A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera

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

(2018) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

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

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

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

Diversity and Transmission of Gut Bacteria in Atta and Acromyrmex Leaf-Cutting Ants during Development

(2017) Mariya Zhukova et al.   Frontiers in Microbiology

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

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

Acromyrmex Leaf-Cutting Ants Have Simple Gut Microbiota with Nitrogen-Fixing Potential

(2015) Panagiotis Sapountzis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

International Code of Nomenclature of Prokaryotes

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

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

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

International Committee on Systematics of ProkaryotesSubcommittee on the taxonomy of Mollicutes: Minutes of the meetings, July 15th and 19th 2012, Toulouse, France

(2013) G. Firrao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Phylum-Level Bacterial Phylogenetic Marker Database

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

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

Phylogeny and molecular typing of Mycoplasma agalactiae and Mycoplasma bovis by multilocus sequencing

(2012) Lucía Manso-Silván et al.   VETERINARY MICROBIOLOGY

Towards a genome based taxonomy of Mycoplasmas

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

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

Spiroplasmas and phytoplasmas: Microbes associated with plant hosts

(2010) Gail E. Gasparich   BIOLOGICALS

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

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

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

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

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