Our research program aims to elucidate how gut microbial species relate to genotypic differences between human individuals, to identify bacterial and archaeal species that share an evolutionary history with humans, and to determine the molecular basis of long-term host-microbial relationships. We approach these aims with a combination of population-level observations and molecular-level investigations in the laboratory. We link inter-microbial and microbial-host interactions at the molecular scale to patterns at population and evolutionary scales. This cross-scale approach has led to the following discoveries:

Key contributions of the Ley Lab:

Human genetics shape the gut microbiome: Ley and colleagues challenged the established paradigm that once a gut microbiome is seeded, its composition is determined solely by environmental factors such as diet. Ley designed and led the first study aimed at identifying heritable gut microbes (i.e., variation in relative abundance across a population could be attributed to variation in host genotype)[3]. Ley’s team generated gut microbiome data and performed twin-based heritability analyses for >1200 genotyped twins sampled by collaborators in the UK. They thus presented the first list of heritable species for the human gut [3]. Ley and colleagues went on to perform the first genome-wide association analyses, leading to the identification of the alleles linked to the heritable species [4]. Their analyses produced a deepened understanding of how the microbiome relates to the virome [5] and yielded a novel phylum for the human gut [6]. Importantly, these studies brought human genetic variation to the fore as an important shaper of the microbiome. Ley has pioneered exploration of the role of the microbiome in human adaptation to new environments over the course of human evolution particularly in the acquisition of new diets [7,8]. With this work, Ley and colleagues has laid a theoretical framework for how the human microbiome may influence host evolutionary processes and opened new conceptual areas for empirical exploration.

Heritable microbiota promote metabolic health: The Ley lab identified Christensenella and Methanobrevibacter as the most highly heritable genera, and further showed that their abundance correlated positively with a lean body mass [3]. Notably, these findings have subsequently been corroborated in studies worldwide [9]. They followed up these observations with gnotobiotic experiments to demonstrate that these correlations are indicative of causality. Her team has shown in animal models that the Christensenella consortium can confer a lean phenotype [3], and recently, increase physical activity [11]. Working with laboratory cultures, Ley’s group has shown that Christensenella and Methanobrevibacter species use protein interactions to form tight biofilms and interact metabolically via hydrogen-transfer [9,10]. Together Ley’s studies have provided the first evidence that human genotype shapes the microbiome to promote metabolically beneficial microbial consortia. The translational impact of this work is a novel target for therapeutic interventions aimed to promote metabolic health.

Gut microbes in host fitness: During pregnancy the immune system of the mother changes to avoid rejection of the fetus. Ley and colleagues, notably Omry Koen, demonstrated that this change in immune milieu could impact the microbiome, and feedback to impact the mother’s metabolic state [11]. They documented a profound alteration in composition of the gut microbiome over the course of pregnancy; their experiments in animal models showed that the altered microbiome could induce metabolic and immunological changes observed in the mothers and that are predicted to support a healthy pregnancy [11]. This work suggests that changes to the immune system not only act to accept the baby but also to alter the microbiome to drive positive metabolic changes. Importantly, the implication of  the Ley lab’s work is that host-microbial interactions have evolved to support host fitness.

Humans share an evolutionary history with their gut microbes: Ley and team members, Taichi Suzuki and Liam Fitzstevens, are the first to elucidate the evolutionary origins of the human gut microbiome. They asked whether any gut microbiota share an evolutionary history with humans. Their approach was to conduct a cophylogeny analysis to compare a human phylogeny with phylogenies of the gut species inhabiting the same individuals. However, a major hurdle was that although human genotype and microbiome datasets were by then publicly available, they rarely came from the same set of individuals. Ley thus led a study of ~1220 individuals sampled for their genotype and microbiome, coordinating with international partners in 6 countries. Her team performed field sampling in Gabon, Germany, and Vietnam, where the participants selected were mothers with infants. The final dataset, consisting of two European countries (Germany, UK from previous Ley studies [3,4]), two African countries (Gabon, Cameroon) and two Asian (Vietnam, Korea), is unparalleled in size and global scope [12]. The team used SNPs indicative of human ancestry to derive a phylogeny for the participants, and generated metagenome-assembled genomes to create strain-based trees for the gut bacterial and archaeal species. For more than half of the ~60 species tested, comparison of host and microbial phylogenies showed statistically significant mirroring. This observed cophylogeny of humans and specific bacterial and archaeal taxa is strong evidence for codiversification from a shared evolutionary history. The Ley lab’s work in this area is highly significant as it implies kin transmission of key taxa over thousands of generations: as humans spread around the globe, they carried their symbionts with them.

