Gut Microbiome Science

Ruth Ley

  • PhD, University of Colorado, Boulder, 2001
  • Postdoctoral training, University of Colorado, 2001-2004; Post-Doc, Instructor, and Research Assistant Professor, Washington University School of Medicine, 2004-2008
  • Assistant and Associate Professor at Cornell University, 2008-2016
  • Director at the MPI for Developmental Biology since 2016

Research Interest

One big focus of our research is how interactions between humans and their gut microbiota influence metabolism and obesity.  Eukaryotic species have harnessed the microbiota to extend their phenotypes, yet gut microbiomes are immensely complex. When new hosts (infants) emerge, microbes are assembled into their microbiomes from the environment. The microbiome is challenged during disturbances, augmented by newly arriving microbes, and supported by synthropic partnerships. Host exudates including peptides, mucus, and antibodies have all been implicated in shaping the composition of these communities. In turn the host can be irreversibly reliant on its microbiome for immune development, nutrient release, and a growing list of other aspects of metabolism. The specifics of the mix at any given time can profoundly affect host metabolism and health. Although we work primarily in the context of human health and use gnotobiotic mice as a model system, we ask similar questions in other contexts, such as plant roots.

  • Illustration RuthLey Nov16
    click to enlarge

Host genetics and the gut microbiome can both influence metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, including 416 twin pairs. We identified many microbial taxa whose abundances were influenced by host genetics.
The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea. Furthermore, Christensenellaceae and its partners were enriched in individuals with low body mass index (BMI). An obese-associated microbiome was amended with Christensenella minuta, a cultured member of the Christensenellaceae, and transplanted to germ-free mice. C. minuta amendment reduced weight gain and altered the microbiome of recipient mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.

Available PhD Projects

Project 1: Genetic manipulation of Christensenella minuta, a keystone species in the human gut.

Project 2: Stable isotope probing of gut bacteria.

Selected Reading

1)  Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG and Ley RE (2014). Human genetics shape the gut microbiome. Cell 159: 789-799.

2)  Koren, O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed H, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S and Ley RE (2012). Remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 1-11.

3)  Cullender, TC, Chassaing B, Janzon A, Kumar K, Muller C, Werner JJ, Angenent LT, Bell ME, Hay AG, Peterson DA, Walter J, Vijay-Kumar M, Gewirtz AT and Ley RE (2013). Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe 14: 571-581.