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!
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.
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.
We are very proud of Mariana Harris for receiving the UCLA GATP fellowship and Ricky Wolff for receiving honorable mention in the NSF GRFP competition!! Congrats!
We are very proud to share our recent preprint:
Correcting for background noise improves phenotype prediction from human gut microbiome
Leah Briscoe, Bruna Balliu, Sriram Sankararaman, Eran Halperin and Nandita Garud
Many technical and biological variables can contribute to variation in microbiome data. For example, in this combined dataset, the study contributes more variation than colorectal disease status.
Many of the popular methods for correcting background noise in microbiome data are supervised. Unsupervised methods may be preferable because they can correct for unmeasured sources of variation. We perform a comparative analysis of background noise correction methods and find that regressing out Principal Components after applying a centered log-ratio transformation is quite effective in removing unwanted variation. In fact, if we correct for background noise, we can even improve phenotype prediction of many phenotypes.
Nandita has been named an Allen Distinguished Investigator! The Garud lab is excited to be collaborating with Drs. Carolina Tropini, Aida Habtezion, and Siddharth Sinha on the following grant: Distinct immune-metabolic niches in inflammatory bowel disease. Link to press release.