Dr. David’s laboratory studies microbiota-gut-brain interactions and implements new computational biology tools to decipher how microbiomes interact with their hosts and their environments. The lab aims to unravel how the gut microbiota can impact our behavior, specifically in Autism Spectrum Disorder. We also work on identifying bottlenecks in microbiome data exploration and leverage deep learning to improve microbial sequence annotation and multi-omics analysis. You can follow our scientific journey on X (formerly twitter): @MDavidLab on X.
Learning microbiome properties using deep learning
The David Lab is leveraging deep learning methods on thousands of publicly available samples to a wide array of applications in microbial ecology. For example, we worked with 16S amplicon sequences, where we sought to learn a set of properties to describe individual taxa and entire microbial communities more effectively than a list of taxa can. We condensed the variable space in the human gut microbiome from thousands of taxa to a latent variable landscape of only hundreds of variables, thereby utilizing community level signatures to increase power and reproducibility in microbiome studies. To accomplish this, we use a system of embeddings that transforms human gut microbiome taxonomic data into a continuous, dense, low-dimensional space. We show that embedded gut microbiome data is more informative of the inflammatory bowel disease (IBD) status of the host than normalized taxonomic counts and other dimensionality reduction methods such as Principal Coordinate ordination. You can find our first paper in Plos Computational Biology, and the package was made available in Frontiers in Bioinformatics. We now moving toward applying deep learning to improve gene annotation, pathway discovery and the integration of multi-omics data.
The M3 project: Microbiome, Metabolites and the Mind: a longitudinal analysis of the microbiota of children with autism
The existence of a link between the gut microbiome and Autism Spectrum Disorder (ASD) is well established in mice, but in human populations efforts to identify microbial biomarkers remain limited due to a lack of appropriately matched controls, stratification of participants within the spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of over 100 families with age-matched sibling pairs between 2-7 years old, where one child had a diagnosis of ASD and the other did not. We performed multi-omics analysis and longitudinal data analysis of 16S amplicon data. You can find a couple of our publications on this project here and here. We're now working toward a better understanding of the mechanisms underlying autism, new publication to come soon!
Sex shapes gut–microbiota–brain communication and disease
Research into the microbiota–gut–brain axis (MGBA) has entered a golden age, raising the hope that therapeutics acting on it may offer breakthroughs in the treatment of many illnesses. However, most of this work overlooks a fundamental, yet understudied, biological variable: sex. Sex differences exist at every level of the MGBA. The laboratory has been working on feeding mice specific microbial taxa, which previously were found enriched in individuals in individual with Autism Spectrum Disorder. Behavior testing has been implemented to evaluate if the microbe being supplemented seems to have an effect on the behavior of the mice, and if sex their response is consistent or differ between sex. Our first opinion on this subject has been published in Trends in Microbiology and can be found here.
Should we feed probiotics to honey bee? (our beehavior study!)
n collaboration with Dr. Ramesh Sagili’s Honey Bee Lab at OSU, we are testing if nutritional complements (such as probiotics) can offset gut pathogen stressors and/or significantly impact the micro-bee-al community. We are measuring if different treatments can affect their floral choice, and therefore alters bee gustatory responses. We have also recently received a USDA grant in collaboration with 4 other universities across the country to study this question when bees are affected by European foulbrood.