1
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Grasso G, Bianciotto V, Marmeisse R. Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities. Microb Biotechnol 2024; 17:e14390. [PMID: 38227345 PMCID: PMC10832523 DOI: 10.1111/1751-7915.14390] [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: 07/28/2023] [Revised: 11/04/2023] [Accepted: 12/10/2023] [Indexed: 01/17/2024] Open
Abstract
By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non-host-associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre-disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.
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Affiliation(s)
- Gianluca Grasso
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversità degli Studi of TurinTurinItaly
- Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS‐MNHN‐Sorbonne Université‐EPHE‐UA)¸ Muséum National d'Histoire NaturelleParisFrance
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
| | - Roland Marmeisse
- Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS‐MNHN‐Sorbonne Université‐EPHE‐UA)¸ Muséum National d'Histoire NaturelleParisFrance
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
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2
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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3
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Paradis E, Claramunt S, Brown J, Schliep K. Confidence intervals in molecular dating by maximum likelihood. Mol Phylogenet Evol 2023; 178:107652. [PMID: 36306994 DOI: 10.1016/j.ympev.2022.107652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Molecular dating has been widely used to infer the times of past evolutionary events using molecular sequences. This paper describes three bootstrap methods to infer confidence intervals under a penalized likelihood framework. The basic idea is to use data pseudoreplicates to infer uncertainty in the branch lengths of a phylogeny reconstructed with molecular sequences. The three specific bootstrap methods are nonparametric (direct tree bootstrapping), semiparametric (rate smoothing), and parametric (Poisson simulation). Our extensive simulation study showed that the three methods perform generally well under a simple strict clock model of molecular evolution; however, the results were less positive with data simulated using an uncorrelated or a correlated relaxed clock model. Several factors impacted, possibly in interaction, the performance of the confidence intervals. Increasing the number of calibration points had a positive effect, as well as increasing the sequence length or the number of sequences although both latter effects depended on the model of evolution. A case study is presented with a molecular phylogeny of the Felidae (Mammalia: Carnivora). A comparison was made with a Bayesian analysis: the results were very close in terms of confidence intervals and there was no marked tendency for an approach to produce younger or older bounds compared to the other.
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Affiliation(s)
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, ON 5S2C6, Canada
| | - Joseph Brown
- Department of Natural History, Royal Ontario Museum, Toronto, ON 5S2C6, Canada
| | - Klaus Schliep
- Institute of Computational Biotechnology, Technology University Graz, Austria
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4
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Chandrarathna HPSU, Nikapitiya C, Dananjaya SHS, Wijerathne CUB, Wimalasena SHMP, Kwun HJ, Heo GJ, Lee J, De Zoysa M. Outcome of co-infection with opportunistic and multidrug resistant Aeromonas hydrophila and A. veronii in zebrafish: Identification, characterization, pathogenicity and immune responses. FISH & SHELLFISH IMMUNOLOGY 2018; 80:573-581. [PMID: 29964197 DOI: 10.1016/j.fsi.2018.06.049] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/17/2018] [Accepted: 06/27/2018] [Indexed: 05/04/2023]
Abstract
Fish can be potentially co-infected by two or more bacterial strains, which can make synergistic influence on the virulence of infection. In this study, two opportunistic and multidrug resistant Aeromonas strains were isolated from wounds of morbid zebrafish with typical deep skin lesions similar to Motile Aeromonas Septicemia. Isolates were genetically identified as A. hydrophila and A. veronii by 16 S rRNA sequencing and phylogenetic analysis. Both isolates were positive for virulent genes (aerA, lip, ser, exu gcaT) and selected phenotypic tests (DNase, protease, gelatinase, lipase, biofilm production and β-haemolysis). A. hydrophila and A. veronii had strong antibiotic resistance against ampicillin, tetracycline, nalidixic acid, kanamycin, erythromycin, clindamycin and trimethoprim-sulfamethoxazole. Histopathological studies revealed that co-infection causes severe necrosis and hypertrophy in the muscles, kidney and liver of zebrafish. Naturally co-infected zebrafish showed highly induced tnf-α, il-1β, il-6, il-12, ifn, ifn-γ, cxcl18 b and ccl34a.4 at transcription level compared to healthy fish, suggesting virulence factors may activate immune and inflammatory responses of zebrafish. Experimentally infected zebrafish showed significantly higher mortality under co-infection with A. hydrohila and A. veronii (87%), followed by individual challenge of A. hydrophila (72%) or A. veronii (67%) suggesting that virulence of A. hydrophila have greater pathogenicity than A. veronii during co-infection.
