Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms.

  title={Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms.},
  author={J{\"o}rg Overmann and Sixing Huang and Ulrich N{\"u}bel and Richard L. Hahnke and Brian J. Tindall},
  journal={Systematic and applied microbiology},
  volume={42 1},

The Taxonomy of Bacteria in the Genomic Era

The use of the single 16S rRNA gene sequence to generate evolutionary phylogenetic trees improved the analysis of the relationships among newly obtained strains and those already described, allowing a faster and more accurate classification than previously used methods.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

This work analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism, and characterized the new ‘oxycline’ clade.

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy and analysis connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information.

Prokaryotic taxonomy and nomenclature in the age of big sequence data

The challenge ahead is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.

Recent trend, biases, and limitations of cultivation based diversity studies of microbes.

Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant, and other fastidious microbes is poor.

Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy.

It is argued here that the proposed changes to ICNP are unlikely to result in a lower focus on isolation efforts since isolating an organism in the laboratory has important advantages for its study and use in downstream applications.

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes

  • N. Salmaso
  • Environmental Science
    Front. Microbiol.
  • 2019
Results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones.

Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials

This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations and calls for an increased deposit of strains and genetic resources.

Microbial Journey: Mount Everest to Mars

A glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity is presented.



Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea.

Uncultivated microbes in need of their own taxonomy

The use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for identification and phylogenetic placement, and the implementation of an independent nomenclatural system for uncultivated taxa, which will facilitate a comprehensive characterization of the ‘uncultivated majority’.

Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

These data give first insight into the genome content and diversity of the ubiquitously distributed but poorly characterized phylum of Acidobacteria, and support the phylogenetic inferences made from 16S rRNA gene libraries, suggesting that Acidob bacteria form a broad group in the same sense and with a similar diversity as that of many well‐studied bacterial phyla.

Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes.

This note is presented in advance of discussions by the International Committee on Systematic Bacteriology at the forthcoming congress (July 1994) so that there may be discussions and reaction by colleagues.

Modest proposals to expand the type material for naming of prokaryotes.

  • W. Whitman
  • Biology
    International journal of systematic and evolutionary microbiology
  • 2016
The Code should be modified to allow gene sequences to serve as the type material for genera in the absence of described species, which will unite the nomenclature of the cultured and uncultured prokaryotes into a single, robust system.

An environmental bacterial taxon with a large and distinct metabolic repertoire

Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei.

Uncultivated microbes—in need of their own nomenclature?

It is high time for microbial ecologists to establish their own official committee that will make recommendations on how to classify uncultured taxa with harmonized high standards, supervise and manage an ‘official’ classification and the rules of the nomenclature of uncultivated taxa, according to the authors of the Perspectives paper.

Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes.

All information, including structural, metabolic, and reproductive features, should be included in the description of a provisional taxon, together with the natural environment in which the organism can be identified by in situ hybridization or other similar techniques for cell identification.

Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria

A ‘digital protologue’ database (DPD) to accompany descriptions of novel Archaeal and Bacterial taxa published in these two journals is developed and believes it has good functionality and fitness for purpose as a repository for taxonomic data.