstedtii in previous studies. The 20 genes showed potential to enhance the methods for the identification and epidemiological investigation of CKC.
Collapse
Affiliation(s)
- Ying Huang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| | - Ming-Hui Song
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China
| | - Shun-Guang Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hong- Yu Shen
- Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215026, China
| | - Ping-Hua Qu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Dao-Feng Zhang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| |
Collapse
|
3
|
Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [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: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
Collapse
Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
| | | |
Collapse
|
4
|
Zielezinski A, Dobrychlop W, Karlowski WM. TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria. Database (Oxford) 2023; 2023:baad058. [PMID: 37555549 PMCID: PMC10410690 DOI: 10.1093/database/baad058] [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: 02/21/2023] [Revised: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
The TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRG-associated, unique features, and characteristics of bacterial organisms. Database URL www.combio.pl/trgdb.
Collapse
Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
| | - Wojciech Dobrychlop
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
| |
Collapse
|
5
|
Plasmid-Encoded Traits Vary across Environments. mBio 2023; 14:e0319122. [PMID: 36629415 PMCID: PMC9973032 DOI: 10.1128/mbio.03191-22] [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] [Indexed: 01/12/2023] Open
Abstract
Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.
Collapse
|
6
|
White H, Vos M, Sheppard SK, Pascoe B, Raymond B. Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades. Mol Ecol 2022; 31:3584-3597. [PMID: 35510788 PMCID: PMC9324797 DOI: 10.1111/mec.16490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan‐genomes to drive and maintain the emergence of clades is unclear. Focusing on the three largest clades in the diverse and well‐studied Bacillus cereus sensu lato group, we identified clade‐specific core genes (present in all clade members) and then used clade‐specific allelic diversity to identify genes under purifying and diversifying selection. Clade‐specific accessory genes (present in a subset of strains within a clade) were characterized as being under selection using presence/absence in specific clades. Gene ontology analyses of genes under selection revealed that different gene functions were enriched in different clades. Furthermore, some gene functions were enriched only amongst clade‐specific core or accessory genomes. Genes under purifying selection were often clade‐specific, while genes under diversifying selection showed signs of frequent HGT. These patterns are consistent with different selection pressures acting on both the core and the accessory genomes of different clades and can lead to ecological divergence in both cases. Examining variation in allelic diversity allows us to uncover genes under clade‐specific selection, allowing ready identification of strains and their ecological niche.
Collapse
Affiliation(s)
- Hugh White
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - Ben Pascoe
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| |
Collapse
|
7
|
Mourkas E, Yahara K, Bayliss SC, Calland JK, Johansson H, Mageiros L, Muñoz-Ramirez ZY, Futcher G, Méric G, Hitchings MD, Sandoval-Motta S, Torres J, Jolley KA, Maiden MCJ, Ellström P, Waldenström J, Pascoe B, Sheppard SK. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter. eLife 2022; 11:73552. [PMID: 35191377 PMCID: PMC8912921 DOI: 10.7554/elife.73552] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/20/2022] [Indexed: 01/16/2023] Open
Abstract
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
Collapse
Affiliation(s)
- Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Jessica K Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmarSweden
| | - Leonardos Mageiros
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Zilia Y Muñoz-Ramirez
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Grant Futcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | | | - Santiago Sandoval-Motta
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Keith A Jolley
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala UniversityUppsalaSweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmarSweden
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom,Faculty of Veterinary Medicine, Chiang Mai UniversityChiang MaiThailand
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of BathBathUnited Kingdom,Department of Zoology, University of OxfordOxfordUnited Kingdom
| |
Collapse
|
8
|
Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2021; 50:D785-D794. [PMID: 34520557 PMCID: PMC8728215 DOI: 10.1093/nar/gkab776] [Citation(s) in RCA: 521] [Impact Index Per Article: 173.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/28/2021] [Indexed: 11/13/2022] Open
Abstract
The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.
