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Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life. mSphere 2019; 4:4/4/e00446-19. [PMID: 31462411 PMCID: PMC6714891 DOI: 10.1128/msphere.00446-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional categories as a scheme to describe the genomic contents of microbes, a method that can be applied to any microbial lineage for which genomes are available. This simple approach allows quantitative comparisons between microbial genomes with different gene compositions from across the microbial tree of life. Our observations demonstrate statistically significant patterns in cluster of orthologous group functional categories at taxonomic levels that span the range from domain to genus. Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy database, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportunity to completely separate taxonomy from traits and therefore to quantify how taxonomic rank corresponds to traits across the microbial tree of life. We quantified the relative abundances of clusters of orthologous group functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database. On average, 41.4% of the variation in COG-FC relative abundance is explained by taxonomic rank, with domain, phylum, class, order, family, and genus explaining, on average, 3.2%, 14.6%, 4.1%, 9.2%, 4.8%, and 5.5% of the variance, respectively (P < 0.001 for all). To our knowledge, this is the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. A qualitative comparison between the COG-FC relative abundances and genus-level phylogenies, generated from published concatenated protein sequence alignments, further supports the idea that metabolic potential is taxonomically coherent at higher taxonomic ranks. The quantitative analyses presented here characterize the integral relationship between diversification of microbial lineages and the metabolisms which they host. IMPORTANCE Recently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional categories as a scheme to describe the genomic contents of microbes, a method that can be applied to any microbial lineage for which genomes are available. This simple approach allows quantitative comparisons between microbial genomes with different gene compositions from across the microbial tree of life. Our observations demonstrate statistically significant patterns in cluster of orthologous group functional categories at taxonomic levels that span the range from domain to genus.
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Bühl H, Eibach D, Nagel M, Greub G, Borel N, Sarpong N, Rettig T, Pesch T, Aeby S, Klöckner A, Brunke M, Krannich S, Kreuels B, Owusu-Dabo E, Hogan B, May J, Henrichfreise B. Chlamydiae in febrile children with respiratory tract symptoms and age-matched controls, Ghana. New Microbes New Infect 2018; 22:44-48. [PMID: 29511568 PMCID: PMC5832669 DOI: 10.1016/j.nmni.2017.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/30/2017] [Accepted: 12/21/2017] [Indexed: 11/29/2022] Open
Abstract
Members of the Chlamydiales order are obligate intracellular pathogens causing acute and chronic infectious diseases. Chlamydiaceae are established agents of community- and zoonotically acquired respiratory tract infections, and emerging pathogens among the Chlamydia-related bacteria have been implicated in airway infections. The role of both in airway infections in Africa is underexplored. We performed a case -control study on the prevalence of Chlamydiaceae and Chlamydia-related emerging pathogens in children with febrile respiratory tract infections in West Africa, Ghana. Using a pan-Chlamydiales broad-range real-time PCR, we detected chlamydial DNA in 11 (1.9%) of 572 hospitalized febrile children with respiratory tract symptoms and in 24 (4.3%) of 560 asymptomatic age-matched controls (p 0.03). Chlamydiaceae were found to be common among both symptomatic and healthy Ghanaian children, with Chlamydia pneumoniae being the most prevalent species. Parachlamydiaceae were detected in two children without symptoms but not in the symptomatic group. We identified neither Chlamydia psittaci nor Simkania negevensis but a member of a new chlamydial family that shared 90.2% sequence identity with the 16S rRNA gene of the zoonotic pathogen Chlamydia pecorum. In addition, we found a new Chlamydia-related species that belonged to a novel family sharing 91.3% 16S rRNA sequence identity with Candidatus Syngnamydia venezia. The prevalence and spectrum of chlamydial species differed from previous results obtained from children of other geographic regions and our study indicates that both, Chlamydiaceae and Chlamydia-related bacteria, are not clearly linked to clinical symptoms in Ghanaian children.
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Affiliation(s)
- H Bühl
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - D Eibach
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - M Nagel
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - G Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - N Borel
- Institute of Veterinary Pathology, University of Zurich, Vetsuisse Faculty, Zurich, Switzerland
| | - N Sarpong
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany.,Agogo Presbyterian Hospital, Department of Child Health, Agogo, Ghana
| | - T Rettig
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - T Pesch
- Institute of Veterinary Pathology, University of Zurich, Vetsuisse Faculty, Zurich, Switzerland
| | - S Aeby
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - A Klöckner
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany.,German Center for Infection Research (DZIF), Bonn, Germany
| | - M Brunke
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - S Krannich
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - B Kreuels
- Division of Tropical Medicine, I. Department of Internal Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - E Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.,Department of Global Health, School of Public Health, College of Health Sciences, KNUST, Kumasi, Ghana
| | - B Hogan
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - J May
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - B Henrichfreise
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
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