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Affiliation(s)
- H P S U Chandrarathna
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Chamilani Nikapitiya
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - S H S Dananjaya
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - C U B Wijerathne
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - S H M P Wimalasena
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyo Jung Kwun
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Gang-Joon Heo
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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5
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Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M. Bacterial diversification through geological time. Nat Ecol Evol 2018; 2:1458-1467. [DOI: 10.1038/s41559-018-0625-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022]
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6
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Lorén JG, Farfán M, Fusté MC. Species Delimitation, Phylogenetic Relationships, and Temporal Divergence Model in the Genus Aeromonas. Front Microbiol 2018; 9:770. [PMID: 29731747 PMCID: PMC5920023 DOI: 10.3389/fmicb.2018.00770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/05/2018] [Indexed: 11/16/2022] Open
Abstract
The definition of species boundaries constitutes an important challenge in biodiversity studies. In this work we applied the Generalized Mixed Yule Coalescent (GMYC) method, which determines a divergence threshold to delimit species in a phylogenetic tree. Based on the tree branching pattern, the analysis fixes the transition threshold between speciation and the coalescent process associated with the intra-species diversification. This approach has been widely used to delineate eukaryote species and establish their diversification process from sequence data. Nevertheless, there are few examples in which this analysis has been applied to a bacterial population. Although the GMYC method was originally designed to assume a constant (Yule) model of diversification at between-species level, it was later evaluated simulating other conditions. Our aim was therefore to determine the species delineation in Aeromonas using the GMYC method and asses which model best explains the speciation process in this bacterial genus. The application of the GMYC method allowed us to clearly delineate the Aeromonas species boundaries, even in the controversial groups, such as the A. veronii or A. media species complexes.
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Affiliation(s)
- J G Lorén
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Maribel Farfán
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - M C Fusté
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
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7
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Marin J, Battistuzzi FU, Brown AC, Hedges SB. The Timetree of Prokaryotes: New Insights into Their Evolution and Speciation. Mol Biol Evol 2017; 34:437-446. [PMID: 27965376 DOI: 10.1093/molbev/msw245] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increasing size of timetrees in recent years has led to a focus on diversification analyses to better understand patterns of macroevolution. Thus far, nearly all studies have been conducted with eukaryotes primarily because phylogenies have been more difficult to reconstruct and calibrate to geologic time in prokaryotes. Here, we have estimated a timetree of 11,784 'species' of prokaryotes and explored their pattern of diversification. We used data from the small subunit ribosomal RNA along with an evolutionary framework from previous multi-gene studies to produce three alternative timetrees. For each timetree we surprisingly found a constant net diversification rate derived from an exponential increase of lineages and showing no evidence of saturation (rate decline), the same pattern found previously in eukaryotes. The implication is that prokaryote diversification as a whole is the result of the random splitting of lineages and is neither limited by existing diversity (filled niches) nor responsive in any major way to environmental changes.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, Temple University, SERC Suite 502, 1925 N 12th Street, Philadelphia, PA.,Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Sorbonne-Universités, Paris, France
| | | | - Anais C Brown
- Department of Biological Sciences, Oakland University, Rochester, MI
| | - S Blair Hedges
- Center for Biodiversity, Temple University, SERC Suite 502, 1925 N 12th Street, Philadelphia, PA
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8
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Lebreton F, Manson AL, Saavedra JT, Straub TJ, Earl AM, Gilmore MS. Tracing the Enterococci from Paleozoic Origins to the Hospital. Cell 2017; 169:849-861.e13. [PMID: 28502769 DOI: 10.1016/j.cell.2017.04.027] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/16/2017] [Accepted: 04/19/2017] [Indexed: 01/16/2023]
Abstract
We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya. Speciation appears to parallel the diversification of hosts, including the rapid emergence of new enterococcal species following the End Permian Extinction. Major drivers of speciation include changing carbohydrate availability in the host gut. Life on land would have selected for the precise traits that now allow pathogenic enterococci to survive desiccation, starvation, and disinfection in the modern hospital, foreordaining their emergence as leading hospital pathogens.
