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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [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] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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Long-term survive of Aliarcobacter butzleri in two models symbiotic interaction with Acanthamoeba castellanii. Arch Microbiol 2022; 204:610. [DOI: 10.1007/s00203-022-03223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/02/2022]
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Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov. Curr Microbiol 2020; 77:1945-1954. [PMID: 32350604 DOI: 10.1007/s00284-020-02004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The genus Metakosakonia, as the closest phylogenetic neighbor of the genus Kosakonia within the family Enterobacteriaceae, when proposed in 2017, consisted of M. massiliensis JC163T and Metakosakonia spp. strains CAV1151 and GT-16. The strain CAV1151 was later classified into a novel species Phytobacter ursingii. Here, we show that the strain GT-16 shares a digital DNA-DNA hybridization (DDH) similarity of 91.0% with P. diazotrophicus DSM 17806 T and thus also belongs to P. diazotrophicus. M. massiliensis and the strains within the genus Phytobacter formed a monophyletic cluster on a phylogenomic tree based on the core proteins of the family Enterobacteriaceae and on a phylogenetic tree based on the 16S rRNA genes. M. massiliensis and the genus Phytobacter share average amino acid identities of 86.80‒87.41% above the threshold (86%) for genus delimitation within the family Enterobacteriaceae. Moreover, they share conserved signature indels in the intracellular growth protein IgaA and the outer membrane assembly protein AsmA. Therefore, we propose to unite the genus Metakosakonia and the genus Phytobacter to a single genus. Because the genus Phytobacter was validly published earlier in 2017 than the genus Metakosakonia in 2017, the genus name Phytobacter has priority over Metakosakonia. We propose to unite the two genera under the name Phytobacter with the type species P. diazotrophicus and reclassify M. massiliensis as P. massiliensis comb. nov. In addition, the analyses of genome relatedness and phylogenomic relationship identified one potential novel species within the genus Phytobacter and three potential novel species within the genus Kosakonia.
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Han KI, Kim JS, Lee KC, Eom MK, Suh MK, Kim HS, Park SH, Lee JH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Lee JH, Lee JS. Senegalimassilia faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces, and emended description of the genus Senegalimassilia. Int J Syst Evol Microbiol 2020; 70:1684-1690. [PMID: 31913113 DOI: 10.1099/ijsem.0.003958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated KGMB04484T, was isolated from healthy human faeces sampled in the Republic of Korea. Cells of strain KGMB04484T were strictly anaerobic, Gram-stain-positive, catalase-positive, oxidase-negative, non-motile coccobacilli and formed tiny colonies on Columbia agar with 5 % horse blood. On the basis of 16S rRNA gene sequence similarity, strain KGMB04484T was affiliated with the genus Senegalimassilia in the family Coriobacteriaceae and its closest relative was Senegalimassilia anaerobia JC110T (96.28 % sequence similarity). The DNA G+C content of strain KGMB04484T was 61.2 mol%. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and three unidentified glycolipids. The predominant cellular fatty acids (>10 %) of strain KGMB04484T were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal. Based on its phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04484T is considered to represent a novel species within the genus Senegalimassilia, for which the name Senegalimassilia faecalis sp. nov. is proposed. The type strain is KGMB04484T (=KCTC 15721T=CCUG 72347T).
