1
|
Borowiaka M, Kreitlow A, Malorny B, Lämmler C, Rau J, Plötz M, Abdulmawjood A. Complete genome sequence of Arcanobacterium wilhelmae strain DSM 102162 isolated from the genital tract of a Rhinoceros unicornis. Microbiol Resour Announc 2024:e0020424. [PMID: 39023269 DOI: 10.1128/mra.00204-24] [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: 03/05/2024] [Accepted: 05/23/2024] [Indexed: 07/20/2024] Open
Abstract
Previous case reports indicate Arcanobacterium's opportunistic pathogenic potential. However, the true diversity of the genus remains understudied. Here, we present the complete genome of Arcanobacterium wilhelmae isolated from a diseased rhinoceros, suspected to play a role in its condition. These genomic data may enable future advancements in understanding Arcanobacterium pathogenicity.
Collapse
Affiliation(s)
- Maria Borowiaka
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Christoph Lämmler
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Jörg Rau
- Chemisches und Veterinärunterschungsamt Stuttgart (CVUAS), Fellbach, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| |
Collapse
|
2
|
Jiao JY, Abdugheni R, Zhang DF, Ahmed I, Ali M, Chuvochina M, Dedysh SN, Dong X, Göker M, Hedlund BP, Hugenholtz P, Jangid K, Liu SJ, Moore ERB, Narsing Rao MP, Oren A, Rossello-Mora R, Rekadwad BN, Salam N, Shu W, Sutcliffe IC, Teo WFA, Trujillo ME, Venter SN, Whitman WB, Zhao G, Li WJ. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. Natl Sci Rev 2024; 11:nwae168. [PMID: 39071100 PMCID: PMC11275469 DOI: 10.1093/nsr/nwae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 07/30/2024] Open
Abstract
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
Collapse
Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig D-38124, Germany
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Kamlesh Jangid
- Bioenergy Group, MACS Collection of Microorganisms, Agharkar Research Institute, Pune 411004, India
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Edward R B Moore
- Department of Infectious Disease, Institute for Biomedicine, and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40234, Sweden
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles 070190, Spain
| | - Bhagwan Narayan Rekadwad
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nimaichand Salam
- National Agri-Food Biotechnology Institute, Knowledge City, Mohali 140306, India
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca 37008, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| |
Collapse
|
3
|
Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024; 12:e0402123. [PMID: 38661349 PMCID: PMC11237764 DOI: 10.1128/spectrum.04021-23] [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: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
Collapse
Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| |
Collapse
|
4
|
Botero J, Peeters C, De Canck E, Laureys D, Vandamme P. Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees. Int J Syst Evol Microbiol 2024; 74. [PMID: 38833293 DOI: 10.1099/ijsem.0.006409] [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: 06/06/2024] Open
Abstract
Strain LMG 33000T was isolated from a Bombus lapidarius gut sample. It shared the highest percentage 16S rRNA sequence identity, average amino acid identity, and amino acid identity of conserved genes with Convivina intestini LMG 28291T (95.86 %, 69.9 and 76.2 %, respectively), and the highest percentage OrthoANIu value with Fructobacillus fructosus DSM 20349T (71.4 %). Phylogenomic analyses by means of 107 or 120 conserved genes consistently revealed Convivina as nearest neighbour genus. The draft genome of strain LMG 33000T was 1.44 Mbp in size and had a DNA G+C content of 46.1 mol%. Genomic and physiological analyses revealed that strain LMG 33000T was a typical obligately fructophilic lactic acid bacterium that lacked the adhE and aldh genes and that did not produce ethanol during glucose or fructose metabolism. In contrast, Convivina species have the adhE and aldh genes in their genomes and produced ethanol from glucose and fructose metabolism, which is typical for heterofermentative lactic acid bacteria. Moreover, strain LMG 33000T exhibited catalase activity, an unusual characteristic among lactic acid bacteria, that is not shared with Convivina species. Given its position in the phylogenomic trees, and the difference in genomic percentage G+C content and in physiological and metabolic characteristics between strain LMG 33000T and Convivina species, we considered it most appropriate to classify strain LMG 33000T into a novel genus and species within the Lactobacillaceae family for which we propose the name Eupransor demetentiae gen. nov., sp. nov., with LMG 33000T (=CECT 30958T) as the type strain.
Collapse
Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
5
|
Botero J, Peeters C, De Canck E, Laureys D, Wieme AD, Cleenwerck I, Depoorter E, Praet J, Michez D, Smagghe G, Vandamme P. A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees. Syst Appl Microbiol 2024; 47:126505. [PMID: 38564984 DOI: 10.1016/j.syapm.2024.126505] [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: 01/18/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.
Collapse
Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000 Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| |
Collapse
|
6
|
Koga R, Moriyama M, Nozaki T, Fukatsu T. Genome analysis of " Candidatus Aschnera chinzeii," the bacterial endosymbiont of the blood-sucking bat fly Penicillidia jenynsii (Insecta: Diptera: Nycteribiidae). Front Microbiol 2024; 14:1336919. [PMID: 38318130 PMCID: PMC10841577 DOI: 10.3389/fmicb.2023.1336919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
Insect-microbe endosymbiotic associations are omnipresent in nature, wherein the symbiotic microbes often play pivotal biological roles for their host insects. In particular, insects utilizing nutritionally imbalanced food sources are dependent on specific microbial symbionts to compensate for the nutritional deficiency via provisioning of B vitamins in blood-feeding insects, such as tsetse flies, lice, and bedbugs. Bat flies of the family Nycteribiidae (Diptera) are blood-sucking ectoparasites of bats and shown to be associated with co-speciating bacterial endosymbiont "Candidatus Aschnera chinzeii," although functional aspects of the microbial symbiosis have been totally unknown. In this study, we report the first complete genome sequence of Aschnera from the bristled bat fly Penicillidia jenynsii. The Aschnera genome consisted of a 748,020 bp circular chromosome and a 18,747 bp circular plasmid. The chromosome encoded 603 protein coding genes (including 3 pseudogenes), 33 transfer RNAs, and 1 copy of 16S/23S/5S ribosomal RNA operon. The plasmid contained 10 protein coding genes, whose biological function was elusive. The genome size, 0.77 Mbp, was drastically reduced in comparison with 4-6 Mbp genomes of free-living γ-proteobacteria. Accordingly, the Aschnera genome was devoid of many important functional genes, such as synthetic pathway genes for purines, pyrimidines, and essential amino acids. On the other hand, the Aschnera genome retained complete or near-complete synthetic pathway genes for biotin (vitamin B7), tetrahydrofolate (vitamin B9), riboflavin (vitamin B2), and pyridoxal 5'-phosphate (vitamin B6), suggesting that Aschnera provides these vitamins and cofactors that are deficient in the blood meal of the host bat fly. Similar retention patterns of the synthetic pathway genes for vitamins and cofactors were also observed in the endosymbiont genomes of other blood-sucking insects, such as Riesia of human lice, Arsenophonus of louse flies, and Wigglesworthia of tsetse flies, which may be either due to convergent evolution in the blood-sucking host insects or reflecting the genomic architecture of Arsenophonus-allied bacteria.
