Home › Studies › PRJNA698986
PRJNA698986 SRP304602

Infant gut microbiome succession with NEC, Pittsburgh cohort

Early-life metagenomes from human infant fecal samples with matched maternal sample

819 fecal samples from infants and neonates (with matched maternal samples) at Magee-Womens Hospital of UPMC, Pittsburgh, including healthy controls and necrotizing enterocolitis cases, in a longitudinal cohort design. machine-written summary

819 samples · 850 runs · US · Infant / toddler · 2021 · 10.10 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 4,442○Abstract / description○Full text✓Supplementary tables 4,537–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive4,442 sample values (age, country, family id, family role, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC10092070, PMC10654741, PMC11322291, PMC11497992, PMC12677589, PMC8484513
✓ Supplementary tables4,537 sample values (antibiotic exposure, birth weight grams, delivery mode, gestational age weeks, health condition, nec status, sex, subject id)
– 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
infant613
neonate105
unknown84
child17
Condition
healthy_control229
nec166
Sex
male433
female302
Country
US819
Body site
primary819
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 2 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 3 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 3 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 7 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 362 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 440 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 1 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 10.18 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalmother–infant

81 of 95 people sampled more than once (805 samples; median 11, up to 24 per person) · follow-up median 2.9 y (max 3.6 y) · median interval between samples 2 mo (time from age at collection). Schedule stated by the source: “archive time labels: year 3, near birth, DOL 31, DOL 61, DOL 122, DOL 64, DOL 92, DOL 30” (time origin: birth).

