1
|
Venkatachalam S, Jabir T, Vipindas PV, Krishnan KP. Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems. Appl Microbiol Biotechnol 2024; 108:128. [PMID: 38229335 DOI: 10.1007/s00253-023-12991-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/08/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.
Collapse
Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| |
Collapse
|
2
|
Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [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: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
Collapse
Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| |
Collapse
|
3
|
Whitman WB, Chuvochina M, Hedlund BP, Konstantinidis KT, Palmer M, Rodriguez‐R LM, Sutcliffe I, Wang F. Why and how to use the SeqCode. MLIFE 2024; 3:1-13. [PMID: 38827511 PMCID: PMC11139209 DOI: 10.1002/mlf2.12092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/16/2023] [Accepted: 11/01/2023] [Indexed: 06/04/2024]
Abstract
The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.
Collapse
Affiliation(s)
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandSt LuciaAustralia
| | | | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Marike Palmer
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevadaUSA
| | - Luis M. Rodriguez‐R
- Department of Microbiology and Digital Science Center (DiSC)University of InnsbruckInnsbruckAustria
| | - Iain Sutcliffe
- Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Fengping Wang
- School of Oceanography, International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina
| |
Collapse
|
4
|
Arahal D, Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Duim B, Emler S, Figge M, Göker M, Moore ERB, Nemec A, Nørskov-Lauritsen N, Nübel U, On SLW, Vandamme P, Ventosa A. The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180015 DOI: 10.1099/ijsem.0.006188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
Collapse
Affiliation(s)
- David Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | | | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, CRBIP, CIP-Collection of Institut Pasteur, F-75015 Paris, France
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, Leiden / Torensteelaan 68, 3281 MA Numansdorp, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CS Utrecht, Netherlands
| | - Stefan Emler
- SmartGene Services SARL, EPFL Innovation Park, PSE-C, CH-1015 Lausanne, Switzerland
| | - Marian Figge
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT, Utrecht, Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Srobarova 48, 100 00 Prague 10, Czech Republic
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, V Úvalu 84, 150 06 Prague 5, Czechia
| | | | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Faculty of Agricultural Science, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| |
Collapse
|
5
|
Pallen MJ. Formation of prokaryote names from personal names: a review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38226641 DOI: 10.1099/ijsem.0.006233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
The practice of naming elements from the natural world after notable individuals stretches back to ancient times. This practice of creating eponyms-terms derived from personal names-has been carried forward into prokaryotic nomenclature, where the International Code of Nomenclature of Prokaryotes (ICNP) sets guidelines for creating scientific names from personal names. However, these guidelines can be seen as culturally biased, disjointed and, on occasion, misguided. Here, with the goal of modernizing these recommendations to render them more user-friendly, coherent and inclusive, I review current practice in the light of precedents and key linguistic and cultural principles, while questioning the applicability of the first-name/last-name paradigm for many cultural traditions. Procedural challenges include romanization of the personal name (including handling of diacritics), creation of a short and agreeable latinized stem, assignment of the stem to a declension and addition of suffixes or compound word components to create genus names or species epithets, customizing the approach for names and stems that end in a vowel. I review the pros and cons of stem augmentation, which involves addition of an extra 'i' to the original stem. Next, I formulate a coherent workflow, which I incorporate into a Python script to enable computer-based automation of name creation. Rather than following the ICNP in limiting discussion to a few dozen mainly European names, I examine how these principles work out when applied to the tens of thousands of last names under which scientists publish in the PubMed database, focusing on edge cases where conventional approaches fail, particularly very short and very long names. Drawing on these explorations and analyses, I propose emendations to the advice currently presented in the ICNP to usher in a modern, consistent, pragmatic and globally inclusive approach to the creation of prokaryotic eponyms.
Collapse
Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
6
|
Bowman JP, Hugo C, Nicholson A, Hahnke R, Lau EF, Holmes B, Sutcliffe I. International Committee on Systematics of Prokaryotes: Subcommittee on the taxonomy of aerobic Bacteroidota. Minutes of the online meeting 25 April 2023. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917547 DOI: 10.1099/ijsem.0.006144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Celia Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Ainsley Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Richard Hahnke
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Ellen Frandsen Lau
- Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
| | - Barry Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle Upon Tyne, Tyne & Wear, UK
| |
Collapse
|
7
|
Kaminsky RA, Reid PM, Altermann E, Kenters N, Kelly WJ, Noel SJ, Attwood GT, Janssen PH. Rumen Lachnospiraceae isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen. Appl Environ Microbiol 2023; 89:e0063423. [PMID: 37800930 PMCID: PMC10617493 DOI: 10.1128/aem.00634-23] [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: 04/16/2023] [Accepted: 08/08/2023] [Indexed: 10/07/2023] Open
Abstract
Hydrogen (H2) is the primary electron donor for methane formation in ruminants, but the H2-producing organisms involved are largely uncharacterized. This work integrated studies of microbial physiology and genomics to characterize rumen bacterial isolate NK3A20 of the family Lachnospiraceae. Isolate NK3A20 was the first recognized isolate of the NK3A20 group, which is among the ten most abundant bacterial genera in 16S rRNA gene surveys of rumen microbiota. NK3A20 produced acetate, butyrate, H2, and formate from glucose. The end product ratios varied when grown with different substrates and at different H2 partial pressures. NK3A20 produced butyrate as a major product using glucose or under high H2 partial pressures and switched to mainly acetate in the presence of galacturonic acid (an oxidized sugar) or in coculture with a methanogen. Growth with galacturonic acid was faster at elevated H2 concentrations, while elevated H2 slowed growth with glucose. Genome analyses revealed the presence of multiple hydrogenases including a membrane-bound Ech hydrogenase, an electron bifurcating butyryl-CoA dehydrogenase (Bcd-Etf), and an Rnf complex that may be involved in modulating the observed metabolic pathway changes, providing insight into H2 formation in the rumen. IMPORTANCE The genus-level NK3A20 group is one of the ten most abundant genera of rumen bacteria. Like most of the rumen bacteria that produce the hydrogen that is converted to methane in the rumen, it is understudied, without any previously characterized isolates. We investigated isolate NK3A20, a cultured member of this genus, and showed that it modulates hydrogen production in response to its growth substrates and the hydrogen concentration in its environment. Low-hydrogen concentrations stimulated hydrogen formation, while high concentrations inhibited its formation and shifted the fermentation to more reduced organic acid products. We found that growth on uronic acids, components of certain plant polymers, resulted in low hydrogen yields compared to glucose, which could aid in the selection of low-methane feeds. A better understanding of the major genera that produce hydrogen in the rumen is part of developing strategies to mitigate biogenic methane emitted by livestock agriculture.
