human_gut_microbiome_compendium — Human Microbiome Compendium of gut samples (2023-2026)

Description

Bipartite networks of human gut microbiome samples and the bacterial and archaeal taxa found in them, from the Human Microbiome Compendium of Abdill et al., which gathers 168,464 publicly available 16S rRNA gene amplicon sequencing samples of the human gut (mostly stool) from 482 studies in the Sequence Read Archive, processed with a uniform pipeline (DADA2), and classified with the SILVA reference database.

Nodes are samples and taxa, and an edge connects a sample to each taxon observed in it, with the number of reads of the taxon in the sample as weight.

v1.0.0, v1.0.1, v1.1.2: the taxonomic tables at the genus level of the releases of the compendium, where the amplicon sequence variants (ASVs) are classified with SILVA 138.0 (v1.0.0, also published as versions 0.1.0 and 0.2.0), with SILVA 138.0 and corrections of the names of 2,881 ASVs whose taxonomic levels were inferred incorrectly (v1.0.1), and with SILVA 138.2, with all the ASVs of the compendium classified together (v1.1.2, the table of the releases 1.1.0 to 1.1.2). Taxa are named by their lineage down to the genus (unclassified levels are NA).
asv (release 1.1.2): the samples and the ASVs (exact sequence variants, shared across studies), from the per-study ASV tables, with the classification of each ASV with SILVA 138.2.
gg2 (release 1.1.2): the samples and the features of the classification with Greengenes2 (2022.10, closed-reference at 99% identity), with their Greengenes2 taxonomy (the 5,018 samples of the table without any classified reads are isolated nodes).

The networks have the following properties:

(Node) is_sample: whether the node is a sample (otherwise it is a taxon).
(Node) name: the identifier of the sample (<BioProject>_<SRA run> in the genus tables, the SRA sample accession in asv and gg2), or the taxon (lineage in the genus tables, ASV identifier in asv, feature identifier in gg2).
(Node) taxonomy (asv, gg2): the lineage of the ASV or feature (empty for samples).
(Node) srs, srr, project: the SRA sample and run accessions and the BioProject of the sample.
(Node) pubdate, total_bases, instrument: the publication date of the run in the SRA (as Unix time), the number of sequenced bases, and the sequencing instrument.
(Node) geo_loc_name, iso, region: the location of the sample as given in BioSample, its country (ISO 3166-1 code, or unknown), and its world region.
(Node) amplicon, bead_beating, kit, sample_type, condition, subjects, publication: the metadata of the study of the sample (annotated by the authors of the compendium): the amplified region of the 16S gene, whether the DNA extraction used mechanical lysis, the extraction kit, the material, the condition studied, the population, and the link to the publication.
(Node) tags: the attributes of the sample in BioSample, as tag=value strings.
(Edge) count: the number of reads of the taxon in the sample.

Tags

Biological Ecological Weighted Bipartite Metadata

Added

2026-10-31

Citation

R. J. Abdill, S. P. Graham, V. Rubinetti, M. Ahmadian, P. Hicks, A. Chetty, D. McDonald, P. Ferretti, E. Gibbons, M. Rossi, A. Krishnan, F. W. Albert, C. S. Greene, S. Davis, R. Blekhman, "Integration of 168,000 samples reveals global patterns of the human gut microbiome." Cell 188, 1100-1118.e17 (2025) 10.1016/j.cell.2024.12.017 Sci-Hub

Upstream URL OK

https://microbiomap.org/
https://doi.org/10.5281/zenodo.8186993

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
v1.0.0	172,482	9,621,652	111.57	1736.64	2029.29	2.81	-0.52	6	1.00	Undirected	Bipartite	is_sample name srs srr project instrument geo_loc_name iso region amplicon bead_beating kit sample_type condition subjects publication pubdate total_bases tags	count	22.3 MiB	49.1 MiB	47.2 MiB	46.8 MiB
v1.0.1	172,482	9,621,652	111.57	1736.64	2029.29	2.81	-0.52	6	1.00	Undirected	Bipartite	is_sample name srs srr project instrument geo_loc_name iso region amplicon bead_beating kit sample_type condition subjects publication pubdate total_bases tags	count	22.5 MiB	49.0 MiB	47.2 MiB	46.8 MiB
v1.1.2	173,144	9,251,903	106.87	1602.94	1959.45	2.98	-0.51	6	1.00	Undirected	Bipartite	is_sample name srs srr project instrument geo_loc_name iso region amplicon bead_beating kit sample_type condition subjects publication pubdate total_bases tags	count	21.6 MiB	47.4 MiB	45.6 MiB	45.1 MiB
asv	3,280,035	22,963,366	14.00	96.29	832.50	987344.14	-0.10	38	0.67	Undirected	Bipartite	is_sample name taxonomy srs srr project instrument geo_loc_name iso region amplicon bead_beating kit sample_type condition subjects publication pubdate total_bases tags	count	63.8 MiB	132.2 MiB	134.9 MiB	132.9 MiB
gg2	228,369	15,050,011	131.80	1115.95	1746.31	25.10	-0.28	9	0.98	Undirected	Bipartite	is_sample name taxonomy srs srr project instrument geo_loc_name iso region amplicon bead_beating kit sample_type condition subjects publication pubdate total_bases tags	count	37.4 MiB	77.2 MiB	76.5 MiB	73.8 MiB