The Earth Hologenome Initiative: Data Release 1

Abstract

Background: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.

Results: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.

Conclusions: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.

Keywords: Bacteria; Genome; Genome-resolved metagenomics; MAG; Metagenome-assembled genome; Metagenomics; Microbiome; Microbiota.

Figure 1:

Phylogenetic placement and geographic origin of the samples. (A) Phylogenetic tree of all vertebrate species represented in the EHI collection in 2025 Q1, with the phylogenetic position of the species included in this data release highlighted. (B) World map indicating the number of samples sourced from each of the represented countries.

Figure 2:

Phylogenetic trees of the EHI-reconstructed bacterial and archaeal genomes. Each tip represents a genus, and the tip size indicates the number of released genomes within the genus.

Figure 3:

Host breadth of the reconstructed bacterial taxa. Only genomes reconstructed from individual assemblies are displayed in this figure. Chalcides striatus, Geospizopsis unicolor, Natrix astreptophora, Plecotus auritus, Salamandra atra, and Zonotrichia capensis did not yield any metagenome-assembled genomes from individual assemblies. Note that only the most abundant bacterial phylum names are displayed for the sake of visualization. Exact data can be found in the supplementary materials.