They went further to demonstrate that codiversified microbes exhibit hallmarks of host restriction, including reduced genome size, loss of key functions, and sensitivity to oxygen and to below-body temperatures [12]. The team demonstrated these functional attributes from genome analysis and corroborated them with laboratory-based culture work. The evidence suggests that a subset of the human gut microbiome has been transmitted from host to host with relatives over thousands of generations, resulting in patterns of codiversification and unique strains within human populations. Importantly, she also demonstrated mother-infant transmission of codiversified taxa within a single generation, using a novel strain-comparison tool developed in her group [13]. This work has major implications for the development of therapeutic strains for use in diverse populations, and for the irreplaceable loss of microbial diversity worldwide.

Codiversifed microbiota show adaptations to human innate immune receptors: The Ley lab’s discovery of codiversification between humans and a suite of gut microbes implies that these species have had time to adapt to the human body.  To assess how human gut microbes have adapted specifically to human biology, Ley has focused on one of the most important innate immune receptors in the gut, toll-like receptor 5 (TLR5). The bacterial ligand of TLR5 is flagellin, the protein subunit of the bacterial flagellum, which confers motility. In early work at Cornell, the team discovered that anti-flagellin antibodies in the gut quench the motility of gut microbes [13]. Tthis work highlighted that the host can regulate the behaviour of commensal microbes. The understanding that the same microbiome can be more or less pro-inflammatory based on host immune responses has important consequences for the treatment of chronic inflammatory disease.

Ley and colleagues, notably Sara Clasen, then went on to challenge the well-established mode of action of TLR5. They demonstrated that the TLR5 does not operate according to the textbook description of ligand-induced dimerization leading to signalling. They showed this model to be incorrect using extensive biochemistry and cell- and organoid-based assays. Instead, they demonstrated signalling requires allosteric binding to preformed TLR5 dimer [14]. They characterised a novel class of flagellin that she termed “silent” based on their ability to bind TLR5 monomer without eliciting a pro-inflammatory response [14]. They showed that silent flagellins are widespread in gut commensal bacteria, many of which she identified as codiversified with their human populations [11]. This important work highlights how commensal microbes have evolved to evade immune stimulation even while maintaining immune recognition. The Ley lab has provided a deepened understanding of flagellin-TLR5 interactions that will require an update of basic immunology textbooks.

Host-like lipids in gut bacteria: Ley and colleagues have impacted on another poorly studied aspect of host-microbial interaction: lipids [15-18]. Sphingolipids are important structural and signalling lipids essential to mammalian biology. The majority are sourced from the diet, and a small fraction is synthesized de-novo in eukaryotic cells. Ley asked if the gut Bacteroidetes could act as an endogenous source of these important lipids. The Bacteroidetes comprise a significant fraction of the human gut microbiome worldwide and they are unique amongst gut bacteria in that they produce sphingolipids. Ley and colleagues, notably Liz Johnson and Sara Di Rienzi, showed that bacterial sphingolipids enter host metabolic pathways and directly affect liver de-novo sphingolipid production rates [15-17]. They went further and developed imaging-mass spectrometry techniques, which she combined with bacterial genetics and gnotobiotics, to show that lipids could enter gut tissue directly from the microbiome [19]. These studies constitute the first demonstrations that gut bacteria can act as an endogenous source of bioactive lipids to the host. This work may have implications for early life development, particularly in the provisioning of sphingomyelin to the brain, under conditions of malnutrition in sphingolipid-poor diets.

In addition, working with Stacey Heaver in the group, they showed that inositol lipids, previously thought of as either mammalian or produced solely by Mycobacteria, are widespread in the Bacteroidetes [20]. They has identified and characterized biochemically two distinct pathways for inositol lipid production and shown that inositol lipids are critical for bacterial fitness in the gut using genetics in species of the Bacteroides, Parabacteroides and Prevotella genera [20]. This work identifies inositol lipids as a novel molecular language in host-microbial interactions. Lipids represent a poorly explored class of fundamentally important compounds; the Ley lab’s unique work in this area is opening up new avenues to explore host-microbial interactions, with potential therapeutic outcomes.

