@article{Frederiksen1970a, year = {1970}, journal = {Publication of the Faculty of Sciences University, J.E. Purkyne, Brno}, volume = {47}, pages = {89-94}, author = {Frederiksen, W.}, title = {\textit{Citrobacter koseri} (n. sp.), a new species within the genus \textit{Citrobacter}, with a comment on the taxonomic position of \textit{Citrobacter intermedium} (Werkman and Gillen).} } @article{YoungEtAl1971a, year = {1971}, journal = {International Journal of Systematic Bacteriology}, volume = {21}, pages = {58-63}, author = {Young, V.M. and Kenton, D.M. and Hobbs, B.J. and Moody, M.R.}, title = {\textit{Levinea}, a new genus of the family \textit{Enterobacteriaceae}.}, doi = {10.1099/00207713-21-1-58}, issue = {1} } @incollection{Farmeriii1981b, year = {1981}, booktitle = {The procaryotes, a handbook on habitats, isolation, and identification of bacteria}, publisher = {Springer-Verlag}, address = {Berlin}, editor = {Starr, M.P. and et al}, author = {Farmer Iii, J.J.}, title = {The genus \textit{Citrobacter}.}, pages = {1140-1147} } @article{YoungEtAl1971a, year = {1971}, journal = {International Journal of Systematic Bacteriology}, volume = {21}, pages = {58-63}, author = {Young, V.M. and Kenton, D.M. and Hobbs, B.J. and Moody, M.R.}, title = {\textit{Levinea}, a new genus of the family \textit{Enterobacteriaceae}.}, doi = {10.1099/00207713-21-1-58}, issue = {1} } @article{BrennerEtAl1982a, year = {1982}, journal = {J Clin Microbiol}, volume = {15}, pages = {703-713}, author = {Brenner, D.J. and Davis, B.R. and Steigerwalt, A.G. and Riddle, C.F. and McWhorter, A.C. and Allen, S.D. and Farmer, J.J. and Saitoh, Y. and Fanning, G.R.}, title = {Atypical biogroups of \textit{Escherichia coli} found in clinical specimens and description of \textit{Escherichia hermannii} sp. nov.}, abstract = {DNA relatedness was used to define the biochemical boundaries of \textit{Escherichia coli}. A large number of biochemically atypical strains were shown to belong to biogroups of \textit{E. coli}. These included strains negative in reactions for indole, all three decarboxylases, D-mannitol, lactose, or methyl red and strains positive in reactions for H2S, urea, citrate, KCN, adonitol, myo-inositol, or phenylalanine deaminase. Frequency and source data are presented for these atypical \textit{E. coli} biogroups. One group of KCN-positive, cellobiose-positive, yellow-pigmented strains was 84 to 91% interrelated but only 35 to 45% related to \textit{E. coli}. The name \textit{Escherichia hermannii} sp. nov. is proposed for this group of organisms that was formerly called Enteric Group 11 by the Enteric Section, Centers for Disease Control, Atlanta, GA. Twenty-nine strains of \textit{E. hermannii} have been isolated in the United States from a variety of clinical sources, principally wounds, sputum, and stools. Three additional strains were isolated from food. \textit{E. hermannii} strains are gram-negative, oxidase-negative, fermentative, motile rods. In addition to yellow pigment and positive KCN and cellobiose tests, the biochemical reactions characteristic of 32 strains of \textit{E. hermannii} were as follows: gas from D-glucose, acid from D-glucose, maltose, D-xylose, L-arabinose, L-rhamnose, and D-mannitol; no acid from adonitol or inositol; variable acid production from lactose and sucrose; positive tests for indole, methyl red, and mucate; negative tests for Voges-Proskauer. Simmons citrate, H2S, urea, phenylalanine deaminase, and gelatin hydrolysis; negative or delayed test for L-lysine decarboxylase and negative test for L-arginine dihydrolase; and positive test for ornithine decarboxylase. \textit{E. hermannii} strains were resistant to penicillin, ampicillin, and carbenicillin and sensitive to other commonly used antibiotics. Wounds account for almost 50% of human isolates of \textit{E. hermannii}, followed by sputum or lung isolates (ca. 25%) and stool isolates (20%).}, issue = {4}, pmid = {7040466} } @article{HuysEtAl2003b, year = {2003}, journal = {Int J Syst Evol Microbiol}, volume = {53}, pages = {807-810}, author = {Huys, G. and Cnockaert, M. and Janda, J.M. and Swings, J.}, title = {\textit{Escherichia albertii} sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children.}, abstract = {The taxonomic position of a group of five D-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), was investigated by DNA-DNA hybridization, phenotypic characterization and 16S rDNA sequencing. These strains were originally identified as '\textit{Hafnia alvei}-like' with the API 20E system but, in fact, show more phenotypic and genotypic resemblance to members of the genus \textit{Escherichia}. By 16S rDNA sequencing, one representative strain of the ICDDR,B group was shown to be closely affiliated to the genera \textit{Escherichia} and \textit{Shigella}. Using the fluorimetric microplate hybridization method, the diarrhoeagenic ICDDR,B isolates were found to constitute a homogeneous taxon (> or = 82% internal DNA relatedness), with the closest affiliation to the type strains of \textit{Escherichia coli} (55-64%) and \textit{Shigella flexneri} (54-60%). The DNA-DNA hybridization levels were much lower with members of other described \textit{Escherichia} species (16-45%) and with the type strain of \textit{H. alvei} (9-17%). The G + C content of the ICDDR,B strains ranged from 50.5 to 50.7 mol%. Together with the diagnostic characteristics reported previously, including the presence of the eaeA gene of enteropathogenic \textit{E. coli} and of the \textit{E. coli} and \textit{Shigella}-specific phoE gene, it is concluded that the ICDDR,B strains represent a novel taxon in the genus \textit{Escherichia}, for which the name \textit{Escherichia albertii} sp. nov. is proposed. Its type strain is Albert 19982\textsuperscript{T} (= LMG 20976\textsuperscript{T} = CCUG 46494\textsuperscript{T}).}, doi = {10.1099/ijs.0.02475-0}, issue = {3}, pmid = {12807204} } @article{GuEtAl2014a, year = {2014}, journal = {Int J Syst Evol Microbiol}, volume = {64}, pages = {2650-2656}, author = {Gu, C.T. and Li, C.Y. and Yang, L.J. and Huo, G.C.}, title = {\textit{Enterobacter xiangfangensis} sp. nov., isolated from Chinese traditional sourdough, and reclassification of \textit{Enterobacter sacchari} Zhu et al. 2013 as \textit{Kosakonia sacchari} comb. nov.