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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Liu Q, Xue L, Wu K, Fan G, Bai X, Yang X, Cao L, Sun H, Song W, Pan Y, Chen S, Xiong Y, Chen H. Nanchangia anserum gen. nov., sp. nov., isolated from feces of greater white-fronted geese ( Anser albifrons). Int J Syst Evol Microbiol 2021; 71. [PMID: 34431769 DOI: 10.1099/ijsem.0.004978] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two rod-shaped and Gram-stain-positive bacteria (strains C64T and C62) were isolated in 2020 from faeces of greater white-fronted geese (Anser albifrons) from Poyang Lake, PR China. Their optimal growth conditions were at 37 °C, pH 7.0 and with 0.5 % (w/v) NaCl. The two isolates showed a highest 16S rRNA gene sequence similarity to Bowdeniella nasicola DSM 19116T (92.1 %). Phylogenetic/phylogenomic analyses indicated that strains C64T and C62 clustered independently in the vicinity of the genera Varibaculum, Winkia and Mobiluncus within the family Actinomycetaceae, but could not be classified clearly as members of any of these known genera. The average amino acid identity values between our isolates and available genomes of members of the family Actinomycetaceae were around the genus threshold value (45-65 %). The major cellular fatty acids of the strains were C18 : 1ω9c and C16 : 0. The predominant polar lipids were phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine, diacylglycerol, triacylglycerol and cardiolipin. The amino acid composition of peptidoglycan contained alanine, glutamic acid and glycine. The major respiratory menaquinones were MK-8(H4) and MK-9(H4). The whole cell sugars included galactose, arabinose and glucose. On the basis of the results of the 16S rRNA gene sequences comparison, whole-genome phylogenomic analysis, phenotypic and chemotaxonomic characteristics, we propose that strains C64T and C62 represent a novel species belonging to a novel genus within the family Actinomycetaceae, for which the name Nanchangia anserum gen. nov., sp. nov. is proposed. The type strain is Nanchangia anserum C64T (=CGMCC 1.18410T=GDMCC 1.1969T=KCTC 49511T=KACC 22143T).
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Affiliation(s)
- Qian Liu
- Jiangxi Province Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330006, PR China
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lin Xue
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
| | - Kui Wu
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
| | - Guoyin Fan
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xi Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lijiao Cao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wentao Song
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
| | - Yanyu Pan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shengen Chen
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Haiying Chen
- Jiangxi Province Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330006, PR China
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-origin and Vector-borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, PR China
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 409] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Gillespie A, Bortolami A, Crosby‐Durrani H, Verin R. An unusual presentation of actinomycosis in a dairy cow. VETERINARY RECORD CASE REPORTS 2017. [DOI: 10.1136/vetreccr-2016-000395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Amy Gillespie
- School of Veterinary ScienceUniversity of LiverpoolNestonUK
| | | | | | - Ranieri Verin
- School of Veterinary ScienceUniversity of LiverpoolNestonUK
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Strong T, Dowd S, Gutierrez AF, Molnar D, Coffman J. Amplicon pyrosequencing and ion torrent sequencing of wild duck eubacterial microbiome from fecal samples reveals numerous species linked to human and animal diseases. F1000Res 2013. [DOI: 10.12688/f1000research.2-224.v2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Our investigation into the composition of the wild duck,Aythya americana, eubacterial microbiome from a fecal sample using amplicon pyrosequencing revealed that the representative bacterial species were quite distinct from a pond water sample, and we were able to classify the major operational taxonomic units withFusobacterium mortiferum,Streptobacillus moniliformis,Lactobacillus intermedius,Actinomyces suimastitidis,Campylobacter Canadensis,Enterococcus cecorum,Lactobacillus aviarus,Actimomyces spp.,Pseudobutyrivibrio spp.and Helicobacter brantaerepresenting the majority of the eubacterial fecal microbiome. Bacterial species present in the analysis revealed numerous organisms linked to human and animal diseases including septicemia, rat bite fever, pig mastitis, endocarditis, malar masses, genital infections, skin lesions, peritonitis, wound infections, septic arthritis, urocystitis, gastroenteritis and drinking water diseases. In addition, to being known carriers of viral pathogens wild ducks should also be recognized as a potential source of a range of bacterial diseases.