Collapse
Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Tomonari Nozaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
7
|
Borowiak M, Kreitlow A, Malorny B, Lämmler C, Prenger-Berninghoff E, Plötz M, Abdulmawjood A. Arcanobacterium canis strain DSM 25104 isolated from an English bulldog suffering from otitis externa: complete genome sequence. Microbiol Resour Announc 2024; 13:e0062423. [PMID: 38099684 DOI: 10.1128/mra.00624-23] [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: 07/12/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
Many species of the genus Arcanobacterium are known as opportunistic pathogens and have been isolated in association with infectious diseases in humans and animals. Here, we present the complete genome sequence of another opportunistic pathogenic representative, namely Arcanobacterium canis, isolated from the otitis externa of an English bulldog.
Collapse
Affiliation(s)
- Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR) , Berlin, Germany
| | - Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR) , Berlin, Germany
| | - Christoph Lämmler
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen, Germany
| | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
| |
Collapse
|
8
|
Faist H, Ankenbrand MJ, Sickel W, Hentschel U, Keller A, Deeken R. Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization. Genome Biol Evol 2023; 15:evad228. [PMID: 38085065 PMCID: PMC10745273 DOI: 10.1093/gbe/evad228] [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] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA. The expression of oncogenes in transformed host cells induces unregulated cell proliferation and metabolic and physiological changes. The crown gall produces opines uncommon to plants, which provide an important nutrient source for A. vitis harboring opine catabolism enzymes. Crown galls host a distinct bacterial community, and the mechanisms establishing a crown gall-specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the tumor-inducing plasmid coexist in the genomes of the microbial species coexisting in crown galls. We isolated 8 bacterial strains from grapevine crown galls, sequenced their genomes, and tested their virulence and opine utilization ability in bioassays. In addition, the 8 genome sequences were compared with 34 published bacterial genomes, including closely related plant-associated bacteria not from crown galls. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. In contrast, homologs of the opine catabolism genes were present in all strains including the nonvirulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighborhood and sequence identity of the opine degradation cluster of virulent and nonvirulent strains together with the results of the opine utilization assay support the important role of opine utilization for cocolonization in crown galls, thereby shaping the crown gall community.
Collapse
Affiliation(s)
- Hanna Faist
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln 3430, Austria
- Julius-von-Sachs Institute for Biological Sciences, Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg 97082, Germany
| | - Markus J Ankenbrand
- Faculty of Biology, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg 97074, Germany
| | - Wiebke Sickel
- Institute of Biodiversity, Thuenen-Institute of Biodiversity, Braunschweig 38116, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
- Sektion Biologie, Christian-Albrechts University of Kiel, Kiel 24105, Germany
| | - Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Rosalia Deeken
- Julius-von-Sachs Institute for Biological Sciences, Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg 97082, Germany
| |
Collapse
|
9
|
de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
Collapse
Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| |
Collapse
|
10
|
Anda M, Yamanouchi S, Cosentino S, Sakamoto M, Ohkuma M, Takashima M, Toyoda A, Iwasaki W. Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nat Commun 2023; 14:7232. [PMID: 37963895 PMCID: PMC10645730 DOI: 10.1038/s41467-023-42681-w] [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: 02/13/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.
Collapse
Affiliation(s)
- Mizue Anda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Salvatore Cosentino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masako Takashima
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Institute for Quantitative Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| |
Collapse
|
11
|
Tian R, Imanian B. VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution. MICROBIOME 2023; 11:247. [PMID: 37936197 PMCID: PMC10631056 DOI: 10.1186/s40168-023-01705-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene's 'phylogenetic fidelity' unexamined. RESULTS From 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene's phylogenetic fidelity by comparing each gene's phylogeny with its corresponding 16S rRNA gene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Compared to the larger gene set, the 20-gene core set resulted in more species having all genes present and fewer species with missing data, thereby enhancing the accuracy of phylogenomic analysis. Using Escherichia coli strains as examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while 16S rRNA gene tree alone could not. CONCLUSION The 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution. Video Abstract.
Collapse
Affiliation(s)
- Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA
| | - Behzad Imanian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA.