}, abstract = {A Gram-stain-negative bacterial strain, 10-17\textsuperscript{T}, was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase beta subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase beta subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 10-17\textsuperscript{T} was phylogenetically related to \textit{Enterobacter hormaechei} CIP 103441\textsuperscript{T}, \textit{Enterobacter cancerogenus} LMG 2693\textsuperscript{T}, \textit{Enterobacter asburiae} JCM 6051\textsuperscript{T}, \textit{Enterobacter mori} LMG 25706\textsuperscript{T}, \textit{Enterobacter ludwigii} EN-119\textsuperscript{T} and \textit{Leclercia adecarboxylata} LMG 2803\textsuperscript{T}, having 99.5%, 99.3%, 98.7%, 98.5%, 98.4% and 98.4% 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, \textit{Enterobacter xiangfangensis} sp. nov., is proposed and the type strain is 10-17\textsuperscript{T} ( = LMG 27195\textsuperscript{T} = NCIMB 14836\textsuperscript{T} = CCUG 62994\textsuperscript{T}). \textit{Enterobacter sacchari} Zhu et al. 2013 was reclassified as \textit{Kosakonia sacchari} comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1\textsuperscript{T}( = CGMCC 1.12102\textsuperscript{T} = LMG 26783\textsuperscript{T}).}, doi = {10.1099/ijs.0.064709-0}, issue = {8}, pmid = {24824638} } @article{ZhuEtAl2013a, year = {2013}, journal = {Int J Syst Evol Microbiol}, volume = {63}, pages = {2577-2582}, author = {Zhu, B. and Zhou, Q. and Lin, L. and Hu, C. and Shen, P. and Yang, L. and An, Q. and Xie, G. and Li, Y.}, title = {\textit{Enterobacter sacchari} sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.).}, abstract = {Five nitrogen-fixing bacterial strains (SP1\textsuperscript{T}, NN143, NN144, NN208 and HX148) were isolated from stem, root or rhizosphere soil of sugar cane (Saccharum officinarum L.) plants. Cells were Gram-negative, motile, rods with peritrichous flagella. DNA G+C content was 55.0 +/- 0.5 mol%. Sequence determinations and phylogenetic analysis of 16S rRNA gene and rpoB indicated that the strains were affiliated with the genus \textit{Enterobacter} and most closely related to \textit{E. radicincitans} DSM 16656\textsuperscript{T} and \textit{E. oryzae} LMG 24251\textsuperscript{T}. Fluorimetric determination of thermal denaturation temperatures after DNA-DNA hybridization, enterobacterial repetitive intergenic consensus PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiated the whole-genome, genotype and protein profiles from those of \textit{E. radicincitans} and \textit{E. oryzae}. The strains' cell fatty acid composition differentiated them from \textit{E. radicincitans} and \textit{E. oryzae} by containing a higher level of summed feature 2 (C16 : 1omega7c and/or C16 : 1omega6c) and a lower level of C17 : 0 cyclo. Their physiological and biochemical profiles differentiated them from \textit{E. radicincitans} by being positive for methyl red test, ornithine decarboxylase and utilization of putrescine, D-arabitol, L-fucose and methyl alpha-D-glucoside and being negative for arginine dihydrolase, and differentiated them from \textit{E. oryzae} by being positive for aesculin hydrolysis and utilization of putrescine, D-arabitol and L-rhamnose and being negative for arginine dihydrolase, lysine decarboxylase and utilization of mucate. The five strains therefore represent a novel species, for which the name \textit{Enterobacter sacchari} sp. nov. is proposed, with the type strain SP1\textsuperscript{T} ( = CGMCC 1.12102\textsuperscript{T} = LMG 26783\textsuperscript{T}).}, doi = {10.1099/ijs.0.045500-0}, issue = {7}, pmid = {23291881} } @book{CastellaniChalmers1919a, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {Manual of Tropical Medicine, 3rd ed.}, publisher = {Williams Wood and Co.}, address = {New York} } @incollection{Migula1895c, year = {1895}, booktitle = {Die Naturlichen Pfanzenfamilien, Teil I, Abteilung Ia}, publisher = {W. Engelmann}, address = {Leipzig}, editor = {Engler, A. and Prantl, K.}, author = {Migula, W.}, title = {\textit{Bacteriaceae} (Stabchenbacterien).}, pages = {20-30} } @article{Burkey1928a, year = {1928}, journal = {Iowa State College Journal of Science}, volume = {3}, pages = {57-100}, author = {Burkey, L.A.}, title = {The fermentation of corn-stalks and their constituents. I. Studies on the pectin-fermenting bacteria.} } @article{WerkmanGillen1932a, year = {1932}, journal = {J Bacteriol}, volume = {23}, pages = {167-182}, author = {Werkman, C.H. and Gillen, G.F.}, title = {\textit{Bacteria} Producing Trimethylene Glycol.}, doi = {10.1128/jb.23.2.167-182.1932}, issue = {2}, pmid = {16559543} } @article{LeminorEtAl1982a, year = {1982}, journal = {Ann. Microbiol.}, volume = {133B}, pages = {245-254}, author = {Le Minor, L. and Véron, M. and Popoff, M.}, title = {Proposition pour une nomenclature des \textit{Salmonella}.} } @article{LeminorPopoff1987a, year = {1987}, journal = {Int. J. Syst. Bacteriol.}, volume = {37}, pages = {465-468}, author = {Le Minor, L. and Popoff, M.Y.}, title = {Request for an Opinion. Designation of \textit{Salmonella enterica} sp. nov., nom. rev., as the type and only species of the genus \textit{Salmonella}.}, doi = {10.1099/00207713-37-4-465}, issue = {4} } @incollection{Borman1957a, year = {1957}, booktitle = {Bergey's Manual of Determinative Bacteriology, 7th edition}, publisher = {The Williams & Wilkins Co}, address = {Baltimore}, editor = {Breed, R.S. and Murray, E.G.D. and Smith, N.R.}, author = {Borman, E.K.}, title = {Genus IV. \textit{Paracolobactrum} Borman et al., 1944,}, pages = {346-348} } @incollection{Kauffmann1964a, year = {1964}, booktitle = {The world problem of salmonellosis}, publisher = {Junk Publications}, address = {The Hague}, editor = {Van Oye, E.}, author = {Kauffmann, F.}, title = {Das Kauffmann-White-Schema.}, pages = {21-46} } @article{WarrenScott1930a, year = {1930}, journal = {J Hyg (Lond)}, volume = {29}, pages = {415-417}, author = {Warren, S.H. and Scott, W.M.}, title = {A New Serological Type of \textit{Salmonella}.}, issue = {4}, pmid = {20475042} } @incollection{Schroeter1889a, year = {1889}, booktitle = {Kryptogamen-Flora von Schlesien, Band 3, Heft 3, Pilze}, publisher = {Max Müller}, address = {Breslau}, editor = {Cohn, F.}, author = {Schroeter, J.