Rapid evolution and strain turnover in the infant gut microbiome

We are pleased to share our latest manuscript on Rapid evolution and strain turnover in the infant gut microbiome. In this paper, we quantify differences in the tempo and mode of evolution in the infant compared to adult gut microbiomes and find that evolution and strain turnover is significantly faster in infants and decays with life stage. Please check out our manuscript and send us any comments!

Figure 2 from Chen and Garud. (B) Rates of number of SNV changes per day due to evolution, (C) rates of number of strain replacements per day, and (D) rates of gene gains and loss per day.

 

Welcome Aina and Alex!

We are thrilled to welcome Alex Flynn-Carroll and Aina Martinez Zurita to the lab this quarter. They are rotation students in Bioinformatics and Human Genetics, respectively and are working on projects related to understanding the evolutionary forces shaping microbiome genetic variation.

 

Aina

 

Alex

Farewell to Daisy Chen

We are very sad to bid Daisy Chen farewell, but excited for her next steps as a PhD student at UCSD. Daisy has been with the lab since its inception in 2019 and has contributed a tremendous amount to its growth. Stay tuned for her papers, which are forthcoming!

 

Ecological and evolutionary responses of the human gut microbiome during antibiotics

We are happy to share that our collaboration on Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment is now out in Genome Research. This was an exciting project to work on with several co-authors, including Morteza Roodgar, Benjamin Good, Michael Snyder, and Katherine Pollard.

UCLA Hellman Fellow

Nandita was recently named a Hellman Fellow at UCLA! This grant will fund work in the lab on Uncovering the Landscape of Mutations in the Human Gut Microbiome.

Bruins in Genomics summer students

We are excited to welcome Sarah Bald and Anna McDonald to our lab this summer for the Bruins in Genomics program!

 

Scialog!

We sincerely thank the Research Corporation for Science Advancement, The Paul G. Allen Frontiers Group, and the Frederick Gardner Cottrell Foundation for funding our research group to collaborate with Dr. Will Ludington’s group on our project: Do Aging Microbiomes Evolve Pathogenicity Via Gene Shedding? Using Evolutionary Theory to Deconstruct Microbiome-based Neurodegeneration. This grant was facilitated via that Scialog! meeting hosted earlier this year.

 

CTEG talk at Berkeley

Nandita recently gave a seminar at Berkeley and her colleague, Alison Feder, drew a graphical abstract of the talk!

CTEG talk at Berkeley

Scialog!

Nandita is a Microbiome, Neurobiology and Disease Scialog Fellow and recently participated in the annual Scialog conference to innovate and pitch new ideas about the connection between the gut and the brian.

Scialog conference

EEB149: Evolutionary Genomics

This quarter, Prof. Nandita and TA Ricky are teaching a new R-based course on Evolutionary Genomics for undergraduates. Our goals for the class are to teach students how to make evolutionary inferences from DNA sequences. We are covering topics ranging from evolutionary dynamics on short time scales within populations to longer-term evolutionary forces across across species. We conclude by examining the microbiome. Here is our syllabus.