Science

Colorectal cancer

There are 1.4 million people in the US with a history of colorectal cancer (CRC). Although the mortality rate has declined in recent decades, incidence rates are expected to rise due to the aging population and increasing occurrence of CRC in younger individuals. Cancerous or precancerous cells in the colon form lesions which are typically detected via colonoscopy, but the technique is invasive, expensive, and only 39% of patients return for subsequent screening. There is a need for improved non-invasive screening methods. We are using an innovative source to detect CRC: the human microbiome. Human microbiome can directly contribute to the development of CRC. We try to identify microbial biomarkers associated with CRC and to develop computational models that improve the non-invasive detection of CRC.

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Clostridium difficile Infection

Clostridium difficile infection (CDI) following therapeutic antibiotic treatment represents a considerable threat to human health, each year causing as many as half a million infections, 29,000 deaths, and a healthcare burden of $4.8 million. CDI can cause severe abdominal pain and diarrhea, and can develop the life-threatening conditions, which it accomplishes through secretion of protein toxins. Infections in healthy individuals are uncommon, as the combination of the innate immune system and gut microbiome prevent colonization under ordinary circumstances. However, disruption of the native gut bacterial communities during antibiotic therapy, often for unrelated illness, provides opportunity for C. difficile to establish infection. Subsequent treatment of CDI with antibiotics is typically effective, but recurrence of disease is common and may be increasing in prevalence. This, in combination with increased prevalence of infection, the emergence of more virulent forms of the pathogen, and the ever-present threat of antibiotic resistance highlight the need to better understand the mechanisms by which the gut immune system and the resident microbiota prevent initial colonization and subsequent recurrence by C. difficile. We use a combination of 16S rRNA gene sequencing, metagenomics, metatranscriptomics, and metabolomics in a mouse model for CDI and in infected patients to identify microbial functions that are important for colonization resistance and clearance of C. difficile.

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Bioinformatic tool development

The ability to generate data that describes the microbial world continues to grow rapidly. This requires that we develop and assess computational tools that allow us to synthesize these data to tell robust and compelling stories that solve important problems. We have been at the fore front of efforts to develop tools that are widely used by microbial ecologists for the past 15 years. Our tools have facilitated the analysis of 16S rRNA gene, metagenomic, and metatranscriptomic sequence data, metabolomics data, and clinical data.

Take a look at our software for links to documentation and other information, and check out our papers below:

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General microbiome research

We take an expansive approach to defining microbiomes. If it’s a community of microorganisms - bacteria, archaea, microeukaryotes, viruses - and it interacts with a biotic or abiotic environment, then it’s a microbiome. Although most of our ongoing work focuses on microbiomes associated with human or murine hosts, we have also studied microbiomes in hydrothermal vents, insects, sand dunes, soil, and more! We have also developed laboratory approaches to improve our ability to study these microbiomes.

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Scientific culture

How we do science and who does it is as important as what we are sciencing. Our research group has been very interested in reproducibility, publishing, and open access. We try to lead by example without drawing much attention to how we are doing it. Sometimes, it’s important to be more vocal about what we think is important.

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