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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [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
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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2
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Trujillo SM, McKenney EA, Hilderbrand GV, Mangipane LS, Rogers MC, Joly K, Gustine DD, Erlenbach JA, Mangipane BA, Lafferty DJR. Intrinsic and extrinsic factors influence on an omnivore's gut microbiome. PLoS One 2022; 17:e0266698. [PMID: 35395042 PMCID: PMC8993001 DOI: 10.1371/journal.pone.0266698] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/24/2022] [Indexed: 01/04/2023] Open
Abstract
Gut microbiomes (GMBs), complex communities of microorganisms inhabiting the gastrointestinal tracts of their hosts, perform countless micro-ecosystem services such as facilitating energy uptake and modulating immune responses. While scientists increasingly recognize the role GMBs play in host health, the role of GMBs in wildlife ecology and conservation has yet to be realized fully. Here, we use brown bears (Ursus arctos) as an ecological model to (1) characterize GMB community composition associated with location, season, and reproductive condition of a large omnivore; (2) investigate how both extrinsic and intrinsic factors influence GMB community membership and structure; and (3) quantify differences in GMB communities among different locations, seasons, sex, and reproductive conditions. To achieve these aims, we subsampled brown bear fecal samples collected during United States National Park Service research activities at three National Parks and Preserves (Katmai, Lake Clark, and Gates of the Arctic) and extracted microbial DNA for 16S rRNA amplicon sequencing and microbial taxonomic classification. We analyzed GMB communities using alpha and beta diversity indices, subsequently using linear mixed models to examine relationships between alpha diversity and extrinsic and intrinsic factors. Katmai brown bears hosted the greatest alpha diversity, whereas Gates brown bears hosted the least alpha diversity. Our results indicate that location and diet drive GMB variation, with bears hosting less phylogenetic diversity as park distance inland increases. Monitoring brown bear GMBs could enable managers to quickly detect and assess the impact of environmental perturbations on brown bear health. By integrating macro and micro-ecological perspectives we aim to inform local and landscape-level management decisions to promote long-term brown bear conservation and management.
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Affiliation(s)
- Sarah M. Trujillo
- Wildlife Ecology and Conservation Science Lab, Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
- * E-mail:
| | - Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Grant V. Hilderbrand
- Natural Resources Team, National Park Service, Anchorage, Alaska, United States of America
| | - Lindsey S. Mangipane
- Marine Mammals Management, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Matthew C. Rogers
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, Alaska, United States of America
| | - Kyle Joly
- Gates of the Arctic National Park and Preserve, National Park Service, Fairbanks, Alaska, United States of America
| | - David D. Gustine
- Marine Mammals Management, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Joy A. Erlenbach
- Kodiak National Wildlife Refuge, U.S. Fish and Wildlife Service, Kodiak, Alaska, United States of America
| | - Buck A. Mangipane
- Lake Clark National Park and Preserve, National Park Service, Anchorage, Alaska, United States of America
| | - Diana J. R. Lafferty
- Wildlife Ecology and Conservation Science Lab, Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
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Volokhov DV, Furtak VA, Blom J, Zagorodnyaya TA, Gao Y, Gulland FM. Mycoplasma miroungirhinis sp. nov. and Mycoplasma miroungigenitalium sp. nov., isolated from northern elephant seals (Mirounga angustirostris), Mycoplasma phocoenae sp. nov., isolated from harbour porpoise (Phocoena phocoena), and Mycoplasma phocoeninasale sp. nov., isolated from harbour porpoise and California sea lions (Zalophus californianus). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005224] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Seven novel independent strains of
Mycoplasma