- Food Science and Nutrition Department, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| |
Collapse
|
12
|
Miyazaki U, Sanari M, Tame A, Kitajima M, Okamoto A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Pyrofollis japonicus gen. nov. sp. nov., a novel member of the family Pyrodictiaceae isolated from the Iheya North hydrothermal field. Extremophiles 2023; 27:28. [PMID: 37843723 DOI: 10.1007/s00792-023-01316-0] [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: 07/31/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023]
Abstract
A novel hyperthermophilic, heterotrophic archaeon, strain YC29T, was isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough, Japan. Cells of strain YC29T were non-motile, irregular cocci with diameters of 1.2-3.0 µm. The strain was an obligatory fermentative anaerobe capable of growth on complex proteinaceous substrates. Growth was observed between 85 and 100 °C (optimum 90-95 °C), pH 4.9-6.4 (optimum 5.1), and in the presence of 1.4-4.0% (w/v) NaCl (optimum 3.0%). Inorganic carbon was required as a carbon source. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the family Pyrodictiaceae. The genome size was 2.02 Mbp with a G+C content of 49.4%. The maximum values for average nucleotide identity (ANI), average amino acid identity (AAI), and in silico DNA-DNA hybridization (dDDH) value of strain YC29T with relatives were 67.9% (with Pyrodictium abyssi strain AV2T), 61.1% (with Pyrodictium occultum strain PL-19T), and 33.8% (with Pyrolobus fumarii strain 1AT), respectively. Based on the phylogenetic, genomic, and phenotypic characteristics, we propose that strain YC29T represents a novel genus and species, Pyrofollis japonicus gen. nov., sp. (type strain YC29T = DSM 113394T = JCM 39171T).
Collapse
Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Masaru Sanari
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Department of Marine and Earth Sciences, Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-Ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-Ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
| |
Collapse
|
13
|
Zhang DF, He W, Shao Z, Ahmed I, Zhang Y, Li WJ, Zhao Z. EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. BMC Bioinformatics 2023; 24:390. [PMID: 37838689 PMCID: PMC10576351 DOI: 10.1186/s12859-023-05527-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. RESULTS EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson-Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines. CONCLUSIONS EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).
Collapse
Affiliation(s)
- Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China.
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Zongze Shao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China.
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Iftikhar Ahmed
- National Agricultural Research Centre (NARC), Land Resources Research Institute (LRRI), National Culture Collection of Pakistan (NCCP), Islamabad, 45500, Pakistan
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China
| |
Collapse
|
14
|
Hettiarachchi A, Cnockaert M, Joossens M, Laureys D, De Clippeleer J, Vereecken NJ, Michez D, Smagghe G, de Graaf DC, Vandamme P. Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina. INSECT MOLECULAR BIOLOGY 2023; 32:510-527. [PMID: 37204105 DOI: 10.1111/imb.12847] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023]
Abstract
We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.
Collapse
Affiliation(s)
- Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
15
|
Vargas C, Bautista D, Jimenez H, Soto-Suarez M, Restrepo S, Gonzalez C, Zuluaga P. Complete genome sequence of Pediococcus acidilactici A40, a bacterium with biocontrol and plant growth-promoting properties. Microbiol Resour Announc 2023; 12:e0053023. [PMID: 37578226 PMCID: PMC10508112 DOI: 10.1128/mra.00530-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
We report the complete genome assembly of Pediococcus acidilactici A40, a bacterium with biocontrol and plant growth-promoting properties, obtained from Colombia.
Collapse
Affiliation(s)
- Christian Vargas
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Bogotá, Colombia
| | | | - Hugo Jimenez
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Bogotá, Colombia
| | - Mauricio Soto-Suarez
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Bogotá, Colombia
| | | | - Carolina Gonzalez
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Bogotá, Colombia
| | - Paola Zuluaga
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Bogotá, Colombia
| |
Collapse
|
16
|
Sombolestani AS, Bongaerts D, Depoorter E, Cleenwerck I, Wieme AD, Britton SJ, Weckx S, De Vuyst L, Vandamme P. Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages. Syst Appl Microbiol 2023; 46:126440. [PMID: 37429096 DOI: 10.1016/j.syapm.2023.126440] [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: 03/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
Polyphasic taxonomic and comparative genomic analyses revealed that a series of lambic beer isolates including strain LMG 32668T and the kombucha isolate LMG 32879 represent a novel species among the acetic acid bacteria, with Acidomonas methanolica as the nearest phylogenomic neighbor with a valid name. Overall genomic relatedness indices and phylogenomic and physiological analyses revealed that this novel species was best classified in a novel genus for which we propose the name Brytella acorum gen. nov., sp. nov., with LMG 32668T (=CECT 30723T) as the type strain. The B. acorum genomes encode a complete but modified tricarboxylic acid cycle, and complete pentose phosphate, pyruvate oxidation and gluconeogenesis pathways. The absence of 6-phosphofructokinase which rendered the glycolysis pathway non-functional, and an energy metabolism that included both aerobic respiration and oxidative fermentation are typical metabolic characteristics of acetic acid bacteria. Neither genome encodes nitrogen fixation or nitrate reduction genes, but both genomes encode genes for the biosynthesis of a broad range of amino acids. Antibiotic resistance genes or virulence factors are absent.
Collapse
Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dries Bongaerts
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Scott J Britton
- Department of Research & Development, Brewery Duvel Moortgat, 2870 Puurs-Sint-Amands, Belgium; International Centre for Brewing and Distilling, Institute of Biological Chemistry, Biophysics, and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, United Kingdom
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| |
Collapse
|
17
|
Gulay A, Fournier G, Smets BF, Girguis PR. Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation. Mol Biol Evol 2023; 40:msad161. [PMID: 37440531 PMCID: PMC10415592 DOI: 10.1093/molbev/msad161] [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: 03/03/2023] [Revised: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.
Collapse
Affiliation(s)
- Arda Gulay
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Greg Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| |
Collapse
|
18
|
Buzzanca D, Kerkhof PJ, Alessandria V, Rantsiou K, Houf K. Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness. Heliyon 2023; 9:e17652. [PMID: 37449094 PMCID: PMC10336517 DOI: 10.1016/j.heliyon.2023.e17652] [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: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.
Collapse
Affiliation(s)
- Davide Buzzanca
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Pieter-Jan Kerkhof
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
19
|
Botero J, Sombolestani AS, Cnockaert M, Peeters C, Borremans W, De Vuyst L, Vereecken NJ, Michez D, Smagghe G, Bonilla-Rosso G, Engel P, Vandamme P. A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont. Anim Microbiome 2023; 5:25. [PMID: 37120592 PMCID: PMC10149009 DOI: 10.1186/s42523-023-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis. RESULTS The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont. CONCLUSION The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.