}, title = {\textit{Schizomycetes} (1886), pp. 131-256.}, pages = {1-814} } @book{CastellaniChalmers1919a, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {Manual of Tropical Medicine, 3rd ed.}, publisher = {Williams Wood and Co.}, address = {New York} } @article{Ewing1949a, year = {1949}, journal = {J Bacteriol}, volume = {57}, pages = {633-638}, author = {Ewing, W.H.}, title = {SHIGELLA NOMENCLATURE.}, doi = {10.1128/jb.57.6.633-638.1949}, issue = {6}, pmid = {16561743} } @article{KampferEtAl2014d, year = {2014}, journal = {Syst Appl Microbiol}, volume = {37}, pages = {17-22}, author = {Kampfer, P. and Glaeser, S.P. and Raza, M.W. and Abbasi, S.A. and Perry, J.D.}, title = {\textit{Pseudocitrobacter} gen. nov., a novel genus of the \textit{Enterobacteriaceae} with two new species \textit{Pseudocitrobacter faecalis} sp. nov., and \textit{Pseudocitrobacter anthropi} sp. nov, isolated from fecal samples from hospitalized patients in Pakistan.}, abstract = {Four isolates of Gram-negative facultatively anaerobic bacteria, three of them producing NDM-1 carbapenemase, were isolated from hospitalized patients and outpatients attending two military hospitals in Rawalpindi, Pakistan, and studied for their taxonomic position. Initially the strains were phenotypically identified as \textit{Citrobacter} species. Comparative analysis of 16S rRNA gene sequences then showed that the four strains shared >97%, but in no case >98.3%, 16S rRNA gene sequence similarities to members of the genera \textit{Citrobacter}, \textit{Kluyvera}, \textit{Pantoea}, \textit{Enterobacter} and \textit{Raoultella}, but always formed a separate cluster in respective phylogenetic trees. Based on multilocus sequence analysis (MLSA) including partial recN, rpoA, thdF and rpoB gene sequence and respective amino acid sequence analysis it turned out that the strains also here always formed separate clusters. Based on further comparative analyses including DNA-DNA hybridizations, genomic fingerprint analysis using rep- and RAPD-PCRs and physiological tests, it is proposed to classify these four strains into the novel genus \textit{Pseudocitrobacter} gen. nov. with a new species \textit{Pseudocitrobacter faecalis} sp. nov. with strain 25 CIT\textsuperscript{T} (=CCM 8479\textsuperscript{T}=LMG 27751\textsuperscript{T}) and \textit{Pseudocitrobacter anthropi} sp. nov. with strain C138\textsuperscript{T} (=CCM 8478\textsuperscript{T}=LMG 27750\textsuperscript{T}), as the type strains, respectively.}, doi = {10.1016/j.syapm.2013.08.003}, issue = {1}, pmid = {24182752} } @article{KampferEtAl2020c, year = {2020}, journal = {Int J Syst Evol Microbiol}, volume = {70}, pages = {1315-1320}, author = {Kampfer, P. and Fuglsang-Damgaard, D. and Overballe-Petersen, S. and Hasman, H. and Hammerum, A.M. and Fuursted, K. and Blom, J. and Glaeser, S.P. and Hansen, F.}, title = {Taxonomic reassessment of the genus \textit{Pseudocitrobacter} using whole genome sequencing: \textit{Pseudocitrobacter anthropi} is a later heterotypic synonym of \textit{Pseudocitrobacter faecalis} and description of \textit{Pseudocitrobacter vendiensis} sp. nov.}, abstract = {The taxonomic status of all \textit{Pseudocitrobacter} species was re-evaluated by comparative genomics based on whole genome sequencing. As a result, it is obvious that \textit{Pseudocitrobacter anthropi} is a later heterotypic synonym of \textit{Pseudocitrobacter faecalis}. In addition, genome-based analysis of strain CPO20170097\textsuperscript{T}, isolated from a patient in northern Denmark was allocated to the genus \textit{Pseudocitrobacter}. This strain showed significant genotypic and phenotypic differences from \textit{P. faecalis} and it is proposed that this strain represents a novel species of the genus, for which the name \textit{Pseudocitrobacter vendiensis} sp. nov. is proposed with the type strain CPO20170097\textsuperscript{T} (=CCUG 73096\textsuperscript{T}=LMG 31042\textsuperscript{T}).}, doi = {10.1099/ijsem.0.003918}, issue = {2}, pmid = {31860429} } @article{LeminorEtAl1982a, year = {1982}, journal = {Ann. Microbiol.}, volume = {133B}, pages = {245-254}, author = {Le Minor, L. and Véron, M. and Popoff, M.}, title = {Proposition pour une nomenclature des \textit{Salmonella}.} } @article{Smith1894a, year = {1894}, journal = {Bulletin of the United States Bureau of Animal Industry}, volume = {6}, pages = {6-40}, author = {Smith, T.}, title = {The hog-cholera group of bacteria.} } @article{Weldin1927a, year = {1927}, journal = {Iowa State Journal of Science}, volume = {1}, pages = {121-197}, author = {Weldin, J.C.}, title = {The colon-typhoid group of bacteria and related forms. Relationships and classification.} } @article{JosephEtAl2012a, year = {2012}, journal = {Int J Syst Evol Microbiol}, volume = {62}, pages = {1277-1283}, author = {Joseph, S. and Cetinkaya, E. and Drahovska, H. and Levican, A. and Figueras, M.J. and Forsythe, S.J.}, title = {\textit{Cronobacter condimenti} sp. nov., isolated from spiced meat, and \textit{Cronobacter universalis} sp. nov., a species designation for \textit{Cronobacter} sp. genomospecies 1, recovered from a leg infection, water and food ingredients.}, abstract = {A re-evaluation of the taxonomic position of five strains, one assigned to \textit{Cronobacter sakazakii} (strain 1330\textsuperscript{T}, isolated from spiced meat purchased in Slovakia), two previously assigned to \textit{Cronobacter} genomospecies 1 (strains NCTC 9529\textsuperscript{T} and 731, isolated from water and a leg infection, respectively) and two previously assigned to \textit{Cronobacter turicensis} (strains 96 and 1435, isolated from onion powder and rye flour, respectively) was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing and multilocus sequence analysis (MLSA) of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, ppsA; 3036 bp). 