Microbiome Research at Yale

The Human Nature Lab (www.HumanNatureLab.net) studies the predicates and implications of human social interactions, including the role of social networks in the spread and physiological impact of the gut microbiome. This work advances both sides of the “social microbiome” — understanding the two-way relationship between social interactions and microbial phenotypes.

ORCID: https://orcid.org/0000-0001-5547-1086

Key Recent Paper: https://pubmed.ncbi.nlm.nih.gov/39567691/

The Crawford laboratory examines Metabolism at the Human-Microbe Interface. High-throughput genome sequencing of bacteria revealed unusual “orphan” biosynthetic gene clusters suspected of synthesizing novel, structurally diverse, biologically active small molecules. These molecules regulate complex interactions with animal hosts and can serve as human drugs and molecular probes to identify new drug targets. Using diverse approaches, the lab exploits interactions between bacteria and animals to discover new molecules with signaling, antimicrobial, immunomodulatory, and anticancer activities.

Our laboratory is interested in understanding the low-dimensional ecology of host-associated microbiomes and harnessing AI and traditional ecological modeling tools to understand how microbiomes relate to host physiology, specifically, how rumen microbiomes contribute to enteric methane production by ruminants.

The Ezenwa Lab focuses on the ecology and evolution of infectious diseases in wild animal populations, studying how within-host interactions between hosts and pathogens translate to larger-scale epidemiological patterns. Dr. Ezenwa has received a National Science Foundation CAREER Award, Zoetis Award for Veterinary Research Excellence, and Fulbright Scholar Award and is a fellow of the American Association for the Advancement of Science.

We study how the microbiota of ticks and mosquitoes influences the transmission of arthropod-borne diseases.

The Flavell lab studies the relationship between the microbiota and the immune system, particularly in the context of human diseases such as IBD, metabolic syndrome and cancer and their mouse models.

Mechanisms of enteric pathogen restriction by the gut microbiota.

Microbiome research in experimental cirrhosis to identify measures to decrease bacterial translocation, a mechanism that leads to systemic inflammation and decompensation in patients with cirrhosis.

Cooperation and competition in the human gut microbiome; role of the gut microbiota in drug metabolism and function.

Our laboratory investigates gene control in Bacteroides thetaiotaomicron, a dominant member of the mammalian gut microbiota.

Our lab is investigating the interplay between human diet, microbiome, genetics, and immune reponses in inflammatory disease.

My lab applies chemical biology to the discovery of enzymes and other proteins whose biochemical activity shapes host-microbe dynamics in the context of gastrointestinal infections and the gut microbiota.

My lab is interested in looking at the effect of the microbiome on responses to biologics and in understanding how the microbiome regulates immune tolerance.

Our research focuses on the structure elucidation and mode of action of small molecules encoded in the human microbiome. We are particularly interested in secondary microbiota metabolites that have been implicated in human cancers.

Applying synthetic biology technologies to engineer clinical and ecological microbiomes.

The Iwasaki laboratory studies the role of microbiome and virome on immunity and inflammatory diseases. Our research showed that signals from the microbiome help optimize the immune response in the respiratory tract against influenza virus infection.

Understanding the role of microbial metabolites in human disease.

Acquisition and maturation of the gut and airway microbiomes in infants with Cystic Fibrosis.

The Konnikova lab is interested in how the microbiome and the associated metabolome regulate immune development and homeostasis at barrier sites.

We are developing a high-throughput cryo-electron tomography (cryo-ET) pipeline for high-resolution structure determination of molecular machines in cells, in order to gain molecular insights into fundamental biochemical processes.