Collapse
Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles, Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - German Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| |
Collapse
|
20
|
Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nat Microbiol 2023; 8:727-744. [PMID: 36928026 PMCID: PMC10066038 DOI: 10.1038/s41564-022-01319-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023]
Abstract
Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
Collapse
|
21
|
Vandamme P, Peeters C, Hettiarachchi A, Cnockaert M, Carlier A. Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria. Syst Appl Microbiol 2023; 46:126405. [PMID: 36905873 DOI: 10.1016/j.syapm.2023.126405] [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: 01/20/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/07/2023]
Abstract
Strain LMG 31809 T was isolated from a top soil sample of a temperate, mixed deciduous forest in Belgium. Comparison of its 16S rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class Alphaproteobacteria and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders Emcibacterales and Sphingomonadales. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which Acidobacteria and Alphaproteobacteria predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 T. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 T represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 T as a novel species within a novel genus, Govania unica gen. nov., sp. nov, within the novel family Govaniaceae of the class Alphaproteobacteria. Its type strain is LMG 31809 T (=CECT 30155 T). The whole-genome sequence of strain LMG 31809 T has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 T are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively.
Collapse
Affiliation(s)
- Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| |
Collapse
|
22
|
Guzman J, Won M, Poehlein A, Sombolestani AS, Mayorga-Ch D, Laureys D, Clippeleer JD, Kämpfer P, Daniel R, Vilcinskas A, Vandamme P, Kwon SW. Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749681 DOI: 10.1099/ijsem.0.005699] [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: 02/08/2023] Open
Abstract
Acetic acid bacteria (family Acetobacteraceae) are found in the gut of most insects. Two clades are currently recognized: Commensalibacter-Entomobacter and Bombella-Oecophyllibacter. The latter group is only found in hymenopteran insects and the described species have been isolated from bees and ants. In this study, two new strains DDB2-T1T (=KACC 21507T=LMG 31759T) and DM15PD (=CCM 9165=DSM 112731=KACC 22353=LMG 32454) were isolated from wasps collected in the Republic of Korea and Germany, respectively. Molecular and phenotypic analysis revealed that the strains are closely related, with 16S rRNA gene sequences showing 100 % identity and genomic average nucleotide identity (ANI) values ≥99 %. The closest related species based on type strain 16S rRNA gene sequences are Swingsia samuiensis, Acetobacter peroxydans, Bombella favorum and Bombella intestini (94.8-94.7% identity), whereas the closest related species based on type strain genome analysis are Saccharibacter floricola and Bombella intestini (ANI values of 68.8 and 68.2 %, respectively). The reconstruction of a phylogenomic tree based on 107 core proteins revealed that the branch leading to DDB2-T1T and DM15PD is localized between Oecophyllibacter and Saccharibacter-Bombella. Further genomic distance metrics such as ANI, percentage of conserved proteins and alignment fraction values were consistent with these strains belonging to a new genus. The key phenotypic characteristics were one MALDI-TOF-MS peak (m/z=4601.9±2.0) and the ability to produce acid from d-arabinose. Based on this polyphasic approach, including phylogenetics, phylogenomics, genome distance calculations, ecology and phenotypic characteristics, we propose to name the novel strains Aristophania vespae gen. nov., sp. nov., with the type strain DDB2-T1T (=KACC 21507T=LMG 31759T).
Collapse
Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daniela Mayorga-Ch
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - David Laureys
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| |
Collapse
|
23
|
Maranha A, Costa M, Ripoll-Rozada J, Manso JA, Miranda V, Mendes VM, Manadas B, Macedo-Ribeiro S, Ventura MR, Pereira PJB, Empadinhas N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 2023; 6:108. [PMID: 36707645 PMCID: PMC9883506 DOI: 10.1038/s42003-023-04448-3] [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: 05/20/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) so far detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria such as Mycobacterium avium, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a previously undescribed α-endomannosidase that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1→4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, whose disruption affected mycobacterial growth rate at low temperature.
Collapse
Affiliation(s)
- Ana Maranha
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mafalda Costa
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jorge Ripoll-Rozada
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal ,grid.507090.b0000 0004 5303 6218Present Address: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, Spain
| | - José A. Manso
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vanessa Miranda
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Vera M. Mendes
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - M. Rita Ventura
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro José Barbosa Pereira
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Empadinhas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| |
Collapse
|
24
|
Arcanobacterium pinnipediorum Strain DSM 28752 Isolated from a Harbour Seal: Complete Genome Sequence. Microbiol Resour Announc 2023; 12:e0118022. [PMID: 36598257 PMCID: PMC9872578 DOI: 10.1128/mra.01180-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genus Arcanobacterium is constantly growing as novel species are identified. In particular, harbor seals have proven to be a common reservoir for bacteria of this genus. Here, we announce the complete genome sequence of another Arcanobacterium species-namely, Arcanobacterium pinnipediorum strain DSM 28752, isolated from a harbor seal.
Collapse
|
25
|
Lynch C, Peeters C, Walsh N, McCarthy C, Coffey A, Lucey B, Vandamme P. Campylobacter majalis sp. nov. and Campylobacter suis sp. nov., novel Campylobacter species isolated from porcine gastrointestinal mucosa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748456 DOI: 10.1099/ijsem.0.005510] [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: 12/14/2022] Open
Abstract
Strains LMG 7974T and LMG 8286T represent single, novel Campylobacter lineages with Campylobacter pinnipediorum and Campylobacter mucosalis as nearest phylogenomic neighbours, respectively. The results of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses of LMG 7974T, LMG 8286T and type strains of species of the genus Campylobacter confirmed that these strains represent novel species of the genus Campylobacter. The 16S rRNA gene sequences of both strains showed highest identity towards C. mucosalis (97.84 and 98.74 %, respectively). Strains LMG 7974T and LMG 8286T shared 72.5 and 73.7% ANI, respectively, with their nearest phylogenomic neighbours and less than 21 % dDDH. The draft genome sizes of LMG 7974T and LMG 8286T are 1 945429 bp and 1 708214 bp in length with percentage DNA G+C contents of 33.8 and 37.2 %, respectively. Anomalous biochemical characteristics and low MALDI-TOF mass spectrometry log scores supported their designation as representing novel species of the genus Campylobacte. We therefore propose to classify strain LMG 7974T (=CCUG 20705T) as the type strain of the novel species Campylobacter majalis sp. nov. and strain LMG 8286T (=CCUG 24193T, NCTC 11879T) as the type strain of the novel species Campylobacter suis sp. nov.
