Neisseria montereyensis sp. nov., Isolated from Oropharynx of California Sea Lion (Zalophus californianus): Genomic, Phylogenetic, and Phenotypic Study

[1]  Lihong Chen,et al.  VFDB 2022: a general classification scheme for bacterial virulence factors , 2021, Nucleic Acids Res..

[2]  C. Rückert,et al.  Paralysiella testudinis gen. nov., sp. nov., isolated from the cloaca of a toad-headed turtle (Mesoclemmys nasuta). , 2021, International journal of systematic and evolutionary microbiology.

[3]  Radhey S. Gupta,et al.  Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov. , 2021, Systematic and applied microbiology.

[4]  M. Jansson,et al.  Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species. , 2021, International journal of systematic and evolutionary microbiology.

[5]  A. Goesmann,et al.  EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure , 2021, Nucleic Acids Res..

[6]  J. Blom,et al.  Streptococcus vicugnae sp. nov., isolated from faeces of alpacas (Vicugna pacos) and cattle (Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions (Zalophus californianus). , 2021, International journal of systematic and evolutionary microbiology.

[7]  Sudhir Kumar,et al.  MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , 2021, Molecular biology and evolution.

[8]  Dmitry Antipov,et al.  Using SPAdes De Novo Assembler , 2020, Current protocols in bioinformatics.

[9]  Geoffrey L. Winsor,et al.  CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database , 2019, Nucleic Acids Res..

[10]  B. Liu,et al.  Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing , 2019, bioRxiv.

[11]  J. Blom,et al.  The synergistic effect of concatenation in phylogenomics: the case in Pantoea , 2019, PeerJ.

[12]  Cuixia Chen,et al.  Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae) , 2019, Antonie van Leeuwenhoek.

[13]  D. Volokhov,et al.  Neisseria zalophi sp. nov., isolated from oral cavity of California sea lions (Zalophus californianus) , 2018, Archives of Microbiology.

[14]  E. Sundberg,et al.  Motility and adhesion through type IV pili in Gram-positive bacteria. , 2016, Biochemical Society transactions.

[15]  Eric P. Nawrocki,et al.  NCBI prokaryotic genome annotation pipeline , 2016, Nucleic acids research.

[16]  J. Blom,et al.  Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes (Vulpes vulpes). , 2016, International journal of systematic and evolutionary microbiology.

[17]  Luis V. Santana-Quintero,et al.  High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis , 2016, Database J. Biol. Databases Curation.

[18]  D. Relman,et al.  Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea , 2016, Nature Communications.

[19]  H. Bratcher,et al.  The genus Neisseria , 2014 .

[20]  J. Chun,et al.  Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. , 2014, International Journal of Systematic and Evolutionary Microbiology.

[21]  T. Tønjum,et al.  Dialects of the DNA Uptake Sequence in Neisseriaceae , 2013, PLoS genetics.

[22]  Alexander F. Auch,et al.  Genome sequence-based species delimitation with confidence intervals and improved distance functions , 2013, BMC Bioinformatics.

[23]  P. Delmonte,et al.  Separation of fatty acid methyl esters by GC-online hydrogenation × GC. , 2013, Analytical chemistry.

[24]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[25]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[26]  P. Delmonte,et al.  Review of methods for preparation and gas chromatographic separation of trans and cis reference fatty acids. , 2009, Journal of AOAC International.

[27]  G. Olsen,et al.  Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes , 2008, Applied and Environmental Microbiology.

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

[29]  C. Keys,et al.  Differentiation of Enterobacter sakazakii from closely related Enterobacter and Citrobacter species using fatty acid profiles. , 2007, Journal of Agricultural and Food Chemistry.

[30]  K. Konstantinidis,et al.  The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[31]  L. Martínez-Chavarría,et al.  Aerobic bacterial flora of the nasal cavity in Gulf of California sea lion (Zalophus californianus) pups. , 2005, Veterinary journal.

[32]  Konstantinos T. Konstantinidis,et al.  Towards a Genome-Based Taxonomy for Prokaryotes , 2005, Journal of bacteriology.

[33]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

[34]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[35]  Francisco P. Chavez,et al.  Seasonal fluctuations of temperature, salinity, nitrate, chlorophyll and primary production at station H3/M1 over 1989-1996 in Monterey Bay, California , 2000 .

[36]  N. Moran,et al.  Calibrating bacterial evolution. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Holmes,et al.  Networks and groups within the genus Neisseria: analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. , 1999, Molecular biology and evolution.

[38]  W. Bowen,et al.  The Evolution of Maternal Care in Pinnipeds , 1996 .

[39]  C Thornsberry,et al.  Comparison of the E Test to agar dilution, broth microdilution, and agar diffusion susceptibility testing techniques by using a special challenge set of bacteria , 1991, Journal of clinical microbiology.

[40]  J. Blom,et al.  Attempts to demonstrate a polysaccharide capsule in Neisseria gonorrhoeae , 1988, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[41]  W. Gilmartin,et al.  Hazards of disease transfer from marine mammals to land mammals: review and recent findings. , 1978, Journal of the American Veterinary Medical Association.

[42]  D. S. Kellogg,et al.  Analysis by gas chromatography of fatty acids found in whole cultural extracts of Neisseria species. , 1971, Canadian journal of microbiology.

[43]  D. S. Kellogg,et al.  Cellular Fatty Acids of Pathogenic Neisseria , 1970, Journal of bacteriology.

[44]  D. Hollis,et al.  Fatty Acid Composition of Neisseria Species as Determined by Gas Chromatography , 1968, Journal of bacteriology.

[45]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[46]  Henrik Christensen,et al.  Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. , 2018, International journal of systematic and evolutionary microbiology.

[47]  W. Whitman.  Bergey's Manual of Systematics of Archaea and Bacteria , 2016 .

[48]  D. Volokhov,et al.  RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae. , 2012, Molecular phylogenetics and evolution.

[49]  T. Maier,et al.  Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. , 2009, The Journal of molecular diagnostics : JMD.

[50]  Didier Raoult,et al.  The rpoB gene as a tool for clinical microbiologists. , 2009, Trends in microbiology.

[51]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[52]  E. Stackebrandt.  Taxonomic parameters revisited : tarnished gold standards , 2006 .

[53]  M. Apicella,et al.  The lipooligosaccharides of pathogenic gram-negative bacteria. , 1996, Critical reviews in microbiology.

[54]  W. M. Huang,et al.  Bacterial diversity based on type II DNA topoisomerase genes. , 1996, Annual review of genetics.

[55]  J. Riou,et al.  Presence of a capsule in Neisseria lactamica, antigenically similar to the capsule of N. meningitidis. , 1986, Annales de l'Institut Pasteur. Microbiologie.

[56]  C. Hoke,et al.  Taxonomy of the Neisseriae: Fatty Acid Analysis, Aminopeptidase Activity, and Pigment Extraction , 1982 .