Host DNA depletion methods in pig and human colon biopsies
138 samples from frozen human and pig intestinal biopsies (San Diego, CA, USA), comparing six host-depletion methods, including ChIP, for microbiome recovery; most human subjects were adults, with some elderly. machine-written summary
138 samples · 382 runs · US · Adult · 2024 · 32.7 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,380 sample values (age, antibiotic exposure, collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11845529 |
| ○ 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 |
longitudinal — not resolved
10 of 10 people sampled more than once (138 samples; median 14, up to 14 per person).
Genera, mean relative abundance over 9 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 | 138 | 100% | ||||
| country | 138 | 100% | 138 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 138 | 100% | 138 | |||
| age_at_collection_days | 138 | 100% | 138 | |||
| antibiotic_exposure | 138 | 100% | 138 | |||
| collection_date | 138 | 100% | 138 | |||
| detailed_location | 138 | 100% | ||||
| latitude | 138 | 100% | 138 | |||
| location_locality | 138 | 100% | 138 | |||
| location_region | 138 | 100% | 138 | |||
| longitude | 138 | 100% | 138 | |||
| sex | 138 | 100% | 138 |
- ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias. 2025 PMID 39982577 PMC11845529 own_data
Archive description
Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies. We find that all methods that rely on differential lysis of host and microbial cells introduce substantial biases as assessed by 16S rRNA gene amplicon profiling. However, ChIP enables 10-fold enrichment of microbial DNA while introducing less bias, sufficient to make assessment possible against background, in both pigs and humans. We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.title · “pig and human colon samples”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “pig and human colon samples”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.host_life_stage · “adult (n=278/382)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA116331147 | age_at_collection_days | 23741.2 | R1 | 0.90 | sample.attr.host_age | 65 |
| SAMEA116331147 | antibiotic_exposure | yes | R1 | 0.90 | biosample_attr | TRUE |
| SAMEA116331147 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA116331147 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA116331147 | latitude | 32.8420 | R1 | 0.90 | biosample.attribute:latitude+longitude | 32.842 -117.258 |
| SAMEA116331147 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA: San Diego |
| SAMEA116331147 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA: San Diego |
| SAMEA116331147 | longitude | -117.2580 | R1 | 0.90 | biosample.attribute:latitude+longitude | 32.842 -117.258 |
| SAMEA116331147 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMEA116331147 | subject_id | UCSD-42.1 | R1 | 0.85 | sample.attr.host_subject_id | UCSD-42.1 |
Sequencing
382 runs over 138 samples · mean 0.55 Gbp per run (median 32.7 Mbp, total 208.86 Gbp; 382 runs with a base count) · layout PAIRED 382 · platform ILLUMINA 382 · models Illumina NovaSeq 6000 (382) · 8% of runs with a Sandpiper profile · first public 2024-10-30
Authors (11)
Bhute S first · Sanders JG · Song SJ · Lavoie S · Swafford A · Guccione C · Patel L · Gonzalez A · Rooks MG · Knight R · Bartko A last
Downloads
PRJEB81804.csv.gz (3.6 KB) · parquet (75.1 KB) — all 138 samples, every field with route and confidence · PRJEB81804_determinations.csv.gz (7.5 KB) — 1,380 evidence rows