Collapse
Affiliation(s)
- Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Christian Rinke
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Aaron J Mussig
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Pierre-Alain Chaumeil
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| |
Collapse
|
9
|
Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
Collapse
Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| |
Collapse
|
10
|
Weissman JL, Dogra S, Javadi K, Bolten S, Flint R, Davati C, Beattie J, Dixit K, Peesay T, Awan S, Thielen P, Breitwieser F, Johnson PLF, Karig D, Fagan WF, Bewick S. Exploring the functional composition of the human microbiome using a hand-curated microbial trait database. BMC Bioinformatics 2021; 22:306. [PMID: 34098872 PMCID: PMC8186035 DOI: 10.1186/s12859-021-04216-2] [Citation(s) in RCA: 6] [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: 11/03/2019] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. RESULTS We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. CONCLUSIONS Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.
Collapse
Affiliation(s)
- J L Weissman
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Sonia Dogra
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Keyan Javadi
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Samantha Bolten
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Rachel Flint
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Cyrus Davati
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Jess Beattie
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Keshav Dixit
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Tejasvi Peesay
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Shehar Awan
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Peter Thielen
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Florian Breitwieser
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Philip L F Johnson
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - David Karig
- Bioengineering Department, Clemson University, Clemson, SC, USA
| | - William F Fagan
- Department of Biology, University of Maryland - College Park, College Park, MD, USA
| | - Sharon Bewick
- Biological Sciences Department, Clemson University, Clemson, SC, USA.
| |
Collapse
|
11
|
Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
Collapse
Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
| |
Collapse
|
12
|
Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
Collapse
Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Stott CM, Bobay LM. Impact of homologous recombination on core genome phylogenies. BMC Genomics 2020; 21:829. [PMID: 33238876 PMCID: PMC7691112 DOI: 10.1186/s12864-020-07262-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/19/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate. RESULTS In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. CONCLUSIONS Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.
Collapse
Affiliation(s)
- Caroline M Stott
- Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA
| | - Louis-Marie Bobay
- Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
| |
Collapse
|
15
|
Zhou Z, Charlesworth J, Achtman M. Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. Genome Res 2020; 30:1667-1679. [PMID: 33055096 PMCID: PMC7605250 DOI: 10.1101/gr.260828.120] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses, including the calculation of trees based on accessory gene content or allelic differences between core genes. To test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated data sets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of approximately 40,000 genes from 3052 representative genomes spanning at least 80 species of Streptococcus The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of the entire Streptococcus genus.
Collapse
Affiliation(s)
- Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jane Charlesworth
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
16
|
VanInsberghe D, Arevalo P, Chien D, Polz MF. How can microbial population genomics inform community ecology? Philos Trans R Soc Lond B Biol Sci 2020; 375:20190253. [PMID: 32200748 PMCID: PMC7133533 DOI: 10.1098/rstb.2019.0253] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2019] [Indexed: 12/22/2022] Open
Abstract
Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Collapse
Affiliation(s)
- David VanInsberghe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Philip Arevalo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Diana Chien
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| |
Collapse
|
17
|
Baker BJ, Crane-Kramer G, Dee MW, Gregoricka LA, Henneberg M, Lee C, Lukehart SA, Mabey DC, Roberts CA, Stodder ALW, Stone AC, Winingear S. Advancing the understanding of treponemal disease in the past and present. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:5-41. [PMID: 31956996 DOI: 10.1002/ajpa.23988] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time.