species were isolated from northern elephant seals (ES2806-NAST, ES2806-GENT, ES3157-GEN-MYC and ES3225-GEN-MYC), a harbour porpoise (C264-GENT and C264-NAST), and a California sea lion (CSL7498). These strains were phenotypically and genetically characterized and compared to the known
Mycoplasma
species. Four strains (C264-GENT, C264-NAST, CSL7498 and ES2806-NAST) hydrolysed arginine but not urea and did not produce acid from carbohydrates. Strains ES2806-GENT, ES3157-GEN-MYC and ES3225-GEN-MYC did not produced acid from carbohydrates and did not hydrolyse arginine or urea; hence, it is assumed that organic acids are used as the energy source for them. All were isolated and propagated in ambient air supplemented with 5±1 % CO2 at +35–37 °C using either SP4 or PPLO medium. Colonies on solid medium showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. The complete genomes were sequenced for all type strains. Average nucleotide and amino acid identity analyses showed that these novel strains were distant from the phylogenetically closely related
Mycoplasma
species. Based on these data, we propose four novel species of the genus
Mycoplasma
, for which the name Mycoplasma miroungirhinis sp. nov. is proposed with the type strain ES2806-NAST (=NCTC 14430T=DSM 110945T), Mycoplasma miroungigenitalium sp. nov. is proposed with the type strain ES2806-GENT (=NCTC 14429T=DSM 110944T) and representative strains ES3157-GEN-MYC and ES3225-GEN-MYC, Mycoplasma phocoenae sp. nov. is proposed with the type strain C264-GENT (=NCTC 14344T=DSM 110687T) and Mycoplasma phocoeninasale sp. nov. is proposed with the type strain C264-NAST (=NCTC 14343T=DSM 110688T) and representative strain CSL7498. The genome G+C contents are 24.06, 30.09, 28.49 and 29.05% and the complete genome sizes are 779 550, 815 486, 693 115, and 776 009 bp for strains ES2806-NAST, ES2806-GENT, C264-GENT and C264-NAST, respectively.
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Affiliation(s)
- Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Vyacheslav A. Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Tatiana A. Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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Ade J, Stadler J, Ritzmann M, Zübert C, Hoelzle K, Hoelzle LE. Occurrence of 'Candidatus Mycoplasma haemosuis' in fattening pigs, sows and piglets in Germany using a novel gap-based quantitative real-time PCR assay. BMC Vet Res 2022; 18:40. [PMID: 35039068 PMCID: PMC8762947 DOI: 10.1186/s12917-022-03147-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background The appearance of the novel porcine haemotrophic mycoplasma (HM) species ‘Candidatus Mycoplasma haemosuis’ was reported in apparently healthy but also in clinically sick animals in China, Korea and in a case report from Germany. Outside of Asia, however, nothing further is known about the frequency of ‘Ca. M. haemosuis’ in pigs to date. To investigate the distribution of this novel HM species in Germany, fattening pigs, sows and pre-suckling piglets were examined using a herein developed quantitative real-time PCR assay (qPCR). Because the piglets were sampled before the first colostrum uptake, additional information on a possible vertical transmission from dams to their offspring was obtained. Results Our novel qPCR assay successfully detected ‘Ca. M. haemosuis’ in all blood samples from the ‘Ca. M. haemosuis’-infected pigs. No cross-reactivity was detected when DNA from non-target Mycoplasma spp. and other bacterial species representing 105 bacteria/reaction were used as a template. The lower limit of detection of the qPCR was thus 10 gap gene copies per reaction and 2.5 x 103 genome equivalents (GE) per mL blood. ‘Candidatus M. haemosuis’ was detected by this qPCR in blood samples from a total out of 6.25% sows (13/208), 4.50% pre-suckling piglets (28/622) and 17.50% fattening pigs (35/200). On farm level, 3 out of 21 piglet producing farms (14.28%) and 9 out of 20 fattening farms (45.00%) were positive for ‘Ca. M. haemosuis’. Co-infections with M. suis were evident in all age groups. Conclusion ‘Candidatus M. haemosuis’ infection is present in German pig farms and the detection of the novel porcine HM species in piglets immediately after birth before colostrum intake indicates vertical transmission. The novel qPCR assay specific for ‘Ca. M. haemosuis’ described herein will be a prerequisite for future studies on the prevalence, epidemiology as well as the clinical and economic impact of ‘Ca. M. haemosuis’ infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03147-1.
