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Jahn MT, Lachnit T, Markert SM, Stigloher C, Pita L, Ribes M, Dutilh BE, Hentschel U. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. ISME J 2021; 15:2001-2011. [PMID: 33603147 PMCID: PMC8245591 DOI: 10.1038/s41396-021-00900-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 01/18/2021] [Indexed: 01/31/2023]
Abstract
Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.
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Affiliation(s)
- M T Jahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- Department of Zoology and Department of Biochemistry, University of Oxford, Oxford, UK.
| | - T Lachnit
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | - S M Markert
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | - C Stigloher
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | - L Pita
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - M Ribes
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - U Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-University of Kiel, Kiel, Germany
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Coutinho FH, von Meijenfeldt FAB, Walter JM, Haro-Moreno JM, Lopéz-Pérez M, van Verk MC, Thompson CC, Cosenza CAN, Appolinario L, Paranhos R, Cabral A, Dutilh BE, Thompson FL. Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome. Sci Total Environ 2021; 765:142758. [PMID: 33183813 DOI: 10.1016/j.scitotenv.2020.142758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/18/2023]
Abstract
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands; Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - F A B von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - J M Walter
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M Lopéz-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M C van Verk
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - C A N Cosenza
- COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - L Appolinario
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Paranhos
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - A Cabral
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - B E Dutilh
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Douterelo I, Dutilh BE, Calero C, Rosales E, Martin K, Husband S. Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks. Water Res 2020; 187:116416. [PMID: 33039899 DOI: 10.1016/j.watres.2020.116416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality.
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Affiliation(s)
- I Douterelo
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, United Kingdom.
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584, CH, Utrecht, Netherlands
| | - C Calero
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, United Kingdom
| | - E Rosales
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, United Kingdom
| | - K Martin
- Dwr Cymru Welsh Water, Pentwyn Road, Nelson, Treharris, Mid Glamorgan CF46 6LY, United Kingdom
| | - S Husband
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, United Kingdom
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Douterelo I, Dutilh BE, Arkhipova K, Calero C, Husband S. Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems. Water Res 2020; 173:115586. [PMID: 32065938 DOI: 10.1016/j.watres.2020.115586] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/22/2020] [Accepted: 02/02/2020] [Indexed: 06/10/2023]
Abstract
Drinking water distribution systems host complex microbial communities as biofilms that interact continuously with delivered water. Understanding the diversity, behavioural and functional characteristics will be a requisite for developing future monitoring strategies and protection against water-borne health risks. To improve understanding, this study investigates mobilisation and accumulation behaviour, microbial community structure and functional variations of biofilms developing on different pipe materials from within an operational network. Samples were collected from four pipes during a repeated flushing operation three months after an initial visit that used hydraulic forces to mobilise regenerating biofilms yet without impacting the upstream network. To minimise confounding factors, test sections were chosen with comparable daily hydraulic regimes, physical dimensions, and all connected straight of a common trunk main and within close proximity, hence similar water chemistry, pressure and age. Taxonomical results showed differences in colonising communities between pipe materials, with several genera, including the bacteria Pseudomonas and the fungi Cladosporium, present in every sample. Diverse bacterial communities dominated compared to more homogeneous fungal, or mycobiome, community distribution. The analysis of bacterial/fungal networks based on relative abundance of operational taxonomic units (OTUs) indicated microbial communities from cast iron pipes were more stable than communities from the non-ferrous pipe materials. Novel analysis of functional traits between all samples were found to be mainly associated to mobile genetic elements that play roles in determining links between cells, including phages, prophages, transposable elements, and plasmids. The use of functional traits can be considered for development in future surveillance methods, capable of delivering network condition information beyond that of limited conventional faecal indicator tests, that will help protect water quality and public health.
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Affiliation(s)
- I Douterelo
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, UK.