Collapse
Affiliation(s)
- Brenda J Baker
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Gillian Crane-Kramer
- Department of Anthropology, State University of New York at Plattsburgh, Plattsburgh, New York
| | - Michael W Dee
- Centre for Isotope Research, University of Groningen, Groningen, Netherlands
| | - Lesley A Gregoricka
- Department of Sociology, Anthropology, and Social Work, University of South Alabama, Mobile, Alabama
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit, Adelaide Medical School, University of Adelaide, Adelaide, Australia.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Christine Lee
- Department of Anthropology, California State University Los Angeles, Los Angeles, California
| | - Sheila A Lukehart
- Department of Medicine/Infectious Diseases and Global Health, University of Washington, Seattle, Washington
| | - David C Mabey
- Communicable Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ann L W Stodder
- Office of Archaeological Studies, The Museum of New Mexico, Santa Fe, New Mexico
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| |
Collapse
|
18
|
Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome Biol Evol 2019; 11:1780-1796. [PMID: 31173069 PMCID: PMC6690169 DOI: 10.1093/gbe/evz119] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.
Collapse
Affiliation(s)
- Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine
| | - Ekpeno Nnah
- Lurie Children's Hospital, Chicago, Illinois
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Rachel J Whitaker
- Department of Microbiology and the Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana-Champaign
| | - Alan R Hauser
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine.,Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine
| |
Collapse
|
19
|
Edgar RC. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics 2019; 34:2371-2375. [PMID: 29506021 DOI: 10.1093/bioinformatics/bty113] [Citation(s) in RCA: 315] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data. Results Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms using four accuracy metrics. All algorithms had comparable accuracy when tuned to a given metric. Optimal identity thresholds were ∼99% for full-length sequences and ∼100% for the V4 hypervariable region. Availability and implementation Reference sequences and source code are provided in the Supplementary Material. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
|
20
|
Vila JCC, Jones ML, Patel M, Bell T, Rosindell J. Uncovering the rules of microbial community invasions. Nat Ecol Evol 2019; 3:1162-1171. [PMID: 31358951 DOI: 10.1038/s41559-019-0952-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/24/2019] [Indexed: 12/30/2022]
Abstract
Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion.
Collapse
Affiliation(s)
- Jean C C Vila
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK. .,Microbial Sciences Institute, West Campus, Yale University, West Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| | - Matt L Jones
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
| | - Matishalin Patel
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Tom Bell
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
| | - James Rosindell
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
| |
Collapse
|
21
|
Fukuyama J. Adaptive gPCA: A method for structured dimensionality reduction with applications to microbiome data. Ann Appl Stat 2019. [DOI: 10.1214/18-aoas1227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
22
|
Díez-Vives C, Nielsen S, Sánchez P, Palenzuela O, Ferrera I, Sebastián M, Pedrós-Alió C, Gasol JM, Acinas SG. Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea. Mol Ecol 2019; 28:2846-2859. [PMID: 30830717 DOI: 10.1111/mec.15068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 01/18/2023]
Abstract
Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.
Collapse
Affiliation(s)
- Cristina Díez-Vives
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Department of Life Sciences (Invertebrate Division), The Natural History Museum of London, London, UK
| | - Shaun Nielsen
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, Australia
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Oswaldo Palenzuela
- Department of Biology, Culture and Pathology of Marine Species, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto Español de Oceanografía, Centro Oceanográfico de Málaga, Fuengirola, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Madrid, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| |
Collapse
|
23
|
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: 13] [Impact Index Per Article: 2.6] [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.
Collapse
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
| |
Collapse
|
24
|
Population Genomics Insights into Adaptive Evolution and Ecological Differentiation in Streptomycetes. Appl Environ Microbiol 2019; 85:AEM.02555-18. [PMID: 30658977 DOI: 10.1128/aem.02555-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Deciphering the genomic variation that represents microevolutionary processes toward species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCE Species are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but it is a challenge in the microbial world. In this study, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps. These findings highlight the role of ecology in structuring recombining bacterial species, making a step toward a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.