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Affiliation(s)
- Julia Ade
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Sonnenstrasse 16, 85764, Oberschleissheim, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Sonnenstrasse 16, 85764, Oberschleissheim, Germany
| | - Christina Zübert
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Katharina Hoelzle
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Ludwig E Hoelzle
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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Volokhov DV, Grózner D, Gyuranecz M, Ferguson-Noel N, Gao Y, Bradbury JM, Whittaker P, Chizhikov VE, Szathmary S, Stipkovits L. Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese ( Anser anser domesticus) with reproductive pathology. Int J Syst Evol Microbiol 2020; 70:2369-2381. [PMID: 32068526 DOI: 10.1099/ijsem.0.004052] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S-23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02-99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00-96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma. Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis. Based on the genetic data, we propose a novel species of the genus Mycoplasma, for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Dénes Grózner
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143, Hungary.,Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, Budapest, 1143, Hungary
| | - Miklós Gyuranecz
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, Budapest, 1143, Hungary.,Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143, Hungary
| | - Naola Ferguson-Noel
- Poultry Diagnostic & Research Center, University of Georgia, 953 College Station Rd., Athens, GA 30602, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Janet M Bradbury
- University of Liverpool, School of Veterinary Science, Leahurst Campus, Neston, CH64 7TE, UK
| | - Paul Whittaker
- Present address: Currently retired from the US FDA, Maryland, USA.,Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Dr., College Park, MD 20740, USA
| | - Vladimir E Chizhikov
- Present address: Currently retired from the US FDA, Maryland, USA.,Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Susan Szathmary
- RT-Europe Research Center, 9200 Var 2, Mosonmagyaróvár, Hungary.,Galen Bio, Inc. Carlsbad, 5922 Farnsworth Ct Carlsbad, CA 92008, USA
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Volokhov DV, Gao Y, Davidson MK, Chizhikov VE. Acholeplasma equirhinis sp. nov. isolated from respiratory tract of horse (Equus caballus) and Mycoplasma procyoni sp. nov. isolated from oral cavity of raccoon (Procyon lotor). Arch Microbiol 2019; 202:411-420. [PMID: 31828363 DOI: 10.1007/s00203-019-01786-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023]
Abstract
We describe two novel species of Acholeplasma sp. strain N93 and Mycoplasma sp. strain LR5794 which were isolated from the nasopharynx of a horse from the United Kingdom and from the oral cavity of a North American raccoon from Canada, respectively. These strains were phenotypically and genetically characterized and compared to other established Mycoplasma and Acholeplasma species. Both strains are facultative anaerobes, resistant to penicillin, and produce acid from glucose but do not hydrolyze arginine and urea. Both strains grew well in microaerophilic and anaerobic atmospheric conditions at 35-37 °C using PPLO (pleuropneumonia-like organisms) medium. Acholeplasma sp. N93 does not require serum for growth. Colonies of both strains showed a typical fried-egg appearance and transmission electron microscopy of bacterial cells revealed a typical mycoplasma cellular morphology. Molecular characterization included assessment of several genetic loci. The genetic analysis indicated that Acholeplasma sp. N93 and Mycoplasma sp. LR5794 were most closely related to A. hippikon and A. equifetale, and M. molare and M. lagogenitalium, respectively. However, both novel strains were genetically unique in comparison to other well-known Mycoplasma and Acholeplasma species. Based on the isolation source history, phenotypic, genotypic, and phylogenetic characteristics of these novel strains, we propose the name Acholeplasma equirhinis sp. nov. for Acholeplasma sp. isolated from the nasopharynx of a horse [the type strain is N93T (= DSM 106692T = ATCC TSD-139T = NCTC 14351T)], and the name Mycoplasma procyoni sp. nov. for the Mycoplasma sp. isolated from the oral cavity of a North American raccoon [the type strain is LR5794T (= DSM 106703T = ATCC TSD-141T = NCTC 14309T)].
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Affiliation(s)
- Dmitriy V Volokhov
- Laboratory of Method Development, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993-0002, USA.
| | - Yamei Gao
- Laboratory of Respiratory Viral Diseases, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993-0002, USA
| | - Maureen K Davidson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA
| | - Vladimir E Chizhikov
- Laboratory of Method Development, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993-0002, USA
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