16S rRNA gene sequence analysis and MLSA showed that strain 1330\textsuperscript{T} formed an independent phylogenetic lineage in the MLSA, with \textit{Cronobacter dublinensis} LMG 23823\textsuperscript{T} as the closest neighbour. DNA-DNA reassociation and phenotypic analysis revealed that strain 1330\textsuperscript{T} represented a novel species, for which the name \textit{Cronobacter condimenti} sp. nov. is proposed (type strain 1330\textsuperscript{T} = CECT 7863\textsuperscript{T} = LMG 26250\textsuperscript{T}). Strains NCTC 9529\textsuperscript{T}, 731, 96 and 1435 clustered together within an independent phylogenetic lineage, with \textit{C. turicensis} LMG 23827\textsuperscript{T} as the closest neighbour in the MLSA. DNA-DNA reassociation and phenotypic analysis confirmed that these strains represent a novel species, for which the name \textit{Cronobacter universalis} sp. nov. is proposed (type strain NCTC 9529\textsuperscript{T} = CECT 7864\textsuperscript{T} = LMG 26249\textsuperscript{T}).}, doi = {10.1099/ijs.0.032292-0}, issue = {6}, pmid = {22661070} } @article{HordtEtAl2020a, year = {2020}, journal = {Front Microbiol}, volume = {11}, pages = {468}, author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.}, title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of \textit{Alphaproteobacteria}.}, abstract = {The class \textit{Alphaproteobacteria} is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. \textit{Alphaproteobacteria} classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 \textit{Alphaproteobacteria} and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.}, doi = {10.3389/fmicb.2020.00468}, pmid = {32373076} } @article{LuoEtAl2012c, year = {2012}, journal = {Int J Syst Evol Microbiol}, volume = {62}, pages = {1271-1276}, author = {Luo, G. and Shi, Z. and Wang, H. and Wang, G.}, title = {\textit{Skermanella stibiiresistens} sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus \textit{Skermanella}.}, abstract = {A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22\textsuperscript{T}, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C(18:1)omega7c (63.5 %), summed feature 2 (C(14:0) 3-OH and/or iso-C(16:1) I, 10.8 %) and C(16:0) (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22\textsuperscript{T} was most closely related to \textit{Skermanella aerolata} 5416T-32\textsuperscript{T} (97.3 %), \textit{Skermanella parooensis} ACM 2042\textsuperscript{T} (95.8 %) and \textit{Skermanella xinjiangensis} 10-1-101\textsuperscript{T} (92.9 %). The DNA-DNA hybridization value between strain SB22\textsuperscript{T} and \textit{S. aerolata} KACC 11604\textsuperscript{T} ( = 5416T-32\textsuperscript{T}) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22\textsuperscript{T} and related species, it is considered that the isolate represents a novel species of the genus \textit{Skermanella}, for which the name \textit{Skermanella stibiiresistens} sp. nov. is proposed. The type strain is SB22\textsuperscript{T} ( = CGMCC 1.10751\textsuperscript{T} = KCTC 23364\textsuperscript{T}). An emended description of the genus \textit{Skermanella} is provided.}, doi = {10.1099/ijs.0.033746-0}, issue = {6}, pmid = {21784960} } @article{HardoimEtAl2013a, year = {2013}, journal = {BMC Microbiol}, volume = {13}, pages = {164}, author = {Hardoim, P.R. and Nazir, R. and Sessitsch, A. and Elhottova, D. and Korenblum, E. and van Overbeek, L.S. and van Elsas, J.D.}, title = {The new species \textit{Enterobacter oryziphilus} sp. nov. and \textit{Enterobacter oryzendophyticus} sp. nov. are key inhabitants of the endosphere of rice.}, abstract = {BACKGROUND: Six independent Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing rod-shaped isolates were obtained from the root endosphere of rice grown at the International Rice Research Institute (IRRI) and investigated in a polyphasic taxonomic study. RESULTS: The strains produced fatty acid patterns typical for members of the family \textit{Enterobacteriaceae}. Comparative sequence analyses of the 16S rRNA as well as rpoB genes allocated the strains to two well-defined groups within the genus \textit{Enterobacter}, family \textit{Enterobacteriaceae}. The analyses indicated \textit{Enterobacter radicincitans}, \textit{Enterobacter arachidis} and \textit{Enterobacter oryzae} to be the closest related species. An RpoB (translated) protein comparison supported the placement in the genus \textit{Enterobacter} and the relatedness of our isolates to the aforementioned species. Genomic DNA:DNA hybridization analyses and biochemical analyses provided further evidence that the novel strains belong to two new species within the genus \textit{Enterobacter}. The two species can be differentiated from each other and from existing enteric species by acid production from L-rhamnose and D-melibiose, decarboxylation of ornithine and utilization of D-alanine, D-raffinose L-proline and L-aspartic acid, among other characteristics. Members of both species revealed capacities to colonise rice roots, including plant-growth-promoting capabilities such as an active supply of fixed nitrogen to the plant and solubilisation of inorganic phosphorus, next to traits allowing adaptation to the plant. CONCLUSIONS: Two novel proposed enterobacterial species, denominated \textit{Enterobacter oryziphilus} sp. nov. (type strain REICA_142\textsuperscript{T}=LMG 26429\textsuperscript{T}=NCCB 100393\textsuperscript{T}) and \textit{Enterobacter oryzendophyticus} sp. nov. (type strain REICA_082\textsuperscript{T}=LMG 26432\textsuperscript{T} =NCCB 100390\textsuperscript{T}) were isolated from rice roots. Both species are capable of promoting rice growth by supplying nitrogen and phosphorus.}, doi = {10.1186/1471-2180-13-164}, pmid = {23865888} } @article{LiEtAl2016t, year = {2016}, journal = {Int J Syst Evol Microbiol}, volume = {66}, pages = {2780-2783}, author = {Li, C.Y. and Zhou, Y.L. and Ji, J. and Gu, C.T.}, title = {Reclassification of \textit{Enterobacter oryziphilus} and \textit{Enterobacter oryzendophyticus} as \textit{Kosakonia oryziphila} comb. nov. and \textit{Kosakonia oryzendophytica} comb. nov.}, abstract = {The taxonomic positions of \textit{Enterobacter oryziphilus} and \textit{Enterobacter oryzendophyticus} were re-examined on the basis of concatenated partial rpoB, atpD, gyrB and infB gene sequence analysis. The reconstructed phylogenetic tree based upon concatenated partial rpoB, atpD, gyrB and infB gene sequences clearly showed that \textit{E. oryziphilus} and \textit{E. oryzendophyticus} and all defined species of the genus \textit{Kosakonia} form a clade separate from other genera of the family \textit{Enterobacteriaceae}, and, therefore, these species of the genus \textit{Enterobacter} should be transferred to the genus \textit{Kosakonia}. \textit{E. oryziphilus} and \textit{E. oryzendophyticus} are reclassified as \textit{K. oryziphila} comb. nov. (type strain REICA_142T=LMG 26429T=NCCB 100393T) and \textit{K. oryzendophytica} comb. nov. (type strain REICA_082T=LMG 26432T=NCCB 100390T), respectively.