Collapse
|
25
|
Palmer M, Venter SN, Coetzee MP, Steenkamp ET. Prokaryotic species are sui generis evolutionary units. Syst Appl Microbiol 2019; 42:145-158. [DOI: 10.1016/j.syapm.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/25/2022]
|
26
|
Abstract
Biological communities are conventionally described as assemblages of species, whose ecological roles are known or predictable from their observable morphology. In microbial ecology, such a taxonomic approach is hindered by limited capacity to discriminate among different microbes, which bear highly dynamic genomes and establish complex associations. Approaches based on culture-independent functional genes profiling might overcome these problems, but a set of usable established genes in a general situation is still lacking. We show that genes related to reduction-oxidation (redox) processes separate microbial communities into their corresponding biomes. This redox-based characterization is linked to the microbial energetics of ecosystems and to most biogeochemical cycles and might be useful for assessing the impact of environmental degradation on the ecosystem services, underpinned by microorganisms. The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases’ description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.
Collapse
|
27
|
Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
Collapse
Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| |
Collapse
|
28
|
Wright ES, Baum DA. Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow. BMC Genomics 2018; 19:724. [PMID: 30285620 PMCID: PMC6171291 DOI: 10.1186/s12864-018-5099-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/21/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization. RESULTS Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species. CONCLUSIONS The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.
Collapse
Affiliation(s)
- Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA.
- Pittsburgh Center for Evolutionary Biology and Medicine, Pittsburgh, USA.
| | - David A Baum
- Department of Botany, University of Wisconsin-Madison, Madison, USA
| |
Collapse
|
29
|
Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
Collapse
Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
| |
Collapse
|
30
|
Akita T, Takuno S, Innan H. Coalescent framework for prokaryotes undergoing interspecific homologous recombination. Heredity (Edinb) 2018; 120:474-484. [PMID: 29358726 PMCID: PMC5889408 DOI: 10.1038/s41437-017-0034-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/04/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
Coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination with individuals of the same species (intraspecific recombination) and with individuals of other species (interspecific recombination). This work particularly focuses on interspecific recombination because intraspecific recombination has been well incorporated in coalescent framework. We present a simulation framework for generating SNP (single-nucleotide polymorphism) patterns that allows external DNA integration into host genome from other species. Using this simulation tool, msPro, we observed that the joint processes of intra- and interspecific recombination generate complex SNP patterns. The direct effect of interspecific recombination includes increased polymorphism. Because interspecific recombination is very rare in nature, it generates regions with exceptionally high polymorphism. Following interspecific recombination, intraspecific recombination cuts the integrated external DNA into small fragments, generating a complex SNP pattern that appears as if external DNA was integrated multiple times. The insight gained from our work using the msPro simulator will be useful for understanding and evaluating the relative contributions of intra- and interspecific recombination events in generating complex SNP patters in prokaryotes.
Collapse
Affiliation(s)
- Tetsuya Akita
- Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan
- National Research Institute of Far Seas Fisheries, Fisheries Research Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Shohei Takuno
- Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan
| | - Hideki Innan
- Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan.
| |
Collapse
|
31
|
Monk J, Bosi E. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences. Methods Mol Biol 2018; 1716:151-175. [PMID: 29222753 DOI: 10.1007/978-1-4939-7528-0_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species. Recently, genome-scale metabolic models of different strains have been assembled to highlight the intra-species diversity at the metabolic level. The strain-specific metabolic capabilities and auxotrophies can be used to identify factors related to the lifestyle diversity of a bacterial species.In this chapter, we present the computational steps to perform genome-scale metabolic modeling in the context of comparative genomics, and the different challenges related to this task.
Collapse
Affiliation(s)
- Jonathan Monk
- Department of Bioengineering, University of California, La Jolla, CA, USA
| | - Emanuele Bosi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| |
Collapse
|
32
|
A Reverse Ecology Framework for Bacteria and Archaea. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
33
|
Brito PH, Chevreux B, Serra CR, Schyns G, Henriques AO, Pereira-Leal JB. Genetic Competence Drives Genome Diversity in Bacillus subtilis. Genome Biol Evol 2018; 10:108-124. [PMID: 29272410 PMCID: PMC5765554 DOI: 10.1093/gbe/evx270] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/18/2022] Open
Abstract
Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.
