PhD defence by Lili Yang

Strain-Resolved ecology and evolution of Escherichia coli and Bifidobacteria longum in the Developing Infant Gut Microbiome

Assessment Committee:
Professor Karsten Kristiansen, Biology, University of Copenhagen (Chairperson)
Professor Mathieu Groussin, University of Kiel
Associate Professor Martin Frederik Laursen, National Food Institute, Technical University of Denmark (DTU)

Supervisor(s):
Professor Søren Johannes Sørensen

Assistant Professor Urvish Sureshchandra Trivedi

Department:
Department of Biology

Place:
Building 1, Room: Ground floor, Auditorium A,Universitetsparken 15, 2100 København Ø

Email address to gain access to the thesis: urvish.trivedi@bio.ku.dk 
You will either receive a copy of the thesis or be informed where you can read a physical copy.

Short description of the thesis:

In the infant gut microbiome, Escherichia coli and Bifidobacterium longum are dominant early colonizers that play important roles in microbial community assembly and host health. However, these bacteria have largely been studied at the species level, overlooking the substantial finer-scale diversity. This thesis applies strain-resolved approaches to investigate the ecology and evolution of E. coli and B. longum within individual hosts and across host populations. By developing analytical frameworks that are broadly applicable to other microbial species, this work reveals how mobile genetic elements, metabolic adaptation, and diet-driven selection shape strain fitness, and how ecological and evolutionary processes together drive microbial colonization in early life.