Chemostat cultivation of mouse and human fecal virome
108 samples from chemostat cultures of mouse cecal and human fecal material, propagated to retain bacteria and phages while limiting eukaryotic virus multiplication, as a proof-of-concept for safer fecal microbiota transplantation. machine-written summary
108 samples · 108 runs · Age unknown · 2023 · 1.06 Gbp / sample
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what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11298661 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure · Chemostat propagation of mouse cecal/human fecal material for FMT prep
Genera, mean relative abundance over 45 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material. 2024 PMID 39104406 PMC11298661 own_data
Archive description
During the last decade it has become evident that () complex diseases such as metabolic syndrome, autoimmune diseases and colon cancer are associated with imbalances of gut microbiome (GM). This makes the GM an attractive therapeutic target for faecal microbiota transplantation (FMT). During FMT in addition to bacteria also archaea and prokaryotic as well as eukaryotic viruses are transferred. Recent studies indicate the role of bacteriophages for successful FMT. However, wider clinical application of FMT is unlikely due to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in chemostat cultures. Environmental conditions supported reproduction of bacteria, archaea, and phages, whilst multiplication of eukaryotic viruses was prevented by the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of contigs of eukaryotic viruses from 0.2 % to below 0.01 %. The number of phage-assigned OTUs remained over 1000 x higher than these of eukaryotic viral OTUs after 5 volumes dilution. The corresponding bacterial virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity. The dominant viral taxa in mice cecal and human fecal matters were Petitvirales and Tubulavirales but the chemostat cultured phageomes contained mainly taxa from Caudoviricetes. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with low risk of infection from the donor material to target a broad spectrum of gut-related diseases.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.50. Assay shotgun_dna.
- host study.description · “mouse cecal and human fecal material”
- body site run.scientific_name · “gut metagenome”
Sequencing
108 runs over 108 samples · mean 1.00 Gbp per run (median 1.06 Gbp, total 108.52 Gbp; 108 runs with a base count) · layout PAIRED 108 · platform ILLUMINA 108 · models Illumina NovaSeq 6000 (108) · 45% of runs with a Sandpiper profile · first public 2023-04-29
Authors (6)
Adamberg S first · Rasmussen TS · Larsen SB · Mao X · Nielsen DS · Adamberg K last
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJEB58787.csv.gz (3.0 KB) · parquet (72.3 KB) — all 108 samples, every field with route and confidence · PRJEB58787_determinations.csv.gz (168 B) — 0 evidence rows