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PRJNA1006039 SRP483425

Phosphorothioation mapping in healthy adult gut microbiomes

Investigation of the Phosphorothioate Landscape in the Human Gut Microbiome

Cross-sectional study of 2 samples from healthy adult controls in Boston, USA, used to map phosphorothioate DNA modifications in human gut microbiome isolates via metagenomic and iodine cleavage sequencing. machine-written summary

2 samples · 2 runs · US · Age unknown · 2024 · 4.13 Gbp / sample

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Sources
✓Sequence archive 13○Abstract / description✓Full text 4○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive13 sample values (collection date, country, latitude, location locality, location region, longitude, subject id)
○ Abstract / descriptionread; no usable statement
✓ Full text4 sample values (health condition, health condition detail) · PMC11931770, PMC12914056
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult2
Condition
healthy_control2
Country
US2
Body site
primary2
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 1 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 1 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 4.13 Gbp per sample0130Gbp
Community composition
Prevotella 13.2%Faecalibacterium 8.4%Holdemanella 5.1%Blautia_A 3.8%Coprococcus 3.6%Anaerostipes 2.1%Dorea_A 2.1%Roseburia 2.1%Alistipes 1.9%Bacteroides 1.9%Phascolarctobacterium 1.9%Fimivicinus 1.7%not assigned to a genus 4.5%other genera 47.5%

Genera, mean relative abundance over 1 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category2 100%
country2 100%2
health_condition2 100%2
subject_id2 100%2
collection_date2 100%2
detailed_location2 100%
health_condition_detail2 100%2
latitude2 100%2
location_locality2 100%2
longitude2 100%2
location_region1 50%1
Papers (2)
  • Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome. 2025 PMID 40128848 PMC11931770 own_data
  • Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome. 2026 PMID 41571653 PMC12914056 own_data
Details
Archive description

Phosphorothioation (PT) is the only known backbone modification in DNA that plays a role in gene regulation and stress response. To survey the landscape of PTs in human gut microbiome in the background of heath and diseases, we applied sequencing technologies to map PTs in human gut microbiome. Dataset including raw reads of metagenomic sequencing of human gut microbiome samples and raw reads of iodine cleavage coupled sequencing of human gut microbiome isolates that locate PTs at a single nucleotide resolution.

How this project entered the registry

Classified as human gut / stool mixed assays of age unknown by sonnet_x2 with confidence 0.65. Assay mixed.

  • host run.host_tax_id · “9606”
  • host run.scientific_name · “human gut metagenome”
  • body site study.title · “Human Gut Microbiome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN39420940collection_date2021-06-01R10.90biosample.attribute:collection_date2021-06-01
SAMN39420940countryUSR10.90sample.attr.geo_loc_nameUSA:Boston
SAMN39420940health_conditionhealthy_controlR30.70paper.fulltext.abstractPT dinucleotides in fecal DNA from 11 healthy humans
SAMN39420940health_condition_detailhealthy humansR30.70paper.fulltext.abstractPT dinucleotides in fecal DNA from 11 healthy humans
SAMN39420940latitude42.3700R10.90biosample.attribute:lat_lon42.37 N 71.10 W
SAMN39420940location_localityBostonR10.85biosample.attribute:geo_loc_nameUSA:Boston
SAMN44015141location_regionMassachusettsR10.60biosample.attribute:lat_lon42.36 N 71.09 W
SAMN39420940longitude-71.1000R10.90biosample.attribute:lat_lon42.37 N 71.10 W
SAMN39420940subject_iddonor5R10.70sample.name_rule:library_nameslibrary_names: donor5_PTseq
Sequencing

2 runs over 2 samples · mean 4.13 Gbp per run (median 4.13 Gbp, total 8.25 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models Illumina MiSeq (1), Illumina NovaSeq 6000 (1) · 50% of runs with a Sandpiper profile · first public 2024-01-14 – 2024-10-03

Authors (24)

Byrne SR first · DeMott MS · Yuan Y · Ghanegolmohammadi F · Kaiser S · Fox JG · Alm EJ · Dedon PC last · Flores K · Poyet M · Groussin M · Berdy B · Bahunde JR · Girard C · Lehtimäki J · Mabulla AZP · Mwikarago IE · Nartey YA · Nguyen LTT · Onyekwere CA · Roberts LR · Shapiro BJ · Vatanen T · Comstock LE

Downloads

PRJNA1006039.csv.gz (994 B) · parquet (70.1 KB) — all 2 samples, every field with route and confidence · PRJNA1006039_determinations.csv.gz (899 B) — 17 evidence rows

Samples (2 · every field this project has values for · hover a cell for its source)
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