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Affiliation(s)
- Kook-Il Han
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Han Sol Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung Yeob Yu
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Byung-Yong Kim
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Je Hee Lee
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea.,University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Bertel Mesa LM, Betancur Hurtado CA, Oviedo Zumaque L. Identificación de Bacillus toyonensis en heces de ganado cebú en el Departamento de Sucre, Colombia. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2019. [DOI: 10.15446/rev.colomb.biote.v21n2.69421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Se evaluaron las características probióticas de cepas nativas aisladas de ganado cebú y se realizó identificación molecular de una de estas cepas, para considerar su posterior aplicación como aditivos microbianos en la alimentación bovina. Se usaron muestras de estiércol de terneros de levante, se aislaron bacterias y levaduras, determinándose la capacidad probiótica de estas cepas mediante pruebas como; resistencia a sales biliares (0.05, 0.1, 0.15 y 0.3 %), resistencia a pH ácido (pH 3, 4, 5.6, 7), tolerancia a NaCl (2, 4, 6, 8,10 %), actividad antagónica (Salmonella spp., y Escherichia coli), producción de gas a partir de la glucosa, y crecimiento a diferentes temperaturas (37 y 40 °C). La identificación preliminar de las cepas se realizó mediante: tinción de Gram, tinción de endosporas (método de Wirtz), prueba de la catalasa, prueba de oxidasa. Se seleccionó una de las cepas que superó las pruebas probióticas para su identificación mediante métodos moleculares y se realizó el análisis filogenético de la misma utilizando la base de datos NCBI Reference Sequence (RefSeq). Los ensayos se organizaron en un diseño completamente al azar, los resultados obtenidos por triplicado se sistematizaron en el software Statgraphics Centurion XVI y el efecto de los diferentes tratamientos se analizó estadísticamente mediante análisis de varianza. Se aislaron 10 cepas nativas, identificándose molecularmente a Bacillus toyonensis. Esta investigación representa el primer reporte molecular de B. toyonensis en estiércol de terneros de levante cebú en el Departamento de Sucre, el cual ha sido ampliamente utilizado como probiótico en la nutrición animal.
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Abdulmawjood A, Herrmann J, Riede S, Jimenez G, Becker A, Breves G. Evaluation of enterotoxin gene expression and enterotoxin production capacity of the probiotic strain Bacillus toyonensis BCT-7112T. PLoS One 2019; 14:e0214536. [PMID: 31022208 PMCID: PMC6483178 DOI: 10.1371/journal.pone.0214536] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
The aim of the present study was to evaluate the safety of the probiotic strain Bacillus toyonensis BCT-7112T (active ingredient of Toyocerin) in relation to the enterotoxins haemolysin BL (Hbl) and the non-haemolytic enterotoxin (Nhe) by performing a quantitative reverse transcription (RT) real-time polymerase chain reaction (PCR) and a Western blot assay. The expression levels of the enterotoxin genes hblA, hblD, nheA, nheB and nheC, determined by means of RT real-time PCR in B. toyonensis, were lower than those in B. cereus reference strains. No expression of hblC was detected. The Western blot assays of native and 25-fold concentrated supernatants from B. toyonensis, using monoclonal antibodies directed against the Hbl component L1 and the Nhe component NheB, showed weak bands. The NheC component was not detected in the native supernatant, but weakly in the 25-fold concentrated supernatant. According to the results of the present study, the enterotoxin expression and protein levels of B. toyonensis BCT-7112T were absent or clearly lower compared to the B. cereus reference strains. Thus, their ability to form functional enterotoxins can also be considered to be lower or unlikely compared to the B. cereus reference strains. This experimental approach can be implemented when studying the health and safety as well as harmlessness of probiotic microorganisms.
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Affiliation(s)
- Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jens Herrmann
- Department of Physiology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Susanne Riede
- Department of Physiology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Andre Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Gerhard Breves
- Department of Physiology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Oren A. Correction of the name Amycolatopsis albidoflavus to Amycolatopsis albidiflava corrig. Request for an Opinion. Int J Syst Evol Microbiol 2017; 67:4284. [PMID: 28893352 PMCID: PMC5845654 DOI: 10.1099/ijsem.0.002352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/06/2017] [Indexed: 03/19/2024] Open
Abstract
The name Amycolatopsis albidoflavus Lee and Hah 2001 is malformed because the genus name Amycolatopsis has the feminine gender. It is here proposed to correct the name to Amycolatopsis albidiflava corrig.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
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Alnajar S, Gupta RS. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. INFECTION GENETICS AND EVOLUTION 2017; 54:108-127. [DOI: 10.1016/j.meegid.2017.06.024] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 01/02/2023]
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10
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Salinarchaeum chitinilyticum sp. nov., a chitin-degrading haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2017; 67:2274-2278. [DOI: 10.1099/ijsem.0.001941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Glenwright H, Pohl S, Navarro F, Miro E, Jiménez G, Blanch AR, Harwood CR. The Identification of Intrinsic Chloramphenicol and Tetracycline Resistance Genes in Members of the Bacillus cereus Group ( sensu lato). Front Microbiol 2017; 7:2122. [PMID: 28101085 PMCID: PMC5209696 DOI: 10.3389/fmicb.2016.02122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022] Open
Abstract
