Data sources

This dataset was constructed using two different bioprojects:
PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.
PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.
PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.
PRJNA944553. 30 samples from 30 animals.
PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.
PRJNA923753 from Ho et al. 2023. 1 sample.

Metagenomic assembly

De novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.

MAGs recovery

MAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).

Non-redundant gene catalog

Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.

MSPs recovery

Samples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.

MAGs and MSPs taxonomic annotation

Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.

Construction of the phylogenetic tree

39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).

Mapping rate distribution across public cohorts

We generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB4391, PRJEB9357, PRJNA758898, PRJNA906124, PRJNA908260, PRJNA923753 and PRJNA944553 used in catalogue assembly.