In vitro fermentation of elderly fecal microbiota, Zurich

Metagenome of fermentation model samples inoculated with human feces

18 samples from in vitro PolyFermS fermentation models inoculated with elderly fecal microbiota (Zurich, Switzerland), studying Clostridium difficile colonization and effects of antibiotic treatment; intervention design. machine-written summary

18 samples · 18 runs · CH · Age unknown · 2016 · 3.7 Mbp / sample

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Sources

✓Sequence archive 126○Abstract / description✓Full text 72○Supplementary tables–External resources–User contribution–Human verified

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

what each source gave

✓ Sequence archive	126 sample values (collection date, country, intervention, latitude, location locality, location region, longitude)
○ Abstract / description	read; no usable statement
✓ Full text	72 sample values (antibiotic exposure, health condition, health condition detail, sex) · PMC5133761
○ Supplementary tables	files read; no table could be matched to the samples
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Interventions

intervention · arms resolved

exposed vs. not exposed (observational)

design observational_with_procedure

Samples at a glance

1 sampling locations · 1 country

Age

elderly18

Condition

healthy_control18

Sex

female18

Country

CH18

Body site

primary18

Sequencing depth per sample · this project all projects

Community composition

No Sandpiper profile for this project's samples yet.

Field coverage

field	samples	coverage	R1	R3
age_category	18	100%
country	18	100%	18
health_condition	18	100%		18
subject_id	0	0%
antibiotic_exposure	18	100%		18
collection_date	18	100%	18
detailed_location	18	100%
health_condition_detail	18	100%		18
intervention	18	100%	18
latitude	18	100%	18
location_locality	18	100%	18
location_region	18	100%	18
longitude	18	100%	18
sex	18	100%		18

Papers (1)

Clostridium difficile colonization and antibiotics response in PolyFermS continuous model mimicking elderly intestinal fermentation. 2016 PMID 27980686 PMC5133761 own_data

Details

Archive description

In vitro fermentation of human feces to study the effect of antibiotics on the gut microbiota

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.

host run.scientific_name · “human gut metagenome”
host study.title · “inoculated with human feces”
body site study.description · “In vitro fermentation of human feces”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN05755736	antibiotic_exposure	no	R3	0.70	paper.fulltext.methods	did not receive antibiotic treatment for at least three months
SAMN05755736	collection_date	2013	R1	0.90	biosample.attribute:collection_date	2013
SAMN05755736	country	CH	R1	0.90	sample.attr.geo_loc_name	Switzerland: Zurich
SAMN05755736	health_condition	healthy_control	R3	0.70	paper.fulltext.methods	obtained from two healthy women aged 72
SAMN05755736	health_condition_detail	healthy women	R3	0.70	paper.fulltext.methods	obtained from two healthy women aged 72
SAMN05755736	intervention	no_intervention	R1	0.85	biosample.attribute:isolation_source	isolation_source: Fermentation effluent_control_B_22
SAMN05755736	latitude	47.3764	R1	0.90	biosample.attribute:lat_lon	47.3764 N 8.5481 E
SAMN05755736	location_locality	Zurich	R1	0.85	biosample.attribute:geo_loc_name	Switzerland: Zurich
SAMN05755736	location_region	Zurich	R1	0.60	biosample.attribute:lat_lon	47.3764 N 8.5481 E
SAMN05755736	longitude	8.5481	R1	0.90	biosample.attribute:lat_lon	47.3764 N 8.5481 E
SAMN05755736	sex	female	R3	0.70	paper.fulltext.methods	fresh fecal samples were obtained from two healthy women aged 72

Sequencing

18 runs over 18 samples · mean 3.6 Mbp per run (median 3.7 Mbp, total 64.9 Mbp; 18 runs with a base count) · layout SINGLE 18 · platform LS454 18 · models 454 GS FLX Titanium (18) · 0% of runs with a Sandpiper profile · first public 2016-10-27

Authors (6)

Fehlbaum S first · Chassard C · Poeker SA · Derrien M · Fourmestraux C · Lacroix C last

Downloads

PRJNA342339.csv.gz (1.3 KB) · parquet (70.9 KB) — all 18 samples, every field with route and confidence · PRJNA342339_determinations.csv.gz (2.1 KB) — 198 evidence rows

Samples (18 · every field this project has values for · hover a cell for its source)

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