Bacillus toyonensis strain BCT-7112T (NCIMB 14858T) has been widely used as an additive in animal nutrition for more than 30 years without reports of adverse toxigenic effects. However, this strain is resistant to chloramphenicol and tetracycline and it is generally considered inadvisable to introduce into the food chain resistance determinants capable of being transferred to other bacterial strains, thereby adding to the pool of such determinants in the gastro-enteric systems of livestock species. We therefore characterized the resistance phenotypes of this strain and its close relatives to determine whether they were of recent origin, and therefore likely to be transmissible. To this end we identified the genes responsible for chloramphenicol (catQ) and tetracycline (tetM) resistance and confirmed the presence of homologs in other members of the B. toyonensis taxonomic unit. Unexpectedly, closely related strains encoding these genes did not exhibit chloramphenicol and tetracycline resistance phenotypes. To understand the differences in the behaviors, we cloned and expressed the genes, together with their upstream regulatory regions, into Bacillus subtilis. The data showed that the genes encoded functional proteins, but were expressed inefficiently from their native promoters. B. toyonensis is a taxonomic unit member of the Bacillus cereus group (sensu lato). We therefore extended the analysis to determine the extent to which homologous chloramphenicol and tetracycline resistance genes were present in other species within this group. This analysis revealed that homologous genes were present in nearly all representative species within the B. cereus group (sensu lato). The absence of known transposition elements and the observations that they are found at the same genomic locations, indicates that these chloramphenicol and tetracycline resistance genes are of ancient origin and intrinsic to this taxonomic group, rather than recent acquisitions. In this context we discuss definitions of what are and are not intrinsic genes, an issue that is of fundamental importance to both Regulatory Authorities, and the animal feed and related industries.
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Affiliation(s)
- Helen Glenwright
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
| | - Susanne Pohl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant PauBarcelona, Spain
| | - Elisenda Miro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant PauBarcelona, Spain
| | | | - Anicet R. Blanch
- Department of Microbiology, University of BarcelonaBarcelona, Spain
| | - Colin R. Harwood
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Risks for public health related to the presence of Bacillus cereus and other Bacillus spp. including Bacillus thuringiensis in foodstuffs. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.4524] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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14
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Caputo A, Lagier J, Azza S, Robert C, Mouelhi D, Fournier P, Raoult D. Microvirga massiliensis sp. nov., the human commensal with the largest genome. Microbiologyopen 2016; 5:307-22. [PMID: 26749561 PMCID: PMC4831475 DOI: 10.1002/mbo3.329] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/12/2015] [Accepted: 11/19/2015] [Indexed: 11/09/2022] Open
Abstract
Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M. massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M. massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M. massiliensis JC119(T), together with the genome sequence information and its annotation.
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Affiliation(s)
- Aurélia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Jean‐Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Saïd Azza
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Donia Mouelhi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Pierre‐Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
- Special Infectious Agents UnitKing Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
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Dione N, Sankar S, Lagier JC, Khelaifia S, Michele C, Armstrong N, Richez M, Abrahão J, Raoult D, Fournier PE. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016; 10:66-76. [PMID: 26937282 PMCID: PMC4753391 DOI: 10.1016/j.nmni.2016.01.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 01/09/2023] Open
Abstract
Anaerosalibacter massiliensis sp. nov. strain ND1(T) (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes.
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Affiliation(s)
- N. Dione
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S.A. Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - C. Michele
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - M. Richez
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
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Fournier PE, Lagier JC, Dubourg G, Raoult D. From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 2015; 36:73-8. [DOI: 10.1016/j.anaerobe.2015.10.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/06/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023]
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Shimane Y, Minegishi H, Echigo A, Kamekura M, Itoh T, Ohkuma M, Tsubouchi T, Usui K, Maruyama T, Usami R, Hatada Y. Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample. Int J Syst Evol Microbiol 2015; 65:3830-3835. [PMID: 28875923 DOI: 10.1099/ijsem.0.000501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange-red-pigmented. Strain MH1-243-3T was able to grow at 15-27 % (w/v) NaCl (optimum 24 °C), at pH 4.5-6.5 (pH 5.5) and at 35-50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew within slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest phylogenetic relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarity. The rpoB' gene sequences of the three strains were also identical, and the closest phylogenetic relative was Halarchaeum acidiphilum JCM 16109T with 92.0 % similarity. The DNA G+C content of MH1-243-3T, MH1-243-5 and MH1-243-6 was 65.2 mol%. The levels of DNA-DNA relatedness amongst the three strains were 84.1-99.8 %, while that between MH1-243-3T and H. salinum MH1-34-1T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3-29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T ( = JCM 19585T = KCTC 4142T), isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 ( = JCM 19586) and MH1-243-6 ( = JCM 18422) are additional strains of the species.
