Human stool samples of healthy donors and active ulcerative colitis patients under donor fecal microbiota filtrate and microbiota transfer raw Illumina sequence reads of shotgun metagenomes and 16S amplicons

Dataset overview

Participants 11

Samples 134

Reuse readiness 7.6/10 evidence-backed score

Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.

Junca H, Steube A, Mrowietz S, Stallhofer J, Vital M, Dos Anjos Borges LG, Pieper DH, Stallmach A. · ISME communications · 2024

Abstract

Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.

doi:10.1093/ismeco/ycae167 ↗ PMID 39830095 ↗ PMC11740987 ↗

Study facts

Organism: human feces metagenome
Platform: Illumina MiSeq
Age group: adult
Disease groups: Non-IBD controls, Ulcerative colitis
Anatomical sites: —

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Feature/OTU tables are advertised
Taxonomic tables are advertised
Participant-to-sample mapping is available
Participant counts are documented
Sample counts are documented

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.paired_end`	True	subjected to 2 × 300-bp Illumina MiSeq sequencing Section `DNA and 16S ribosomal RNA (rRNA) gene amplicon sequencing`, offset 6800
`assay.platform`	Illumina MiSeq from source	ENA instrument_model=Illumina MiSeq Section `ENA study report`, offset —
`assay.primers_reported`	True	PCR with primers 27Fbif and 338R Section `DNA and 16S ribosomal RNA (rRNA) gene amplicon sequencing`, offset 6400
`assay.target_region`	V1–V2	A 2-step PCR-approach was used to amplify the V1–V2 variable region of the 16S rRNA gene Section `DNA and 16S ribosomal RNA (rRNA) gene amplicon sequencing`, offset 6200

Cohort

Field	Value	Evidence
`cohort.age_group`	adult	Six adult patients with active disease Section `Patients, treatment regimes, and sample collection`, offset 1840
`cohort.disease_activity_metadata_available`	True	Six adult patients with active disease Section `Patients, treatment regimes, and sample collection`, offset 1800
`cohort.non_ibd_controls`	5	Fecal microbiota and fecal microbiota filtrate were prepared from healthy donors D1–D5 Section `Patients, treatment regimes, and sample collection`, offset 2100
`cohort.study_design`	longitudinal	Stool samples were collected during the treatment every week Section `Patients, treatment regimes, and sample collection`, offset 2450
`cohort.total_participants`	11 computed	Six adult patients with active disease... Fecal microbiota and fecal microbiota filtrate were prepared from healthy donors D1–D5 Section `Patients, treatment regimes, and sample collection`, offset 1800
`cohort.treatment_exposure_documented`	True	long-term, multi-donor, oral-capsule based FMFT (12 weeks) followed by FMT (12 weeks) Section `Patients, treatment regimes, and sample collection`, offset 1300
`cohort.treatment_response_metadata_available`	True	Efficacy of FMFT/FMT was measured by clinical response... and clinical remission Section `Patients, treatment regimes, and sample collection`, offset 3000
`cohort.ulcerative_colitis_participants`	6	Six adult patients with active disease and failure of response to conventional UC therapy were enrolled Section `Patients, treatment regimes, and sample collection`, offset 1800

Data_Assets

Field	Value	Evidence
`data_assets.feature_or_otu_table`	True	The data matrices comprising 667 species level taxa were used Section `Bioinformatic and statistical analysis`, offset 7600
`data_assets.open_access`	True from source	"license": "cc by" Section `publication metadata`, offset —
`data_assets.pipeline_or_tool_versions`	True	The fastQ files were analyzed with the dada2 package version 1.21.0 in R Section `Bioinformatic and statistical analysis`, offset 7350
`data_assets.raw_reads`	True	includes datasets of raw fastq Illumina reads Section `study.description`, offset —
`data_assets.taxonomic_table`	True	Relative abundances of sequence types, species and genera were used for downstream analyses (Supplementary Table S3) Section `Bioinformatic and statistical analysis`, offset 7200

Specimens

Field	Value	Evidence
`specimens.body_site`	stool	Stool samples were collected during the treatment every week Section `Patients, treatment regimes, and sample collection`, offset 2300
`specimens.inflamed_status_available`	True	Six adult patients with active disease Section `Patients, treatment regimes, and sample collection`, offset 1800
`specimens.longitudinal_sampling`	True	Stool samples were collected during the treatment every week Section `Patients, treatment regimes, and sample collection`, offset 2300
`specimens.number_of_samples`	134 from source	ENA sample_count=134 Section `ENA study report`, offset —
`specimens.participant_to_sample_mapping_available`	True	Six chronic UC patients P1–P6... healthy donors D1–D5 Section `Patients, treatment regimes, and sample collection`, offset 2050
`specimens.sample_type`	stool	Stool samples were collected during the treatment every week Section `Patients, treatment regimes, and sample collection`, offset 2300