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PRJNA916952 SRP415387

Infant & maternal gut virome development, California cohort

Stanford's Outcomes Research in Kids (STORK) Virome

1,144 stool samples from a longitudinal cohort of 53 infants (age 2 weeks–3 years) and their mothers in California, profiling viral metagenomes to compare infant and maternal gut virome development over time. machine-written summary

1,144 samples · 1,144 runs · US · Infant / toddler · 2023 · 1.32 Gbp / sample

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Sources
✓Sequence archive 6,856○Abstract / description✓Full text 1,144✓Supplementary tables 831–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive6,856 sample values (collection date, country, family id, family role, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
✓ Full text1,144 sample values (location region) · PMC11322291, PMC13434738, PMC9950819
✓ Supplementary tables831 sample values (age)
– 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 country
Age
infant819
unknown313
child6
neonate6
Country
US1,144
Body site
primary1,144
Collected 2011–2018
2011: 6 samples2012: 162 samples2013: 276 samples2014: 289 samples2015: 237 samples2016: 124 samples2017: 48 samples2018: 2 samples20112018
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 60 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 114 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 114 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 236 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 335 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 231 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 52 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 2 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 1.32 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalmother–infant

102 of 105 people sampled more than once (1,137 samples; median 10, up to 18 per person) · follow-up median 18 mo (max 2.8 y) · median interval between samples 4 mo (time from collection dates). Schedule stated by the source: “Stool samples collected longitudinally from infants age 2 weeks to 3 years; mothers also sampled, up to 18 samples/subject (median 10).” (time origin: birth); stated follow-up 3.0 y.

