This October, Nandita spoke at the ISB virtual microbiome symposium featuring talks from the field on evolution in commensal gut bacteria on short and long time scales. A link to view the talks is available here: https://youtu.be/u12G6tSLpjY.
We are very excited to share our latest manuscript entitled Ecological stability emerges at the level of strains in the human gut microbiome. To date, there has been an intensive focus on quantifying ecological dynamics from gut mirobiome data at the species level using 16S amplicon data. However, each species within hosts can be comprised of multiple strains, and it is not clear whether this ecological stability that is observed at the species level can extend down to the strain level. Here we quantify this and find that strains are indeed stable ecological units whose fluctuations in frequencies over time can be described by macroecological laws.
Figure 2 from Wolff et al. in which a stochastic logistic model was fit to the fluctuations in strain abundance for two strains from a given host quantified over 2 years.
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.
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
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!
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.
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.
We are excited to welcome Sarah Bald and Anna McDonald to our lab this summer for the Bruins in Genomics program!
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.
Nandita recently gave a seminar at Berkeley and her colleague, Alison Feder, drew a graphical abstract of the talk!