101101 (child): day 0101 (child): day 0101 (child): day 9101 (child): day 9101 (child): day 16101 (child): day 24101 (child): day 24101 (child): day 30101 (child): day 38101 (child): day 48101 (child): day 61101 (child): day 118101 (child): day 118101 (child): day 242101 (child): day 242101 (child): day 361101 (child): day 361101 (child): day 494101 (child): day 603101 (child): day 928101 (child): day 1095102102 (child): day 0102 (child): day 0102 (child): day 30102 (child): day 30102 (child): day 57102 (child): day 57102 (child): day 91102 (child): day 211102 (child): day 211102 (child): day 329102 (child): day 329102 (child): day 329102 (child): day 455102 (child): day 580102 (child): day 580102 (child): day 582102 (child): day 700102 (child): day 904102 (child): day 1064105105 (child): day 0105 (child): day 20105 (child): day 44105 (child): day 79105 (child): day 204105 (child): day 316106106 (child): day 0106 (child): day 30106 (child): day 54106 (child): day 71106 (child): day 115106 (child): day 363114114 (child): day 0114 (child): day 2114 (child): day 11114 (child): day 20114 (child): day 26114 (child): day 26114 (child): day 26114 (child): day 38114 (child): day 118114 (child): day 118114 (child): day 232114 (child): day 232114 (child): day 355114 (child): day 355114 (child): day 489114 (child): day 607121121 (child): day 0121 (child): day 0121 (child): day 34121 (child): day 34121 (child): day 68121 (child): day 68121 (child): day 98121 (child): day 98121 (child): day 219121 (child): day 219121 (child): day 339121 (child): day 339121 (child): day 339121 (child): day 465121 (child): day 659121 (child): day 734121 (child): day 885121 (child): day 1078122122 (child): day 0122 (child): day 0122 (child): day 33122 (child): day 33122 (child): day 61122 (child): day 61122 (child): day 92122 (child): day 92122 (child): day 211122 (child): day 211122 (child): day 337122 (child): day 337122 (child): day 456122 (child): day 655122 (child): day 725122 (child): day 881122 (child): day 1068129129 (child): day 0129 (child): day 32129 (child): day 63129 (child): day 92129 (child): day 215129 (child): day 331129 (child): day 455129 (child): day 592129 (child): day 704129 (child): day 876129 (child): day 10661313 (child): day 013 (child): day 813 (child): day 913 (child): day 1113 (child): day 1513 (child): day 1713 (child): day 1913 (child): day 2713 (child): day 3013 (child): day 3113 (child): day 3713 (child): day 11613 (child): day 23913 (child): day 36513 (child): day 61013 (child): day 63813 (child): day 72513 (child): day 91513 (child): day 1092130130 (child): day 0130 (child): day 28130 (child): day 59130 (child): day 92130 (child): day 215130 (child): day 341130 (child): day 468130 (child): day 746130 (child): day 889130 (child): day 1074131131 (child): day 0131 (child): day 28131 (child): day 58131 (child): day 89131 (child): day 210131 (child): day 334131 (child): day 457131 (child): day 705131 (child): day 883131 (child): day 1066132132 (child): day 0132 (child): day 31132 (child): day 63132 (child): day 95132 (child): day 216132 (child): day 337132 (child): day 463132 (child): day 715132 (child): day 880132 (child): day 1071133133 (child): day 0133 (child): day 32133 (child): day 62133 (child): day 94133 (child): day 213133 (child): day 332133 (child): day 458133 (child): day 578133 (child): day 718133 (child): day 878133 (child): day 1075144144 (child): day 0144 (child): day 30144 (child): day 59144 (child): day 90144 (child): day 213144 (child): day 333144 (child): day 454144 (child): day 579144 (child): day 712144 (child): day 883144 (child): day 1060145145 (child): day 0145 (child): day 5145 (child): day 18145 (child): day 29145 (child): day 54145 (child): day 115145 (child): day 238145 (child): day 361145 (child): day 693145 (child): day 711145 (child): day 740145 (child): day 910145 (child): day 1098162162 (child): day 0162 (child): day 34162 (child): day 62162 (child): day 90162 (child): day 208162 (child): day 328162 (child): day 490162 (child): day 579162 (child): day 697162 (child): day 888162 (child): day 1060166166 (child): day 0166 (child): day 24166 (child): day 58166 (child): day 210166 (child): day 327166 (child): day 454166 (child): day 578166 (child): day 697166 (child): day 880166 (child): day 1066168168 (child): day 0168 (child): day 3168 (child): day 6168 (child): day 30168 (child): day 33168 (child): day 35168 (child): day 43168 (child): day 240168 (child): day 593168 (child): day 712168 (child): day 906168 (child): day 1087169169 (child): day 0169 (child): day 24169 (child): day 47169 (child): day 52169 (child): day 120169 (child): day 126169 (child): day 235169 (child): day 368169 (child): day 604169 (child): day 723169 (child): day 907169 (child): day 1085171171 (child): day 0171 (child): day 19171 (child): day 25171 (child): day 25171 (child): day 49171 (child): day 53171 (child): day 58171 (child): day 71171 (child): day 115171 (child): day 241171 (child): day 362171 (child): day 587171 (child): day 717171 (child): day 909171 (child): day 1103174174 (child): day 0174 (child): day 32174 (child): day 62174 (child): day 90174 (child): day 217174 (child): day 339174 (child): day 454174 (child): day 577174 (child): day 705174 (child): day 878174 (child): day 1073179179 (child): day 0179 (child): day 17179 (child): day 109179 (child): day 247179 (child): day 604179 (child): day 755187187 (child): day 0187 (child): day 27187 (child): day 55187 (child): day 82187 (child): day 228187 (child): day 468187 (child): day 570187 (child): day 677187 (child): day 879187 (child): day 10151919 (child): day 019 (child): day 119 (child): day 219 (child): day 719 (child): day 1119 (child): day 1619 (child): day 2219 (child): day 2819 (child): day 2919 (child): day 3619 (child): day 3619 (child): day 5319 (child): day 6219 (child): day 7619 (child): day 11119 (child): day 23619 (child): day 35719 (child): day 48019 (child): day 59619 (child): day 59619 (child): day 72319 (child): day 90019 (child): day 10872222 (child): day 022 (child): day 2922 (child): day 7222 (child): day 9322 (child): day 21522 (child): day 33522 (child): day 45722 (child): day 57722 (child): day 69522 (child): day 88222 (child): day 10742626 (child): day 026 (child): day 3426 (child): day 6226 (child): day 10126 (child): day 22026 (child): day 34426 (child): day 46326 (child): day 58326 (child): day 70226 (child): day 89026 (child): day 10673131 (child): day 031 (child): day 3131 (child): day 6031 (child): day 9431 (child): day 21731 (child): day 33931 (child): day 45431 (child): day 57931 (child): day 70331 (child): day 88231 (child): day 12513737 (child): day 037 (child): day 437 (child): day 437 (child): day 1137 (child): day 1237 (child): day 1937 (child): day 3537 (child): day 3937 (child): day 4337 (child): day 5637 (child): day 11937 (child): day 23637 (child): day 36737 (child): day 48537 (child): day 60237 (child): day 71837 (child): day 91437 (child): day 12963838 (child): day 038 (child): day 2938 (child): day 6238 (child): day 18238 (child): day 30738 (child): day 42538 (child): day 66738 (child): day 85738 (child): day 12543939 (child): day 039 (child): day 439 (child): day 1939 (child): day 2339 (child): day 2939 (child): day 3039 (child): day 4039 (child): day 4039 (child): day 4639 (child): day 4939 (child): day 10639 (child): day 22439 (child): day 34739 (child): day 7044040 (child): day 040 (child): day 240 (child): day 940 (child): day 1640 (child): day 3040 (child): day 5240 (child): day 5840 (child): day 6340 (child): day 8140 (child): day 8140 (child): day 8940 (child): day 9240 (child): day 11640 (child): day 21740 (child): day 35740 (child): day 48540 (child): day 60040 (child): day 71940 (child): day 90840 (child): day 12554747 (child): day 047 (child): day 3147 (child): day 6047 (child): day 8847 (child): day 32947 (child): day 46047 (child): day 57347 (child): day 69647 (child): day 88147 (child): day 10635757 (child): day 057 (child): day 657 (child): day 957 (child): day 1157 (child): day 1257 (child): day 3157 (child): day 3757 (child): day 4057 (child): day 4357 (child): day 5357 (child): day 6457 (child): day 11457 (child): day 23657 (child): day 48157 (child): day 59557 (child): day 71857 (child): day 90657 (child): day 11715858 (child): day 058 (child): day 658 (child): day 1558 (child): day 2158 (child): day 2958 (child): day 3658 (child): day 4058 (child): day 4558 (child): day 5658 (child): day 6558 (child): day 13758 (child): day 24958 (child): day 3756363 (child): day 063 (child): day 363 (child): day 1163 (child): day 1763 (child): day 2363 (child): day 2363 (child): day 3463 (child): day 4663 (child): day 5563 (child): day 5563 (child): day 12063 (child): day 12063 (child): day 12063 (child): day 24463 (child): day 24463 (child): day 36263 (child): day 36263 (child): day 48263 (child): day 60363 (child): day 72763 (child): day 90963 (child): day 11566868 (child): day 068 (child): day 068 (child): day 3168 (child): day 3168 (child): day 5868 (child): day 9068 (child): day 9068 (child): day 21168 (child): day 21168 (child): day 33668 (child): day 33668 (child): day 45468 (child): day 57668 (child): day 69968 (child): day 10650 d11 mo21 mo2.7 y3.5 y

