Longitudinal gut microbiome of FMT donors, Massachusetts

Dense longitudinal metagenomic analysis of the gut microbiome of FMT donors

469 longitudinal gut metagenome samples from fecal microbiota transplant (FMT) donors in Massachusetts, USA; 383 samples labeled as healthy control. machine-written summary

469 samples · 469 runs · US · Adult · 2020 · 0.80 Gbp / sample

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Sources

✓Sequence archive 3,158–Abstract / description–Full text–Supplementary tables✓External resources 766–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	3,158 sample values (bmi, collection date, country, health condition, health condition detail, latitude, location region, longitude)
– Abstract / description	no abstract or project description
– Full text	no open-access full text linked
– Supplementary tables	no supplementary tables available (or none open access)
✓ External resources	766 sample values (health condition, health condition detail) · from GMrepo v3
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 sampling locations · 1 country

Age

adult469

Condition

healthy_control469

Sex

male82

female4

Country

US469

Body site

primary469

Collected 2014–2016

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

40 of 44 people sampled more than once (465 samples; median 2, up to 172 per person) · follow-up median 5 mo (max 15 mo) · median interval between samples 2 d (time from collection dates).

Each row is one person (36 shown of 40); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 28.4%Phocaeicola 21.7%Roseburia 5.8%Faecalibacterium 4.4%Alistipes 3.4%Parabacteroides 2.9%Lachnospira 2.5%Hominimerdicola 2.0%Ruminococcoides 1.7%Prevotella 1.7%Gemmiger 1.5%Blautia_A 1.0%not assigned to a genus 11.4%other genera 11.7%

Genera, mean relative abundance over 415 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R2
age_category	469	100%
country	469	100%	469
health_condition	469	100%	86	383
subject_id	469	100%	469
collection_date	469	100%	469
detailed_location	469	100%
health_condition_detail	469	100%	86	383
latitude	469	100%	469
location_region	469	100%	469
longitude	469	100%	469
bmi	86	18%	86
sex	86	18%	86

Details

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
body site study.title · “analysis of the gut microbiome of FMT”
body site external_curation.infant_catalog · “body_site_call stool”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN08865949	bmi	31.0	R1	0.90	sample.attr.host_body_mass_index	31
SAMN08865949	collection_date	2014-07-10	R1	0.90	biosample.attribute:collection_date	2014-07-10
SAMN08865949	country	US	R1	0.90	sample.attr.geo_loc_name	USA: Massachusetts
SAMN08865949	health_condition	healthy_control	R1	0.60	biosample.attribute:host_age	Healthy
SAMN10410084	health_condition	healthy_control	R2	0.75	external.gmrepo source	phenotype: Health
SAMN08865949	health_condition_detail	Healthy	R1	0.60	biosample.attribute:host_age	Healthy
SAMN08865957	health_condition_detail	Omnivore; Avoids some fruits	R1	0.90	sample.attr.host_disease	Omnivore; Avoids some fruits
SAMN10410084	health_condition_detail	Health	R2	0.75	external.gmrepo source	phenotype: Health
SAMN08865949	latitude	42.3700	R1	0.90	biosample.attribute:lat_lon	42.37 N 71.08 W
SAMN08865949	location_region	Massachusetts	R1	0.85	biosample.attribute:geo_loc_name	USA: Massachusetts
SAMN08865949	longitude	-71.0800	R1	0.90	biosample.attribute:lat_lon	42.37 N 71.08 W
SAMN08865949	sex	male	R1	0.60	biosample.attribute:host_subject_id	M
SAMN08865949	subject_id	M	R1	0.60	biosample.attribute:host_subject_id	M
SAMN10410084	subject_id	am	R1	0.70	sample.name_rule:sample_alias	sub_am0053

Sequencing

469 runs over 469 samples · mean 1.00 Gbp per run (median 0.80 Gbp, total 469.38 Gbp; 469 runs with a base count) · layout PAIRED 469 · platform ILLUMINA 469 · models Illumina HiSeq 2500 (469) · 88% of runs with a Sandpiper profile · first public 2020-05-02 – 2020-12-02

Authors (0)

No author record.

Downloads

PRJNA448876.csv.gz (12.8 KB) · parquet (88.7 KB) — all 469 samples, every field with route and confidence · PRJNA448876_determinations.csv.gz (29.2 KB) — 3,924 evidence rows

Samples (469 · every field this project has values for · hover a cell for its source)

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