Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazi

Rodentibacter gen. nov. is proposed based on isolation and phenotypic characterization of strains, predominantly from rodents. The strains showed 86 % or higher rpoB gene sequence similarity and indicated a genus-level relationship within Pasteurellaceae. The strains compared at 16S rRNA gene sequence level showed 93.8 % or higher similarity, and their genus-level relationship within Pasteurellaceae was confirmed by phenotypic analysis. The type species Rodentibacter pneumotropicus comb. nov. is reclassified from [Pasteurella] pneumotropica with type strain NCTC 8141T (=CCUG 12398T). Whole genomic comparison allowed the estimation of DNA-DNA renaturation. Rodentibacter heylii sp. nov. was proposed for a group that included the biovar Heyl of [Pasteurella] pneumotropica with the type strain ATCC 12555T (=CCUG 998T). A group was proposed as Rodentibacter ratti sp. nov., which included the taxon 22 of Bisgaard; the type strain is F75T (=CCUG 69665T=DSM 103977T). Taxon 41 of Bisgaard was proposed as Rodentibacter myodis sp. nov. with type strain Ac151T (=CCUG 69666T=DSM 103994T). Rodentibacter heidelbergensis sp. nov. included the type strain 1996025094T (=Ac69T) (=CCUG 69667T=DSM 103978T). A group strains of was proposed as Rodentibacter trehalosifermentans sp. nov. with type strain H1987082031T (=CCUG 69668T=DSM 104075T). Two strains including the reference strain of taxon 17 of Bisgaard that showed 16S rRNA gene similarity of 97.3 % were proposed as Rodentibacter rarus sp. nov. 2325/79T (=CCUG 17206T=DSM 103980T). Rodentibacter mrazii sp. nov. was proposed with type strain Ppn418T (Bisgaard taxon 21) (=CCUG 69669T=DSM 103979T). The eight species could be separated based on phenotypic characteristics such as NAD requirement, ornithine decarboxylase and indole formation, α-glucosidase, β-galactosidase and in acid formation from (+)-l-arabinose, (-)-d-ribose, (+)-d-xylose, myo-inositol, (-)-d-mannitol, lactose, melibiose and trehalose. Forty-six strains including taxon 48 of Bisgaard formed a monophyletic group by rpoB and 16S rRNA gene sequence analysis, but could not be separated phenotypically from R. pneumotropicus and R. heylii, and it was left as an unnamed genomospecies 1 of Rodentibacter with reference strain Ppn416. Another taxon that included 13 strains, mainly isolated from Apodemus sylvaticus, could not be separated phenotypically from R. pneumotropicus or R. heylii and was designated as genomospecies 2. Strain Ppn85 with 95 % or less rpoB gene sequence similarity and with 16S rRNA gene sequence similarity of 97 % or less to the other members of Rodentibacter was left as an unnamed singleton.

[1]  A. Benner,et al.  Prevalence and biochemical properties of V factor-dependent Pasteurellaceae from rodents. , 1993, Zentralblatt fur Bakteriologie : international journal of medical microbiology.

[2]  M. Bertelsen,et al.  Bisgaardia miroungae sp. nov., a new member of the family Pasteurellaceae isolated from the oral cavity of northern elephant seals (Mirounga angustirostris), and emended description of the genus Bisgaardia. , 2015, International journal of systematic and evolutionary microbiology.

[3]  J. E. Olsen,et al.  Reclassification of Bisgaard taxon 33, with proposal of Volucribacter psittacicida gen. nov., sp. nov. and Volucribacter amazonae sp. nov. as new members of the Pasteurellaceae. , 2004, International journal of systematic and evolutionary microbiology.

[4]  R. Mutters,et al.  Characterization of some previously unclassified "Pasteurella" spp. obtained from the oral cavity of dogs and cats and description of a new species tentatively classified with the family Pasteurellaceae Pohl 1981 and provisionally called taxon 16. , 2009, Acta pathologica, microbiologica, et immunologica Scandinavica. Section B, Microbiology.

[5]  H. Christensen,et al.  Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis 'Haemophilus somnus', 'Haemophilus agni' and 'Histophilus ovis'. , 2003, International journal of systematic and evolutionary microbiology.

[6]  I. Mikaelian,et al.  Proposal of Bisgaardia hudsonensis gen. nov., sp. nov. and an additional genomospecies, isolated from seals, as new members of the family Pasteurellaceae. , 2011, International journal of systematic and evolutionary microbiology.

[7]  M. Kilian,et al.  Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov. , 2005, International journal of systematic and evolutionary microbiology.

[8]  B. Korczak,et al.  Phylogeny of the family Pasteurellaceae based on rpoB sequences. , 2004, International journal of systematic and evolutionary microbiology.

[9]  W. Whitman,et al.  Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. , 2002, International journal of systematic and evolutionary microbiology.

[10]  Henrik Christensen,et al.  Revised definition of Actinobacillus sensu stricto isolated from animals. A review with special emphasis on diagnosis. , 2004, Veterinary microbiology.

