Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

(2018) Radhey S. Gupta et al.   Frontiers in Microbiology

Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage

(2018) et al.   Genes

Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family

(2017) Seema Alnajar et al.   INFECTION GENETICS AND EVOLUTION

Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717)

(2017) Alan G. Barbour et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales

(2017) Radhey S. Gupta et al.   PLoS One

Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

(2017) Bijendra Khadka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato

(2017) Chrizelle W. Beukes et al.   Frontiers in Microbiology

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2017) David W. Waite et al.   Frontiers in Microbiology

Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938

(2016) Paul A. Lawson et al.   ANAEROBE

A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov.

(2016) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Description and prevalence of Mycoplasma ciconiae sp. nov. isolated from white stork nestlings (Ciconia ciconia)

(2016) Franca Möller Palau-Ribes et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.

(2016)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome-Based Microbial Taxonomy Coming of Age

(2016) Philip Hugenholtz et al.   Cold Spring Harbor Perspectives in Biology

Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

(2015) Chantal Campbell et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

International Code of Nomenclature of Prokaryotes

(2015) Charles T Parker et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome sequences as the type material for taxonomic descriptions of prokaryotes

(2015) William B. Whitman   SYSTEMATIC AND APPLIED MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Insertion/Deletion-Based Approach for the Detection of Escherichia coli O157:H7 in Freshwater Environments

(2014) Shirley Y. Wong et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Phylogenomics of “Candidatus Hepatoplasma crinochetorum,” a Lineage of Mollicutes Associated with Noninsect Arthropods

(2014) Sébastien Leclercq et al.   Genome Biology and Evolution

The Request for an Opinion that the current use of the genus name Mycoplasma be maintained and Mycoplasma coccoides be considered a legitimate name is denied. Opinion 92.: Judicial Commission of the International Committee on Systematics of Prokaryotes

(2014) B. J. Tindall   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

International Committee on Systematics of Prokaryotes * Subcommittee on the taxonomy of Mollicutes: Minutes of the meetings (closed and open), 1 and 5 June 2014, Blumenau SC, Brazil

(2014) M. May et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.

(2014) R. S. Gupta et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria

(2014) H. S. Naushad et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease

(2014) Jennifer M. Fettweis et al.   PLoS One

Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes

(2014) Henri Grosjean et al.   PLoS Genetics

Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations

(2013) Vaibhav Bhandari et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

A Phylum-Level Bacterial Phylogenetic Marker Database

(2013) Zhang Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

LPSN—list of prokaryotic names with standing in nomenclature

(2013) Aidan C. Parte   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Mycoplasma feriruminatoris sp. nov., a fast growing Mycoplasma species isolated from wild Caprinae

(2013) Joerg Jores et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

(2012) B. Gao et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Towards a genome based taxonomy of Mycoplasmas

(2011) Cristiane C. Thompson et al.   INFECTION GENETICS AND EVOLUTION

International Committee on Systematics of ProkaryotesSubcommittee on the taxonomy of Mollicutes

(2011) G. Firrao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mycoplasma neophronis sp. nov., isolated from the upper respiratory tract of Canarian Egyptian vultures (Neophron percnopterus majorensis)

(2011) A. Suarez-Perez et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group

(2011) Nadia Z. Ahmod et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2011) Dmitriy V. Volokhov et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs

(2010) J. Spergser et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function

(2010) Allyn J. Schoeffler et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

(2010) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri

(2009) L. Manso-Silvan et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth

(2009) Bhag Singh et al.   MOLECULAR GENETICS AND GENOMICS

A New Lineage of Halophilic, Wall-Less, Contractile Bacteria from a Brine-Filled Deep of the Red Sea

(2008) A. Antunes et al.   JOURNAL OF BACTERIOLOGY

RNase P RNA Gene (rnpB) Phylogeny of Hemoplasmas and Other Mycoplasma Species

(2008) I. R. Peters et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Signature Genes as a Phylogenomic Tool

(2008) B. E. Dutilh et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Molecular detection of Mycoplasma wenyonii and ‘Candidatus Mycoplasma haemobos’ in cattle in Hokkaido, Japan

(2008) Michihito Tagawa et al.   VETERINARY MICROBIOLOGY