Longitudinal gut metagenomes of healthy Boston donors
563 longitudinal gut metagenome samples from healthy adult stool donors (FMT donors) in Boston, USA, part of a longitudinal study design. machine-written summary
563 samples · 563 runs · US · Adult · 2019 · 1.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,941 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,689 sample values (antibiotic exposure, health condition, health condition detail) · PMC10039858, PMC10820491, PMC10932609, PMC11796403, PMC12505567 |
| ○ 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
82 of 84 people sampled more than once (561 samples; median 2, up to 206 per person) · follow-up median 3 mo (max 18 mo) · median interval between samples 2 d (time from collection dates). Schedule stated by the source: “not specified; only subject-level repeated sampling counts given (564 metagenomic samples from 84 donors)”.
Each row is one person (36 shown of 82); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 497 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 | 563 | 100% | ||||
| country | 563 | 100% | 563 | |||
| health_condition | 563 | 100% | 563 | |||
| subject_id | 563 | 100% | 563 | |||
| antibiotic_exposure | 563 | 100% | 563 | |||
| collection_date | 563 | 100% | 563 | |||
| detailed_location | 563 | 100% | ||||
| health_condition_detail | 563 | 100% | 563 | |||
| latitude | 563 | 100% | 563 | |||
| location_locality | 563 | 100% | 563 | |||
| location_region | 563 | 100% | 563 | |||
| longitude | 563 | 100% | 563 |
- A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. 2019 PMID 31477907 own_data
- Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. 2020 PMID 32753501 PMC7406220 own_data
- Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering. 2021 PMID 33901198 PMC8102008 own_data
- A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome. 2021 PMID 34669476 PMC8528411 own_data
- Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. 2023 PMID 36757364 PMC9977275 own_data
20 more
- Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome. 2023 PMID 36809109 PMC10127601
- The genomic landscape of reference genomes of cultivated human gut bacteria. 2023 PMID 36966151 PMC10039858
- Stability of human gut microbiome: Comparison of ecological modelling and observational approaches. 2023 PMID 37745638 PMC10511340
- Polyethylene Terephthalate Hydrolases in Human Gut Microbiota and Their Implications for Human Health. 2024 PMID 38257965 PMC10820491
- Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. 2024 PMID 38376180 PMC10997323
- Genomic and functional diversity of cultivated <i>Bifidobacterium</i> from human gut microbiota. 2024 PMID 38463766 PMC10923715
- MetaQuad: shared informative variants discovery in metagenomic samples. 2024 PMID 38476299 PMC10932609
- CRISPR-Cas spacer acquisition is a rare event in human gut microbiome. 2025 PMID 39719706 PMC11770219
- Virulence factor discovery identifies associations between the Fic gene family and Fap2<sup>+</sup> fusobacteria in colorectal cancer microbiomes. 2025 PMID 39807864 PMC11796403
- Members of Lachnospiraceae produce valerate and caproate in response to short-chain fatty acids. 2025 PMID 41057964 PMC12505567
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. 2020 PMID 32093762 PMC7038607
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196
- Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. 2023 PMID 37709733 PMC10502120
- Cataloging the phylogenetic diversity of human bladder bacterial isolates. 2024 PMID 38515176 PMC10958879
- Gut microbiota strain richness is species specific and affects engraftment. 2025 PMID 39604726 PMC12547691
- Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria. 2025 PMID 40670725 PMC12313528
- Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization. 2025 PMID 40742180 PMC12363224
- Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway. 2025 PMID 41118772 PMC13059687
- Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes. 2025 PMID 41413769 PMC12853991
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies. 2026 PMID 42683728 PMC13540108
Archive description
We introduce a comprehensive library of human gut bacteria: a library of 7,758 bacterial isolates, characterized by 16S sanger sequences, which were obtained from healthy FMT donors recruited in the Boston area. This library covers most of the phylogenetic diversity found in the human gut and contains extensive strain diversity. Isolates can be requested at this address: XXX.</p><p>We report Whole Genome Sequences (WGSs) for a phylogenetically-comprehensive subset of these isolates, representing a library of 3,632 WGSs, to enable researchers to test and predict phenotypes in vitro and in vivo. We also provide longitudinal 16S (1,169 samples from 90 donors), metagenomic (564 samples from 84 donors) and metabolomic data (179 samples from 83 donors) for a large cohort of FMT donors.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “healthy FMT donors recruited in the Boston area”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11950000 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not taking any drugs during the last month |
| SAMN11950000 | collection_date | 2014-07-10 | R1 | 0.90 | biosample.attribute:collection_date | 2014-07-10 |
| SAMN11950000 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Boston |
| SAMN11950000 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 299 healthy human donors not taking any drugs |
| SAMN11950000 | health_condition_detail | healthy donors, no diagnosed disease | R3 | 0.70 | paper.fulltext.methods | 299 healthy human donors not taking any drugs |
| SAMN11950000 | latitude | 42.3600 | R1 | 0.90 | biosample.attribute:lat_lon | 42.36 N 71.06 W |
| SAMN11950000 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Boston |
| SAMN11950000 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.36 N 71.06 W |
| SAMN11950000 | longitude | -71.0600 | R1 | 0.90 | biosample.attribute:lat_lon | 42.36 N 71.06 W |
| SAMN11950000 | subject_id | aa | R1 | 0.85 | sample.attr.host_subject_id | aa |
Sequencing
563 runs over 563 samples · mean 1.88 Gbp per run (median 1.56 Gbp, total 1,061.03 Gbp; 563 runs with a base count) · layout PAIRED 563 · platform ILLUMINA 563 · models Illumina HiSeq 2500 (563) · 88% of runs with a Sandpiper profile · first public 2019-08-01
Authors (88)
Poyet M first · Groussin M · Gibbons SM · Avila-Pacheco J · Jiang X · Kearney SM · Perrotta AR · Berdy B · Zhao S · Lieberman TD · Swanson PK · Smith M · Roesemann S · Alexander JE · Rich SA · Livny J · Vlamakis H · Clish C · Bullock K · Deik A · Scott J · Pierce KA · Xavier RJ · Alm EJ last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last · Levy S · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Tang G first · Carr AV · Perez C · Ramos Sarmiento K · Levy L · Lampe JW · Diener C · Jacoby C first · Scorza K · Ecker L · Nol Bernardino P · Little AS · McMillin M · Ramaswamy R · Sundararajan A · Sidebottom AM · Lin H · Dufault-Thompson K · Hall B · Light SH last · Medina-Méndez JM first · Iruzubieta P · Fernández-López R · Crespo J · de la Cruz F last · Zhang Z first · Holton M · Ferrer DM · Tripp AD · Richter A · Dixit PD · Urtecho G last
Downloads
PRJNA544527.csv.gz (15.2 KB) · parquet (92.4 KB) — all 563 samples, every field with route and confidence · PRJNA544527_determinations.csv.gz (33.3 KB) — 5,630 evidence rows