[11]  M. Raspa,et al.  FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units , 2014, Laboratory animals.

[12]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[13]  H. Busse,et al.  Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae. , 2007, International journal of systematic and evolutionary microbiology.

[14]  H. Christensen,et al.  Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov. , 2015, International journal of systematic and evolutionary microbiology.

[15]  M. Bisgaard,et al.  Reclassification of 30 Pasteurellaceae strains isolated from rodents , 1995, Laboratory animals.

[16]  J. Heyl A study ofPasteurella strains from animal sources , 2005, Antonie van Leeuwenhoek.

[17]  M. Bisgaard ISOLATION AND CHARACTERIZATION OF SOME PREVIOUSLY UNREPORTED TAXA FROM POULTRY WITH PHENOTYPICAL CHARACTERS RELATED TO ACTINOBACILLUS- AND PASTEURELLA SPECIES , 2009 .

[18]  J. E. Olsen,et al.  Phylogenetic analysis by 16S rDNA gene sequence comparison of avian taxa of Bisgaard and characterization and description of two new taxa of Pasteurellaceae , 2003, Journal of applied microbiology.

[19]  B. Korczak,et al.  Nicoletella semolina gen. nov., sp. nov., a New Member of Pasteurellaceae Isolated from Horses with Airway Disease , 2004, Journal of Clinical Microbiology.

[20]  B. Korczak,et al.  Classification of the taxon 2 and taxon 3 complex of Bisgaard within Gallibacterium and description of Gallibacterium melopsittaci sp. nov., Gallibacterium trehalosifermentans sp. nov. and Gallibacterium salpingitidis sp. nov. , 2009, International journal of systematic and evolutionary microbiology.

[21]  M. Kilian,et al.  Reclassification of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, Haemophilus paraphrophilus and Haemophilus segnis as Aggregatibacter actinomycetemcomitans gen. nov., comb. nov., Aggregatibacter aphrophilus comb. nov. and Aggregatibacter segnis comb. nov., and emended description o , 2006, International journal of systematic and evolutionary microbiology.

[22]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[23]  H. Christensen,et al.  Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov. , 2014, International journal of systematic and evolutionary microbiology.

[24]  M. Bisgaard,et al.  The Family Pasteurellaceae , 2014 .

[25]  L. Banu,et al.  Assessment of rpoB and 16S rRNA genes as targets for PCR-based identification of Pasteurella pneumotropica. , 2010, Comparative medicine.

[26]  J. E. Olsen,et al.  Final classification of Bisgaard taxon 9 as Actinobacillus arthritidis sp. nov. and recognition of a novel genomospecies for equine strains of Actinobacillus lignieresii. , 2002, International journal of systematic and evolutionary microbiology.

[27]  Werner Nicklas,et al.  Chapter 19 – Pasteurellaceae , 2007 .

[28]  A. Bojesen,et al.  Comparative studies on [Pasteurella] testudinis and [P.] testudinis-like bacteria and proposal of Chelonobacter oris gen. nov., sp. nov. as a new member of the family Pasteurellaceae. , 2009, International journal of systematic and evolutionary microbiology.

[29]  H. Christensen,et al.  The Genus Pasteurella , 2006 .

[30]  N. nørskov-lauritsen,et al.  Multilocus sequence phylogenetic analysis of Avibacterium. , 2012, Microbiology.

[31]  R. Kroppenstedt,et al.  Lipoquinones in members of the family Pasteurellaceae , 1989 .

[32]  T. Itoh,et al.  Genetic Diversity on 16S rDNA Sequence and Phylogenic Tree Analysis in Pasteurella pneumotropica Strains Isolated from Laboratory Animals , 2005, Current Microbiology.

[33]  J. E. Olsen,et al.  Taxonomic relationships of the [Pasteurella] haemolytica complex as evaluated by DNA-DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen. nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheim , 1999, International journal of systematic bacteriology.

[34]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[35]  M. Bertelsen,et al.  Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds. , 2012, International journal of systematic and evolutionary microbiology.

[36]  M. Kilian A taxonomic study of the genus Haemophilus, with the proposal of a new species. , 1976, Journal of general microbiology.

[37]  S. D. Henriksen Some Pasteurella strains from the human respiratory tract. A correction and supplement. , 2009, Acta pathologica et microbiologica Scandinavica.

[38]  L. Blackall,et al.  Reclassification of Pasteurella gallinarum, [Haemophilus] paragallinarum, Pasteurella avium and Pasteurella volantium as Avibacterium gallinarum gen. nov., comb. nov., Avibacterium paragallinarum comb. nov., Avibacterium avium comb. nov. and Avibacterium volantium comb. nov. , 2005, International journal of systematic and evolutionary microbiology.

[39]  Hans-Peter Klenk,et al.  Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison , 2010, Standards in genomic sciences.

