Earth Microbiome Vuegen Demo Notebook

init_notebook_modetrusted

The Earth Microbiome Project (EMP) is a systematic attempt to characterize global microbial taxonomic and functional diversity for the benefit of the planet and humankind. It aimed to sample the Earth’s microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial community structure. The EMP dataset is generated from samples that individual researchers have compiled and contributed to the EMP. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

You can find more information about the Earth Microbiome Project at https://earthmicrobiome.org/ and in the original article.

Exploratory Data Analysis

This section contains the exploratory data analysis of the Earth Microbiome Project (EMP) dataset.

Sample Exploration

Metadata Random Subset

^ⓘ#SampleID	BarcodeSequence	LinkerPrimerSequence	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	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	emp_release1	qc_filtered	subset_10k	subset_5k	subset_2k	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	latitude_deg	longitude_deg	depth_m	altitude_m	elevation_m	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	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
1056.Mel.urs.ino.SanDi.1	CGATAGGCCTTA	GTGCCAGCMGCCGCGGTAA	fecal sample from Sri Lankan sloth bear	1056:Mel.urs.ino.SanDi.1	1056	Convergence of gut microbiomes in myrmecophagous mammals	Frederic Delsuc	10.1111/mec.12501	ERP003782	16S rRNA	V4	FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT	MiSeq	CCME-Boulder	CCME	10/9/12	151	19043	17318.0	17597.0	18497.0	13608.0	13265.0	10851.0	True	True	True	True	True	749906	gut metagenome	9636.0	Sri Lankan sloth bear	sloth bear	Melursus ursinus	sk__Eukaryota	k__Metazoa	p__Chordata	c__Mammalia	o__Carnivora	f__Ursidae	g__Melursus	s__Melursus_ursinus	2012-08-03	GAZ:United States of America	32.780000	-117.070000	0.000	0.0	72.0000	terrestrial biome	animal-associated habitat	feces	biome	terrestrial biome	NaN	NaN	NaN	NaN	EMP sample	Host-associated	Animal	Animal distal gut	173.0	208.775000	4.013517	22.370232	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
1036.P.N.14.2.s.4.1.sequences	GGTTCCATTAGG	GTGCCAGCMGCCGCGGTAA	soil metagenome P_N_14_2	XXQIITAXX	1036	Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability?	Jenni Hultman	10.1038/ismej.2011.163*	ERP016588	16S rRNA	V4	FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT	HiSeq	ANL-Chicago	CCME	2/15/12	100	201124	165896.0	171547.0	198921.0	107368.0	77423.0	0.0	True	True	True	False	False	410658	soil metagenome	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	2009-04-01	GAZ:United States of America	64.490000	-157.750000	0.700	0.0	593.0000	tundra biome	permafrost	soil	biome	terrestrial biome	tundra biome	NaN	NaN	NaN	EMP sample	Free-living	Non-saline	Soil (non-saline)	481.0	706.857143	6.932894	56.337594	NaN	6.20	NaN	NaN	NaN	NaN	NaN	NaN
1034.CHI7	CTGAAGGGCGAA	GTGCCAGCMGCCGCGGTAA	soil metagenome, AB	CHI7	1034	Distinct microbial communities associated with buried soils in the Siberian tundra	Antje Gittel	10.1038/ismej.2013.219	ERP016735	16S rRNA	V4	FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT	HiSeq	ANL-Chicago	CCME	8/28/12	100	94168	74417.0	77196.0	92153.0	46391.0	46128.0	0.0	True	True	False	False	False	410658	soil metagenome	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	2011-08-10	GAZ:Russia	68.747920	161.601180	NaN	0.0	315.0000	tundra biome	tundra	soil	biome	terrestrial biome	tundra biome	NaN	NaN	NaN	EMP sample	Free-living	Non-saline	Soil (non-saline)	1087.0	1704.946903	8.403612	90.602021	NaN	5.46	NaN	NaN	NaN	NaN	NaN	NaN
(97 more rows not shown)

Animal Samples Map

Plant Samples Map

Saline Samples Map

Physicochemical properties of the EMP samples

Pairwise scatter plots of available physicochemical metadat are shown for temperature, salinity, oxygen, and pH, and for phosphate, nitrate, and ammonium

Metagenomics

Alpha Diversity

This subsection contains the alpha diversity analysis of the EMP dataset.