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Affiliation(s)
- Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Hiroaki Minegishi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Research Institute of Industrial Technology, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Research Institute of Industrial Technology, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda, Chiba 278-0043, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Ron Usami
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Research Institute of Industrial Technology, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
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Sankar SA, Rathored J, Metidji S, Lagier JC, Khelaifia S, Labas N, Musso D, Raoult D, Fournier PE. Clostridium polynesiense sp. nov., a new member of the human gut microbiota in French Polynesia. Anaerobe 2015; 36:79-87. [PMID: 26485191 DOI: 10.1016/j.anaerobe.2015.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
Strain MS1, a Gram-positive, obligately anaerobic, motile and spore-forming rod belonging to the Clostridium genus, was isolated from the feces of a healthy Polynesian male living in French Polynesia. The temperature range for growth was 30-45 °C. We sequenced its complete genome and studied its phenotypic characteristics. The 3,560,738-bp long genome (one chromosome, no plasmid, G + C content 34%) contained 3535 protein-coding and 70 RNA genes. Strain MS1 exhibited a 98.24% 16S rRNA similarity with Clostridium amylolyticum, the phylogenetically closest species. When compared with other Clostridium species with standing in nomenclature, it had an average genomic similarity of 68.8-70%, a unique MALDI-TOF spectrum, and differed in nitrate reduction, motility and L-arabinose and D-lactose metabolism with most of the closest species. Therefore, strain MS1 is sufficiently distinct from type strains of the genus Clostridium to represent a novel species within this genus, for which the name Clostridium polynesiense sp. nov. is proposed. The type strain of C. polynesiense is MS1(T) (= CSUR P630 = DSM 27072).
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Affiliation(s)
- Senthil Alias Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Sarah Metidji
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Noemie Labas
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Musso
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Kämpfer P, McInroy JA, Glaeser SP. Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2015; 65:4093-4099. [PMID: 26294947 DOI: 10.1099/ijsem.0.000547] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA-DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA-DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
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Yuan PP, Ye WT, Pan JX, Han D, Zhang WJ, Cui HL. Halorussus amylolyticus sp. nov., isolated from an inland salt lake. Int J Syst Evol Microbiol 2015; 65:3734-3738. [PMID: 26228463 DOI: 10.1099/ijsem.0.000487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A halophilic archaeal strain, YC93T, was isolated from Yuncheng salt lake in Shanxi Province, China. Cells were pleomorphic rods, stained Gram-negative and formed light-red-pigmented colonies on agar plates. Strain YC93T was able to grow at 25–50 °C (optimum 37 °C), with 1.4–4.8 M NaCl (optimum 2.0 M), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 6.0–9.5 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). 16S rRNA gene sequence analysis revealed that strain YC93T had two dissimilar 16S rRNA genes both of which were phylogenetically related to those of the two recognized members of the genus Halorussus (93.0–95.3 % similarity). The rpoB′ gene of strain YC93T was phylogenetically related to the corresponding gene of Halorussus rarus TBN4T (91.3 % similarity) and Halorussus ruber YC25T (90.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and five glycolipids chromatographically identical to those of Halorussus rarus CGMCC 1.10122T. The DNA G+C content of strain YC93T was 64.6 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YC93T represents a novel species of the genus Halorussus, for which the name Halorussus amylolyticus sp. nov. is proposed. The type strain is YC93T ( = CGMCC 1.12126T = JCM 18367T).
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Affiliation(s)
- Pan-Pan Yuan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Wei-Tao Ye
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jia-Xiang Pan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Dong Han
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Wen-Jiao Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE. The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 2015; 38:276-86. [DOI: 10.1016/j.syapm.2015.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/16/2023]
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