Baby’s First Microbiome

In other words, the formation of this community of microorganisms during infancy has lifelong consequences. Despite this great impact, however, very little is known about how microbes colonize the gut during infancy or how the composition of the microbiome affects pediatric disease. Yassour, who is cross-appointed to the Faculty of Medicine and the School of Computer Science and Engineering, explores this scientifically rich niche at the Hebrew University, where she earned all three of her degrees and to which she returned in 2018 after a postdoctoral fellowship at the Broad Institute of MIT and Harvard. While in Boston, she found herself wondering about the factors contributing to differences in infant gut microbes. “Being a mother myself,” she says, “it intrigued me.”

Yassour who grows bacterial cell cultures in her lab that simulate the infant gut and performs computational analyses.

Today, Yassour works in her lab with a dozen or so students, from undergraduates to PhDs, with backgrounds ranging from microbiology and medicine to pure computer science. Together, they grow bacterial cell cultures in anaerobic environments that simulate the infant gut, sequence bacterial DNA from stool samples and use machine learning algorithms to map out not only what type of microbes inhabit our guts, but also the specific strains and their functionality, and how they may play a role in pediatric health. 

Yassour has made significant progress in the eight years since starting her research in this field. She has debunked the belief that the vaginal microbiome seeds the infant gut microbiome during birth (the source appears to be rectal) and traced mother-to-child transmission of the microbes that colonize the infant gut. She has also continued to lay the groundwork for more ambitious and applied work. Eventually, thanks to her research, infant formula could better mimic breastmilk’s ability to nurture healthy children, and lifesaving caesarean deliveries won’t deny babies the microbial boost experienced from vaginal births.

“We still need to answer many of the basic science questions,” says Yassour, “before we can move on to address the big important ones.” Infants born by caesarian, for example, have a greater chance of developing autoimmune diseases than those who are born vaginally. Yassour wants to find out whether differences in their microbiomes are at the root of this disparity. At six months of age, a child born by caesarian has a different microbial signature in their gut than one who is born vaginally. The signs are so strong that if you were to give her a stool sample from an infant’s diaper, she could tell you how that baby was born with 80 per cent accuracy. Breastfed infants also have unique signatures in their gut microbes compared with formula-fed infants.

Yassour is interested in teasing apart the precise impact of these variations. One way to do this is by decoding the microbial make-up of stool samples collected from individuals across multiple points in their early lives. “We can collect longitudinal cohorts of infants or older children that have a medical condition that is associated with immunity early on in life, profile their microbiome and search for differential features, such as specific microbial taxa,” she says. She is collaborating with researchers at Massachusetts General Hospital in Boston to study an allergy that some infants develop to the proteins in cow’s milk. Although the allergy resolves on its own, children who develop it have a higher chance of developing life-threatening food allergies, such as to nuts or shellfish, later in life. 

Yassour and her colleagues are analyzing stool samples from ninety babies who developed this allergy during the first year of their lives and ninety who did not to compare their gut microbiomes. “We find some overall differences in microbial diversity between the groups,” she says of their findings so far, “and also identify bacterial species that have a higher abundance in one group than the other.” Moreover, the researchers found differences during the period that the allergy presents and after it resolves, and they are examining the specific bacteria at play. 

Moran Yassour (middle) with students Nadav Moriel and Sivan Kijner in her lab, where their research is deepening our understanding of the infant gut microbiome.