Collapse
Affiliation(s)
- Patrícia H Brito
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Portugal
| | - Bastien Chevreux
- DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA
| | - Cláudia R Serra
- Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Ghislain Schyns
- DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA
| | | | - José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Ophiomics—Precision Medicine, Lisbon, Portugal
| |
Collapse
|
34
|
Nakajima T. Ecological extension of the theory of evolution by natural selection from a perspective of Western and Eastern holistic philosophy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 131:298-311. [DOI: 10.1016/j.pbiomolbio.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 01/29/2023]
|
35
|
Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J. A Robust Framework for Microbial Archaeology. Annu Rev Genomics Hum Genet 2017; 18:321-356. [PMID: 28460196 PMCID: PMC5581243 DOI: 10.1146/annurev-genom-091416-035526] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.
Collapse
Affiliation(s)
- Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
| | - Allison Mann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse 31000, France
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
| |
Collapse
|
36
|
Millán-Aguiñaga N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 2017; 7:3564. [PMID: 28620214 PMCID: PMC5472633 DOI: 10.1038/s41598-017-02845-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
Collapse
Affiliation(s)
- Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Krystle L Chavarria
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Juan A Ugalde
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bella, Santiago, Chile
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Greg W Rouse
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States. .,Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
| |
Collapse
|
37
|
Larkin AA, Martiny AC. Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:55-70. [PMID: 28185400 DOI: 10.1111/1758-2229.12523] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood. Here, we present two theoretical models outlining the evolutionary mechanisms that drive the formation of microdiverse 'sub-taxa.' Additionally, we review recent literature and reveal that microdiversity influences a wide range of functional traits across diverse ecosystems and microbes. Moving to higher levels of organization, we use laboratory data from marine, soil, and host-associated bacteria to demonstrate that the aggregated trait-based response of microdiverse sub-taxa modifies the fundamental niche of microbes. The correspondence between microdiversity and niche space represents a critical tool for future studies of microbial ecology. By combining growth experiments on diverse isolates with examinations of environmental abundance patterns, researchers can better quantify the fundamental and realized niches of microbes and improve understanding of microbial biogeography and response to future environmental change.
Collapse
Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| |
Collapse
|
38
|
Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection. Appl Environ Microbiol 2017; 83:AEM.02589-16. [PMID: 27881415 DOI: 10.1128/aem.02589-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features-for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria. IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.
Collapse
|
39
|
Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
Collapse
Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
| |
Collapse
|
40
|
Morgan GJ. What is a virus species? Radical pluralism in viral taxonomy. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 59:64-70. [PMID: 26994934 DOI: 10.1016/j.shpsc.2016.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 02/27/2016] [Indexed: 06/05/2023]
Abstract
Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) has refined its definition of a virus species to include an appeal to evolutionary history. The current ICTV definition defines a viral species in terms of monophyly. The existence of prolific horizontal genetic transfer (HGT) among various groups of viruses presents a challenge to this definition. I argue that the proper response to this mode of evolution is to allow for radical pluralism. Some viruses can be members of more than one species; others don't form species at all and should be classified using new reticulate categories.
Collapse
Affiliation(s)
- Gregory J Morgan
- College of Arts and Letters, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| |
Collapse
|
41
|
Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS Comput Biol 2016; 12:e1005071. [PMID: 27532298 PMCID: PMC4988722 DOI: 10.1371/journal.pcbi.1005071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/20/2016] [Indexed: 12/30/2022] Open
Abstract
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.