Collapse
Affiliation(s)
- Rachel A. Kaminsky
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter M. Reid
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Nikki Kenters
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J. Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Samantha J. Noel
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T. Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| |
Collapse
|
8
|
On SLW. Minutes of the inaugural 25 October 2022 meeting of International Committee on Systematics of Prokaryotes (ICSP) Subcommittees on Taxonomy representatives: challenges, trends, and perspectives for microbial taxonomists. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787396 DOI: 10.1099/ijsem.0.006075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Affiliation(s)
- Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| |
Collapse
|
9
|
Vigneron A, Vincent WF, Lovejoy C. Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog. ISME COMMUNICATIONS 2023; 3:82. [PMID: 37596370 PMCID: PMC10439189 DOI: 10.1038/s43705-023-00287-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/20/2023]
Abstract
Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.
Collapse
Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
| |
Collapse
|
10
|
Bowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37589187 DOI: 10.1099/ijsem.0.005991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.
Collapse
Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania, 7005, Australia
| |
Collapse
|
11
|
Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol 2023; 5:acmi000558.v3. [PMID: 37424544 PMCID: PMC10323806 DOI: 10.1099/acmi.0.000558.v3] [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: 01/09/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Background The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva. Results Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts. Conclusions Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.
Collapse
Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mina E. Adam
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Bhaskar Kumar
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
12
|
Sreya P, Suresh G, Rai A, Ria B, Vighnesh L, Agre VC, Jagadeeshwari U, Sasikala C, Ramana CV. Revisiting the taxonomy of the genus Rhodopirellula with the proposal for reclassification of the genus to Rhodopirellula sensu stricto, Aporhodopirellula gen. nov., Allorhodopirellula gen. nov. and Neorhodopirellula gen. nov. Antonie Van Leeuwenhoek 2023; 116:243-264. [PMID: 36547858 DOI: 10.1007/s10482-022-01801-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The current genus Rhodopirellula consists of marine bacteria which belong to the family Pirellulaceae of the phylum Planctomycetota. Members of the genus Rhodopirellula are aerobic, mesophiles and chemoheterotrophs. The here conducted analysis built on 16S rRNA gene sequence and multi-locus sequence analysis based phylogenomic trees suggested that the genus is subdivided into four clades. Existing Rhodopirellula species were studied extensively based on phenotypic, genomic and chemotaxonomic parameters. The heterogeneity was further confirmed by overall genome-related indices (OGRI) including digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and percentage of conserved proteins (POCP). AAI and POCP values between the clades of the genus Rhodopirellula were 62.2-69.6% and 49.5-62.5%, respectively. Comparative genomic approaches like pan-genome analysis and conserved signature indels (CSIs) also support the division of the clades. The genomic incoherence of the members of the genus is further supported by variations in phenotypic characteristics. Thus, with the here applied integrated comparative genomic and polyphasic approaches, we propose the reclassification of the genus Rhodopirellula to three new genera: Aporhodopirellula gen. nov., Allorhodopirellula gen. nov., and Neorhodopirellula gen. nov.
Collapse
Affiliation(s)
- Pannikurungottu Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Lakshmanan Vighnesh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Vaibhav Chandrakant Agre
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India.
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India.
| |
Collapse
|
13
|
Oren A. Naming new taxa of prokaryotes in the 21st century. Can J Microbiol 2023; 69:151-157. [PMID: 36852830 DOI: 10.1139/cjm-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.
Collapse
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| |
Collapse
|
14
|
Kannan S, Sharma S, Ciufo S, Clark K, Turner S, Kitts PA, Schoch CL, DiCuccio M, Kimchi A. Collection and curation of prokaryotic genome assemblies from type strains at NCBI. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748495 DOI: 10.1099/ijsem.0.005707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
Collapse
Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Shobha Sharma
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Seán Turner
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Avi Kimchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| |
Collapse
|