}, doi = {10.1099/ijsem.0.001054}, issue = {8}, pmid = {27045188} } @article{IversenEtAl2007a, year = {2007}, journal = {BMC Evol Biol}, volume = {7}, pages = {64}, author = {Iversen, C. and Lehner, A. and Mullane, N. and Bidlas, E. and Cleenwerck, I. and Marugg, J. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {The taxonomy of \textit{Enterobacter sakazakii}: proposal of a new genus \textit{Cronobacter} gen. nov. and descriptions of \textit{Cronobacter sakazakii} comb. nov. \textit{Cronobacter sakazakii} subsp. \textit{sakazakii}, comb. nov., \textit{Cronobacter sakazakii} subsp. \textit{malonaticus} subsp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov. and \textit{Cronobacter} genomospecies 1.}, abstract = {BACKGROUND: \textit{Enterobacter sakazakii} is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as \textit{E. sakazakii} was further investigated. RESULTS: Strains identified as \textit{E. sakazakii} were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified. CONCLUSION: This study clarifies the taxonomy of \textit{E. sakazakii} and proposes a reclassification of these organisms.}, doi = {10.1186/1471-2148-7-64}, pmid = {17439656} } @article{IversenEtAl2008a, year = {2008}, journal = {Int J Syst Evol Microbiol}, volume = {58}, pages = {1442-1447}, author = {Iversen, C. and Mullane, N. and McCardell, B. and Tall, B.D. and Lehner, A. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {\textit{Cronobacter} gen. nov., a new genus to accommodate the biogroups of \textit{Enterobacter sakazakii}, and proposal of \textit{Cronobacter sakazakii} gen. nov., comb. nov., \textit{Cronobacter malonaticus} sp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov., \textit{Cronobacter} genomospecies 1, and of three subspecies, \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov., \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov.}, abstract = {[\textit{Enterobacter}] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, \textit{Cronobacter} gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, \textit{Cronobacter dublinensis} sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: \textit{Cronobacter sakazakii} gen. nov., comb. nov. [type strain ATCC 29544\textsuperscript{T} (=NCTC 11467\textsuperscript{T})]; \textit{Cronobacter malonaticus} sp. nov. [type strain CDC 1058-77\textsuperscript{T} (=LMG 23826\textsuperscript{T}=DSM 18702\textsuperscript{T})]; \textit{Cronobacter turicensis} sp. nov. [type strain z3032\textsuperscript{T} (=LMG 23827\textsuperscript{T}=DSM 18703\textsuperscript{T})]; \textit{Cronobacter muytjensii} sp. nov. [type strain ATCC 51329\textsuperscript{T} (=CIP 103581\textsuperscript{T})]; \textit{Cronobacter dublinensis} sp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. [type strain E515\textsuperscript{T} (=LMG 23824=DSM 18706\textsuperscript{T})], and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov. [type strain E464\textsuperscript{T} (=LMG 23825\textsuperscript{T}=DSM 18707\textsuperscript{T})].}, doi = {10.1099/ijs.0.65577-0}, issue = {6}, pmid = {18523192} } @article{IversenEtAl2007a, year = {2007}, journal = {BMC Evol Biol}, volume = {7}, pages = {64}, author = {Iversen, C. and Lehner, A. and Mullane, N. and Bidlas, E. and Cleenwerck, I. and Marugg, J. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {The taxonomy of \textit{Enterobacter sakazakii}: proposal of a new genus \textit{Cronobacter} gen. nov. and descriptions of \textit{Cronobacter sakazakii} comb. nov. \textit{Cronobacter sakazakii} subsp. \textit{sakazakii}, comb. nov., \textit{Cronobacter sakazakii} subsp. \textit{malonaticus} subsp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov. and \textit{Cronobacter} genomospecies 1.}, abstract = {BACKGROUND: \textit{Enterobacter sakazakii} is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as \textit{E. sakazakii} was further investigated. RESULTS: Strains identified as \textit{E. sakazakii} were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified. CONCLUSION: This study clarifies the taxonomy of \textit{E. sakazakii} and proposes a reclassification of these organisms.}, doi = {10.1186/1471-2148-7-64}, pmid = {17439656} } @article{IversenEtAl2008a, year = {2008}, journal = {Int J Syst Evol Microbiol}, volume = {58}, pages = {1442-1447}, author = {Iversen, C. and Mullane, N. and McCardell, B. and Tall, B.D. and Lehner, A. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {\textit{Cronobacter} gen. nov., a new genus to accommodate the biogroups of \textit{Enterobacter sakazakii}, and proposal of \textit{Cronobacter sakazakii} gen. nov., comb. nov., \textit{Cronobacter malonaticus} sp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov., \textit{Cronobacter} genomospecies 1, and of three subspecies, \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov., \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov.}, abstract = {[\textit{Enterobacter}] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, \textit{Cronobacter} gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, \textit{Cronobacter dublinensis} sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: \textit{Cronobacter sakazakii} gen. nov., comb. nov. [type strain ATCC 29544\textsuperscript{T} (=NCTC 11467\textsuperscript{T})]; \textit{Cronobacter malonaticus} sp. nov. [type strain CDC 1058-77\textsuperscript{T} (=LMG 23826\textsuperscript{T}=DSM 18702\textsuperscript{T})]; \textit{Cronobacter turicensis} sp. nov. [type strain z3032\textsuperscript{T} (=LMG 23827\textsuperscript{T}=DSM 18703\textsuperscript{T})]; \textit{Cronobacter muytjensii} sp. nov. [type strain ATCC 51329\textsuperscript{T} (=CIP 103581\textsuperscript{T})]; \textit{Cronobacter dublinensis} sp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. [type strain E515\textsuperscript{T} (=LMG 23824=DSM 18706\textsuperscript{T})], and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov. [type strain E464\textsuperscript{T} (=LMG 23825\textsuperscript{T}=DSM 18707\textsuperscript{T})].