emp_microbiome — Earth Microbiome Project sample-microbe networks (2017)

Description

Bipartite networks of environmental samples and the microbes (bacteria and archaea) found in them, from release 1 of the Earth Microbiome Project (EMP), a collaborative effort that collected and sequenced (16S rRNA gene amplicons, V4 region) about 27,000 samples from 97 studies of all kinds of environments: soils, sediments, fresh and salt water, plants, animal bodies and guts, built environments, etc., with a common protocol, and classified them with the EMP ontology of habitats (EMPO).

Nodes are samples and microbial taxa (sequence variants or OTUs), 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. There is one network for each of the published observation tables of the release, which differ in how the reads were grouped into taxa:

deblur_90bp, deblur_100bp, deblur_150bp: exact sequence variants (sub-OTUs) obtained with Deblur from the reads trimmed to 90, 100 and 150 base pairs (the 150 bp table contains fewer samples, those with longer reads).
cr_gg_13_8, cr_silva_123: OTUs of closed-reference picking (97% identity) against the Greengenes 13.8 and SILVA 123 references.
or_gg_13_8: OTUs of open-reference picking against Greengenes 13.8 (without the OTUs found in a single sample).

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 (in lower case in or_gg_13_8, as given in its table), or of the taxon (the sequence itself for the Deblur tables, the OTU identifier otherwise).
(Node) taxonomy: the taxonomy of the taxon (from kingdom to species, separated by ;; empty for samples).
(Node) The sample metadata, all the columns of the mapping file of the release (empty, NaN or false for taxa; strings unless said otherwise):
(Node) barcode_sequence, linker_primer_sequence, description, host_subject_id: the barcode and primer sequences, the description of the sample and the identifier of its host individual, as given by the study.
(Node) study_id, title, principal_investigator, doi, ebi_accession: the EMP study of the sample, its title, principal investigator, the DOI of its publication, and its accession in the European Nucleotide Archive.
(Node) target_gene, target_subfragment, pcr_primers, illumina_technology, extraction_center, run_center, run_date, read_length_bp (number): the sequencing of the sample.
(Node) sequences_split_libraries, observations_closed_ref_greengenes, observations_closed_ref_silva, observations_open_ref_greengenes, observations_deblur_90bp, observations_deblur_100bp, observations_deblur_150bp (numbers): the numbers of sequences of the sample after demultiplexing, and in each observation table.
(Node) emp_release1, qc_filtered, subset_10k, subset_5k, subset_2k (booleans): whether the sample is in release 1, whether it passed the quality filters of the EMP, and whether it belongs to the even subsets of 10,000, 5,000 and 2,000 samples used in the paper.
(Node) sample_taxid, sample_scientific_name: the NCBI taxon and name of the kind of sample (e.g. soil metagenome).
(Node) host_taxid, host_common_name_provided, host_common_name, host_scientific_name, host_superkingdom, host_kingdom, host_phylum, host_class, host_order, host_family, host_genus, host_species: the host of the sample and its taxonomy.
(Node) collection_timestamp: the date of collection of the sample (as given).
(Node) country, latitude_deg, longitude_deg, depth_m, altitude_m, elevation_m (numbers, except the country): the location of the sample (NaN if unknown).
(Node) env_biome, env_feature, env_material, envo_biome_0 ... envo_biome_5: the environment of the sample (ENVO terms), and the levels of the hierarchy of its biome.
(Node) empo_0, empo_1, empo_2, empo_3: the habitat of the sample in the levels of the EMP ontology (e.g. EMP sample / Free-living / Saline / Water (saline)).
(Node) adiv_observed_otus, adiv_chao1, adiv_shannon, adiv_faith_pd (numbers): the alpha diversity of the sample (observed OTUs, Chao1, Shannon, Faith's phylogenetic diversity), as computed by the EMP.
(Node) temperature_deg_c, ph, salinity_psu, oxygen_mg_per_l, phosphate_umol_per_l, ammonium_umol_per_l, nitrate_umol_per_l, sulfate_umol_per_l (numbers): physicochemical measurements of the sample (NaN if not given).
(Edge) count: the number of reads of the taxon in the sample.

Tags

Biological Ecological Weighted Bipartite Metadata

Added

2026-10-31

Citation

L. R. Thompson, J. G. Sanders, D. McDonald, A. Amir, J. Ladau, K. J. Locey, R. J. Prill, A. Tripathi, S. M. Gibbons, G. Ackermann, et al., "A communal catalogue reveals Earth's multiscale microbial diversity." Nature 551, 457-463 (2017) 10.1038/nature24621 Sci-Hub

Upstream URL OK

https://earthmicrobiome.org/
https://doi.org/10.5281/zenodo.890000

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
deblur_90bp	343,495	23,585,148	137.32	451.35	1529.88	28.54	-0.30	7	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	51.6 MiB	109.9 MiB	110.6 MiB	109.8 MiB
deblur_100bp	354,878	25,275,634	142.45	475.98	1588.52	33.46	-0.33	7	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	54.5 MiB	116.8 MiB	117.4 MiB	116.8 MiB
deblur_150bp	215,194	13,052,393	121.31	392.52	1227.83	50.20	-0.34	7	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	27.8 MiB	60.5 MiB	61.2 MiB	62.4 MiB
cr_gg_13_8	97,299	37,193,012	764.51	1173.28	2778.12	9.57	-0.05	6	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	52.8 MiB	138.0 MiB	137.7 MiB	127.7 MiB
cr_silva_123	154,141	49,921,901	647.74	1189.84	2967.49	10.59	-0.17	6	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	72.1 MiB	186.7 MiB	185.2 MiB	172.5 MiB
or_gg_13_8	8,051,550	158,521,504	39.38	534.11	3297.57	19.00	-0.50	7	1.00	Undirected	Bipartite	is_sample name taxonomy barcode_sequence linker_primer_sequence description host_subject_id study_id title principal_investigator doi ebi_accession target_gene target_subfragment pcr_primers illumina_technology extraction_center run_center run_date sample_taxid sample_scientific_name host_taxid host_common_name_provided host_common_name host_scientific_name host_superkingdom host_kingdom host_phylum host_class host_order host_family host_genus host_species collection_timestamp country env_biome env_feature env_material envo_biome_0 envo_biome_1 envo_biome_2 envo_biome_3 envo_biome_4 envo_biome_5 empo_0 empo_1 empo_2 empo_3 read_length_bp sequences_split_libraries observations_closed_ref_greengenes observations_closed_ref_silva observations_open_ref_greengenes observations_deblur_90bp observations_deblur_100bp observations_deblur_150bp latitude_deg longitude_deg depth_m altitude_m elevation_m adiv_observed_otus adiv_chao1 adiv_shannon adiv_faith_pd temperature_deg_c ph salinity_psu oxygen_mg_per_l phosphate_umol_per_l ammonium_umol_per_l nitrate_umol_per_l sulfate_umol_per_l emp_release1 qc_filtered subset_10k subset_5k subset_2k	count	288.1 MiB	708.6 MiB	682.0 MiB	645.7 MiB