Infant colonization

Also see separate page on the microbiome in pregnancy and human breast milk microbiome. Updated January, 2016.

Research papers

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability – Moran Yassour – Science Translational Medicine – June 2016

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.

Antibiotics, birth mode, and diet shape microbiome maturation during early life – Nicholas A. Bokulich – Science Translational Medicine – June 2016

We profiled microbial development during the first 2 years of life in a cohort of 43 U.S. infants and identified multiple disturbances associated with antibiotic exposures, cesarean section, and formula feeding.

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes – January 2016

A subset of 21 isolates among 126 unique bacteria from breast milk and infant stools from 15 mother-infant pairs were examined for simulated GI transit survival, adherence to Caco-2 cells, bacteriocin production, and lack of antibiotic resistance.

The Placenta Harbors a Unique Microbiome – Kjersti Aagaard – Science Translational Medicine – May 2014

A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA–based and whole-genome shotgun (WGS) metagenomic studies.

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months – Meghan B. Azad, Theodore Konya, et al. – Canadian Medical Association Journal – 2013

We included a subset of 24 term infants from the Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort. (…) Fecal samples were collected at 4 months of age, and we characterized the microbiota composition using high-throughput DNA sequencing.

Human gut microbiome viewed across age and geography – Tanya Yatsunenko,  Federico E. Rey, Mark J. Manary, et al. – Nature – 2012

…we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins.

Succession of microbial consortia in the developing infant gut microbiome – Jeremy E. Koenig,  Aymé Spor, Nicholas Scalfone, Ashwana D. Fricker, Jesse Stombaugh, Rob Knight, Largus T. Angenent, and Ruth E. Ley – PNAS – 2010

Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient.

Development of the Human Infant Intestinal Microbiota – Chana Palmer, Elisabeth M Bik, Daniel B DiGiulio, David A Relman, Patrick O Brown – PLOS Biology – 2007

We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life.

Molecular Monitoring of Succession of Bacterial Communities in Human Neonates – Christine F. Favier, Elaine E. Vaughan, Willem M. De Vos, and Antoon D. L. Akkermans – Applied and Environmental Microbiology – 2002

The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes.

Allergy development and the intestinal microflora during the first year of life – Bengt Björkstén, Epp Sepp, Kaja Julge, Tiia Voor, Marika Mikelsaar – The Journal of Allergy and Clinical Immunology – 2001

Newborn infants were followed prospectively through the first 2 years of life in Estonia (n = 24) and Sweden (n = 20). By that age, 9 Estonian and 9 Swedish infants had developed atopic dermatitis and/or positive skin prick test results. Stool samples were obtained at 5 to 6 days and at 1, 3, 6, and 12 months, and 13 groups of aerobic and anaerobic microorganisms were cultivated through use of standard methods.

Review papers

Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition – December 2015

Microbial programming of health and disease starts during fetal life – Petya T. Koleva – Birth Defects Research (Part C) – December 2015

The developing intestinal microbiome and its relationship to health and disease in the neonate – R. Murgas Torrazza – Journal of Perinatology – 2011

Popular press

Nurturing a baby’s microbiome, before and after birth – Kate Gammon – Popular Science – 2015