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Rao JU, Rash BA, Nobre MF, da Costa MS, Rainey FA, Moe WM. Actinomyces naturae sp. nov., the first Actinomyces sp. isolated from a non-human or animal source. Antonie van Leeuwenhoek 2011; 101:155-68. [PMID: 21965039 DOI: 10.1007/s10482-011-9644-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
Abstract
Three facultatively anaerobic, Gram-positive staining, rod-shaped, non-spore forming, flagellated bacterial strains, BL-75, BL-79(T) and BL-104, were isolated from chlorinated solvent-contaminated groundwater. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed them to represent a distinct lineage within the genus Actinomyces with sequence identities in the range of <88-95.4% with previously described Actinomyces species. The strains were oxidase and catalase negative. Nitrate was not reduced. Esculin was hydrolyzed. Growth occurred in the temperature range of 20-43°C (optimum 30-37°C) and pH range 4.5-9.0 (optimum pH 6.5). Substrates supporting growth included various mono-, di-, and tri-saccharides. The end products of glucose fermentation were acetate, lactate, succinate and formate. Fermentative growth was observed in the presence of near saturation concentrations of perchloroethene (PCE) and toluene and in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 24.4 mM and 11.2 mM, respectively. The dominant cellular fatty acids when grown in peptone/yeast extract/glucose (PYG) medium were C(18:1) ω9c, C(16:0), and C(14:0). The peptidoglycan was found to contain the amino acids alanine, glutamic acid, lysine, and ornithine at approximate molar ratios of 1.7 Ala: 2.3 Glu: 1.3 Lys: 1.0 Orn. The cell wall sugars were found to include rhamnose and mannose. The polar lipids were found to include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), phosphoglycolipids (PGL), and glycolipids (GL). The main respiratory quinone of strain BL-79(T) was MK-9(H(4)), with minor components MK-10(H(4)) and MK-8(H(4)). The DNA mol% G+C content of the type strain is 69.8%. On the basis of phylogenetic and phenotypic characteristics, these strains could be differentiated from previously described species of the genus Actinomyces. Strains BL-75, BL-79(T) and BL-104 are designated as a novel species, for which the name Actinomyces naturae sp. nov. is proposed. This is the first Actinomyces species isolated from an environmental rather than human or animal sources. The type strain of Actinomyces naturae is BL-79(T) (= CCUG 56698(T) = NRRL B-24670(T)).
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Affiliation(s)
- Jyoti U Rao
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
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An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043-2048. [PMID: 16957097 DOI: 10.1099/ijs.0.64059-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two obligate anaerobic bacterial strains, B71Tand D471, were isolated from cattle rumen. The novel strains were Gram-positive and rod-shaped. The strains hydrolysed xylan and starch, fermented some mono-, di- and oligosaccharides and produced formic, acetic and lactic acids as end products from glucose. Growth of the isolates was observed at 20–55 °C and pH 6.5–9.0. The DNA G+C contents of strains B71Tand D471 were 68.06 and 68.26 mol%, respectively. Although the two novel strains met the genus description forActinomyces, some phenotypic characteristics, such as optimum growth temperature, requirement for O2and the end products of fermentation, distinguished them from previously described members of the genus. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strains belonged to the genusActinomyces(88.3–93.6 % sequence similarity) and formed a distinct line within the clade containingActinomyces bovis. On the basis of these results, a novel species,Actinomyces ruminicolasp. nov., is proposed. The type strain is B71T(=JCM 13352T=CGMCC 1.5030T).
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Affiliation(s)
- Dengdi An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences. Beijing 100080, PR China
| | - Shichun Cai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences. Beijing 100080, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences. Beijing 100080, PR China
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Woo PCY, Fung AMY, Lau SKP, Teng JLL, Wong BHL, Wong MKM, Hon E, Tang GWK, Yuen KY. Actinomyces hongkongensis sp. nov. – A Novel Actinomyces species Isolated from a Patient with Pelvic Actinomycosis. Syst Appl Microbiol 2003; 26:518-22. [PMID: 14666979 DOI: 10.1078/072320203770865819] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A bacterium was isolated from the pus of a patient with pelvic actinomycosis. The cells were strictly anaerobic, straight, non-sporulating, Gram-positive rods. It grows on sheep blood agar as non-haemolytic, pinpoint colonies after 24 hours of incubation at 37 degrees C in anaerobic environment. It is non-motile and does not produce catalase. 16S ribosomal RNA (rRNA) gene sequencing showed that there were 6.6% difference between the 16S rRNA gene sequence of the bacterium that of Actinomyces marimammalium (GenBank Accession no. AJ276405), a new species described in 2001, isolated from two seals and a porpoise. For these reasons a new species, Actinomyces hongkongensis sp. nov., is proposed, for which HKU8(T) is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an important cause of actinomycosis.
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Affiliation(s)
- Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong
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