PRJNA417343 SRP124375
Preterm infant gut metagenome time series, Pittsburgh NICU
preterm infant gut metagenomes (NIH Y5 Cohort)
Longitudinal cohort study of 269 fecal metagenome samples from premature infants in a NICU at Magee-Womens Hospital of UPMC, Pittsburgh, USA, spanning neonate and infant age categories. machine-written summary
269 samples · 269 runs · US · Infant / toddler · 2019 · 3.07 Gbp / sample
One study deposited as 2 BioProjects (574 catalog samples together): PRJNA396794 · PRJNA417343 · show together
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Sources
✓ Sequence archive 1,345 ✓ Abstract / description 269 ○ Full text○ Supplementary tables✓ External resources 269 – User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive1,345 sample values (age, collection date, country, subject id, timepoint) ✓ Abstract / description269 sample values (preterm status) ○ Full textread; no usable statement or table · PMC10175488 ○ Supplementary tablesfiles read; no table could be matched to the samples ✓ External resources269 sample values (sex) · from MicrobiomeDB (VEuPathDB) – User contributionnothing uploaded yet – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
Sequencing depth per sample ·
all projects, 0–0.03 Gbp: 25,080 samples (4 %) this project, 0–0.03 Gbp: 2 samples all projects, 0.03–0.1 Gbp: 17,066 samples (3 %) this project, 0.03–0.1 Gbp: 5 samples all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) this project, 0.1–0.3 Gbp: 6 samples all projects, 0.3–1 Gbp: 47,044 samples (8 %) this project, 0.3–1 Gbp: 8 samples all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 104 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 141 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 3 samples 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 3.07 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
longitudinal
53 of 53 people sampled more than once (269 samples; median 4, up to 19 per person) · follow-up median 37 d (max 4 mo) · median interval between samples 9 d (time from age at collection) .
Schedule stated by the source: “Repeated fecal sampling at multiple Day-Of-Life (DOL) timepoints per infant (67 distinct DOL labels across cohort).”.
N5_215 N5_215: day 0 N5_215: day 2 N5_215: day 10 N5_215: day 14 N5_215: day 22 N5_215: day 30 N5_215: day 40 N5_216 N5_216: day 0 N5_216: day 1 N5_216: day 10 N5_216: day 15 N5_216: day 20 N5_216: day 27 N5_216: day 34 N5_217 N5_217: day 0 N5_217: day 9 N5_217: day 22 N5_218 N5_218: day 0 N5_218: day 9 N5_218: day 16 N5_218: day 26 N5_218: day 35 N5_223 N5_223: day 0 N5_223: day 11 N5_223: day 19 N5_223: day 40 N5_224 N5_224: day 0 N5_224: day 5 N5_224: day 20 N5_224: day 37 N5_224: day 44 N5_224: day 57 N5_224: day 70 N5_225 N5_225: day 0 N5_225: day 5 N5_225: day 6 N5_225: day 8 N5_225: day 9 N5_225: day 15 N5_225: day 39 N5_225: day 46 N5_226 N5_226: day 0 N5_226: day 7 N5_226: day 33 N5_227 N5_227: day 0 N5_227: day 15 N5_227: day 49 N5_227: day 59 N5_228 N5_228: day 0 N5_228: day 8 N5_228: day 26 N5_229 N5_229: day 0 N5_229: day 1 N5_229: day 1 N5_229: day 2 N5_229: day 16 N5_229: day 19 N5_229: day 22 N5_229: day 41 N5_229: day 42 N5_232 N5_232: day 0 N5_232: day 14 N5_232: day 29 N5_232: day 39 N5_232: day 52 N5_232: day 67 N5_233 N5_233: day 0 N5_233: day 0 N5_233: day 4 N5_233: day 17 N5_233: day 24 N5_233: day 39 N5_234 N5_234: day 0 N5_234: day 6 N5_234: day 11 N5_234: day 19 N5_234: day 21 N5_234: day 28 N5_234: day 41 N5_234: day 55 N5_234: day 65 N5_235 N5_235: day 0 N5_235: day 20 N5_235: day 48 N5_238 N5_238: day 0 N5_238: day 10 N5_238: day 19 N5_239 N5_239: day 0 N5_239: day 17 N5_239: day 43 N5_239: day 55 N5_239: day 71 N5_239: day 77 N5_239: day 112 N5_241 N5_241: day 0 N5_241: day 30 N5_241: day 58 N5_244 N5_244: day 0 N5_244: day 6 N5_244: day 17 N5_244: day 24 N5_244: day 34 N5_244: day 43 N5_244: day 55 N5_245 N5_245: day 0 N5_245: day 15 N5_245: day 27 N5_245: day 45 N5_245: day 62 N5_245: day 81 N5_245: day 94 N5_246 N5_246: day 0 N5_246: day 3 N5_246: day 4 N5_246: day 7 N5_246: day 14 N5_248 N5_248: day 0 N5_248: day 2 N5_248: day 22 N5_248: day 43 N5_249 N5_249: day 0 N5_249: day 7 N5_249: day 18 N5_249: day 26 N5_249: day 27 N5_249: day 30 N5_252 N5_252: day 0 N5_252: day 13 N5_252: day 28 N5_252: day 71 N5_252: day 79 N5_253 N5_253: day 0 N5_253: day 28 N5_253: day 63 N5_253: day 77 N5_254 N5_254: day 0 N5_254: day 3 N5_254: day 9 N5_254: day 20 N5_254: day 28 N5_254: day 46 N5_254: day 52 N5_254: day 57 N5_254: day 64 N5_255 N5_255: day 0 N5_255: day 10 N5_255: day 16 N5_255: day 17 N5_255: day 33 N5_255: day 55 N5_255: day 72 N5_258 N5_258: day 0 N5_258: day 1 N5_258: day 1 N5_258: day 2 N5_258: day 57 N5_260 N5_260: day 0 N5_260: day 0 N5_260: day 17 N5_260: day 27 N5_261 N5_261: day 0 N5_261: day 1 N5_261: day 2 N5_261: day 3 N5_261: day 3 N5_261: day 4 N5_261: day 4 N5_261: day 5 N5_261: day 5 N5_267 N5_267: day 0 N5_267: day 6 N5_267: day 10 N5_267: day 15 N5_267: day 22 N5_269 N5_269: day 0 N5_269: day 7 N5_269: day 16 N5_269: day 30 N5_269: day 30 N5_269: day 46 N5_271 N5_271: day 0 N5_271: day 2 N5_271: day 3 N5_271: day 3 N5_271: day 14 N5_272 N5_272: day 0 N5_272: day 0 N5_272: day 1 N5_272: day 2 N5_272: day 2 N5_272: day 3 N5_272: day 4 N5_272: day 4 N5_272: day 5 N5_272: day 16 N5_272: day 37 N5_273 N5_273: day 0 N5_273: day 0 N5_273: day 1 N5_273: day 2 N5_273: day 5 N5_273: day 5 N5_273: day 9 N5_273: day 9 N5_273: day 10 N5_273: day 28 N5_273: day 49 N5_278 N5_278: day 0 N5_278: day 1 N5_278: day 4 N5_278: day 4 N5_278: day 5 N5_278: day 6 N5_278: day 8 N5_278: day 8 N5_278: day 10 N5_278: day 12 N5_278: day 13 N5_278: day 16 N5_278: day 17 N5_278: day 17 N5_278: day 32 N5_278: day 41 N5_278: day 47 N5_278: day 80 N5_278: day 88 0 d 28 d 56 d 3 mo 4 mo
Each row is one person (36 shown of 53); dots are samples at days since that person's first sample.
How longitudinal and relatedness information is derived
Community composition
Klebsiella 23.5%Enterobacter 15.3%Escherichia 9.3%Veillonella 7.1%Serratia 6.2%Bifidobacterium 5.0%Enterococcus 4.8%Sarcina 4.4%Staphylococcus 3.7%Clostridium 3.6%Bacteroides 2.3%Pseudomonas 1.7%
Genera, mean relative abundance over 237 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Papers (1)
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
Details
Archive description Time-series fecal samples for a cohort of premature infants in NICU
How this project entered the registry Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna .
host external_curation.infant_catalog · “infant triage verdict include”body site study.title · “preterm infant gut metagenomes (NIH Y5”body site study.description · “Time-series fecal samples for a”life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”life stage study.title · “preterm infant gut metagenomes (NIH”life stage study.title · “preterm infant gut metagenomes”life stage study.description · “a cohort of premature infants in NICU”Evidence examples (one per field × route)
sample field value route conf. source quote
SAMN07982907 age_at_collection_days 10 R1 0.85 sample.title DOL 10 SAMN07982907 collection_date 2015 R1 0.85 biosample.attribute:collection_date collection_date: 2015 SAMN07982907 country US R1 0.90 biosample_attr USA: Pittsburgh, Magee-Womens Hospital of UPMC SAMN07982907 preterm_status preterm R4 0.50 study.description premature infants in NICU SAMN07982907 sex male R2 0.75 external.microbiomedb source Sex: Male SAMN07982907 subject_id N5_215 R1 0.70 sample.name_rule:isolation_source fecal sample from infant N5_215 DOL 10, sample 1 SAMN07982907 timepoint_label DOL 10 R1 0.70 sample.title Infant N5_215 DOL 10
Sequencing 269 runs over 269 samples · mean 3.22 Gbp per run (median 3.07 Gbp, total 865.79 Gbp; 269 runs with a base count) · layout PAIRED 269 · platform ILLUMINA 269 · models Illumina HiSeq 2500 (269) · 88% of runs with a Sandpiper profile · first public 2019-08-01
Authors (16) Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last · Olm MR first · West PT · Brooks B · Firek BA · Baker R · Morowitz MJ · Banfield JF last
Downloads PRJNA417343.csv.gz (9.6 KB) · parquet (82.3 KB) — all 269 samples, every field with route and confidence · PRJNA417343_determinations.csv.gz (16.6 KB) — 1,883 evidence rows
Samples (269 · every field this project has values for · hover a cell for its source)
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