GlobDB & AASTK
These are the citations for the core resources described on this website. Please scroll down for the references to the data sources included in the GlobDB and the tools used to generate some of the analysis products available for the GlobDB genomes
GlobDB
a manuscript introducing the GlobDB (Speth et al. 2025) is published in Bioinformatics Advances.
AASTK
There is no publication describing AASTK yet, so please cite the github repository (https://github.com/dspeth/aastk) when you use AASTK.
In addition, several parts of the software were developed independently and should be credited.
If you use AASTK with the GlobDB protein dataset, please cite:
Speth et al. (2025) GlobDB: a comprehensive species-dereplicated microbial genome resource
https://doi.org/10.1093/bioadv/vbaf280
If you use aastk pasr, please cite:
Speth and Orphan (2018) Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
https://doi.org/10.7717/peerj.5614
The environmental data from aastk meta is derived from the MetaCoOc software. A manuscript is in preparation, but in the meantime please cite:
https://github.com/bcoltman/metacooc
Data sources
This section provides links to papers of the datasets included in the GlobDB, organized by the GlobDB release they were first included, and then alphabetically by dataset name. Note that the GTDB and MGnify have been updated since they were first included in the GlobDB, and these updates have also been integrated subsequent version. The other included datasets are static.
Added in Release 232
CRBC - Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns
CRLG - 236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient
DAWW - Metagenome-assembled genomes from microbial communities in lab-scale anaerobic bioreactors treating simulated dairy wastewater
GCMETA - gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research
HOGU - Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse
NGDC - All "direct submission" entries to the genomic warehouse (GWH) of the CNCB-NGDC (China National Center for Bioinformation / National Genomics Data Center)
PREC - A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary
QXLSG - A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms
SCSSF - Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea
TG2G - A genome and gene catalog of glacier microbiomes
TPLM - Functional traits and adaptation of lake microbiomes on the Tibetan Plateau
TPMCS - Data-mining of sediment microbiomes of the Tibetan Plateau revealed a genomic repository of ancient lineages and adaptive evolution of Asgardarchaeota
Added in Release 226
AMXMAG - A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota
cFMD - Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
GOMC - Global marine microbial diversity and its potential in bioprospecting
HRGM2 - A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models
MGnify - MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues
mOTU - The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
MRGM - MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes
RBG - Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes
SHGO - Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization
TPMC - A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau
Added in Release 220
GTDB - GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
GEM - A genomic catalog of Earth’s microbiomes
SMAG - A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
SPIRE - SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Tools
This section is organized to first credit tools used in all versions of the GlobDB, and then those used in specific versions
General
Anvi'o - Anvi'o contigs databases for the GlobDB genomes, as well as the protein files and GFF files were created using anvi'o, development version, described in Eren et al. 2021. In addition, anvi'o provides a wide range of functionalities, some of which come with their own citations. If you use the GlobDB anvi'o databases in your work please check here whether there's work that would be appropriate to cite.
Prodigal - The gene calling for protein coding genes in the GlobDB genomes was done using Prodigal, version 2.6.3, described in Hyatt et al. 2010. If you use the protein data files in your work, please cite prodigal.
GTDB-tk - Taxonomic assignment for the genomes in the GlobDB that are not derived from the GTDB is described on the methods page and uses GTDB-tk, described in Chaumeil et al. 2022.
CheckM2 - Completeness, contamination, and basic statistics on the GlobDB genomes were calculated using CheckM2, described in Chklovski et al. 2023.
Release 232
Galah - Starting with release 232 dereplication of constittuenta datasets is done using Galah, version 0.4.2. There is no paper yet, but the suggested citation is this Zenodo doi Aroney et al. 2024.
Pyrodigal-gv - The gene calling for protein coding genes in the release 232 GlobDB genomes was done using using pyrodigal-gv, described in Cook et al. 2024. Pyrodigal-gv is an extension of pyrodigal, which was described in Larralde 2022. If you use the protein data files in your work, please cite pyrodigal and pyrodigal-gv.
Release 226
fastANI - Dereplication of the datasets is done using fastANI, version 1.3.4, described in Jain et al. 2018.
dRep - The cFMD, SHGO, and AMXMAG datasets did not provide species dereplicated datasets for download. After sequential dereplication against the GlobDB, the remainder of genomes in these datasets was dereplicated using dRep, described in Olm et al. 2017
BacDive - availability of GlobDB genomes in culture collections is assessed using BacDive, described in Schober et al. 2025
ProtTrans - Protein language model embeddings were calculated using the ProtT5-XL-U50 model described in Elnaggar et al. 2022