Collapse
Affiliation(s)
- Caoimhe Lynch
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Niamh Walsh
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Conor McCarthy
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
26
|
Urvashi, Gundawar K, Sharma S, Choksket S, Sharma M, Grover V, Patil PB, Korpole S. Lacrimispora defluvii PI-S10-B5AT sp. nov., an Obligate Anaerobe, Isolated from an Industrial Waste and Reclassification of Hungatella xylanolytica as Lacrimispora xylanolytica and Clostridium indicum as Lacrimispora indica Comb. nov. Curr Microbiol 2022; 79:397. [DOI: 10.1007/s00284-022-03096-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
|
27
|
Zhu J, Chen Y, Wu Y, Wang Y, Zhu K. Commensal bacteria contribute to the growth of multidrug-resistant Avibacterium paragallinarum in chickens. Front Microbiol 2022; 13:1010584. [PMID: 36406434 PMCID: PMC9672371 DOI: 10.3389/fmicb.2022.1010584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/03/2022] [Indexed: 07/30/2024] Open
Abstract
Avibacterium paragallinarum-associated infectious coryza (IC) is an important threat in commercial poultry. Previous studies about the characteristics of A. paragallinarum are succeeded in revealing the course of IC disease, but whether and how resident microbes contribute to the infection remains unclear. To understand the role of commensal bacteria, we isolated 467 commensal bacteria, including 38 A. paragallinarum, from the respiratory tract of IC chicken. The predominant commensal isolates were Gram-positive bacteria belonging to Staphylococcus spp. [33.19%, 95% confidence interval (CI): 28.93-37.66%], Enterococcus spp. (16.49%, 95% CI: 13.23-20.17%), and Bacillus spp. (16.27%, 95% CI: 13.04-19.94%). These isolates were closely correlated with the survival of A. paragallinarum. We examined and found that commensal bacteria aggravate A. paragallinarum-associated infections because certain commensal species (28.57%, 95% CI: 15.72-44.58%) induced hemolysis and promoted the growth of A. paragallinarum in vitro. Notably, A. paragallinarum showed high resistance to routine antibiotics such as erythromycin (84.21%, 95% CI: 68.75-93.98%), tetracycline (73.68%, 95% CI: 56.90-86.60%) and carried diverse mobile resistance gene clusters. Overall, we found commensal bacteria especially Gram-positive bacteria facilitate the survival of multidrug-resistant A. paragallinarum to exacerbate infections, suggesting that novel strategies may diminish A. paragallinarum-associated infections by modulating the population dynamics of commensal bacteria.
Collapse
Affiliation(s)
- Jiajia Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yunsheng Chen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yifan Wu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongqiang Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
28
|
Wang S, Li G, Liao Z, Liu T, Ma T. A novel alkane monooxygenase ( alkB) clade revealed by massive genomic survey and its dissemination association with IS elements. PeerJ 2022; 10:e14147. [PMID: 36193440 PMCID: PMC9526415 DOI: 10.7717/peerj.14147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.
Collapse
Affiliation(s)
- Shaojing Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guoqiang Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Zitong Liao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Tongtong Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
29
|
Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
Collapse
Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
30
|
Guzman J, Poehlein A, Glaeser SP, Schwengers O, Blom J, Hollensteiner J, Kämpfer P, Vilcinskas A. Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterial strain, G163CMT, was isolated from the gut of the Asian emerald cockroach Corydidarum magnifica. The 16S rRNA gene sequence (1416 bp) of strain G163CMT showed 99.22% similarity to
Pseudocitrobacter faecalis
CCM 8479T and
Pseudocitrobacter vendiensis
CPO20170097T. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values of strain G163CMT were 92.4, 48.8 and 95.7% to
P. faecalis
CCM 8479T, and 93.3, 52.4 and 95.7% to
P. vendiensis
CPO20170097T. This strongly supports the designation of G163CMT as representing a new species in the genus
Pseudocitrobacter
. Phylogenetic trees based on the alignment of 16S rRNA, multilocus sequence analysis of six single-copy genes (fusA, pyrG, leuS, rpoB, recN and mnmE) and 107 core protein sequences consistently showed G163CMT to be a member of the genus
Pseudocitrobacter
, closely related to
P. vendiensis
CPO20170097T. In contrast to
P. faecalis
CCM 8479T and
P. vendiensis
CPO20170097T, the genome of G163CMT did not encode for proteins conferring resistance to antibiotics. However, all three genomes encoded a similar number of virulence factors and specialized metabolite biosynthetic proteins. The major fatty acids of strain G163CMT were C16:0 (31.5 %), C18:1 ω7c (22.6 %), C17:0 cyclo (15.3 %) and C14:0 (6.5 %). Based on the polyphasic results, we conclude that strain G163CMT represents a novel species of the genus
Pseudocitrobacter
and we propose the name Pseudocitrobacter corydidari sp. nov. with the type strain G163CMT (=DSM 112648T=CCM 9160T).