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Affiliation(s)
- François Lebreton
- Department of Ophthalmology and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jose T Saavedra
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA.
| | - Michael S Gilmore
- Department of Ophthalmology and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA.
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9
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Talagrand-Reboul E, Roger F, Kimper JL, Colston SM, Graf J, Latif-Eugenín F, Figueras MJ, Petit F, Marchandin H, Jumas-Bilak E, Lamy B. Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case. Front Microbiol 2017; 8:621. [PMID: 28458658 PMCID: PMC5394120 DOI: 10.3389/fmicb.2017.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Frédéric Roger
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Jean-Luc Kimper
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Sophie M Colston
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Fadua Latif-Eugenín
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Maria José Figueras
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Fabienne Petit
- Normandie Univ, UNIROUEN, UNICAEN, Centre National de la Recherche Scientifique, M2CRouen, France.,Sorbonne Universités, UPMC, Centre National de la Recherche Scientifique, EPHE, UMR 7619 METISParis, France
| | - Hélène Marchandin
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHRU de MontpellierMontpellier, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHU de NiceNice, France
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10
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Sanglas A, Albarral V, Farfán M, Lorén JG, Fusté MC. Evolutionary Roots and Diversification of the Genus Aeromonas. Front Microbiol 2017; 8:127. [PMID: 28228750 PMCID: PMC5296313 DOI: 10.3389/fmicb.2017.00127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/18/2017] [Indexed: 12/02/2022] Open
Abstract
Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes.
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Affiliation(s)
- Ariadna Sanglas
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona Barcelona, Spain
| | - Vicenta Albarral
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona Barcelona, Spain
| | - Maribel Farfán
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de BarcelonaBarcelona, Spain; Institut de Recerca de la Biodiversitat, Universitat de BarcelonaBarcelona, Spain
| | - J G Lorén
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona Barcelona, Spain
| | - M C Fusté
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de BarcelonaBarcelona, Spain; Institut de Recerca de la Biodiversitat, Universitat de BarcelonaBarcelona, Spain
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11
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Ghatak S, Blom J, Das S, Sanjukta R, Puro K, Mawlong M, Shakuntala I, Sen A, Goesmann A, Kumar A, Ngachan SV. Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila. Antonie van Leeuwenhoek 2016; 109:945-56. [PMID: 27075453 DOI: 10.1007/s10482-016-0693-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/30/2016] [Indexed: 11/26/2022]
Abstract
Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.
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Affiliation(s)
- Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Samir Das
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
| | - Rajkumari Sanjukta
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
| | - Kekungu Puro
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
| | | | - Ingudam Shakuntala
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
| | - Arnab Sen
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Ashok Kumar
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - S V Ngachan
- ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
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Sanglas A, Albarral V, Farfán M, Lorén JG, Fusté MC. Direct evidence of recombination in the recA gene of Aeromonas bestiarum. Syst Appl Microbiol 2016; 39:106-14. [PMID: 26934994 DOI: 10.1016/j.syapm.2016.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 11/25/2022]
Abstract
Two hundred and twenty-one strains representative of all Aeromonas species were characterized using the recA gene sequence, assessing its potential as a molecular marker for the genus Aeromonas. The inter-species distance values obtained demonstrated that recA has a high discriminatory power. Phylogenetic analysis, based on full-length gene nucleotide sequences, revealed a robust topology with clearly separated clusters for each species. The maximum likelihood tree showed the Aeromonas bestiarum strains in a well-defined cluster, containing a subset of four strains of different geographical origins in a deep internal branch. Data analysis provided strong evidence of recombination at the end of the recA sequences in these four strains. Intergenomic recombination corresponding to partial regions of the two adjacent genes recA and recX (248 bp) was identified between A. bestiarum (major parent) and Aeromonas eucrenophila (minor parent). The low number of recombinant strains detected (1.8%) suggests that horizontal flow between recA sequences is relatively uncommon in this genus. Moreover, only a few nucleotide differences were detected among these fragments, indicating that recombination has occurred recently. Finally, we also determined if the recombinant fragment could have influenced the structure and basic functions of the RecA protein, comparing models reconstructed from the translated amino acid sequences of our A. bestiarum strains with known Escherichia coli RecA structures.