Alpha Diversity Host Associated Samples

Alpha Diversity Free Living Samples

Average Copy Number

Average Copy Number Emp Ontology Level2

Average Copy Number Emp Ontology Level3

Nestedness

Nestedness Random Subset

^ⓘUnnamed: 0	SAMPLE_RANK	OBSERVATION_RANK	SAMPLE_ID	OBSERVATION_ID	empo_3	METADATA_NUMERIC_CODE
15917	1577	84	808.AK.19.15a.s.4.1.sequences	k__Bacteria;p__Bacteroidetes	Soil (non-saline)	9
6395	1871	70	807.S.S.11.b	k__Archaea;p__Euryarchaeota	Sediment (non-saline)	11
4461	779	83	722.M11Tong.6.s.7.1.sequence	k__Bacteria;p__Actinobacteria	Animal secretion	12
(97 more rows not shown)

All Samples

Plant Samples

Animal Samples

Non Saline Samples

Shanon entropy analysis

This subsection contains the Shannon entropy analysis of the EMP dataset.

Specificity of sequences and higher taxonomic groups for environment

Environment distribution in all genera and 400 randomly chosen tag sequence. b) and c) Shannon entropy within each taxonomic group.

Network Analysis

Phyla Association Networks

Phyla Counts Subset

^ⓘUnnamed: 0	807.E.S.11.b	1883.2008.269.Crump.Artic.LTREB.main.lane2.NoIndex	1627.ZCCK1	1711.KAM6.3	1034.ZKD2	722.TRRsed3.4.s.4.1.sequence	1883.2007.214.Crump.Artic.LTREB.main.lane2.NoIndex	1222.B4.5.8.06	1288.NSB30jul08E.McMahon.Pool.3.and.1percentPhiX.110310.HWUSI.EAS552R.0357.s.3.1.sequence	1242.ME07Aug08EB2R2	1453.47548SDZ2.C8.Cang.stom	1642.MS00567	1198.ANT02.S1M2	1034.ZKE4	1580.1CA.sed.D1	550.L1S264.s.1.sequence	1001.SKM9	1747.DZF.6202012.RJ.glass.window	809.PLRP15.mat	861.H10.mar09	1773.Columb.passer8.lgi	933.Phylospora.comosa.1.5	1774.53Fecal23.10.09	678.T.RFLP.Sample.636	1883.2011.54.Crump.Artic.LTREB.main.lane3.NoIndex	1642.MS00602	910.PocTA2	1039.L.Vermelha.SC.2.3	1748.5.15.12.FI.11.V	807.C.F.11.b	2382.SH004.C1.RH.2.609.leav.9.12.lane8.NoIndex.L008.sequences	807.S.F.11.b	1773.Columb.passer5.ugi	1642.MS00635	1713.McG.L3B1020	804.LS11.70a	2080.S39D435	722.M31Fcsw.3.s.3.1.sequence	933.T.1.1.S.E.4	1064.W.CV123	1627.LBC1	1883.2011.498.Crump.Artic.LTREB.main.lane4.NoIndex	662.M23	2382.SH004.C1.RH.1.605.gp.9.12.lane8.NoIndex.L008.sequences	861.C15.dec08	1883.2008.151.Crump.Artic.LTREB.main.lane2.NoIndex	2382.RU006.C181.RH.4.794.leav.9.12.lane8.NoIndex.L008.sequences	1642.MS00454	722.M31Plmr.7.s.8.1.sequence	1883.2011.494.Crump.Artic.LTREB.main.lane4.NoIndex
Bacteroidetes	0.037649	0.051275	0.123926	0.016145	0.027898	0.027252	0.048886	0.025186	0.029577	0.056765	0.104488	0.026542	0.052696	0.000000	0.094801	0.113335	0.049984	0.042686	0.069616	0.038876	0.008783	0.058573	0.028350	0.023184	0.048563	0.023636	0.002583	0.018211	0.020923	0.025831	0.000000	0.038037	0.005554	0.027833	0.001227	0.035389	0.003746	0.195221	0.052954	0.000065	0.010010	0.022538	0.038295	0.000000	0.035389	0.035002	0.000000	0.026994	0.045140	0.046238
WS3	0.012869	0.000000	0.000000	0.054504	0.000000	0.030280	0.016654	0.000000	0.000000	0.000757	0.000000	0.018925	0.000000	0.000000	0.010598	0.000000	0.000000	0.000000	0.006056	0.065102	0.000000	0.000000	0.000000	0.052233	0.004542	0.034065	0.000000	0.008327	0.000000	0.018925	0.000000	0.026495	0.000000	0.017411	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.019682	0.003028	0.000000	0.000000	0.000000	0.001514	0.000000	0.019682	0.000000	0.018168
Elusimicrobia	0.021100	0.000000	0.000000	0.040693	0.000000	0.000000	0.018839	0.000000	0.000000	0.000000	0.000000	0.022607	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.002261	0.000754	0.003768	0.016579	0.000000	0.003014	0.000000	0.024868	0.000000	0.023361	0.000000	0.023361	0.006029	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000754	0.000000	0.016579	0.000000	0.000000
(78 more rows not shown)

Phyla Correlation Network With 0.5 Threshold Edgelist

Number of nodes: 33

Number of edges: 42