Gut microbiome in ME/CFS vs healthy controls, New York, USA

gut microbiome of Myalgic Encephlomyelitis/Chronic Fatigue Syndrome patients

197 fecal samples from adults and elderly in New York, USA, comparing ME/CFS patients (106) to healthy controls (91) in a case-control study of butyrate-producing gut microbiota and fatigue. machine-written summary

197 samples · 197 runs · US · Adult · 2021 · 1.84 Gbp / sample

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Sources

✓Sequence archive 2,548○Abstract / description○Full text○Supplementary tables✓External resources 197–User contribution–Human verified

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

what each source gave

✓ Sequence archive	2,548 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region)
○ Abstract / description	read; no usable statement
○ Full text	read; no usable statement or table · PMC10183837, PMC13526866
○ Supplementary tables	files read; no table could be matched to the samples
✓ External resources	197 sample values (antibiotic exposure) · from Meta2DB (LLNL)
– 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

adult181

elderly16

Condition

other_disease106

healthy_control91

Sex

female144

male53

Country

US197

Body site

primary197

Sequencing depth per sample · this project all projects

Community composition

Bacteroides 25.9%Phocaeicola 16.2%Alistipes 9.9%Parabacteroides 2.8%Faecalibacterium 2.7%Prevotella 2.6%Roseburia 2.6%Oscillibacter 1.3%Blautia_A 1.1%Ruminiclostridium_E 0.8%Acetatifactor 0.8%Akkermansia 0.8%not assigned to a genus 9.0%other genera 23.6%

Genera, mean relative abundance over 181 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	197	100%
country	197	100%	197
health_condition	197	100%	197
subject_id	197	100%	197
age_at_collection_days	197	100%	197
antibiotic_exposure	197	100%		197
bmi	197	100%	197
collection_date	197	100%	197
detailed_location	197	100%
health_condition_detail	197	100%	197
latitude	197	100%	197
location_region	197	100%	197
location_site	197	100%	197
longitude	197	100%	197
sex	197	100%	197
medication	184	93%	184

Papers (2)

Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. 2023 PMID 36758522 PMC10183837 own_data
Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis. 2026 PMID 42289444 PMC13526866 unsure

Details

Archive description

Deficient butyrate-producing capacity in the gut microbiome of MECFS patients and its association with fatigue symptoms

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site study.title · “gut microbiome of Myalgic Encephlomyelitis”
life stage sample.attr.age_at_a1_cat · “Adult (n=181/197)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN20518494	age_at_collection_days	7741.0	R1	0.85	biosample.attribute:age_at_a1	age_at_a1: 21.19370294
SAMN20518499	age_at_collection_days	23825.0	R1	0.85	sample.attr.age_at_a1	65.33607118
SAMN20518494	antibiotic_exposure	no	R2	0.70	external.meta2db source	antibiotics: FALSE
SAMN20518494	bmi	27.7	R1	0.90	sample.attr.bmi	27.7031338
SAMN20518494	collection_date	2019-01-01	R1	0.90	biosample.attribute:collection_date	2019-01-01
SAMN20518494	country	US	R1	0.90	sample.attr.geo_loc_name	USA: NewYork
SAMN20518494	health_condition	healthy_control	R1	0.85	biosample.attribute:mecfs_status	mecfs_status: N
SAMN20518495	health_condition	other_disease	R1	0.90	biosample_attr	Y
SAMN20518494	health_condition_detail	N	R1	0.90	sample.attr.mecfs_status	N
SAMN20518494	latitude	40.7100	R1	0.90	biosample.attribute:lat_lon	40.71 N 74.00 W
SAMN20518494	location_region	New York	R1	0.75	biosample.attribute:geo_loc_name	USA: NewYork
SAMN20518494	location_site	nevada	R1	0.85	biosample.attribute:site	nevada
SAMN20518494	longitude	-74.0000	R1	0.90	biosample.attribute:lat_lon	40.71 N 74.00 W
SAMN20518494	medication	probiotic_or_prebiotic	R1	0.85	biosample.attribute:probiotic	probiotic: Y
SAMN20518497	medication	other_medication	R1	0.85	biosample.attribute:pain_narc_rx	pain_narc_rx: Y
SAMN20518499	medication	antidepressant_or_antipsychotic	R1	0.85	biosample.attribute:anti_depressant_rx	anti_depressant_rx: Y
SAMN20518555	medication	probiotic_or_prebiotic	R1	0.85	biosample.attribute:prebiotic	prebiotic: Y
SAMN20518494	sex	male	R1	0.90	sample.attr.sex	male
SAMN20518494	subject_id	EF009	R1	0.85	sample.attr.participant_id	EF009

Sequencing

197 runs over 197 samples · mean 1.89 Gbp per run (median 1.84 Gbp, total 372.41 Gbp; 197 runs with a base count) · layout SINGLE 197 · platform ILLUMINA 197 · models NextSeq 550 (197) · 92% of runs with a Sandpiper profile · first public 2021-08-25

Authors (26)

Guo C first · Che X · Briese T · Ranjan A · Allicock O · Yates RA · Cheng A · March D · Hornig M · Komaroff AL · Levine S · Bateman L · Vernon SD · Klimas NG · Montoya JG · Peterson DL · Lipkin WI · Williams BL last · Masuoka H first · Miyatake T · Park J · Negishi H · Kurokawa R · Tsuchihashi H · Makino S · Suda W last

Downloads

PRJNA751448.csv.gz (8.1 KB) · parquet (81.9 KB) — all 197 samples, every field with route and confidence · PRJNA751448_determinations.csv.gz (25.2 KB) — 2,745 evidence rows

Samples (197 · every field this project has values for · hover a cell for its source)

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