}, doi = {10.1099/ijs.0.65577-0}, issue = {6}, pmid = {18523192} } @article{LiuEtAl2015s, year = {2015}, journal = {Int J Syst Evol Microbiol}, volume = {65}, pages = {2130-2134}, author = {Liu, S. and Jin, D. and Lan, R. and Wang, Y. and Meng, Q. and Dai, H. and Lu, S. and Hu, S. and Xu, J.}, title = {\textit{Escherichia marmotae} sp. nov., isolated from faeces of Marmota himalayana.}, abstract = {The taxonomic position of a group of seven closely related lactose-negative enterobacterial strains, which were isolated from fresh faecal samples of Marmota himalayana collected from the Qinghai-Tibetan plateau, China, was determined by using a polyphasic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods (0.5-1 x 1-2.5 mum). By 16S rRNA gene sequences, the representative strain, HT073016\textsuperscript{T}, showed highest similarity values with \textit{Escherichia fergusonii} ATCC 35469\textsuperscript{T} at 99.3%, \textit{Escherichia coli} ATCC 11775\textsuperscript{T} at 99.2%, \textit{Escherichia albertii} LMG 20976\textsuperscript{T} at 98.9%, \textit{Escherichia hermannii} CIP 103176\textsuperscript{T} at 98.4%, and \textit{Escherichia vulneris} ATCC 33821\textsuperscript{T} at 97.7%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the seven strains formed a monophyletic group with five other species of the genus \textit{Escherichia}. Digital DNA-DNA hybridization studies between strain HT073016\textsuperscript{T} and five other species of the genus \textit{Escherichia} showed that it shared less than 70% DNA-DNA relatedness with all known species of the genus \textit{Escherichia}, supporting the novel species status of the strain. The DNA G+C content of strain HT073016\textsuperscript{T} was 53.8 mol%. On the basis of phenotypic and phylogenetic characteristics, strain HT073016\textsuperscript{T} and the six other HT073016\textsuperscript{T}-like strains were clearly distinct from the type strains of other recognized species of the genus \textit{Escherichia} and represent a novel species of the genus \textit{Escherichia}, for which the name \textit{Escherichia marmotae} sp. nov. is proposed, with HT073016\textsuperscript{T} ( = CGMCC 1.12862\textsuperscript{T} = DSM 28771\textsuperscript{T}) as the type strain.}, doi = {10.1099/ijs.0.000228}, issue = {7}, pmid = {25851592} } @article{FarmeriiiEtAl1980a, year = {1980}, journal = {Int. J. Syst. Bacteriol.}, volume = {30}, pages = {569-584}, author = {Farmer Iii, J.J. and Asbury, M.A. and Hickman, F.W. and Brenner, D.J. and The, E.}, title = {\textit{Enterobacter sakazakii}: a new species of "\textit{Enterobacteriaceae}" isolated from clinical specimens.}, doi = {10.1099/00207713-30-3-569}, issue = {3} } @article{IversenEtAl2007a, year = {2007}, journal = {BMC Evol Biol}, volume = {7}, pages = {64}, author = {Iversen, C. and Lehner, A. and Mullane, N. and Bidlas, E. and Cleenwerck, I. and Marugg, J. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {The taxonomy of \textit{Enterobacter sakazakii}: proposal of a new genus \textit{Cronobacter} gen. nov. and descriptions of \textit{Cronobacter sakazakii} comb. nov. \textit{Cronobacter sakazakii} subsp. \textit{sakazakii}, comb. nov., \textit{Cronobacter sakazakii} subsp. \textit{malonaticus} subsp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov. and \textit{Cronobacter} genomospecies 1.}, abstract = {BACKGROUND: \textit{Enterobacter sakazakii} is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as \textit{E. sakazakii} was further investigated. RESULTS: Strains identified as \textit{E. sakazakii} were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified. CONCLUSION: This study clarifies the taxonomy of \textit{E. sakazakii} and proposes a reclassification of these organisms.}, doi = {10.1186/1471-2148-7-64}, pmid = {17439656} } @article{IversenEtAl2008a, year = {2008}, journal = {Int J Syst Evol Microbiol}, volume = {58}, pages = {1442-1447}, author = {Iversen, C. and Mullane, N. and McCardell, B. and Tall, B.D. and Lehner, A. and Fanning, S. and Stephan, R. and Joosten, H.}, title = {\textit{Cronobacter} gen. nov., a new genus to accommodate the biogroups of \textit{Enterobacter sakazakii}, and proposal of \textit{Cronobacter sakazakii} gen. nov., comb. nov., \textit{Cronobacter malonaticus} sp. nov., \textit{Cronobacter turicensis} sp. nov., \textit{Cronobacter muytjensii} sp. nov., \textit{Cronobacter dublinensis} sp. nov., \textit{Cronobacter} genomospecies 1, and of three subspecies, \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov., \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov.}, abstract = {[\textit{Enterobacter}] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, \textit{Cronobacter} gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, \textit{Cronobacter dublinensis} sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: \textit{Cronobacter sakazakii} gen. nov., comb. nov. [type strain ATCC 29544\textsuperscript{T} (=NCTC 11467\textsuperscript{T})]; \textit{Cronobacter malonaticus} sp. nov. [type strain CDC 1058-77\textsuperscript{T} (=LMG 23826\textsuperscript{T}=DSM 18702\textsuperscript{T})]; \textit{Cronobacter turicensis} sp. nov. [type strain z3032\textsuperscript{T} (=LMG 23827\textsuperscript{T}=DSM 18703\textsuperscript{T})]; \textit{Cronobacter muytjensii} sp. nov. [type strain ATCC 51329\textsuperscript{T} (=CIP 103581\textsuperscript{T})]; \textit{Cronobacter dublinensis} sp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{dublinensis} subsp. nov. [type strain DES187\textsuperscript{T} (=LMG 23823\textsuperscript{T}=DSM 18705\textsuperscript{T})]; \textit{Cronobacter dublinensis} subsp. \textit{lausannensis} subsp. nov. [type strain E515\textsuperscript{T} (=LMG 23824=DSM 18706\textsuperscript{T})], and \textit{Cronobacter dublinensis} subsp. \textit{lactaridi} subsp. nov. [type strain E464\textsuperscript{T} (=LMG 23825\textsuperscript{T}=DSM 18707\textsuperscript{T})].}, doi = {10.1099/ijs.0.65577-0}, issue = {6}, pmid = {18523192} } @article{HoffmannEtAl2005a, year = {2005}, journal = {Syst Appl Microbiol}, volume = {28}, pages = {196-205}, author = {Hoffmann, H. and Stindl, S. and Ludwig, W. and Stumpf, A. and Mehlen, A. and Heesemann, J. and Monget, D. and Schleifer, K.H. and Roggenkamp, A.