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Supplementary Tables - Cross-species engraftment biases and metabolic divergence in gnotobiotic mice humanized with ulcerative colitis microbiota

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Dataset overview

Participants 8
Samples None
Reuse readiness 8.4/10 evidence-backed score

Cross-species engraftment biases and metabolic divergence in gnotobiotic mice humanized with ulcerative colitis microbiota.

Guggeis MA, Andreani NA, López-Agudelo VA, Tran F, Kadibalban AS, Moors KA, Marinos G, Saboukh A, et al. · Gut microbes · 2025

Abstract

Ulcerative colitis (UC) is a chronic inflammatory disease of the human colon. Dysbiotic gut microbiota play a central role in its pathogenesis, and alterations in microbial composition and function are closely linked to disease activity. Humanized gnotobiotic mice are increasingly used to study how dysbiotic, human-derived microbial communities shape intestinal inflammation. However, the fidelity of microbiota engraftment and its impact on host physiology and metabolism remain incompletely understood. In this study, we performed a multiomics analysis following fecal microbiota transfer (FMT) from eight patients with active UC into germ-free C57BL/6N mice (five mice per donor). The mice were monitored over three weeks. Longitudinal analysis of microbial communities was performed using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing. Microbial metabolic flux was inferred via genome-scale metabolic modeling, and plasma metabolites were assessed by targeted metabolomics. We observed donor-specific physiological changes in recipient mice, including variations in body weight and adipose tissue. Spontaneous colonic inflammation occurred in one group and was subsequently linked to unintended transfer of <i>Clostridioides difficile</i>, which was previously clinically unrecognised in the donor. While bacterial engraftment overall was generally donor-specific and stable across mice, fungal taxa were transferred inconsistently and at low abundance. Despite similar overall plasma metabolomic profiles, select metabolites, including 3-indoleacetic acid, were differentially associated with specific microbial taxa. Moreover, metabolic modeling revealed disrupted metabolic exchange networks in the mouse microbiota compared to the original human donor communities. In conclusion, while human FMT into germ-free mice reliably transmits bacterial features, it introduces metabolic alterations and fails to fully reproduce the fungal microbiome. These findings underscore the need for cautious interpretation of microbiota-driven effects in gnotobiotic models and highlight the limitations of current approaches in replicating the full complexity of human gut ecosystems.

doi:10.1080/19490976.2025.2581445 ↗ PMID 41277418 ↗ PMC12645861 ↗

Study facts

Organism
—
Platform
Illumina MiSeq
Age group
—
Disease groups
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
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.paired_end True
sequenced with 250 bp paired-end reads

Section V1–V2 region sequencing for fecal and tissue samples, offset 13000
assay.platform Illumina MiSeq
sequenced on an Illumina MiSeq sequencer

Section V3–V4 region sequencing for the fecal samples, offset 11200
assay.primers_reported True
using 515F and 806 R

Section V3–V4 region sequencing for the fecal samples, offset 11100
assay.sequencing_type amplicon_16s
The V3–V4 region of the 16S rRNA gene was amplified

Section V3–V4 region sequencing for the fecal samples, offset 11100
assay.target_region V3–V4 and V1–V2
The V1–V2 hypervariable region of the 16S rRNA gene was amplified

Section V1–V2 region sequencing for fecal and tissue samples, offset 12700

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Colonic inflammation was quantified using the Mayo score.

Section Stool sample collection and preparation, offset 5200
cohort.study_design longitudinal
The mice were extracted from the cages under aseptic conditions once a week for weighing and fecal sample collection.

Section Experimental animals, offset 7000
cohort.total_participants 8
Stool from eight anti-TNF-naïve patients with UC with acute intestinal inflammation was collected

Section Stool sample collection and preparation, offset 5050
cohort.treatment_exposure_documented True
Patients received treatment with either oral or topical corticosteroids and/or 5-aminosalicylic acid and/or azathioprine

Section Results—Donor characteristics and fecal microbiota transfer, offset 28500
cohort.ulcerative_colitis_participants 8
Stool from eight anti-TNF-naïve patients with UC with acute intestinal inflammation was collected

Section Stool sample collection and preparation, offset 5050

Data_Assets

FieldValueEvidence
data_assets.feature_or_otu_table True
Supplementary Table 7: Rarefied ASV table of the 16S gene sequencing data

Section Data availability statement, offset 86800
data_assets.open_access True
"isOpenAccess": "Y"

Section Publication metadata, offset —
data_assets.pipeline_or_tool_versions True
Raw 16S rRNA gene sequencing data were processed using the DADA2 pipeline, implemented in the DADA2 R package, version 1.16.0.

Section V3–V4 region sequencing for the fecal samples, offset 11400
data_assets.qc_or_negative_controls_reported True
The prevalence method Decontam package version 3.19.0 was employed to computationally identify potential contaminants based on the microbial composition of both the true samples and the negative controls.

Section Data processing, offset 14800
data_assets.raw_reads True
The sequencing data that support the findings of this study will be openly available in the Sequence Read Archive (SRA) with the following project number: PRJNA1248768.

Section Data availability statement, offset 85800
data_assets.sample_metadata True
Supplementary Table 17: Physiological data of the recipient mice and fecal lipocalin-2 concentration of the mice.

Section Data availability statement, offset 87800
data_assets.taxonomic_table True
the taxonomic annotation of ASVs was obtained using the SILVA 138 database

Section V3–V4 region sequencing for the fecal samples, offset 11500

Specimens

FieldValueEvidence
specimens.body_site feces, skin, and lung
The analysis was conducted on lung, skin, and a combination of all bodily sites (mouse lung, mouse skin, and mouse feces)

Section Data processing, offset 15700
specimens.inflamed_status_available True
Histological scoring was performed... increased histological inflammation scores in the colons of mice from G8

Section Results—Physiological consequences of FMT from different UC donors to germ-free mice, offset 30000
specimens.longitudinal_sampling True
The mice were extracted from the cages under aseptic conditions once a week for weighing and fecal sample collection.

Section Experimental animals, offset 7000
specimens.participant_to_sample_mapping_available True
Supplementary Table 16: Data of the respective human donor per recipient mouse.

Section Data availability statement, offset 87200
specimens.sample_type mixed
mouse lung, mouse skin, and mouse feces

Section Results—Effect of fecal transfer on skin and lung microbiota, offset 41800