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Shotgun metagenomes enriched for viromes from stool samples of healthy donors and active ulcerative colitis patients under donor fecal microbiota filtrate and microbiota transfer raw Illumina sequence reads

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Dataset overview

Participants 11
Samples None
Reuse readiness 6.3/10 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
—
Platform
Illumina NovaSeq
Age group
—
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.

File types application/x-gzip

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Participant-to-sample mapping is available
  • Participant counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables are advertised
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.paired_end True
Illumina paired-end data (R1 and R2)

Section dataset description, offset —
assay.platform Illumina NovaSeq
Illumina NovaSeq sequencing of test stool samples yielded datasets

Section Fecal virome extraction, DNA purification, and sequencing, offset 11000
assay.read_length 250
16.3 10 6 ± 0.7 10 6 250b paired-end reads per sample

Section Fecal virome extraction, DNA purification, and sequencing, offset 11100
assay.sequencing_type shotgun_metagenomics
Shotgun metagenomes enriched for viromes

Section dataset title, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
active ulcerative colitis patients

Section dataset description, offset —
cohort.non_ibd_controls 5
from 5 healthy stool donors

Section dataset description, offset —
cohort.study_design longitudinal
patients ... at different times of treatment

Section dataset description, offset —
cohort.total_participants 11 computed
Human stool samples of six Ulcerative Colitis patients ... from 5 healthy stool donors

Section dataset description, offset —
cohort.treatment_exposure_documented True
patients under donor fecal microbiota filtrate and microbiota transfer

Section dataset description, offset —
cohort.ulcerative_colitis_participants 6
Human stool samples of six Ulcerative Colitis patients

Section dataset description, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True from source
openAccess

Section datacite_record rights, offset —
data_assets.raw_reads True
raw fastq Illumina reads of shotgun metagenomes

Section dataset description, offset —

Specimens

FieldValueEvidence
specimens.longitudinal_sampling True
patients ... at different times of treatment

Section dataset description, offset —
specimens.participant_to_sample_mapping_available True
healthy donors (D1-D5) and Ulcerative colitis patients (P1-P6) at different days

Section dataset description, offset —
specimens.sample_type stool
Human stool samples of six Ulcerative Colitis patients

Section dataset description, offset —