Workshop Series 2: Path Forward for Naming the Uncultivated (February 2021)

“Practical barriers to naming uncultivated microorganisms” (February 4/5 2021)
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

Pre-recorded talks and presenters are listed below along with associated papers
How did we get here? Ramon Rossello-Mora
   Associated paper:
   Uncultivated microbes in need of their own taxonomy -  Konstantinidis et al. The ISME Journal

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

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

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

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

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

“Path forward to implementation and adoption of the SeqCode” (February 11/12 2021)
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

Pre-recorded talks and presenters are listed below along with associated papers

Translating between nomenclature systems

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

Out of the Box Vincent Robert

Virus taxonomy in a data rich world Arvind Varsani

Eukaryotic plankton diversity in the sunlit ocean Chris Lane

Integration of international organizations, standards, and databases

Introduction to ICSP Iain Sutcliffe

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

The Leibniz Institute DSMZ Jörg Overmann

ISME Nicole Dubilier, Phil Hugenholtz

NCBI Conrad Schoch

Genome taxonomy database Donovan Parks

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

Microbial Genomes Atlas Kostas Konstantinidis

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