The healthy human body harbors trillions of microorganisms, including bacteria, archaea, fungi, and viruses. These microbes play important roles starting with the birth of human babies, and on throughout life, affecting the digestive system, immune system, nervous system and others.

Our long-term goal is to investigate the interactions between humans and their microbes, and the effects of these interactions on human health. Our research will involve the development and implementation of various biomedical technologies, multi-omics approaches, bioinformatics methodologies, model animals and clinical samples. The long-term outcomes will deliver basic knowledge in microbiome research and provide potential directions for microbiome-based therapies and interventions.

In the short term, we focus on the virome, the viral component of the gut microbiome, in the health and disease.

1) We will center on the establishment of human virome in the neonates. My research interests focus on the interactions between humans and their microbes that have the positive effects on human health. The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized. Our previous research found that the colonization of the viral community in infant gut is stepwise. The first wave of viruses is mainly comprised of temperate bacteriophages induced from pioneer bacteria, and the second phase involves viruses that replicate in human cells, which can be modulated by breastfeeding.

2) We are interested in the mechanisms of virome perturbations in diseases. Our previous studies documented the dynamics of virome in different diseases, such as IBD and COVID-19. These studies provided potential directions for microbiome-based diagnosis, therapies and interventions.

3) We are eager to explore the virome “Dark Matter”. Our previous research identified thousands of viral genomes from the virome data that cannot be annotated.