}, title = {Reassignment of enterobacter dissolvens to \textit{Enterobacter cloacae} as \textit{E. cloacae} subspecies dissolvens comb. nov. and emended description of \textit{Enterobacter asburiae} and \textit{Enterobacter kobei}.}, abstract = {The taxonomic position of \textit{Enterobacter dissolvens} was re-evaluated based on the analysis of the type strain ATCC 23373T and three clinical isolates. The strains were assigned to the genetic cluster of the species by phylogenetic sequence analysis in the frame of a recent population genetic study. The relatedness of E. dissolves to the other species of the \textit{E. cloacae} complex was analyzed by DNA-DNA hybridization studies based on melting profiles in microplates. The genetic cluster of \textit{E. dissolvens} fell into the same DNA-relatedness group like \textit{E. cloacae} with mean deltaTm-values of 3.9 degrees C confirming the hybridization results of three former studies. Phenotypic analysis of the \textit{E. cloacae} and \textit{E. dissolvens} strains, respectively, based on 115 biochemical reactions yielded the esculin test as the only one differentiating between them by being positive for \textit{E. dissolvens} and negative for \textit{E. cloacae} strains. The name \textit{E. cloacae} subsp. \textit{dissolvens} comb. nov. is proposed for the group of organisms formerly referred to as \textit{E. dissolvens}, and the name \textit{E. cloacae} subsp. \textit{cloacae} comb. nov. for the group of organisms formerly referred to as \textit{E. cloacae}. The species descriptions of \textit{Enterobacter kobei} and \textit{Enterobacter asburiae} were emended based on the data collected on 17 and 15 strains, respectively. The strains were assigned to the respective species by a combination of phylogenetic sequence analyzes and DNA-DNA hybridizations. Phenotypic analyzes of 115 reactions gave detailed species profiles with new differentiating phenotypic properties.}, doi = {10.1016/j.syapm.2004.12.010}, issue = {3}, pmid = {15900966} } @article{HormaecheEdwards1960a, year = {1960}, journal = {International Bulletin of Bacteriological Nomenclature and Taxonomy}, volume = {10}, pages = {71-74}, author = {Hormaeche, E. and Edwards, P.R.}, title = {A proposed genus \textit{Enterobacter}.}, doi = {10.1099/0096266x-10-2-71} } @book{CastellaniChalmers1919s, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {A Manual of Tropical Medicine. 3rd ed}, publisher = {William Wood and Co}, address = {New York} } @book{LehmannNeumann1896b, author = {Lehmann, K.B. and Neumann, R.}, year = {1896}, title = {Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen bakteriologischen Diagnostik. Teil 2: Text, 1st ed.}, publisher = {J.F. Lehmann}, address = {München} } @incollection{Jordan1890a, year = {1890}, booktitle = {A report of the biological work of the Lawrence Experiment Station, including an account of methods employed and results obtained in the microscopical and bacteriological investigation of sewage and water. Report on water supply and sewerage (Part II). Report of the Massachusetts Board of Public Health}, publisher = {Massachusetts Board of Public Health}, address = {Boston}, editor = {Sedgewick, W.T.}, author = {Jordan, E.O.}, title = {A report on certain species of bacteria observed in sewage.}, pages = {821-844} } @article{BurgessEtAl1973a, year = {1973}, journal = {Journal of Hygiene (Cambridge)}, volume = {71}, pages = {1-7}, author = {Burgess, N.R.H. and McDermott, S.N. and Whiting, J.}, title = {Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis.}, doi = {10.1017/s0022172400046155} } @article{PriestBarker2010a, year = {2010}, journal = {Int J Syst Evol Microbiol}, volume = {60}, pages = {828-833}, author = {Priest, F.G. and Barker, M.}, title = {Gram-negative bacteria associated with brewery yeasts: reclassification of \textit{Obesumbacterium proteus} biogroup 2 as \textit{Shimwellia pseudoproteus} gen. nov., sp. nov., and transfer of \textit{Escherichia blattae} to \textit{Shimwellia blattae} comb. nov.}, abstract = {Phylogenetic analyses of type and reference strains of \textit{Obesumbacterium proteus} biogroups 1 and 2 plus a novel isolate of biogroup 2 were carried out based on 16S rRNA gene sequences and partial sequences of four protein-coding genes (fusA, leuS, pyrG and rpoB). Both approaches revealed that \textit{O. proteus} biogroup 1 strains were closely related to \textit{Hafnia alvei}. Biogroup 2 strains, however, formed a distinct monophyletic clade of generic status that included \textit{Escherichia blattae}. Phenotypic tests were consistent with the molecular classification and provided diagnostic features. It is proposed that biogroup 2 strains be placed in a new genus, \textit{Shimwellia} gen. nov., as \textit{Shimwellia pseudoproteus} sp. nov., with strain 521\textsuperscript{T} (=DSM 3038\textsuperscript{T}=LMG 24835\textsuperscript{T}=NCIMB 14534\textsuperscript{T}) as the type strain, and that \textit{Escherichia blattae} be transferred to the genus \textit{Shimwellia} as \textit{Shimwellia blattae} comb. nov., with strain ATCC 29907( T) (=DSM 4481\textsuperscript{T}) as the type strain.}, doi = {10.1099/ijs.0.013458-0}, issue = {4}, pmid = {19661513} } @article{FarmerEtAl1985a, year = {1985}, journal = {J Clin Microbiol}, volume = {21}, pages = {77-81}, author = {Farmer, J.J. and Fanning, G.R. and Davis, B.R. and O'Hara, C.M. and Riddle, C. and Hickman-Brenner, F.W. and Asbury, M.A. and Lowery, V.A. and Brenner, D.J.}, title = {\textit{Escherichia fergusonii} and \textit{Enterobacter taylorae}, two new species of \textit{Enterobacteriaceae} isolated from clinical specimens.