Each row is one person (36 shown of 81); 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).

43 mother–infant families (84 maternal stools near birth / near year 3); 9 further infants without a maternal sample · 43 families with 86 sampled people (43 with a parent and a child).

motherMchildC
43 × mother + child
family infant_101mother_of_infant_101 — mother · 3 samplesMmothe…101 — child · 21 samplesC101
family infant_102mother_of_infant_102 — mother · 3 samplesMmothe…102 — child · 19 samplesC102
family infant_105mother_of_infant_105 — mother · 1 sampleMmothe…105 — child · 6 samplesC105
family infant_106mother_of_infant_106 — mother · 1 sampleMmothe…106 — child · 6 samplesC106
family infant_114mother_of_infant_114 — mother · 2 samplesMmothe…114 — child · 16 samplesC114
family infant_121mother_of_infant_121 — mother · 3 samplesMmothe…121 — child · 18 samplesC121
family infant_122mother_of_infant_122 — mother · 3 samplesMmothe…122 — child · 17 samplesC122
family infant_129mother_of_infant_129 — mother · 2 samplesMmothe…129 — child · 11 samplesC129
family infant_13mother_of_infant_13 — mother · 2 samplesMmothe…13 — child · 19 samplesC13
family infant_130mother_of_infant_130 — mother · 2 samplesMmothe…130 — child · 10 samplesC130
family infant_131mother_of_infant_131 — mother · 2 samplesMmothe…131 — child · 10 samplesC131
family infant_132mother_of_infant_132 — mother · 2 samplesMmothe…132 — child · 10 samplesC132
family infant_133mother_of_infant_133 — mother · 2 samplesMmothe…133 — child · 11 samplesC133
family infant_144144 — child · 11 samplesC144mother_of_infant_144 — mother · 2 samplesMmothe…
family infant_145145 — child · 13 samplesC145mother_of_infant_145 — mother · 2 samplesMmothe…
family infant_162162 — child · 11 samplesC162mother_of_infant_162 — mother · 2 samplesMmothe…
family infant_166166 — child · 10 samplesC166mother_of_infant_166 — mother · 2 samplesMmothe…
family infant_168168 — child · 12 samplesC168mother_of_infant_168 — mother · 1 sampleMmothe…
family infant_169mother_of_infant_169 — mother · 1 sampleMmothe…169 — child · 12 samplesC169
family infant_171171 — child · 15 samplesC171mother_of_infant_171 — mother · 3 samplesMmothe…
family infant_174174 — child · 11 samplesC174mother_of_infant_174 — mother · 2 samplesMmothe…
family infant_179mother_of_infant_179 — mother · 1 sampleMmothe…179 — child · 6 samplesC179
family infant_187187 — child · 10 samplesC187mother_of_infant_187 — mother · 2 samplesMmothe…
family infant_19mother_of_infant_19 — mother · 2 samplesMmothe…19 — child · 23 samplesC19