10081008 (child): day 01008 (child): day 01008 (child): day 1121008 (child): day 1121008 (child): day 2561008 (child): day 2561008 (child): day 3681008 (child): day 3681008 (child): day 4881008 (child): day 4881008 (child): day 6141008 (child): day 6141008 (child): day 7331008 (child): day 7331008 (child): day 8581008 (child): day 8581008 (child): day 9771008 (child): day 977M1008M1008 (mother): day 0M1008 (mother): day 0M1008 (mother): day 117M1008 (mother): day 117M1008 (mother): day 227M1008 (mother): day 227M1008 (mother): day 368M1008 (mother): day 36810611061 (child): day 01061 (child): day 01061 (child): day 1331061 (child): day 1331061 (child): day 2551061 (child): day 2551061 (child): day 3901061 (child): day 3901061 (child): day 4971061 (child): day 4971061 (child): day 6401061 (child): day 6401061 (child): day 7391061 (child): day 7391061 (child): day 8711061 (child): day 8711061 (child): day 9831061 (child): day 983M1061M1061 (mother): day 0M1061 (mother): day 0M1061 (mother): day 135M1061 (mother): day 135M1061 (mother): day 233M1061 (mother): day 233M1061 (mother): day 359M1061 (mother): day 359M1061 (mother): day 481M1061 (mother): day 48110921092 (child): day 01092 (child): day 01092 (child): day 1191092 (child): day 1191092 (child): day 2381092 (child): day 2381092 (child): day 3601092 (child): day 3601092 (child): day 4791092 (child): day 4791092 (child): day 5981092 (child): day 5981092 (child): day 7281092 (child): day 7281092 (child): day 8541092 (child): day 8541092 (child): day 9721092 (child): day 972M1092M1092 (mother): day 0M1092 (mother): day 0M1092 (mother): day 127M1092 (mother): day 127M1092 (mother): day 243M1092 (mother): day 243M1092 (mother): day 360M1092 (mother): day 360M1092 (mother): day 482M1092 (mother): day 48220482048 (child): day 02048 (child): day 02048 (child): day 1272048 (child): day 1272048 (child): day 1742048 (child): day 1742048 (child): day 3792048 (child): day 3792048 (child): day 6812048 (child): day 6812048 (child): day 7582048 (child): day 7582048 (child): day 8312048 (child): day 8312048 (child): day 9162048 (child): day 916M2048M2048 (mother): day 0M2048 (mother): day 0M2048 (mother): day 122M2048 (mother): day 122M2048 (mother): day 250M2048 (mother): day 250M2048 (mother): day 370M2048 (mother): day 370M2048 (mother): day 417M2048 (mother): day 41720712071 (child): day 02071 (child): day 02071 (child): day 2442071 (child): day 2442071 (child): day 3562071 (child): day 3562071 (child): day 4962071 (child): day 4962071 (child): day 6022071 (child): day 6022071 (child): day 7212071 (child): day 7212071 (child): day 8472071 (child): day 8472071 (child): day 9742071 (child): day 974M2071M2071 (mother): day 0M2071 (mother): day 0M2071 (mother): day 133M2071 (mother): day 133M2071 (mother): day 252M2071 (mother): day 252M2071 (mother): day 496M2071 (mother): day 49620842084 (child): day 02084 (child): day 02084 (child): day 1192084 (child): day 1192084 (child): day 2452084 (child): day 2452084 (child): day 3962084 (child): day 3962084 (child): day 4802084 (child): day 4802084 (child): day 6062084 (child): day 6062084 (child): day 7322084 (child): day 7322084 (child): day 8512084 (child): day 851M2084M2084 (mother): day 0M2084 (mother): day 0M2084 (mother): day 138M2084 (mother): day 138M2084 (mother): day 253M2084 (mother): day 253M2084 (mother): day 379M2084 (mother): day 379M2084 (mother): day 498M2084 (mother): day 49820852085 (child): day 02085 (child): day 02085 (child): day 1262085 (child): day 1262085 (child): day 2452085 (child): day 2452085 (child): day 3352085 (child): day 3352085 (child): day 4542085 (child): day 4542085 (child): day 5742085 (child): day 5742085 (child): day 8122085 (child): day 812M2085M2085 (mother): day 0M2085 (mother): day 0M2085 (mother): day 110M2085 (mother): day 110M2085 (mother): day 235M2085 (mother): day 235M2085 (mother): day 354M2085 (mother): day 35420932093 (child): day 02093 (child): day 02093 (child): day 1122093 (child): day 1122093 (child): day 2312093 (child): day 2312093 (child): day 3502093 (child): day 3502093 (child): day 5072093 (child): day 5072093 (child): day 5902093 (child): day 5902093 (child): day 7092093 (child): day 7092093 (child): day 8292093 (child): day 829M2093M2093 (mother): day 0M2093 (mother): day 0M2093 (mother): day 125M2093 (mother): day 125M2093 (mother): day 251M2093 (mother): day 251M2093 (mother): day 370M2093 (mother): day 370M2093 (mother): day 492M2093 (mother): day 49221122112 (child): day 02112 (child): day 02112 (child): day 1182112 (child): day 1182112 (child): day 2442112 (child): day 2442112 (child): day 3632112 (child): day 3632112 (child): day 4822112 (child): day 4822112 (child): day 6082112 (child): day 6082112 (child): day 7272112 (child): day 7272112 (child): day 