Collapse
Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Jacqueline Hollensteiner
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| |
Collapse
|
31
|
Van Dingenen J, Garcia Mendez S, Beirinckx S, Vlaminck L, De Keyser A, Stuer N, Verschaete S, Clarysse A, Pannecoucque J, Rombauts S, Roldan-Ruiz I, Willems A, Goormachtig S. Flemish soils contain rhizobia partners for Northwestern Europe-adapted soybean cultivars. Environ Microbiol 2022; 24:3334-3354. [PMID: 35212122 DOI: 10.1111/1462-2920.15941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 11/28/2022]
Abstract
In Europe, soybean (Glycine max) used for food and feed has to be imported, causing negative socioeconomic and environmental impacts. To increase the local production, breeding generated varieties that grow in colder climates, but the yield using the commercial inoculants is not satisfactory in Belgium because of variable nodulation efficiencies. To look for indigenous nodulating strains possibly adapted to the local environment, we initiated a nodulation trap by growing early-maturing cultivars under natural and greenhouse conditions in 107 garden soils in Flanders. Nodules occurred in 18 and 21 soils in the garden and greenhouse experiments respectively. By combining 16S rRNA PCR on single isolates with HiSeq 16S metabarcoding on nodules, we found a large bacterial richness and diversity from different soils. Furthermore, using Oxford Nanopore Technologies sequencing of DNA from one nodule, we retrieved the entire genome of a Bradyrhizobium species, not previously isolated, but profusely present in that nodule. These data highlight the need of combining diverse identification techniques to capture the true nodule rhizobial community. Eight selected rhizobial isolates were subdivided by whole-genome analysis in three genera containing six genetically distinct species that, except for two, aligned with known type strains and were all able to nodulate soybean in the laboratory.
Collapse
Affiliation(s)
- Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Sonia Garcia Mendez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, 9000, Belgium
| | - Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Lena Vlaminck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Severine Verschaete
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Alexander Clarysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Joke Pannecoucque
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, 9820, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, 9820, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, 9000, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| |
Collapse
|
32
|
Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022; 11:e1298. [PMID: 35765182 PMCID: PMC9179125 DOI: 10.1002/mbo3.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.
Collapse
Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| |
Collapse
|
33
|
Complete Genome Sequence of an Aeromonas rivuli Strain Isolated from Ready-to-Eat Food. Microbiol Resour Announc 2022; 11:e0113021. [PMID: 35442062 PMCID: PMC9119039 DOI: 10.1128/mra.01130-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Aeromonads can be associated with diseases in animals and humans. Knowledge regarding Aeromonas rivuli, a species recently discovered in creek water in Germany, is still fragmentary. Here, we announce the complete genome sequence of Aeromonas rivuli strain 20-VB00005, which was recovered from ready-to-eat food.
Collapse
|
34
|
Soares F, Trovão J, Ahn AC, Wilmotte A, Cardoso SM, Tiago I, Portugal A. Introducing Petrachlorosaceae fam. nov., Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. (Synechococcales, Cyanobacteria) Isolated from a Portuguese UNESCO monument. JOURNAL OF PHYCOLOGY 2022; 58:219-233. [PMID: 35133645 DOI: 10.1111/jpy.13241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/03/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
The Synechococcales is a large cyanobacterial order comprising both unicellular and filamentous forms, with parietal thylakoid arrangement. Previously, this order has been the subject of taxonomic revisions with new families being erected. During studies of the phototrophic communities on the limestone walls of the Old Cathedral of Coimbra (UNESCO monument), a coccoid Aphanocapsa-like cyanobacterium was isolated. It was characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic and phylogenomic analyses, internal transcribed spacer (ITS) secondary structure, and ecology. The 16S rRNA phylogenetic analyses showed that this strain is placed in a separate and highly supported family-level clade, as part of a large group comprising the families Prochlorococcaceae and Prochlorotrichaceae, with Lagosinema as the closest (although quite distant) taxon. Additionally, the phylogenomic analysis also placed this strain in a separate lineage, situated distantly apart from the family Thermosynechococcaceae, but with strains assigned to Acaryochloris marina MBIC 11017 and Aphanocapsa montana BDHKU210001 as the closest taxa. Based on these data, as well as on the results from the secondary ITS structure, morphology, and ecology, we here propose the establishment of Petrachlorosaceae fam. nov., along with the description of Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. We also address additional considerations regarding some cyanobacterial taxa within the order Synechococcales, which we believe deserve further revisions.
Collapse
Affiliation(s)
- Fabiana Soares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - João Trovão
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - Anne-Catherine Ahn
- BCCM/ULC Culture Collection, InBios-Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Annick Wilmotte
- BCCM/ULC Culture Collection, InBios-Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Susana M Cardoso
- QOPNA &, LAQV-REQUIMTE, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - António Portugal
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| |
Collapse
|
35
|
Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov. Antonie Van Leeuwenhoek 2022; 115:461-472. [PMID: 35107701 DOI: 10.1007/s10482-022-01712-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
Abstract
We present polyphasic taxonomic data to demonstrate that strain 125703-2019T, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov. Upon primary isolation, strain 125703-2019T could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that it belonged to the genus Pseudoclavibacter. Average nucleotide identity and digital DNA-DNA hybridisation analyses confirmed that it represented a novel species within this genus. A detailed physiological characterisation yielded differential tests between the novel species and its nearest neighbor taxa, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify this strain into the novel species Pseudoclavibacter triregionum sp. nov., with strain 125703-2019T (= R-76471T, LMG 31777T, CCUG 74796T) as the type strain. The whole-genome assembly of strain 125703-2019T has a size of 2.4 Mb and a G + C content of 72.74%. A Pseudoclavibacter pangenome analysis revealed that 667 gene clusters were exclusively present in strain 125703-2019T. While these gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that explained the occurrence of this species in human infection. Finally, several phylogenetic and phylogenomic analyses demonstrated that the genus Pseudoclavibacter is polyphyletic with Pseudoclavibacter soli and Pseudoclavibacter caeni representing a unique and deeply branching line of descent within the family Microbacteriaceae. We therefore also propose to reclassify both species into the novel genus Caespitibacter gen. nov. as Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov., respectively, and with C. soli comb. nov. as the type species.
Collapse
|
36
|
Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A. Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus
Agromyces
. The type strain with the highest pairwise similarity was
Agromyces marinus
H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus
Agromyces
, and only
Agromyces atrinae
P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus
Agromyces
indicated that G127ATT represented a previously undescribed species of the genus
Agromyces
. Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus
Agromyces
. The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus
Agromyces
, for which we propose the name Agromyces archimandritae sp. nov.