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Affiliation(s)
- Ariadna Sanglas
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
| | - Vicenta Albarral
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
| | - Maribel Farfán
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - J Gaspar Lorén
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
| | - M Carmen Fusté
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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13
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Paradis E. Random phylogenies and the distribution of branching times. J Theor Biol 2015; 387:39-45. [DOI: 10.1016/j.jtbi.2015.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 11/15/2022]
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Goberna M, Verdú M. Predicting microbial traits with phylogenies. ISME JOURNAL 2015; 10:959-67. [PMID: 26371406 DOI: 10.1038/ismej.2015.171] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/24/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.
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Affiliation(s)
- Marta Goberna
- Centro de Investigaciones Sobre Desertificación (CIDE; CSIC-UV-GV), Valencia, Spain
| | - Miguel Verdú
- Centro de Investigaciones Sobre Desertificación (CIDE; CSIC-UV-GV), Valencia, Spain
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Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136. [PMID: 25406383 PMCID: PMC4251997 DOI: 10.1128/mbio.02136-14] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Prokaryotic taxonomy is the underpinning of microbiology, as it provides a framework for the proper identification and naming of organisms. The “gold standard” of bacterial species delineation is the overall genome similarity determined by DNA-DNA hybridization (DDH), a technically rigorous yet sometimes variable method that may produce inconsistent results. Improvements in next-generation sequencing have resulted in an upsurge of bacterial genome sequences and bioinformatic tools that compare genomic data, such as average nucleotide identity (ANI), correlation of tetranucleotide frequencies, and the genome-to-genome distance calculator, or in silico DDH (isDDH). Here, we evaluate ANI and isDDH in combination with phylogenetic studies using Aeromonas, a taxonomically challenging genus with many described species and several strains that were reassigned to different species as a test case. We generated improved, high-quality draft genome sequences for 33 Aeromonas strains and combined them with 23 publicly available genomes. ANI and isDDH distances were determined and compared to phylogenies from multilocus sequence analysis of housekeeping genes, ribosomal proteins, and expanded core genes. The expanded core phylogenetic analysis suggested relationships between distant Aeromonas clades that were inconsistent with studies using fewer genes. ANI values of ≥96% and isDDH values of ≥70% consistently grouped genomes originating from strains of the same species together. Our study confirmed known misidentifications, validated the recent revisions in the nomenclature, and revealed that a number of genomes deposited in GenBank are misnamed. In addition, two strains were identified that may represent novel Aeromonas species. Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high-quality draft genomes and led to a dramatic increase in the number of publically available genomes. This has allowed researchers to characterize microorganisms using genome data. Advantages of genome sequence-based classification include data and computing programs that can be readily shared, facilitating the standardization of taxonomic methodology and resolving conflicting identifications by providing greater uniformity in an overall analysis. Using Aeromonas as a test case, we compared and validated different approaches. Based on our analyses, we recommend cutoff values for distance measures for identifying species. Accurate species classification is critical not only to obviate the perpetuation of errors in public databases but also to ensure the validity of inferences made on the relationships among species within a genus and proper identification in clinical and veterinary diagnostic laboratories.
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