9702112 (child): day 970M2112M2112 (mother): day 0M2112 (mother): day 0M2112 (mother): day 142M2112 (mother): day 142M2112 (mother): day 252M2112 (mother): day 252M2112 (mother): day 378M2112 (mother): day 37821172117 (child): day 02117 (child): day 02117 (child): day 1262117 (child): day 1262117 (child): day 2512117 (child): day 2512117 (child): day 3492117 (child): day 3492117 (child): day 4752117 (child): day 4752117 (child): day 6082117 (child): day 6082117 (child): day 7212117 (child): day 7212117 (child): day 8402117 (child): day 8402117 (child): day 9732117 (child): day 973M2117M2117 (mother): day 0M2117 (mother): day 0M2117 (mother): day 119M2117 (mother): day 119M2117 (mother): day 249M2117 (mother): day 249M2117 (mother): day 369M2117 (mother): day 369M2127M2127 (mother): day 0M2127 (mother): day 0M2127 (mother): day 148M2127 (mother): day 148M2127 (mother): day 288M2127 (mother): day 288M2127 (mother): day 391M2127 (mother): day 39121272127 (child): day 02127 (child): day 1052127 (child): day 2402127 (child): day 3502127 (child): day 46921332133 (child): day 02133 (child): day 02133 (child): day 1332133 (child): day 1332133 (child): day 2542133 (child): day 2542133 (child): day 3782133 (child): day 3782133 (child): day 5062133 (child): day 5062133 (child): day 6262133 (child): day 6262133 (child): day 7382133 (child): day 7382133 (child): day 8642133 (child): day 8642133 (child): day 9872133 (child): day 987M2133M2133 (mother): day 0M2133 (mother): day 0M2133 (mother): day 118M2133 (mother): day 118M2133 (mother): day 249M2133 (mother): day 249M2133 (mother): day 370M2133 (mother): day 37021372137 (child): day 02137 (child): day 02137 (child): day 1192137 (child): day 1192137 (child): day 2382137 (child): day 2382137 (child): day 3662137 (child): day 3662137 (child): day 4782137 (child): day 4782137 (child): day 6042137 (child): day 6042137 (child): day 7232137 (child): day 7232137 (child): day 8492137 (child): day 849M2137M2137 (mother): day 0M2137 (mother): day 0M2137 (mother): day 118M2137 (mother): day 118M2137 (mother): day 237M2137 (mother): day 237M2137 (mother): day 363M2137 (mother): day 363M2137 (mother): day 482M2137 (mother): day 48221462146 (child): day 02146 (child): day 02146 (child): day 1332146 (child): day 1332146 (child): day 2592146 (child): day 2592146 (child): day 3852146 (child): day 3852146 (child): day 5112146 (child): day 5112146 (child): day 6262146 (child): day 6262146 (child): day 7452146 (child): day 7452146 (child): day 8812146 (child): day 8812146 (child): day 9982146 (child): day 998M2146M2146 (mother): day 0M2146 (mother): day 0M2146 (mother): day 94M2146 (mother): day 94M2146 (mother): day 211M2146 (mother): day 211M2146 (mother): day 340M2146 (mother): day 340M2146 (mother): day 466M2146 (mother): day 466M2169M2169 (mother): day 0M2169 (mother): day 0M2169 (mother): day 84M2169 (mother): day 84M2169 (mother): day 247M2169 (mother): day 247M2169 (mother): day 364M2169 (mother): day 364M2169 (mother): day 484M2169 (mother): day 48421692169 (child): day 02169 (child): day 02169 (child): day 1192169 (child): day 2452169 (child): day 3642169 (child): day 48321752175 (child): day 02175 (child): day 02175 (child): day 1342175 (child): day 1342175 (child): day 2472175 (child): day 2472175 (child): day 3662175 (child): day 3662175 (child): day 4852175 (child): day 4852175 (child): day 6042175 (child): day 6042175 (child): day 7292175 (child): day 7292175 (child): day 8492175 (child): day 8492175 (child): day 9812175 (child): day 981M2175M2175 (mother): day 0M2175 (mother): day 0M2175 (mother): day 117M2175 (mother): day 117M2175 (mother): day 364M2175 (mother): day 36422012201 (child): day 02201 (child): day 02201 (child): day 1682201 (child): day 1682201 (child): day 2582201 (child): day 2582201 (child): day 3782201 (child): day 3782201 (child): day 4972201 (child): day 4972201 (child): day 6282201 (child): day 6282201 (child): day 7402201 (child): day 7402201 (child): day 8542201 (child): day 8542201 (child): day 10062201 (child): day 1006M2201M2201 (mother): day 0M2201 (mother): day 0M2201 (mother): day 107M2201 (mother): day 107M2201 (mother): day 296M2201 (mother): day 296M2201 (mother): day 365M2201 (mother): day 36522112211 (child): day 02211 (child): day 02211 (child): day 1202211 (child): day 1202211 (child): day 2392211 (child): day 2392211 (child): day 3702211 (child): day 3702211 (child): day 4892211 (child): day 4892211 (child): day 6152211 (child): day 6152211 (child): day 7442211 (child): day 744M2211M2211 (mother): day 0M2211 (mother): day 0M2211 (mother): day 119M2211 (mother): day 119M2211 (mother): day 250M2211 (mother): day 250M2211 (mother): day 377M2211 (mother): day 377M2211 (mother): day 489M2211 (mother): day 4890 d8 mo17 mo2.1 y2.8 y