Collapse
|
42
|
Biogeographical Patterns of Legume-Nodulating Burkholderia spp.: from African Fynbos to Continental Scales. Appl Environ Microbiol 2016; 82:5099-115. [PMID: 27316955 DOI: 10.1128/aem.00591-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Rhizobia of the genus Burkholderia have large-scale distribution ranges and are usually associated with South African papilionoid and South American mimosoid legumes, yet little is known about their genetic structuring at either local or global geographic scales. To understand variation at different spatial scales, from individual legumes in the fynbos (South Africa) to a global context, we analyzed chromosomal (16S rRNA, recA) and symbiosis (nifH, nodA, nodC) gene sequences. We showed that the global diversity of nodulation genes is generally grouped according to the South African papilionoid or South American mimosoid subfamilies, whereas chromosomal sequence data were unrelated to biogeography. While nodulation genes are structured on a continental scale, a geographic or host-specific distribution pattern was not detected in the fynbos region. In host range experiments, symbiotic promiscuity of Burkholderia tuberum STM678(T) and B phymatum STM815(T) was discovered in selected fynbos species. Finally, a greenhouse experiment was undertaken to assess the ability of mimosoid (Mimosa pudica) and papilionoid (Dipogon lignosus, Indigofera filifolia, Macroptilium atropurpureum, and Podalyria calyptrata) species to nodulate in South African (fynbos) and Malawian (savanna) soils. While the Burkholderia-philous fynbos legumes (D lignosus, I filifolia, and P calyptrata) nodulated only in their native soils, the invasive neotropical species M pudica did not develop nodules in the African soils. The fynbos soil, notably rich in Burkholderia, seems to retain nodulation genes compatible with the local papilionoid legume flora but is incapable of nodulating mimosoid legumes that have their center of diversity in South America. IMPORTANCE This study is the most comprehensive phylogenetic assessment of root-nodulating Burkholderia and investigated biogeographic and host-related patterns of the legume-rhizobial symbiosis in the South African fynbos biome, as well as at global scales, including native species from the South American Caatinga and Cerrado biomes. While a global investigation of the rhizobial diversity revealed distinct nodulation and nitrogen fixation genes among South African and South American legumes, regionally distributed species in the Cape region were unrelated to geographic and host factors.
Collapse
|
43
|
García FC, García-Martín EE, Taboada FG, Sal S, Serret P, López-Urrutia Á. The allometry of the smallest: superlinear scaling of microbial metabolic rates in the Atlantic Ocean. ISME JOURNAL 2015; 10:1029-36. [PMID: 26636550 PMCID: PMC5029206 DOI: 10.1038/ismej.2015.203] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/27/2015] [Accepted: 10/04/2015] [Indexed: 11/24/2022]
Abstract
Prokaryotic planktonic organisms are small in size but largely relevant in marine biogeochemical cycles. Due to their reduced size range (0.2 to 1 μm in diameter), the effects of cell size on their metabolism have been hardly considered and are usually not examined in field studies. Here, we show the results of size-fractionated experiments of marine microbial respiration rate along a latitudinal transect in the Atlantic Ocean. The scaling exponents obtained from the power relationship between respiration rate and size were significantly higher than one. This superlinearity was ubiquitous across the latitudinal transect but its value was not universal revealing a strong albeit heterogeneous effect of cell size on microbial metabolism. Our results suggest that the latitudinal differences observed are the combined result of changes in cell size and composition between functional groups within prokaryotes. Communities where the largest size fraction was dominated by prokaryotic cyanobacteria, especially Prochlorococcus, have lower allometric exponents. We hypothesize that these larger, more complex prokaryotes fall close to the evolutionary transition between prokaryotes and protists, in a range where surface area starts to constrain metabolism and, hence, are expected to follow a scaling closer to linearity.
