Infant colonization

Also see separate page on the microbiome in pregnancy and human breast milk microbiome. Updated October 2017.

Research papers

Breast Milk Transforming Growth Factor b Is Associated With Neonatal Gut Microbial Composition – Alexandra R. Sitarik – Journal of Pediatric Gastroenterology and Nutrition – September 2017

The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota – Tiina Drell – Scientific Reports – August 2017

Early gut mycobiota and mother-offspring transfer – Kasper Schei – Microbiome – August 2017

Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures – Harro M. Timmerman – Scientific Reports – August 2017

The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elena Biagi – Frontiers in Microbiology – June 2017

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling – Francesco Asnicar – mSystems – January 2017

Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery – Derrick M. Chu – Nature Medicine – January 2017

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.

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
– Fredrik Bäckhed – Cell Host & Microbe – June 2015

Applying metagenomic analysis on fecal samples from a large cohort of Swedish infants and their mothers, we characterized the gut microbiome during the first year of life and assessed the impact of mode of delivery and feeding on its establishment.

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.

Comparative Analysis of Salivary Bacterial Microbiome Diversity in Edentulous Infants and Their Mothers or Primary Care Givers Using Pyrosequencing – Kimberly D. Cephas – PLOS ONE – August 2011

Development of gut microbiota in infants not exposed to medical interventions – Merete Eggesbø – APMIS – January 2011

We describe the colonization process, during the first four months after birth, in 85 infants who have experienced no major medical or dietary interventions.

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns – Maria G. Dominguez-Bello – PNAS – June 2010

We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers’ skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates’ skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode.

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.

Establishment of the gut microbiota in Western infants

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

The Maternal Infant Microbiome: Considerations for Labor and Birth – Alexis Dunn – MCN – August 2017

The shape of the microbiome in early life – Erika von Mutius – Nature Medicine – March 2017

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

Establishment of the gut microbiota in Western infants – I Adlerberth – Acta Paediatrica – January 2009

Popular press

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