Collaborative Projects

human microbiome project.

UB researchers are working across disciplines to find solutions to multi-faceted challenges and to advance the frontiers of knowledge. Many of these are pilot projects funded through Genome, Environment and Microbiome Community of Excellence (GEM) and the Clinical and Translational Science Award (CTSA).

Oral microbiome and periodontitis: A prospective study in postmenopausal women


NIH grant: $772,373 (one year); $3,799,486 (five years)

This is a longitudinal study over 15-17 years of a cohort of more than 1,000 post-menopausal women in the Women’s health Initiative Study. 

We have measured periodontal disease progression and now will determine shifts in the subgingival flora which are associated with the progression of periodontal disease. This study is one of the first to assess the microbiome in an epidemiologic study which allows us to study many factors interacting with the microbiome including smoking, obesity, diet and medications.

Developing advanced algorithms to address major computational challenges in current microbiome research


NIH grant: $311.449 (one year); $973,277 (three years)

The study of the microbiome, reveals a complex community of a thousand or more bacteria in and on the human body. It also shows changes in the microbiome that are associated with disease. We are assessing the microbiome by sequencing the genes of the bacterium. This will produce massive amounts of data to be analyzed by complex bioinformatics techniques.

We are developing accurate algorithms for analyzing the bacterial composition as well as the dynamic changes associated with the beginning and progression of disease. Our goal is to determine if we can predict microbial changes associated with the progression of a disease over time. We are performing these analyses across large populations at varying stages of a disease in a cross-sectional study.

If successful this analysis will eliminate the economic and time constraints involved with a longitudinal study of disease progression.

Proton-Pump Inhibitor (PPI) related gut microbiota dysbiosis role in diabetic nephropathy: A cross-sectional analysis


Genome, Environment and Microbiome Community of Excellence seed grant: $50,000

There is recent evidence suggesting the gut microbiome plays a role in chronic kidney disease.

There also is evidence of increased chronic kidney disease in people who take proton-pump inhibitors including Nexium and Prevacid—among the most widely sold drugs worldwide—to reduce stomach acid. By reducing stomach acid, they are thought to change the gut microbiome which can lead to inflammation and increase the risk of chronic kidney disease.

This pilot study is looking at patients suffering from diabetic nephropathy and assessing the effects of the proton-pump inhibitors on their gut microbiomes. This project is a precursor to intervention trials of probiotics or other strategies that might be used to prevent adverse changes in the gut microbiome.

Gut microbiome keystone species for probiotic-treatment of obesity and its co-morbidities


Genome, Environment and Microbiome Community of Excellence seed grant: $50,000

Recently studies have shown severely reduced numbers of bacterial species in the gut flora of obese patients. Probiotics have been proposed as a reasonable strategy for restoring the normal diversity of the gut flora as well as reducing obesity and its co-morbidities.

In order to design an effective probiotic combination of bacteria, we are identifying keystone species—those species whose activities and abundances are required for the integrity of a healthy gut microbial community. We will combine these keystone species in a novel probiotic and test its effectiveness in restoring the normal gut microbiome to help reduce obesity.