We are delighted to share our latest preprint on “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history“. Please check out our paper and below is an animation we made sharing a few highlights from the paper!
Congratulations to Mariana Harris for winning Best Poster Award at the UCLA QCBio retreat on her work on hard sweep enrichment on the X chromosomes of Drosophila melanogaster!
We are extremely grateful to the NIH for awarding our lab an R35 grant. We will be working on furthering our understanding the evolutionary dynamics of gut bacteria during gut colonization. Stay tuned for results on this work!
Lead by Mariana Harris and in collaboration with Bernard Kim, we recently posted a preprint showing that hard sweeps are enriched on the X chromosome of six Drosophila species, generalizing findings that we previously made in a single population of D. melanogaster.
Please check out our video on the paper!
We are thrilled to welcome Jooeun Jeon, Radha Ganesh, and Rahul Natarajan this summer to our lab for the Bruins in Genomics summer program!
Radha Ganesh
Jooeun Jeon
Rahul Natarajan
Our first PhD student, Leah Briscoe, defended her PhD this past month! Leah’s work spanned several topics, including background noise correction in the microbiome and source tracking in the microbiome with SNVs. She has one more paper coming out, please stay tuned! Congratulations Leah!
The lab celebrating Leah’s defense!
The Garud lab attended the Southern California Evolution meeting (SCALE) this past weekend and had a strong showing of presenters!
From left to right: Mariana, Michael, Aina, Peter, Ricky, and Jon
PhD student Mariana Harris gave a talk at SMBE Everywhere this month on her work on enrichment of hard sweeps on the X chromosome relative to autosomes. Congrats Mariana!
We are excited to share that our lab has received an NSF CAREER award to study rapid, repeatable adaptation in the human gut microbiome! Please stay tuned for results on this work!
We are delighted to share that our paper entitled Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome is now accepted at mBio! This work is with the very talented first author and PhD student Richard Wolff and postdoc William Shoemaker.
In healthy hosts, species abundance fluctuations in the microbiome have been frequently described as stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. Here, we analyze the daily dynamics of intra-specific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that overall genetic diversity in a large majority of species is stationary over time, despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM)—an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.
Figure from the paper: Figure 1: A & B) FST ′ trajectories for B. vulgatus (am) and F. prausnitzii (ao), respectively. C & D): SNV frequencies of three inferred strains for B. vulgatus (C) and two inferred strains for F. prauznitzii (D). In black are the inferred strain trajectories. Highlighted in blue are example strains featured further in (E) and (F). E & F) Frequencies of the example strains in blue, with simulations of the corresponding SLM overlaid in red. At right, the empirical distribution of strain abundances is plotted in blue, and the stationary Gamma distribution of abundances (see Equation 2) predicted by the SLM in red. G & H) Sampling time points. Blue lines indicate that a sample was taken on that day.