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584, CH, Utrecht, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525, GA, Nijmegen, the Netherlands
| | - K Arkhipova
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - C Calero
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, UK
| | - S Husband
- Pennine Water Group, Department of Civil and Structural Engineering, Sir Frederick Mappin Building, University of Sheffield, Sheffield, S1 3JD, UK
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Coutinho FH, Thompson CC, Cabral AS, Paranhos R, Dutilh BE, Thompson FL. Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks. Sci Total Environ 2019; 677:205-214. [PMID: 31059870 DOI: 10.1016/j.scitotenv.2019.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 05/13/2023]
Abstract
Guanabara Bay is a tropical estuarine ecosystem that receives massive anthropogenic impacts from the metropolitan region of Rio de Janeiro. This ecosystem suffers from an ongoing eutrophication process that has been shown to promote the emergence of potentially pathogenic bacteria, giving rise to public health concerns. Although previous studies have investigated how environmental parameters influence the microbial community of Guanabara Bay, they often have been limited to small spatial and temporal gradients and have not been integrated into predictive mathematical models. Our objective was to fill this knowledge gap by building models that could predict how temperature, salinity, phosphorus, nitrogen and transparency work together to regulate the abundance of bacteria, chlorophyll and Vibrio (a potential human pathogen) in Guanabara Bay. To that end, we built artificial neural networks to model the associations between these variables. These networks were carefully validated to ensure that they could provide accurate predictions without biases or overfitting. The estimated models displayed high predictive capacity (Pearson correlation coefficients ≥0.67 and root mean square error ≤ 0.55). Our findings showed that temperature and salinity were often the most important factors regulating the abundance of bacteria, chlorophyll and Vibrio (absolute importance ≥5) and that each of these has a unique level of dependence on nitrogen and phosphorus for their growth. These models allowed us to estimate the Guanabara Bay microbiome's response to changes in environmental conditions, which allowed us to propose strategies for the management and remediation of Guanabara Bay.
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Affiliation(s)
- F H Coutinho
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, the Netherlands; Utrecht University, Theorethical Biology and Bioinformatics, Utrecht, the Netherlands.
| | - C C Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - A S Cabral
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - R Paranhos
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - B E Dutilh
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, the Netherlands; Utrecht University, Theorethical Biology and Bioinformatics, Utrecht, the Netherlands
| | - F L Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Universidade Federal do Rio de Janeiro (UFRJ), COPPE, SAGE, Rio de Janeiro, Brazil.
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Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL. Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes. Nat Commun 2019; 10:502. [PMID: 30700713 PMCID: PMC6353887 DOI: 10.1038/s41467-018-08286-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/28/2018] [Indexed: 11/08/2022] Open
Affiliation(s)
- F H Coutinho
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, 21944970, Brazil
- Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht, 3584 CH, The Netherlands
| | - C B Silveira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, 21944970, Brazil
- Biology Department, San Diego State University (SDSU), San Diego, 92182, USA
| | - G B Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Baixada Santista, 11070100, Brazil
| | - C C Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, 21944970, Brazil
| | - R A Edwards
- Biology Department, San Diego State University (SDSU), San Diego, 92182, USA
| | - C P D Brussaard
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), Texel, 1790 AB, The Netherlands
- Department of Aquatic Microbiology, University of Amsterdam/Institute for Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, 1090 GE, The Netherlands
| | - B E Dutilh
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, 21944970, Brazil
- Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht, 3584 CH, The Netherlands
| | - F L Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, 21944970, Brazil.
- Universidade Federal do Rio de Janeiro (UFRJ)/COPPE/SAGE, Rio de Janeiro, 21941950, Brazil.
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Coutinho FH, Dutilh BE, Thompson CC, Thompson FL. Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features. Arch Microbiol 2016; 198:973-986. [PMID: 27339259 DOI: 10.1007/s00203-016-1256-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- COPPE, SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- CCS, IB, BIOMAR, Laboratório de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho. S/N, BLOCO A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, 21941-599, Brazil.
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Dutilh BE, van Noort V, van der Heijden RTJM, Boekhout T, Snel B, Huynen MA. Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 2007; 23:815-24. [PMID: 17237036 DOI: 10.1093/bioinformatics/btm015] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology. RESULTS Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content. CONCLUSIONS Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- B E Dutilh
- Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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