Each row is one person (36 shown of 102); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).

Cohort of 53 infants and their biological mothers; stool virome compared longitudinally between infant and maternal pairs. · 51 families with 106 sampled people (51 with a parent and a child).

motherMchildC
50 × mother + child
motherMchildCchildCchildCchildCchildC
1 × mother + child×5
family 10081008 — child · 18 samplesC1008M1008 — mother · 8 samplesMM1008
family 26262626 — child · 14 samplesC2626nan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnannan — child · 1 sampleCnanM2626 — mother · 4 samplesMM2626
family 10611061 — child · 18 samplesC1061M1061 — mother · 10 samplesMM1061
family 10921092 — child · 18 samplesC1092M1092 — mother · 10 samplesMM1092
family 20482048 — child · 16 samplesC2048M2048 — mother · 10 samplesMM2048
family 20712071 — child · 16 samplesC2071M2071 — mother · 8 samplesMM2071
family 20842084 — child · 16 samplesC2084M2084 — mother · 10 samplesMM2084
family 20852085 — child · 14 samplesC2085M2085 — mother · 8 samplesMM2085
family 20932093 — child · 16 samplesC2093M2093 — mother · 10 samplesMM2093
family 21122112 — child · 16 samplesC2112M2112 — mother · 8 samplesMM2112
family 21172117 — child · 18 samplesC2117M2117 — mother · 8 samplesMM2117
family 21272127 — child · 5 samplesC2127M2127 — mother · 8 samplesMM2127
family 21332133 — child · 18 samplesC2133M2133 — mother · 8 samplesMM2133
family 21372137 — child · 16 samplesC2137M2137 — mother · 10 samplesMM2137
family 21462146 — child · 18 samplesC2146M2146 — mother · 10 samplesMM2146
family 21692169 — child · 6 samplesC2169M2169 — mother · 10 samplesMM2169
family 21752175 — child · 18 samplesC2175M2175 — mother · 6 samplesMM2175
family 22012201 — child · 18 samplesC2201M2201 — mother · 8 samplesMM2201
family 22112211 — child · 14 samplesC2211M2211 — mother · 10 samplesMM2211
family 22502250 — child · 18 samplesC2250M2250 — mother · 4 samplesMM2250
family 22602260 — child · 18 samplesC2260M2260 — mother · 5 samplesMM2260
family 22712271 — child · 18 samplesC2271M2271 — mother · 4 samplesMM2271
family 22842284 — child · 18 samplesC2284M2284 — mother · 5 samplesMM2284
family 22962296 — child · 17 samplesC2296M2296 — mother · 4 samplesMM2296

motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 51 families (one per family structure, then more). 105 people in the project overall.