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 43 families (one per family structure, then more). 95 people in the project overall.

Families (25 of 43)
familymemberssamples
infant_72mother + childSAMN17764023 · SAMN17764024 · SAMN17764025 · SAMN17764026 · SAMN17764027 · SAMN17764028 · SAMN17764029 · SAMN17764030 · SAMN17764031 · SAMN17764032 · SAMN17764033 · SAMN17764034
infant_98mother + childSAMN17764058 · SAMN17764059 · SAMN17764060 · SAMN17764061 · SAMN17764062 · SAMN17764063 · SAMN17764064 · SAMN17764065 · SAMN17764066 · SAMN17764067 · SAMN17764068 · SAMN17764069
infant_19mother + childSAMN17763815 · SAMN17763816 · SAMN17763817 · SAMN17763818 · SAMN17763819 · SAMN17763820 · SAMN17763821 · SAMN17763822 · SAMN17763823 · SAMN17763824 · SAMN17763825 · SAMN17763826
infant_101mother + childSAMN17764070 · SAMN17764071 · SAMN17764072 · SAMN17764073 · SAMN17764074 · SAMN17764075 · SAMN17764076 · SAMN17764077 · SAMN17764078 · SAMN17764079 · SAMN17764080 · SAMN37313866
infant_63mother + childSAMN17763990 · SAMN17763991 · SAMN17763992 · SAMN17763993 · SAMN17763994 · SAMN17763995 · SAMN17763996 · SAMN17763997 · SAMN17763998 · SAMN17763999 · SAMN17764000 · SAMN17764001
infant_40mother + childSAMN17763902 · SAMN17763903 · SAMN17763904 · SAMN17763905 · SAMN17763906 · SAMN17763907 · SAMN17763908 · SAMN17763909 · SAMN17763910 · SAMN17763911 · SAMN17763912 · SAMN17763913
infant_102mother + childSAMN17764081 · SAMN17764082 · SAMN17764083 · SAMN17764084 · SAMN17764085 · SAMN17764086 · SAMN17764087 · SAMN37313879 · SAMN37313880 · SAMN37313881 · SAMN37313882 · SAMN37313883
infant_13mother + childSAMN17763800 · SAMN17763801 · SAMN17763802 · SAMN17763803 · SAMN17763804 · SAMN17763805 · SAMN17763806 · SAMN17763807 · SAMN17763808 · SAMN17763809 · SAMN17763810 · SAMN17763811
infant_121mother + childSAMN17764122 · SAMN17764123 · SAMN17764124 · SAMN17764125 · SAMN17764126 · SAMN17764127 · SAMN17764128 · SAMN17764129 · SAMN37313911 · SAMN37313912 · SAMN37313913 · SAMN37313914
infant_79mother + childSAMN17764036 · SAMN17764037 · SAMN17764038 · SAMN17764039 · SAMN17764040 · SAMN17764041 · SAMN17764042 · SAMN17764043 · SAMN37313819 · SAMN37313820 · SAMN37313821 · SAMN37313822
infant_122mother + childSAMN17764130 · SAMN17764131 · SAMN17764132 · SAMN17764133 · SAMN17764134 · SAMN17764135 · SAMN17764136 · SAMN37313924 · SAMN37313925 · SAMN37313926 · SAMN37313927 · SAMN37313928
infant_82mother + childSAMN17764044 · SAMN17764045 · SAMN17764046 · SAMN17764047 · SAMN17764048 · SAMN17764049 · SAMN17764050 · SAMN17764051 · SAMN37313831 · SAMN37313832 · SAMN37313833 · SAMN37313834
infant_57mother + childSAMN17763936 · SAMN17763937 · SAMN17763938 · SAMN17763939 · SAMN17763940 · SAMN17763941 · SAMN17763942 · SAMN17763943 · SAMN17763944 · SAMN17763945 · SAMN17763946 · SAMN17763947
infant_37mother + childSAMN17763868 · SAMN17763869 · SAMN17763870 · SAMN17763871 · SAMN17763872 · SAMN17763873 · SAMN17763874 · SAMN17763875 · SAMN17763876 · SAMN17763877 · SAMN17763878 · SAMN17763879
infant_171mother + childSAMN37314053 · SAMN37314054 · SAMN37314055 · SAMN37314056 · SAMN37314057 · SAMN37314058 · SAMN37314059 · SAMN37314060 · SAMN37314061 · SAMN37314062 · SAMN37314063 · SAMN37314064
infant_68mother + childSAMN17764002 · SAMN17764003 · SAMN17764004 · SAMN17764005 · SAMN17764006 · SAMN17764007 · SAMN17764008 · SAMN37313794 · SAMN37313795 · SAMN37313796 · SAMN37313797 · SAMN37313798
infant_114mother + childSAMN17764113 · SAMN17764114 · SAMN17764115 · SAMN17764116 · SAMN17764117 · SAMN17764118 · SAMN17764119 · SAMN17764120 · SAMN17764121 · SAMN37313902 · SAMN37313903 · SAMN37313904
infant_8mother + childSAMN17763793 · SAMN17763794 · SAMN17763795 · SAMN17763796 · SAMN17763797 · SAMN17763798 · SAMN17763799 · SAMN37313692 · SAMN37313693 · SAMN37313694 · SAMN37313695 · SAMN37313696
infant_39mother + childSAMN17763888 · SAMN17763889 · SAMN17763890 · SAMN17763891 · SAMN17763892 · SAMN17763893 · SAMN17763894 · SAMN17763895 · SAMN17763896 · SAMN17763897 · SAMN17763898 · SAMN17763899
infant_145mother + childSAMN37313987 · SAMN37313988 · SAMN37313989 · SAMN37313990 · SAMN37313991 · SAMN37313992 · SAMN37313993 · SAMN37313994 · SAMN37313995 · SAMN37313996 · SAMN37313997 · SAMN37313998
infant_58mother + childSAMN17763964 · SAMN17763965 · SAMN17763966 · SAMN17763967 · SAMN17763968 · SAMN17763969 · SAMN17763970 · SAMN17763971 · SAMN17763972 · SAMN17763973 · SAMN17763974 · SAMN17763975
infant_69mother + childSAMN17764009 · SAMN17764010 · SAMN17764011 · SAMN17764012 · SAMN17764013 · SAMN17764014 · SAMN17764015 · SAMN17764016 · SAMN17764017 · SAMN17764018 · SAMN17764019 · SAMN17764020
infant_144mother + childSAMN37313974 · SAMN37313975 · SAMN37313976 · SAMN37313977 · SAMN37313978 · SAMN37313979 · SAMN37313980 · SAMN37313981 · SAMN37313982 · SAMN37313983 · SAMN37313984 · SAMN37313985
infant_133mother + childSAMN17764183 · SAMN17764184 · SAMN17764185 · SAMN17764186 · SAMN17764187 · SAMN17764188 · SAMN17764189 · SAMN37313691 · SAMN37313969 · SAMN37313970 · SAMN37313971 · SAMN37313972
infant_169mother + childSAMN37314040 · SAMN37314041 · SAMN37314042 · SAMN37314043 · SAMN37314044 · SAMN37314045 · SAMN37314046 · SAMN37314047 · SAMN37314048 · SAMN37314049 · SAMN37314050 · SAMN37314051