}, abstract = {\textit{Escherichia fergusonii} (formerly known as Enteric Group 10) and \textit{Enterobacter taylorae} (formerly known as Enteric Group 19) are proposed as new species in the family \textit{Enterobacteriaceae}. By DNA hybridization (32P, 60 degrees C, hydroxyapatite), strains of \textit{E. fergusonii} were 90 to 97% related to the type strain (holotype) ATCC 35469. They were most closely related to \textit{Escherichia coli} and more distantly related to species in other genera. \textit{E. fergusonii} strains are positive for indole production, methyl red, lysine decarboxylase, ornithine decarboxylase, and motility. They ferment D-glucose with gas production and also ferment adonitol, L-arabinose, L-rhamnose, maltose, D-xylose, trehalose, cellobiose, and D-arabitol. They are negative for Voges-Proskauer, citrate utilization (17% positive), urea hydrolysis, phenylalanine deamination, arginine dihydrolase, growth in KCN, and fermentation of lactose, sucrose, myo-inositol, D-sorbitol, raffinose, and alpha-methyl-D-glucoside. By DNA hybridization (32P, 60 degrees C, hydroxyapatite), strains of \textit{E. taylorae} were 84 to 95% related to the type strain (holotype) ATCC 35317. Their nearest relative was \textit{E. cloacae}, to which they were 61% related. Other named species were more distantly related. Strains of \textit{E. taylorae} are positive for Voges-Proskauer, citrate utilization, arginine dihydrolase, ornithine decarboxylase, motility, growth in KCN medium, and malonate utilization. They ferment D-glucose with gas production and also ferment D-mannitol, L-arabinose, L-rhamnose, maltose, D-xylose, trehalose, and cellobiose. They are negative for indole production, methyl red, H2S production on triple sugar-iron agar, urea hydrolysis, phenylalanine deamination, lysine decarboxylase, gelatin hydrolysis, and fermentation of adonitol, i-inositol, D-sorbitol, and raffinose. Both new species occur in human clinical specimens. Two strains of \textit{E. fergusonii} were isolated from blood. Five stains of \textit{E. taylorae} were isolated from blood, and one was from spinal fluid. These blood and spinal fluid isolates suggest possible clinical significance, but this point requires further study.}, doi = {10.1128/jcm.21.1.77-81.1985}, issue = {1}, pmid = {3968204} } @article{LeminorPopoff1987a, year = {1987}, journal = {Int. J. Syst. Bacteriol.}, volume = {37}, pages = {465-468}, author = {Le Minor, L. and Popoff, M.Y.}, title = {Request for an Opinion. Designation of \textit{Salmonella enterica} sp. nov., nom. rev., as the type and only species of the genus \textit{Salmonella}.}, doi = {10.1099/00207713-37-4-465}, issue = {4} } @article{Loeffler1892a, year = {1892}, journal = {Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene, Abteilung I}, volume = {11}, pages = {129-141}, author = {Loeffler, F.}, title = {Über Epidemieen unter den im hygienischen Institut zu Greifswald gehaltenen Mäusen und über die Bekämpfung der Feldmausplage.} } @book{CastellaniChalmers1919a, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {Manual of Tropical Medicine, 3rd ed.}, publisher = {Williams Wood and Co.}, address = {New York} } @article{Loeffler1892a, year = {1892}, journal = {Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene, Abteilung I}, volume = {11}, pages = {129-141}, author = {Loeffler, F.}, title = {Über Epidemieen unter den im hygienischen Institut zu Greifswald gehaltenen Mäusen und über die Bekämpfung der Feldmausplage.} } @book{CastellaniChalmers1919a, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {Manual of Tropical Medicine, 3rd ed.}, publisher = {Williams Wood and Co.}, address = {New York} } @article{Levine1920a, year = {1920}, journal = {Journal of Infectious Diseases}, volume = {27}, pages = {31-39}, author = {Levine, M.}, title = {Dysentery and allied bacilli.}, doi = {10.1093/infdis/27.1.31} } @article{Weldin1927a, year = {1927}, journal = {Iowa State Journal of Science}, volume = {1}, pages = {121-197}, author = {Weldin, J.C.}, title = {The colon-typhoid group of bacteria and related forms. Relationships and classification.} } @article{Shiga1897a, year = {1897}, journal = {Saikingaku-Zasshi}, volume = {25}, pages = {790-810}, author = {Shiga, K.}, title = {Sekiri Byogen Kenkyu Hokoku Dai-Ichi (First report on etiologic research on dysentery).} } @book{CastellaniChalmers1919a, author = {Castellani, A. and Chalmers, A.J.}, year = {1919}, title = {Manual of Tropical Medicine, 3rd ed.}, publisher = {Williams Wood and Co.}, address = {New York} } @article{LeminorEtAl1982a, year = {1982}, journal = {Ann. Microbiol.}, volume = {133B}, pages = {245-254}, author = {Le Minor, L. and Véron, M. and Popoff, M.}, title = {Proposition pour une nomenclature des \textit{Salmonella}.} } @article{LeminorPopoff1987a, year = {1987}, journal = {Int. J. Syst. Bacteriol.}, volume = {37}, pages = {465-468}, author = {Le Minor, L. and Popoff, M.Y.}, title = {Request for an Opinion. Designation of \textit{Salmonella enterica} sp. nov., nom. rev., as the type and only species of the genus \textit{Salmonella}.}, doi = {10.1099/00207713-37-4-465}, issue = {4} } @article{ReevesEtAl1989a, year = {1989}, journal = {J Clin Microbiol}, volume = {27}, pages = {313-320}, author = {Reeves, M.W. and Evins, G.M. and Heiba, A.A. and Plikaytis, B.D. and Farmer, J.J.}, title = {Clonal nature of \textit{Salmonella typhi} and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of \textit{Salmonella bongori} comb. nov.}, abstract = {Crude cell extracts of 26 isolates of \textit{Salmonella} serotype typhi (\textit{S. typhi}) and 48 other \textit{Salmonella} isolates representing 28 serotypes and seven DNA hybridization subgroups were analyzed for electrophoretic variants of 24 metabolic enzymes by starch gel electrophoresis. All strains of \textit{S. typhi} had identical isoenzyme patterns, indicating that they were a single clone. All of the enzymes detected in the remaining strains were polymorphic, and the degree of genetic variation was quite high. The average number of alleles per enzyme locus was 4.7, and the mean genetic diversity per locus was 0.556. Thirty-two distinct allele profiles, or electrophoretic types (ETs), were found in these 48 strains of \textit{Salmonella} serotypes other than \textit{S. typhi}. Analysis of the genetic relationships of the ETs to each other showed that, with one exception, the ETs formed subgroups that were consistent with the subgroupings based on DNA hybridization studies. ET profiles were not always linked to specific serologic patterns. These data show that multilocus enzyme electrophoresis has a potential application in epidemiologic and taxonomic studies of salmonellae, although it is not differential for \textit{S. typhi}. We also propose a new species, \textit{Salmonella bongori} comb. nov., a new combination base on the elevation of \textit{Salmonella choleraesuis} subsp. \textit{bongori} to the level of species.}, doi = {10.1128/jcm.27.2.313-320.1989}, issue = {2}, pmid = {2915026} }