Families (25 of 51)
familymemberssamples
1061mother + childSAMN32525399 · SAMN32525400 · SAMN32525401 · SAMN32525402 · SAMN32525403 · SAMN32525404 · SAMN32525405 · SAMN32525406 · SAMN32525407 · SAMN32525408 · SAMN32525409 · SAMN32525410
1092mother + childSAMN32525417 · SAMN32525418 · SAMN32525419 · SAMN32525420 · SAMN32525421 · SAMN32525422 · SAMN32525423 · SAMN32525424 · SAMN32525425 · SAMN32525426 · SAMN32525427 · SAMN32525428
2146mother + childSAMN32525586 · SAMN32525587 · SAMN32525588 · SAMN32525589 · SAMN32525590 · SAMN32525591 · SAMN32525592 · SAMN32525593 · SAMN32525594 · SAMN32525595 · SAMN32525596 · SAMN32525597
2117mother + childSAMN32525529 · SAMN32525530 · SAMN32525531 · SAMN32525532 · SAMN32525533 · SAMN32525534 · SAMN32525535 · SAMN32525536 · SAMN32525537 · SAMN32525538 · SAMN32525539 · SAMN32525540
2201mother + childSAMN32525628 · SAMN32525629 · SAMN32525630 · SAMN32525631 · SAMN32525632 · SAMN32525633 · SAMN32525634 · SAMN32525635 · SAMN32525636 · SAMN32525637 · SAMN32525638 · SAMN32525639
2137mother + childSAMN32525570 · SAMN32525571 · SAMN32525572 · SAMN32525573 · SAMN32525574 · SAMN32525575 · SAMN32525576 · SAMN32525577 · SAMN32525578 · SAMN32525579 · SAMN32525580 · SAMN32525581
2133mother + childSAMN32525552 · SAMN32525553 · SAMN32525554 · SAMN32525555 · SAMN32525556 · SAMN32525557 · SAMN32525558 · SAMN32525559 · SAMN32525560 · SAMN32525561 · SAMN32525562 · SAMN32525563
1008mother + childSAMN32525381 · SAMN32525382 · SAMN32525383 · SAMN32525384 · SAMN32525385 · SAMN32525386 · SAMN32525387 · SAMN32525388 · SAMN32525389 · SAMN32525390 · SAMN32525391 · SAMN32525392
2093mother + childSAMN32525497 · SAMN32525498 · SAMN32525499 · SAMN32525500 · SAMN32525501 · SAMN32525502 · SAMN32525503 · SAMN32525504 · SAMN32525505 · SAMN32525506 · SAMN32525507 · SAMN32525508
2084mother + childSAMN32525467 · SAMN32525468 · SAMN32525469 · SAMN32525470 · SAMN32525471 · SAMN32525472 · SAMN32525473 · SAMN32525474 · SAMN32525475 · SAMN32525476 · SAMN32525477 · SAMN32525478
2048mother + childSAMN32525435 · SAMN32525436 · SAMN32525437 · SAMN32525438 · SAMN32525439 · SAMN32525440 · SAMN32525441 · SAMN32525442 · SAMN32525443 · SAMN32525444 · SAMN32525445 · SAMN32525446
2112mother + childSAMN32525513 · SAMN32525514 · SAMN32525515 · SAMN32525516 · SAMN32525517 · SAMN32525518 · SAMN32525519 · SAMN32525520 · SAMN32525521 · SAMN32525522 · SAMN32525523 · SAMN32525524
2071mother + childSAMN32525451 · SAMN32525452 · SAMN32525453 · SAMN32525454 · SAMN32525455 · SAMN32525456 · SAMN32525457 · SAMN32525458 · SAMN32525459 · SAMN32525460 · SAMN32525461 · SAMN32525462
2175mother + childSAMN32525610 · SAMN32525611 · SAMN32525612 · SAMN32525613 · SAMN32525614 · SAMN32525615 · SAMN32525616 · SAMN32525617 · SAMN32525618 · SAMN32525619 · SAMN32525620 · SAMN32525621
2211mother + childSAMN32525646 · SAMN32525647 · SAMN32525648 · SAMN32525649 · SAMN32525650 · SAMN32525651 · SAMN32525652 · SAMN32525653 · SAMN32525654 · SAMN32525655 · SAMN32525656 · SAMN32525657
2284mother + childSAMN32525714 · SAMN32525715 · SAMN32525716 · SAMN32525717 · SAMN32525718 · SAMN32525719 · SAMN32525720 · SAMN32525721 · SAMN32525722 · SAMN32525723 · SAMN32525724 · SAMN32525725
2673mother + childSAMN32527424 · SAMN32527425 · SAMN32527426 · SAMN32527427 · SAMN32527428 · SAMN32527429 · SAMN32527430 · SAMN32527431 · SAMN32527432 · SAMN32527433 · SAMN32527434 · SAMN32527435
2595mother + childSAMN32527288 · SAMN32527289 · SAMN32527290 · SAMN32527291 · SAMN32527292 · SAMN32527293 · SAMN32527294 · SAMN32527295 · SAMN32527296 · SAMN32527297 · SAMN32527298 · SAMN32527299
2547mother + childSAMN32525914 · SAMN32525915 · SAMN32525916 · SAMN32525917 · SAMN32525918 · SAMN32525919 · SAMN32525920 · SAMN32525921 · SAMN32525922 · SAMN32525923 · SAMN32525924 · SAMN32525925
2461mother + childSAMN32525847 · SAMN32525848 · SAMN32525849 · SAMN32525850 · SAMN32525851 · SAMN32525852 · SAMN32525853 · SAMN32525854 · SAMN32525855 · SAMN32525856 · SAMN32525857 · SAMN32525858
2599mother + childSAMN32527306 · SAMN32527307 · SAMN32527308 · SAMN32527309 · SAMN32527310 · SAMN32527311 · SAMN32527312 · SAMN32527313 · SAMN32527314 · SAMN32527315 · SAMN32527316 · SAMN32527317
2341mother + childSAMN32525777 · SAMN32525778 · SAMN32525779 · SAMN32525780 · SAMN32525781 · SAMN32525782 · SAMN32525783 · SAMN32525784 · SAMN32525785 · SAMN32525786 · SAMN32525787 · SAMN32525788
2260mother + childSAMN32525678 · SAMN32525679 · SAMN32525680 · SAMN32525681 · SAMN32525682 · SAMN32525683 · SAMN32525684 · SAMN32525685 · SAMN32525686 · SAMN32525687 · SAMN32525688 · SAMN32525689
2586mother + childSAMN32525966 · SAMN32525967 · SAMN32525968 · SAMN32525969 · SAMN32525970 · SAMN32525971 · SAMN32525972 · SAMN32525973 · SAMN32525974 · SAMN32525975 · SAMN32525976 · SAMN32525977
2271mother + childSAMN32525696 · SAMN32525697 · SAMN32525698 · SAMN32525699 · SAMN32525700 · SAMN32525701 · SAMN32525702 · SAMN32525703 · SAMN32525704 · SAMN32525705 · SAMN32525706 · SAMN32525707