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 17.9%Bacteroides 8.0%Klebsiella 6.2%Phocaeicola 4.9%Escherichia 4.6%Enterobacter 4.3%Faecalibacterium 3.2%Veillonella 3.0%Blautia_A 2.8%Clostridium 2.8%Mediterraneibacter 2.3%Sarcina 2.1%not assigned to a genus 2.5%other genera 35.4%

Genera, mean relative abundance over 743 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category735 90%
country819 100%819
health_condition395 48%395
subject_id819 100%73584
timepoint_label787 96%787
age_at_collection_days735 90%735
birth_weight_grams735 90%735
delivery_mode735 90%735
gestational_age_weeks735 90%735
sex735 90%735
antibiotic_exposure729 89%729
family_id683 83%683
family_role683 83%683
nec_status389 47%389
Papers (6)
  • Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. PMID 34622230 PMC8484513 curated
  • Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
  • Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. PMID 37973815 PMC10654741 curated
  • Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291 curated
  • Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992 curated
1 more
  • The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589
Details
Archive description

Using genome-resolved metagenomics to investigate the early-life gut microbiome succession at the strain-level.

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.title · “from human infant fecal samples with matched”
  • body site study.description · “investigate the early-life gut microbiome succession at”
  • life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
  • life stage study.title · “Early-life metagenomes from human”
  • life stage study.title · “samples with matched maternal sample”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN17763787age_at_collection_days29R10.85sample.titleDOL 29
SAMN37313719age_at_collection_days1339.0R10.70biosample.attribute:isolation_sourceisolation_source: Gut sample from infant #21 DOL 1339
SAMN17763787antibiotic_exposurenoR20.75paper.supp.tableInfant antibiotics=no
SAMN17763787birth_weight_grams3130R20.75paper.supp.tableBirth weight (gram)=3130
SAMN17763786countryUSR10.90biosample_attrUSA: Pittsburgh, Magee-Womens Hospital of UPMC
SAMN17763787delivery_modec_sectionR20.75paper.supp.tableDelivery mode=CS
SAMN17763786family_idinfant_7R10.85biosample.attribute:TITLEMother of infant #7
SAMN17763786family_rolemotherR10.85biosample.attribute:TITLEMother of infant #7
SAMN17763787gestational_age_weeks38.0R20.75paper.supp.tableGestational age (weeks)=38
SAMN17763801health_conditionhealthy_controlR20.70paper.supp.tablePreNEC=noNEC
SAMN17763802nec_statusnoR20.75paper.supp.tablePreNEC=noNEC
SAMN17763787sexfemaleR20.75paper.supp.tableGender=female
SAMN17763787subject_id7R10.70sample.titleInfant #7 DOL 29
SAMN17763786subject_idmother_of_infant_7R20.80archive
SAMN17763787timepoint_labelDOL 29R10.70sample.titleInfant #7 DOL 29
SAMN37313766timepoint_labelnear birthR10.70biosample.attribute:isolation_sourceisolation_source: Gut sample from the mother of infant #40 near birth
Sequencing

850 runs over 819 samples · mean 9.74 Gbp per run (median 10.10 Gbp, total 8,283.20 Gbp; 850 runs with a base count) · layout PAIRED 850 · platform ILLUMINA 850 · models Illumina NovaSeq 6000 (850) · 90% of runs with a Sandpiper profile · first public 2021-02-04 – 2023-09-10

Authors (73)

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 · Rubin BE · Schoelmerich MC · DiMarco KS · Borges AL · Rovinsky R · Song L · Doudna JA · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last · Zeng S first · Wang H · Zhang L · Li S · Yuan Y · Tian M · Qu Y · Ying J · Zhou M · Hu Y · Huang J · Zou R · Zhao F · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Zhou Z · Shen W · Mu D · Wang S last · Lou YC first · Olm MR · Diamond S · Crits-Christoph A · Firek BA · Baker R · Morowitz MJ · Banfield JF last

Downloads

PRJNA698986.csv.gz (29.3 KB) · parquet (107.7 KB) — all 819 samples, every field with route and confidence · PRJNA698986_determinations.csv.gz (88.1 KB) — 8,979 evidence rows

Samples (819 · every field this project has values for · hover a cell for its source)
Loading the sample table…