[40]  R. E. Buchanan,et al.  THE FAMILIES AND GENERA OF THE BACTERIA FINAL REPORT OF THE COMMITTEE OF THE SOCIETY OF AMERICAN BACTERIOLOGISTS ON CHARACTERIZATION AND CLASSIFICATION OF BACTERIAL TYPES , 1917, Journal of bacteriology.

[41]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[42]  S. Octavia,et al.  The Family Enterobacteriaceae , 2014 .

[43]  M. Bertelsen,et al.  Testudinibacter aquarius gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of freshwater turtles. , 2016, International journal of systematic and evolutionary microbiology.

[44]  J. Hedegaard,et al.  Phylogeny of the genus Haemophilus as determined by comparison of partial infB sequences. , 2001, Microbiology.

[45]  M. Bisgaard Actinobacillus muris sp. nov. isolated from mice. , 2009, Acta pathologica, microbiologica, et immunologica Scandinavica. Section B, Microbiology.

[46]  Lawrence G. Wayne,et al.  International Committee on Systematic Bacteriology: Announcement of the Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics , 1988 .

[47]  P. Rehbinder,et al.  Recommendations for the health monitoring of rodent and rabbit colonies in breeding and experimental units , 2002, Laboratory animals.

[48]  W. Frederiksen,et al.  Reclassification of the genus Pasteurella Trevisan 1887 on the basis of deoxyribonucleic acid homology, with proposals for the new species Pasteurella dagmatis, Pasteurella canis, Pasteurella stomatis, Pasteurella anatis, and Pasteurella langaa , 1985 .

[49]  E. Jawetz A pneumotropic pasteurella of laboratory animals; bacteriological and serological characteristics of the organism. , 1950, The Journal of infectious diseases.

[50]  M. Collins,et al.  Phocoenobacter uteri gen. nov., sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from a harbour porpoise (Phocoena phocoena). , 2000, International journal of systematic and evolutionary microbiology.

[51]  B. Korczak,et al.  Classification of organisms previously reported as the SP and Stewart-Letscher groups, with descriptions of Necropsobacter gen. nov. and of Necropsobacter rosorum sp. nov. for organisms of the SP group. , 2011, International journal of systematic and evolutionary microbiology.

[52]  F. Dewhirst,et al.  Phylogeny of the Pasteurellaceae as determined by comparison of 16S ribosomal ribonucleic acid sequences. , 1993, Zentralblatt fur Bakteriologie : international journal of medical microbiology.

[53]  A. Kodjo,et al.  Identification by 16S rDNA fragment amplification and determination of genetic diversity by random amplified polymorphic DNA analysis of Pasteurella pneumotropica isolated from laboratory rodents. , 1999, Laboratory animal science.

[54]  F. Dewhirst,et al.  Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences , 1992, Journal of bacteriology.

[55]  G. Wibbelt,et al.  Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats. , 2014, International journal of systematic and evolutionary microbiology.

[56]  R. E. Buchanan,et al.  THE FAMILIES AND GENERA OF THE BACTERIA PRELIMINARY REPORT OF THE COMMITTEE OF THE SOCIETY OF AMERICAN BACTERIOLOGISTS ON CHARACTERIZATION AND CLASSIFICATION OF BACTERIAL TYPES , 1917, Journal of bacteriology.

[57]  Hans-Peter Klenk,et al.  Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs , 2010, Standards in genomic sciences.

[58]  A. Hensel,et al.  Discrimination of Members of the Family Pasteurellaceae Based on Polyamine Patterns , 1997 .

[59]  Elke Lang,et al.  Lonepinella koalarum gen. nov., sp. nov., a New Tannin-Protein Complex Degrading Bacterium , 1995 .

[60]  A. Stenzel,et al.  Reclassification of German, British and Dutch isolates of so-called Pasteurella multocida obtained from pneumonic calf lungs. , 1991, Veterinary microbiology.

[61]  B. Korczak,et al.  Frederiksenia canicola gen. nov., sp. nov. isolated from dogs and human dog-bite wounds , 2014, Antonie van Leeuwenhoek.

[62]  M. Bisgaard Isolation and characterization of some previously unreported taxa from poultry with phenotypical characters related to Actinobacillus-an Pasteurella species. , 1982, Acta pathologica, microbiologica, et immunologica Scandinavica. Section B, Microbiology.

[63]  Joachim Frey,et al.  Basfia succiniciproducens gen. nov., sp. nov., a new member of the family Pasteurellaceae isolated from bovine rumen. , 2010, International journal of systematic and evolutionary microbiology.

[64]  A. Bojesen,et al.  Rapid and accurate identification of Streptococcus equi subspecies by , 2015 .

[65]  A. Bojesen,et al.  Rapid and accurate identification of Streptococcus equi subspecies by MALDI-TOF MS. , 2015, Systematic and applied microbiology.

[66]  A. Bojesen,et al.  Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov. , 2007, International journal of systematic and evolutionary microbiology.

[67]  M. Bisgaard,et al.  Ecology and significance of Pasteurellaceae in animals. , 1993, Zentralblatt fur Bakteriologie : international journal of medical microbiology.