How longitudinal and relatedness information is derived

Community composition
CAG-302 5.6%Bacteroides 5.3%Prevotella 4.8%Nanosynbacter 3.7%Phocaeicola 3.4%CAG-417 2.6%Romboutsia 2.5%Ruminococcoides 2.0%Clostridium 1.5%Intestinibacter 1.4%Roseburia 1.1%Thomasclavelia 1.0%not assigned to a genus 48.7%other genera 16.4%

Genera, mean relative abundance over 366 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category831 73%
country1,144 100%1,144
health_condition0 0%
subject_id1,140 100%1,140
collection_date1,144 100%1,144
detailed_location1,144 100%
family_id1,144 100%1,144
family_role1,144 100%1,144
location_region1,144 100%1,144
timepoint_label1,140 100%1,140
age_at_collection_days831 73%831
Papers (3)
  • Longitudinal comparison of the developing gut virome in infants and their mothers. PMID 36758519 PMC9950819 curated
  • Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291 curated
  • A meta-analysis of infant gut viromes reveals global patterns in bacteriophage community assembly and functional capacity over the first three years of life. PMID 42315844 PMC13434738 curated
Details
Archive description

The virome of the human gut and its development in early life are poorly understood. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to describe and compare their viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary / environmental viruses, and human-host viruses, predominated by picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Novel, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As the infants aged, the phage component of the infant virome evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, infant virome development in early life is shaped predominantly by dietary, infectious, and environmental factors rather than from direct acquisition from the mother.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage verdict include”
  • body site study.description · “of the human gut and its development”
  • body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
  • life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
  • life stage study.description · “its development in early life are poorly understood.”
  • life stage study.description · “and from their mothers (9.8 billion reads)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN32525381age_at_collection_days84.0R20.75paper.supp.human_viruses.txt[AgeBabyDays]AgeBabyDays: 84
SAMN32525381collection_date2012-01-25R10.85biosample.attribute:collection_date2012-01-25
SAMN32525381countryUSR10.90biosample_attrUSA: California
SAMN32525381family_id1008R10.70sample.name_rule:library_namelibrary_name=1008_B1_DNA
SAMN32525381family_rolechildR10.70sample.name_rule:library_namelibrary_name=1008_B1_DNA
SAMN32525381location_regionCaliforniaR30.70paper.fulltext.methodsStanford University (Stanford, CA, USA), the Santa Clara Valley Medical Center
SAMN32525381subject_id1008R10.70sample.name_rule:replicate1008_B1_DNA
SAMN32525381timepoint_labelB1R10.70sample.name_rule:replicate1008_B1_DNA
SAMN32527530timepoint_labelM1R10.70run.library_nameM1008_M1_DNA
Sequencing

1,144 runs over 1,144 samples · mean 2.43 Gbp per run (median 1.32 Gbp, total 2,777.27 Gbp; 1,144 runs with a base count) · layout SINGLE 1,144 · platform ILLUMINA 1,144 · models Illumina NovaSeq 6000 (1,144) · 39% of runs with a Sandpiper profile · first public 2023-01-03 – 2023-01-04

Authors (19)

Walters WA first · Granados AC · Ley C · Federman S · Stryke D · Santos Y · Haggerty T · Sotomayor-Gonzalez A · Servellita V · Ley RE · Parsonnet J · Chiu CY last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Shamash M first · Maurice CF last

Downloads

PRJNA916952.csv.gz (37.1 KB) · parquet (122.3 KB) — all 1,144 samples, every field with route and confidence · PRJNA916952_determinations.csv.gz (72.4 KB) — 8,831 evidence rows

Samples (1,144 · every field this project has values for · hover a cell for its source)
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