Caltech Joins National Human Virome Program

Caltech has joined a major program through the National Institutes of Health (NIH) to help characterize the trillions of viruses that live harmlessly within our bodies. Dubbed the Human Virome Program (HVP) the effort is aimed at better understanding the role these microorganisms play in human health.

From 2007 until 2016, the NIH funded the Human Microbiome Project to characterize the full collection of microorganisms (bacteria, viruses, and fungi) that live within the human body, including their genes. Ultimately, that initial program focused mainly on bacteria, revealing volumes about the influence bacteria have on human health, development, and disease.

In contrast, viruses have remained somewhat elusive. Although viruses are among the most abundant microorganisms on the planet, most of the viruses that have been studied in detail belong to the subset that cause disease, such as the influenza and coronaviruses. Yet, it is well known that many other viruses, such as the common anellovirus, are present in the vast majority of humans without causing disease.

In 2023, the NIH Common Fund announced it would invest $171 million over five years for the first phase of the HVP. As part of the effort, they put out a call for novel and innovative tools to improve studies of the human virome. Now, the first round of awards has been announced, and an initial consortium of grantees is being encouraged to work together and share resources and data.

Rustem Ismagilov, Caltech's Ethel Wilson Bowles and Robert Bowles Professor of Chemistry and Chemical Engineering, Merkin Institute Professor, and director of the Jacobs Institute for Molecular Engineering for Medicine, has received a four-year grant to develop two innovative tools that hold the promise of greatly improving scientists' ability to detect, sequence, and identify viruses. His lab has a long history of developing precise quantitative measurements of biological entities down to the single-molecule level, including in complex sample types such as human biopsy samples.

The first of these tools is called Viral MEM (Microbial-Enrichment Method), which builds on technology the Ismagilov lab previously developed and validated for studies of bacteria in tissue-rich samples such as biopsies. MEM represented a significant breakthrough for microbiome studies; most human microbiome studies have had to use stool samples because it has not been possible to deeply sequence microbes in samples that are dominated by host material. However, stool is known to be a poor proxy for resident gut microbiome communities, motivating the lab's development of technologies that would enable the direct study of microbes in important sample types, including biopsies, mucosal scrapings, saliva, and sputum.

The team is now applying the MEM technology to virus samples to remove nucleic acids related to the human host while preserving and separating genetic information related to viruses, thereby increasing the relative amount of viral DNA in a sample.

"We became interested in the human virome when studying human intestinal biopsies to characterize how the microbiome contributes to human health and disease, such as in celiac disease, inflammatory bowel disease, irritable bowel syndrome, and Parkinson's disease. During our analysis, we noticed a surprising number of sequencing reads identified as phage," says Natalie Wu-Woods, a bioengineering graduate student in Ismagilov's group. Phages, short for bacteriophages, are viruses that infect bacteria. "We weren't expecting to be able to pick up viruses in our original microbial enrichment method, but that was our first insight that maybe our method could work to improve the study of viruses."

The second tool, known as Viral StochQuant, is a novel approach to count and analyze small numbers of viruses via sequencing. "When you start trying to analyze really rare things, like viruses in host-rich samples, sequencing can be quite hard," says Matt Cooper, a graduate student in biochemistry and molecular biophysics from Ismagilov's group. He explains that there have traditionally been two strategies for dealing with this problem: developing better tools in the wet lab and developing computational tools that leverage math and statistics to make reliable conclusions based on the sequencing data. "Our approach sits at the intersection of the two," Cooper says. "You really need to combine the two approaches to get better, reliable, and more informative quantitative data."

The group's goal is to pair Viral MEM and Viral StochQuant to enhance the accuracy, cost- effectiveness, and scalability of virome analyses in human tissues, thus enabling a more comprehensive integration of viral data with the broader human microbiome research. "We think pairing StochQuant with this work is what's really going to squeeze as much information out of it as possible and allow other people to reproduce these results, providing much more reliable data across the whole consortium," Cooper says. The lab has developed collaborations with clinicians across the US to demonstrate the technologies in various clinical sample types, including gut biopsies, vaginal swabs, and saliva.

The Ismagilov lab will recruit several new graduate students to work on the NIH Human Virome Program starting in 2025. The work is supported by NIH Common Fund grant 1U01DE034199-01.