US term infant gut microbiome survey, five states

During the neonatal period, the gut microbiome plays an important role in protecting infants from infections while favoring the development of the immune system. However, there are few studies surveying the gut microbiome of term infants across the United States during this critical developmental window. To address this gap, we performed a multi-site survey to profile the gut microbiome of term infants in five states using shotgun metagenomics. Our survey found that Bifidobacterium are less abundant among term infants than generally assumed, B. infantis was missing in 97% of the population, resulting in a limitation of human milk oligosaccharide utilization capacity. Antibiotic resistance genes and bacteria associated with inflammation and gut dysbiosis are also widespread in the United States, independent of location, age, and diet. These findings may provide additional insight into the current state of the term infant gut microbiome and the potential risks for infant health and development.

Classified as human gut / stool / human milk 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 · “survey of the gut microbiome of term”
• body site study.description · “neonatal period, the gut microbiome plays an”
• body site study.description · “a limitation of human milk oligosaccharide utilization capacity.”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.title · “microbiome of term infants in the United”
• life stage study.description · “During the neonatal period, the gut”

227 runs over 227 samples · mean 8.11 Gbp per run (median 8.20 Gbp, total 1,840.06 Gbp; 227 runs with a base count) · layout PAIRED 227 · platform ILLUMINA 227 · models Illumina NovaSeq 6000 (227) · 91% of runs with a Sandpiper profile · first public 2021-03-01

Casaburi G first · Duar RM · Brown H · Mitchell RD · Kazi S · Chew S · Cagney O · Flannery RL · Sylvester KG · Frese SA · Henrick BM · Freeman SL last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S · Song D first · Duncan-Lowey B · Khetrapal V · Hamchand R · Deng T · Wu A · Martin AL · Bauer KM · Zhao Y · Nguyen MT · Sonnert ND · Leopold SR · Wu Q · Crawford JM · Palm NW last

PRJNA633576.csv.gz (9.3 KB) · parquet (82.7 KB) — all 227 samples, every field with route and confidence · PRJNA633576_determinations.csv.gz (20.4 KB) — 2,238 evidence rows