Publications cited herein:

1. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R and Gordon JI. (2008). Evolution of mammals and their gut microbes. Science 320:1647-1651.

         DOI: https://doi.org/10.1126/science.1155725.

2. Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH and Ley RE. (2021). Vertebrate host phylogeny influences gut archaeal diversity. Nature Microbiology 6:1443–1454.

         DOI: https://doi.org/10.1038/s41564-021-00980-2.

3. 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.

         DOI: https://doi.org/10.1016/j.cell.2014.09.053.

4. Goodrich JK, Davenport ER, Jackson MA, Beaumont M, Knight R, Spector TD, Bell JT, Clark AG and Ley RE. (2016). Genetic determinants of the gut microbiome in UK twins. Cell Host & Microbe 19:731-743.

         DOI: https://doi.org/10.1016/j.chom.2016.04.017.

5. Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector T, Bell JT, Youngblut ND, Hewson I, Reyes A and Ley RE. (2019).  Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins. Cell Host & Microbe 25:261-272.

         DOI: https://doi.org/10.1016/j.chom.2019.01.019.

6. Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF and Ley RE. (2013). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2:e01102.

         DOI: https://doi.org/10.7554/elife.01102.

7. Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG and Ley RE. (2019). Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host & Microbe 25:553-564.

         DOI: https://doi.org/10.1016/j.chom.2019.03.001.

8. Schmidt V, Enav H, Spector T, Youngblut ND and Ley RE. (2020). Strain-level analysis of Bifidobacterium spp. from gut microbiomes of adults of differing lactase persistence genotypes. mSystems 5:e00911-20.

         DOI: 10.1128/mSystems.00911-20

9. Ruaud A, Esquivel-Elizondo S, de la Cuesta-Zuluaga J, Waters JL, Angenent LT, Youngblut ND and Ley RE. (2020). Syntrophy via interspecies H₂ transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut. mBio 11:e03235-19.

         DOI: https://doi.org/10.1128/mbio.03235-19.

10. Akbuğa-Schön T, Suzuki T, Jakob D, Vu DL, Waters JL and Ley RE. (2024). The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice. mBio15:e02836-23.

         DOI: https://doi.org/10.1128/mbio.02836-23.

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

         DOI: https://doi.org/10.1016/j.cell.2012.07.008.

12. Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Mbong Ngwese M, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P and Ley RE. (2022). Codiversification of gut microbiota with humans. Science 377:1328-1332.

         DOI: https://doi.org/10.1126/science.abm7759.

13. Enav H, Paz I and Ley RE. (2024). Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nature Biotechnology 43: 773–783.

         DOI: https://doi.org/10.1038/s41587-024-02276-2.

14. 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.

         DOI: https://doi.org/10.1016/j.chom.2013.10.009.

15. Clasen SJ, Bell MEW, Borbón A, Lee DH, Henseler ZM, de la Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y and Ley RE. (2023). Silent recognition of flagellins from human gut commensal bacteria by toll-like receptor5. Science Immunology.8:eabq7001.

         DOI: https://doi.org/10.1126/sciimmunol.abq7001.

16. Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS and Ley RE. (2020). Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels. Nature Communications 11:2471.

         DOI: https://doi.org/10.1038/s41467-020-16274-w.

17. Di Rienzi S, Johnson E, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT and Ley RE. (2021). The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. The Journal of Nutritional Biochemistry 97:108808.

         DOI: https://doi.org/10.1016/j.jnutbio.2021.108808.

18. Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J and Ley RE. (2018). Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. eLife 7:e32581.

         DOI: https://doi.org/10.7554/eLife.32581.

19. Mirretta Barone C, Heaver SL, Gruber L, Zundel F, Vu DL and Ley RE. (2024). Spatially resolved lipidomics shows conditional transfer of lipids produced by Bacteroides thetaiotaomicron into the mouse gut. Cell Host & Microbe 32:1025-1036.

         DOI: https://doi.org/10.1016/j.chom.2024.04.021

20. Heaver SL, Le HH, Tang P, Baslé A, Mirretta Barone C, Vu DL, Waters JL, Marles-Wright J, Johnson EL, Campopiano DJ and Ley RE. (2022). Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nature Microbiology 7:986–1000.

         DOI: https://doi.org/10.1038/s41564-022-01152-