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Microbiome


The Microbiome Program provides high-quality services as well as training in innovative microbiological techniques.  The following specific services are provided:

1) High-quality and quality-controlled microbial diversity analysis, including nucleic acid isolation from biospecimens, 16S rRNA PCR and high-throughput sequencing, and metagenomic /metatranscriptome library generation and sequencing on a fee-for-service basis.

2) Consultation and training in data analysis and bioinformatics programs associated with microbial diversity studies.

3) Access and technical assistance for state of the art metabolomics and proteomics services.

4) Consultation and subsequent training in cutting-edge technologies for measuring microbes and microbial products as well as inflammatory mediators in tissue samples and in blood.

5) Assistance with procurement or isolation and expansion of enteric commensal bacterial species.

6) Consultation and training for established or developmental assays of microbe-immune cell interactions using tissue or blood samples.

7) Biorepository services including specimen processing, storage, and transport.

 

  Microbiome Collaborations

  • Microbial diversity analysis
  • Pre and post study design bioinformatics consultation and analysis
  • Procurement and expansion of enteric commensal bacteria  



 

Directors:

Catherine Lozupone, PhD Dr. Catherine Lozupone's main focus is to understand factors that shape human microbiome composition in health and disease and to elucidate the functional consequences of compositional differences, both in terms of the biological/metabolic properties of individual bacteria and host interactions. She has substantial experience in the development and application of computational tools for the analysis of metagenomic and bacterial genome sequences for culture-independent analysis of microbial populations. She is the primary developer of the UniFrac algorithm for comparing microbial diversity among many samples using phylogenetic information, and am a contributor to the QIIME software package. Her work has included extensive meta-analyses of 16S rRNA and genomic sequences in the public domain, analysis of new datasets that she hads had access to through an extensive network of collaborators or generated in her lab. Her substantial publication record in human microbiome research includes studies of the relationships between lung and gut microbiome composition and HIV infection and gut microbiome and age, culture, diet, obesity, and inflammatory bowel diseases. Working across such a breadth of datasets has given her a unique perspective towards understanding parallels between compositional changes that occur in different developmental, physiological and disease states. Her lab currently couples 16S rRNA based analyses of microbial distribution with comparative genomics, metabolic networks, metabolomics and functional experiments with cultured isolates to predict and test which biological/metabolic functions are shared by bacteria that change in relative abundance in disease states, with a particular focus on HIV infection. In particular, her lab had been pairing genomic predictions with immunologic assays with cultured isolates to predict and test immune-modulatory activities of human gut bacteria. 

daniel_frank.jpgDan Frank, PhD

Dr. Dan Frank's primary long-term goal for his research program is to understand how the communities of microorganisms colonizing humans (the human “microbiome”) either nurture health or promote disease.  His work uses a variety of culture-based and DNA/RNA-sequence based, culture-independent microbiological methodologies to study the mechanisms by which the human host and its associated microbial communities adapt and respond to one another.  Because disruptions in the normal composition of the microbiome (“dysbiosis”) are associated with myriad diseases, a central focus of this work is directed towards understanding how dysbiosis arises and its consequences to pathophysiology.  The growing excitement directed towards studying the human microbiome has presented his group significant opportunities to develop and implement cutting-edge, multi-disciplinary research projects across a variety of clinical and basic sciences domains.  He works closely with a number of clinicians and translational scientists who are essential to the process of establishing and studying well-defined cohorts of human subjects.  This work has benefited greatly from a team science approach, which allows him to leverage the expertise of his collaborators; in turn, his program adds value to these studies by applying innovative, state-of-the-art technologies and analytic tools to the collected human specimens.
Current research projects examine the human microbiome in the context of 1) the upper airways microbiome and its influence on carriage and infection by pathogens such as Staphylococcus aureus and Streptococcus pneumoniae; 2) chronic inflammatory conditions of the intestines and upper airways (e.g., inflammatory bowel disease, chronic rhinosinusitis); 3) early development of the human microbiome and immune system, with a focus on nutrition and maternal programming of metabolic disease; and 4) diet-microbiome-host crosstalk in the development of metabolic disease through experimental murine models.
He is committed to not only to building his  lab’s research capacity, but to nurturing the study of the microbiome among colleagues in the University of Colorado system.  He maintains an open-doors policy that has allowed a constant stream of students, residents, post-doctoral fellows, and faculty members to learn about microbiome research through participation either in ongoing research or in their own research projects.  In return, he and his lab personnel gain valuable insight into the clinical/translational relevance of their research projects.  This dialog has been essential to the development of his lab and has stimulated much interdisciplinary research.