Natural history of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability

By Moran Yassour, Tommi Vatanen, Heli Siljander, A. Hämäläinen, T. Härkönen, S. Ryhänen, Eric A. Franzosa, H. Vlamakis, Curtis Huttenhower, Dirk Gevers and 3 more. Science Translational Medicine, 2015

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A longitudinal strain-level analysis of the infant gut microbiome after repeated antibiotic treatments reveals decreased diversity and stability, as well as transient increases in antibiotic resistance genes. Elucidating the effects of drugs on bugs Despite widespread use of antibiotics in children, the effects of antibiotic exposure on the developing infant gut microbiome have remained underexplored. Here, Yassour et al. present a longitudinal study capturing how the gut microbiome responds to and recovers from antibiotic perturbations. Antibiotic-treated children had less stable and less diverse bacterial communities. Antibiotic resistance genes within the guts of these children peaked after antibiotic treatment but generally returned rapidly to baseline. Delivery mode (vaginal versus cesarean) also had strong long-term effects on microbial diversity. These data give insights into the consequences of early life factors such as birth mode and antibiotic treatment on the infant gut microbiome. The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.

Subfields: Epidemiology, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bfe84fd9f339df3b42521ecc591daf2b9ffb4b35

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Citations in the corpus

The Central Nervous System and the Gut Microbiome (2016, background): “The infant microbiome is highly sensitive to various perturbations like changes in diet and antibiotic treatment (Bäckhed et al., 2015; Koenig et al., 2011; Yassour et al., 2016).”
Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration (2017, background): “Some preliminary studies in humans indicate that intra-nasally administered oxytocin may positively alter social behaviour patterns (Yatawara et al. 2016), and a series of large clinical trials are underway to test oxytocin and related therapies for autism spectrum disorder (Shen, 2015).”
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients (2017, background): “(XLSX 9 kb) Additional file 6: Figure S1.”
Antibiotics as Major Disruptors of Gut Microbiota (2020, background): “The gut microbiota affects the development of the adaptive immune system by stimulating the growth of lymphoid structures, T- and B-cell differentiation and the establishment of immune tolerance (Zhao and Elson, 2018).”
The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017, background): “In contrast, the relative abundances of Bifidobacteriaceae, Actinomycetaceae, Veillonellaceae, Enterobacteriaceae, Lactobacillaceae, Enterococcaceae, Clostridiales incertae sedis XI, Carnobacteriaceae, and Fusobacteriaceae decreased during the transition from the infant to the toddler stage (115), w”
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome (2018, background): “, 2014), as well as other influencing factors including maternal and infant antibiotic usage (Lemas et al., 2016; Yassour et al., 2016) and feeding method (formula or breastfeeding) (Backhed et al.”
Impact of antibiotics on the human microbiome and consequences for host health (2022, background): “The authors also re- ported the presence of ARGs on mobile genetic elements long after cessation of treatment (Yassour et al., 2016).”
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography (2016, background): “Other studies have examined the development of the infant gut microbiome (Koenig et al. 2011), including at the strain level (Luo et al. 2015; Yassour et al. 2016), but did not assess vertical transmission.”