Collapse
Affiliation(s)
- Francisca C García
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| | - Enma Elena García-Martín
- Universidad de Vigo, Departamento de Ecología y Biología Animal, Carretera Colegio Universitario, Vigo, Spain
| | | | - Sofía Sal
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| | - Pablo Serret
- Universidad de Vigo, Departamento de Ecología y Biología Animal, Carretera Colegio Universitario, Vigo, Spain.,Estación de Ciencias Marinas de Toralla, Universidad de Vigo, Toralla Island, Vigo, Spain
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| |
Collapse
|
44
|
Migration and horizontal gene transfer divide microbial genomes into multiple niches. Nat Commun 2015; 6:8924. [PMID: 26592443 PMCID: PMC4673824 DOI: 10.1038/ncomms9924] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/16/2015] [Indexed: 02/01/2023] Open
Abstract
Horizontal gene transfer is central to microbial evolution, because it enables genetic regions to spread horizontally through diverse communities. However, how gene transfer exerts such a strong effect is not understood. Here we develop an eco-evolutionary model and show how genetic transfer, even when rare, can transform the evolution and ecology of microbes. We recapitulate existing models, which suggest that asexual reproduction will overpower horizontal transfer and greatly limit its effects. We then show that allowing immigration completely changes these predictions. With migration, the rates and impacts of horizontal transfer are greatly increased, and transfer is most frequent for loci under positive natural selection. Our analysis explains how ecologically important loci can sweep through competing strains and species. In this way, microbial genomes can evolve to become ecologically diverse where different genomic regions encode for partially overlapping, but distinct, ecologies. Under these conditions ecological species do not exist, because genes, not species, inhabit niches. Horizontal gene transfer is central to microbial evolution. Here, the authors develop an eco-evolutionary model and show that migration can greatly promote horizontal gene transfer, which explains how ecologically-important loci can sweep through the species in a microbial community.
Collapse
|
45
|
Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MTG, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Front Microbiol 2015; 6:1191. [PMID: 26583006 PMCID: PMC4631834 DOI: 10.3389/fmicb.2015.01191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022] Open
Abstract
Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.
Collapse
Affiliation(s)
- Abiyad Baig
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Kate J Howell
- Department of Paediatrics, University of Cambridge Cambridge, UK
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield Sheffield, UK
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | | | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Cambridge, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
| | | | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine London, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| |
Collapse
|
46
|
Abstract
What are species? How do they arise? These questions are not easy to answer and have been particularly controversial in microbiology. Yet, for those microbiologists studying environmental questions or dealing with clinical issues, the ability to name and recognize species, widely considered the fundamental units of ecology, can be practically useful. On a more fundamental level, the speciation problem, the focus here, is more mechanistic and conceptual. What is the origin of microbial species, and what evolutionary and ecological mechanisms keep them separate once they begin to diverge? To what extent are these mechanisms universal across diverse types of microbes, and more broadly across the entire the tree of life? Here, we propose that microbial speciation must be viewed in light of gene flow, which defines units of genetic similarity, and of natural selection, which defines units of phenotype and ecological function. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and population genomics studies. These studies suggest a continuous "speciation spectrum," which microbial populations traverse in different ways depending on their balance of gene flow and natural selection.
Collapse
Affiliation(s)
- B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal QC H3C 3J7, Canada
| | - Martin F Polz
- Parsons Laboratory for Environmental Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| |
Collapse
|
47
|
Krause DJ, Whitaker RJ. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes. Syst Biol 2015; 64:926-35. [PMID: 26316424 PMCID: PMC4604833 DOI: 10.1093/sysbio/syv050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.
Collapse
Affiliation(s)
- David J Krause
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
48
|
Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
Collapse
Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| |
Collapse
|
49
|
Papke RT, Corral P, Ram-Mohan N, de la Haba RR, Sánchez-Porro C, Makkay A, Ventosa A. Horizontal gene transfer, dispersal and haloarchaeal speciation. Life (Basel) 2015; 5:1405-26. [PMID: 25997110 PMCID: PMC4500145 DOI: 10.3390/life5021405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022] Open
Abstract
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.
Collapse
Affiliation(s)
- R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
- Author to whom correspondence should be addressed; E-Mail:
| | - Paulina Corral
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Nikhil Ram-Mohan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Andrea Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| |
Collapse
|
50
|
Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 2014; 197:359-70. [PMID: 25533848 DOI: 10.1007/s00203-014-1071-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
Collapse
|