A complete domain-to-species taxonomy for Bacteria and Archaea

By Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig, Philip Hugenholtz. Nature Biotechnology, 2020

1,210 citations recorded by the source corpus.

Subfields: Food Science, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/99d439ebad7d9aa7305207b1677881cd0cd0802a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Food Science

1. Curtis Huttenhower
2. Nicola Segata
3. Eric A. Franzosa
4. F. Asnicar
5. Edoardo Pasolli
6. Adrian Tett
7. Donovan H. Parks
8. Rob Knight

In Molecular Biology

1. Curtis Huttenhower
2. Nicola Segata
3. Philip Hugenholtz
4. Donovan H. Parks
5. Aaron J. Mussig
6. Pierre-Alain Chaumeil
7. Eric A. Franzosa
8. Edoardo Pasolli

In Plant Science

1. Philip Hugenholtz
2. Nikos Kyrpides
3. Donovan H. Parks

Citations in the corpus

• Polypolish: Short-read polishing of long-read bacterial genome assemblies (2021, neutral): “…isolates used in the real-read tests each belong to a different species: Acinetobacter baumannii , Citrobacter koseri , Enterobacter kobei , an unnamed Haemophilus species (given the placeholder name Haemophilus sp002998595 in GTDB R202 [28, 29]), Klebsiella oxytoca and Klebsiella variicola .”
• Identification of mobile genetic elements with geNomad (2023, neutral): “Next, scaffolds with ANI ≥ 97% over at least 95% of the length of the shorter sequence were clustered using a greedy algorithm 62 , and the longest sequence within each cluster was selected as the representative.”
• Genomes OnLine Database (GOLD) v.8: overview and updates (2020, background): “Once the bacterial and archaeal members of the soil community are identified it is important to classify them taxonomically (3) and assign proper nomenclature (4).”
• Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (2023, background): “This definition permits arbitrary microbial genomes to be organized in a manner not unlike amplicons into operational taxonomic units (OTUs) and matches remarkably well the expected boundaries of the existing taxonomy 42,47,48 .”
• GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy (2021, methodology): “This issue is of interest as the GTDB uses a species definition based on the ANI to genomes selected as species representatives (5).”