Rustem Ismagilov

What they work on

1. Optimize T-BEAM in germ-free tissue spiked with defined bacteria, targeting over 1,000-fold removal of host nucleic acids while preserving bacterial transcriptional profiles and RNA yield.
2. Establish detection and quantification limits for T-BEAM in vivo using mice colonized by a single bacterial species and by hCom2, a defined human-derived gut community.
3. Apply T-BEAM to biopsies from patients with subclinical perianal Crohn's disease and matched controls to find joint microbial and host expression patterns that predict radiological progression.
4. Develop and validate MEM, a microbial enrichment and metagenomic sequencing method, using defined communities and milk-derived isolates to recover whole bacterial, archaeal and fungal genomes while excluding reagent contaminants.
5. Apply MEM to repeated paired breast milk and stool samples from full-term and pre-term mother-infant dyads to assess milk microbiome stability and candidate transmission routes.
6. Optimize FRAMES using differential lysis, RNase treatment and chemical fixation on vaginal swabs, verifying host RNA depletion and fungal transcript recovery by digital PCR and RNA sequencing.
7. Use FRAMES across the menstrual cycle and in a recurrent vulvovaginal candidiasis cohort to identify Candida and human gene-expression signatures that separate benign colonization from disease.
8. Create Viral-MEM for particle-independent viral enrichment from host-heavy tissue and Viral StochQuant for absolute, anchored viral quantification, validating both in vaginal swabs, saliva with small-intestine biopsies, and paired lower gastrointestinal biopsies.

More about the research

Why it matters

Trustworthy measurements of what microbes are doing inside human tissue could expose targets for diagnostics and therapies in diseases where tissue-associated microbes are suspected but unproven, including inflammatory bowel disease, colorectal cancer, Parkinson's disease and periodontitis. Women with recurrent yeast infections could gain tests that distinguish colonization from disease, and infants, especially pre-term ones at risk of necrotizing enterocolitis and sepsis, could benefit from clearer evidence on milk-borne microbes and probiotic strain choice.

Known grants

From NIH and NSF research grants. Labs often have other funding we can't see.

Closest labs

The school

California Institute of Technology: 18 labs on PI Pages, $445M a year on research, 200 research doctorates a year.

More about California Institute of Technology

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