Collapse
Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Maite Ortúzar
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Martha E. Trujillo
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| |
Collapse
|
37
|
Goussarov G, Claesen J, Mysara M, Cleenwerck I, Leys N, Vandamme P, Van Houdt R. Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics. ENVIRONMENTAL MICROBIOME 2022; 17:9. [PMID: 35248155 PMCID: PMC8898458 DOI: 10.1186/s40793-022-00403-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Although the total number of microbial taxa on Earth is under debate, it is clear that only a small fraction of these has been cultivated and validly named. Evidently, the inability to culture most bacteria outside of very specific conditions severely limits their characterization and further studies. In the last decade, a major part of the solution to this problem has been the use of metagenome sequencing, whereby the DNA of an entire microbial community is sequenced, followed by the in silico reconstruction of genomes of its novel component species. The large discrepancy between the number of sequenced type strain genomes (around 12,000) and total microbial diversity (106-1012 species) directs these efforts to de novo assembly and binning. Unfortunately, these steps are error-prone and as such, the results have to be intensely scrutinized to avoid publishing incomplete and low-quality genomes. RESULTS We developed MAGISTA (metagenome-assembled genome intra-bin statistics assessment), a novel approach to assess metagenome-assembled genome quality that tackles some of the often-neglected drawbacks of current reference gene-based methods. MAGISTA is based on alignment-free distance distributions between contig fragments within metagenomic bins, rather than a set of reference genes. For proper training, a highly complex genomic DNA mock community was needed and constructed by pooling genomic DNA of 227 bacterial strains, specifically selected to obtain a wide variety representing the major phylogenetic lineages of cultivable bacteria. CONCLUSIONS MAGISTA achieved a 20% reduction in root-mean-square error in comparison to the marker gene approach when tested on publicly available mock metagenomes. Furthermore, our highly complex genomic DNA mock community is a very valuable tool for benchmarking (new) metagenome analysis methods.
Collapse
Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
| |
Collapse
|
38
|
Vanwijnsberghe S, Peeters C, Cnockaert M, De Canck E, Vandamme P. Paraburkholderia gardini sp. nov. and Paraburkholderia saeva sp. nov.: novel aromatic compound degrading bacteria isolated from garden and forest soil samples. Syst Appl Microbiol 2022; 45:126318. [DOI: 10.1016/j.syapm.2022.126318] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
|
39
|
Abstract
A culture collection of 41 bacteria isolated from the rhizosphere of cultivated barley (Hordeum vulgare subsp. vulgare) is available at the Division of Plant Sciences, University of Dundee (UK). The data include information on genes putatively implicated in nitrogen fixation, HCN channels, phosphate solubilization, and linked whole-genome sequences.
Collapse
|
40
|
Cotroneo CE, Gormley IC, Shields DC, Salter-Townshend M. Computational modelling of chromosomally clustering protein domains in bacteria. BMC Bioinformatics 2021; 22:593. [PMID: 34906073 PMCID: PMC8670047 DOI: 10.1186/s12859-021-04512-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/16/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND In bacteria, genes with related functions-such as those involved in the metabolism of the same compound or in infection processes-are often physically close on the genome and form groups called clusters. The enrichment of such clusters over various distantly related bacteria can be used to predict the roles of genes of unknown function that cluster with characterised genes. There is no obvious rule to define a cluster, given their variability in size and intergenic distances, and the definition of what comprises a "gene", since genes can gain and lose domains over time. Protein domains can cluster within a gene, or in adjacent genes of related function, and in both cases these are chromosomally clustered. Here, we model the distances between pairs of protein domain coding regions across a wide range of bacteria and archaea via a probabilistic two component mixture model, without imposing arbitrary thresholds in terms of gene numbers or distances. RESULTS We trained our model using matched gene ontology terms to label functionally related pairs and assess the stability of the parameters of the model across 14,178 archaeal and bacterial strains. We found that the parameters of our mixture model are remarkably stable across bacteria and archaea, except for endosymbionts and obligate intracellular pathogens. Obligate pathogens have smaller genomes, and although they vary, on average do not show noticeably different clustering distances; the main difference in the parameter estimates is that a far greater proportion of the genes sharing ontology terms are clustered. This may reflect that these genomes are enriched for complexes encoded by clustered core housekeeping genes, as a proportion of the total genes. Given the overall stability of the parameter estimates, we then used the mean parameter estimates across the entire dataset to investigate which gene ontology terms are most frequently associated with clustered genes. CONCLUSIONS Given the stability of the mixture model across species, it may be used to predict bacterial gene clusters that are shared across multiple species, in addition to giving insights into the evolutionary pressures on the chromosomal locations of genes in different species.
Collapse
Affiliation(s)
- Chiara E Cotroneo
- School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis C Shields
- School of Medicine, University College Dublin, Dublin, Ireland. .,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| | | |
Collapse
|
41
|
Kerkhof PJ, On SLW, Houf K. Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig. Int J Syst Evol Microbiol 2021; 71. [PMID: 34797211 DOI: 10.1099/ijsem.0.005113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A study on the polyphasic taxonomic classification of an Arcobacter strain, R-73987T, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus Arcobacter and suggested that strain R-73987T belongs to a novel undescribed species. Comparative analysis of the rpoB gene sequence confirmed the findings. Arcobacter faecis LMG 28519T was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and in silico DNA-DNA hybridization between the genome of strain R-73987T and the genomes of validly named Arcobacter species resulted in values below 95-96 and 70 %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987T represents a novel Arcobacter species, for which the name Arcobacter vandammei sp. nov. is proposed. The type strain is R-73987T (=LMG 31429T=CCUG 75005T). This appears to be the first Arcobacter species recovered from porcine intestinal mucus.
