Infant gut microbiota, preterm NICU cohort, USA

The microbial composition of the gut likely contributes to a wide-range of health and disease states including intestinal inflammation, atopic disease, and possibly diseases of adulthood, such as heart disease and obesity. The early establishment of the gut microflora is suspected to have a particularly profound impact protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. In contrast to the large-scale efforts of the Human Microbiome Project to characterize the microbial flora of healthy adults, relatively little has been accomplished to characterize the early establishment of the microbiota in infants. <p> The administration of antibiotics to infants has the capacity to profoundly affect the early acquisition, establishment, and natural maturation of commensal microflora. Prematurity is another major factor that is thought to influence 'normal' gut microbial composition in early life. A high number of pre-term infants receive antibiotic therapy prophylactically the immediate and long-term effects of antibiotic treatment on infant and later health outcomes are unknown. We hypothesize that gestational age influences the ability to support 'normal' gut microbiota, and that antibiotic administration in the first few weeks of life can alter or delay the development of a 'normal' microbiota and may lead to adverse health outcomes. If we hope to promote the healthy establishment of early gut colonization and thereby improve health outcomes, we need to establish what 'normal' colonization looks like across gestational ages and apply this knowledge as a benchmark to understand the impact of antibiotic treatment in early postnatal life. <p> In this project, we propose to examine the microbiome in four cohorts ranging from extremely preterm to term, with birth weights appropriate for gestational age: Group 1) 23 to 27 weeks and extremely low birth weight [ELBW, <1000 grams] Group 2) 28 to 32 weeks and very low birth weight [VLBW, >1000 to <1500 grams] Group 3) 33 to 36 weeks and low birth weight [LBW, >1500 to <2500 grams] and Group 4) term (37 to 42 weeks) and normal [>2500 to <4000 gram] birth weight. The infant gut microbiome will be assessed longitudinally in study infants from the first postnatal week to 18 months of age, and will include untreated and antibiotic-treated infants.

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate 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 · “samples from infant gut”
• body site study.description · “composition of the gut likely contributes to”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.title · “of samples from infant gut”
• life stage study.description · “of commensal microflora. Prematurity is another major”
• life stage study.description · “flora of healthy adults , relatively little”

3,489 runs over 667 samples · mean 0.47 Gbp per run (median 0.40 Gbp, total 1,649.98 Gbp; 3,489 runs with a base count) · layout PAIRED 3,070, SINGLE 419 · platform ILLUMINA 3,070, LS454 419 · models Illumina HiSeq 2000 (3,070), 454 GS FLX Titanium (419) · 74% of runs with a Sandpiper profile · first public 2011-08-02 – 2015-04-04

Taft DH first · Ambalavanan N · Schibler KR · Yu Z · Newburg DS · Ward DV · Morrow AL last · Deshmukh H · Chen Y first · Brook TC · Soe CZ · O'Neill I · Alcon-Giner C · Leelastwattanagul O · Phillips S · Caim S · Clarke P · Hall LJ · Hoyles L last · Tisza MJ first · Buck CB last · Xiao L first · Wang J · Zheng J · Li X · Zhao F last · Tarracchini C first · Milani C · Longhi G · Fontana F · Mancabelli L · Pintus R · Lugli GA · Alessandri G · Anzalone R · Viappiani A · Turroni F · Mussap M · Dessì A · Cesare Marincola F · Noto A · De Magistris A · Vincent M · Bernasconi S · Picaud JC · Fanos V · Ventura M last · Casaburi G first · Wei J · Kazi S · Liu J · Wang K · Tao GZ · Lin PY · Dunn JCY · Henrick BM · Frese SA · Sylvester KG last · van Sinderen D · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · Cosic A first · Halwachs B · Schild-Prüfert K · Zechner EL · Kienesberger S last

PRJNA63661.csv.gz (23.8 KB) · parquet (106.6 KB) — all 667 samples, every field with route and confidence · PRJNA63661_determinations.csv.gz (51.2 KB) — 4,969 evidence rows