Path Forward for Naming the Uncultivated workshop series:

Workshop 1  “Practical barriers to naming uncultivated microorganisms”
Objective: To tackle roadblock issues and concerns with the Uncultivated Code
Format: Pre-recorded talks and resources, moderated round table discussion, and breakout discussion groups

Watch Workshop Recording 1a  February 4/5 2021

Watch Workshop Recording 1b  February 4/5 2021

▼ Pre-recorded talks and background reading

Presentation:
How did we get here? Ramon Rossello-Mora
Associated paper:
Uncultivated microbes in need of their own taxonomy -  Konstantinidis et al. The ISME Journal 

Presentation:
Can MAGs be of same quality as isolate genomes for taxonomic descriptions? Kostas Konstantinidis
Associated paper:
Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy Konstantinidis et al. Environmental microbiology

Presentation:
Nomenclature of Candidatus taxa: establishing order in the current chaos Aharon Oren
Associated paper:
Lists of names of prokaryotic Candidatus taxa Oren et al. Systematic and Evolutionary Microbiology

Presentation:
The importance of a type to be cultivable, according to the ICNP Ed Moore
Associated paper:
A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature Marakeby et al. Plos one

Presentation:
Roadmap to naming uncultivated Archaea and Bacteria Alison Murray
Associated paper:
Roadmap for naming uncultivated Archaea and Bacteria Murrey et al. Nature Microbiology

Presentation:
The SeqCode: a code for naming prokaryotes with DNA sequences as the type Barny Whitman
Associated paper:
Dialogue on the nomenclature and classification of prokaryotes Whitman et al. Systematic and Applied Microbiology
Genome sequences as the type material for taxonomic descriptions of prokaryotes Whitman. Systematic and Applied Microbiology

Breakout Group Feedback Fanus Venter


Workshop 2   “Path forward to implementation and adoption of the SeqCode”
Objective: To determine a path forward for implementation and adoption
Format: Pre-recorded talks and resources:

  • Topic 1: What can we learn from other "modern" nomenclature systems?
  • Topic 2: Path forward through international organizations, standards, and databases
  • Panel discussion and open community forum for moving forward to name the uncultivated

Watch Workshop Recording 2a  February 11/12 2021

Watch Workshop Recording 2b  February 11/12 2021

▼ Pre-recorded talks and background reading

Translating between nomenclature systems

Presentation:
A Return to Linnaeus's Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species Susanne S. Renner
Associated paper: 
A Return to Linnaeus’s Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species Renner. Systematic Biology

Presentation:
Out of the Box Vincent Robert

Presentation:
Virus taxonomy in a data rich world Arvind Varsani

Presentation:
Eukaryotic plankton diversity in the sunlit ocean Chris Lane

Integration of international organizations, standards, and databases

Presentation:
Introduction to ICSP Iain Sutcliffe

Presentation:
WDCM Data Resources: GCM & gcType Juncai Ma, Linhuan Wu

Presentation:
The Leibniz Institute DSMZ Jörg Overmann

Presentation:
ISME Nicole Dubilier, Phil Hugenholtz

Presentation:
NCBI Conrad Schoch

Presentation:
Genome taxonomy database Donovan Parks

Presentation:
Genomics Standards Consortium
Scott Tighe GSC - Panelist-GSC-tighe.pdf  Emiley Eloe-Fadrosh, Scott Tighe

Presentation:
Microbial Genomes Atlas Kostas Konstantinidis

Presentation:
EzBioCloud Database Jongsik Chun

 

▼ Supplementary Literature

Amann et al., 2014:
Bisgaard et al., 2019:
Cowan, 1970:
Dykhuizen, 1998:
Karthikeyan et al., 2019:
Konstantinidis and Rossello-Mora, 2015:
Konstantinidis et al., 2018:
Konstantinidis et al., 2020:
Konstantinidis et al., 2020:
Meziti et al., 2021:
Mora et al., 2011:
Murray and Schleifer, 1994:
Murray and Stackebrandt, 1995:
Oren and Garrity, 2017:
Oren et al., 2019:
Oren et al., 2020:
Overmann et al., 2019:
Padial et al. 2010:
Pallen et al., 2020:
Parker et al., 2019:
Rossello-Mora and Amann, 2001:
Rossello-Mora and Whitman, 2019:
Rossello-Mora, 2011:
Tindall et al., 2010:
Tindall et al., 2010:
Whitman 2015:
Whitman 2016:
Whitman et al., 1998:
Yarza et al., 2014:
Zoological Code:
A precursor workshop was conducted in 2018. Details about that event, along with recorded presentations, and background reading, can be found here