Collapse
Affiliation(s)
- Pieter-Jan Kerkhof
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Springs Road, Lincoln 7467, New Zealand
| | - Kurt Houf
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium, 9000 Ghent, Belgium
| |
Collapse
|
42
|
Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
Collapse
|
43
|
Draft Genome Sequence of Rhodococcus rhodochrous Strain G38GP, Isolated from the Madagascar Hissing Cockroach. Microbiol Resour Announc 2021; 10:e0077721. [PMID: 34617793 PMCID: PMC8496360 DOI: 10.1128/mra.00777-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus rhodochrous is a bacterial species with applications in biocatalysis and bioremediation. Here, we report the draft genome sequence of strain G38GP, isolated from the gut of the cockroach Gromphadorhina portentosa. The genome consists of 76 contigs, with a total length of 6,256,198 bp and a GC content of 67.82%.
Collapse
|
44
|
Tahon G, Gök D, Lebbe L, Willems A. Description and functional testing of four species of the novel phototrophic genus Chioneia gen. nov., isolated from different East Antarctic environments. Syst Appl Microbiol 2021; 44:126250. [PMID: 34592543 DOI: 10.1016/j.syapm.2021.126250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Seven Gram-negative, aerobic, non-sporulating, motile strains were isolated from terrestrial (R-67880T, R-67883, R-36501 and R-36677T) and aquatic (R-39604, R-39161T and R-39594T) East Antarctic environments (i.e. soil and aquatic microbial mats), between 2007 and 2014. Analysis of near-complete 16S rRNA gene sequences revealed that the strains potentially form a novel genus in the family Sphingomonadaceae (Alphaproteobacteria). DNA-DNA reassociation and average nucleotide identity values indicated distinction from close neighbors in the family Sphingomonadaceae and showed that the seven isolates form four different species. The main central pathways present in the strains are the glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The strains can use only a limited number of carbon sources and mainly depend on ammonia and sulfate as a nitrogen and sulfur source, respectively. The novel strains showed the potential of aerobic anoxygenic phototrophy, based on the presence of bacteriochlorophyll a pigments, which was corroborated by the presence of genes for all building blocks for a type 2 photosynthetic reaction center in the annotated genomes. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the strains could be assigned four new species in the novel genus Chioneia gen. nov. in the family Sphingomonadaceae, for which the names C. frigida sp. nov. (R-67880T, R-67883 and R-36501), C. hiemis sp. nov. (R-36677T), C. brumae sp. nov. (R-39161T and R-39604) and C. algoris sp. nov. (R-39594T) are proposed.
Collapse
Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Duygu Gök
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| |
Collapse
|
45
|
Vandamme P, Peeters C, Seth-Smith HMB, Graf L, Cnockaert M, Egli A, Goldenberger D. Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections. Antonie van Leeuwenhoek 2021; 114:1841-1854. [PMID: 34480670 DOI: 10.1007/s10482-021-01644-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/13/2021] [Indexed: 01/22/2023]
Abstract
We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that they belonged to the genus Gulosibacter. Overall genomic relatedness indices between the draft genome sequences of the three isolates and of the type strains of established Gulosibacter species confirmed that the three isolates represented a single novel Gulosibacter species. A biochemical characterisation yielded differential tests between the novel and established Gulosibacter species, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify these three isolates into Gulosibacter hominis sp. nov., with 401352-2018 T (= LMG 31778 T, CCUG 74795 T) as the type strain. The whole-genome sequence of strain 401352-2018 T has a size of 2,340,181 bp and a G+C content of 62.04 mol%. A Gulosibacter pangenome analysis revealed 467 gene clusters that were exclusively present in G. hominis genomes. While these G. hominis specific gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that suggested a role in the human microbiome, nor did it explain the occurrence of G. hominis in ear infections. The absence of acquired antimicrobial resistance determinants and virulence factors in the G. hominis genomes, and an analysis of publicly available 16S rRNA gene sequences and 16S rRNA amplicon sequencing data sets suggested that G. hominis is a member of the human skin microbiota that may occasionally be involved in opportunistic infections.
Collapse
Affiliation(s)
- Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Lukas Graf
- Ear, Nose and Throat Department, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Daniel Goldenberger
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
| |
Collapse
|
46
|
Herpell JB, Vanwijnsberghe S, Peeters C, Schindler F, Fragner L, Bejtović M, Weckwerth W, Vandamme P. Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor. Int J Syst Evol Microbiol 2021; 71:004969. [PMID: 34542391 PMCID: PMC8549267 DOI: 10.1099/ijsem.0.004969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).
Collapse
Affiliation(s)
- Johannes B. Herpell
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sarah Vanwijnsberghe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Florian Schindler
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Mersad Bejtović
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
47
|
Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
Collapse
Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
48
|
Complete Genome Sequence of Arcanobacterium phocisimile Strain DSM 26142, Isolated from a Harbor Seal. Microbiol Resour Announc 2021; 10:e0021521. [PMID: 34264110 PMCID: PMC8281070 DOI: 10.1128/mra.00215-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacteria of the genus Arcanobacterium can be found in a variety of hosts. The species Arcanobacterium phocisimile was originally identified in a free-living harbor seal in the German North Sea in 2004. Here, we announce the complete genome sequence of Arcanobacterium phocisimile strain DSM 26142.
Collapse
|
49
|
Vanwijnsberghe S, Peeters C, De Ridder E, Dumolin C, Wieme AD, Boon N, Vandamme P. Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov. Int J Mol Sci 2021; 22:ijms22137003. [PMID: 34209778 PMCID: PMC8268980 DOI: 10.3390/ijms22137003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022] Open
Abstract
We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.
Collapse
Affiliation(s)
- Sarah Vanwijnsberghe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
| | - Emmelie De Ridder
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
| | - Charles Dumolin
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
| | - Nico Boon
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium;
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (S.V.); (C.P.); (E.D.R.); (C.D.); (A.D.W.)
- Correspondence:
| |
Collapse
|
50
|
Kim J, Na SI, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609-615. [PMID: 34052993 DOI: 10.1007/s12275-021-1231-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022]
Abstract
Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2 .
Collapse
Affiliation(s)
- Jihyeon Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Seong-In Na
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Dongwook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea.
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 00826, Republic of Korea.
| |
Collapse
|