Meet the Researchers

Microbiome Research Interest

Researchers in Dr. Baiz's lab are focused on understanding the evolutionary processes of speciation and adaptation. In particular, they are interested in understanding how symbiotic interactions shape these processes in natural host populations. Researchers use free-living birds as study systems to investigate the relationship between host evolution and microbiome differentiation, the impact of interspecific hybridization on host-associated microbiomes, and genetic and environmental determinants of microbiome assembly.

Prior to joining UB, Dr. Baiz completed a postdoctoral fellowship at the Pennsylvania State University. She earned a PhD in ecology and evolutionary biology from the University of Michigan.

Dr. Armbruster is a researcher focused on determining the ability of common colonizers to modulate risk of symptomatic infection and adverse outcomes in patients, and to utilize an experimental model of infection to uncover host and microbial mechanisms that contribute to disease severity and have the potential to be targeted for treatment or prevention. She started an independent lab in Buffalo in 2017, which focuses on combining basic science techniques with patient-oriented research to investigate the consequences of polymicrobial urine colonization, particularly in catheterized nursing home residents. Armrbuster earned her PhD from Wake Forest University in 2011, where she studied the contribution of AI-2 quorum sensing to polymicrobial biofilm formation, antibiotic resistance, and persistence of chronic otitis media. She then pursued postdoctoral research at the University of Michigan, where she received an NIH F32 and a K99/R00 for her research on Proteus mirabilis and polymicrobial catheter-associated urinary tract infection. 

Microbiome Research Interest

Diagnosis and effective treatment of catheter-associated urinary tract infection (CAUTI) is hindered by numerous challenges, especially in patient populations with long-term indwelling catheters. In a recent prospective longitudinal study, we made two critical observations: 1) patients with long-term catheters exhibit persistent asymptomatic colonization by numerous pathogenic bacteria, and 2) the bacteria identified as the causative agents of symptomatic CAUTIs were generally present asymptomatically for several weeks prior to diagnosis. Thus, in direct challenge to the traditional approach for UTI diagnosis and treatment, new acquisition of pathogenic bacteria was not the cause of infection symptoms. By applying precision metagenomic sequencing to the saved urine specimens from our longitudinal study, we aim to:

1. Characterize the full composition of microbes (bacteria, fungi, parasites, viruses) in urine of individuals with long-term indwelling urinary catheters.
2. Examine the stability of the microbial community over time, and
3. Assess the contribution of specific constituents, dysbiosis, and functional capacity to the development of CAUTI signs and symptoms. 

We expect shotgun metagenomics will reveal new potential CAUTI pathogens and/or genomic elements that are undetected by standard culture methods or amplicon-based methods but correlate with sign and symptom onset.

Michael Buck's research is focused on uncovering how epigenetics and the microbiome regulate cellular events. 

The Buck Lab develops new genomic and bioinformatics methods to uncover biological principles that can be applied to improve health and reduce illness. In the microbiome, the Buck Lab has ongoing projects examining:

• Gut microbiome and metabolic health after fiber dietary intervention,
• The role of the oral microbiome in periodontal and systemic disorders,
• The development of methods to examine bacterial strains from low-biomass or high host-contaminated samples, and
• The use of AI to diagnose diseases from microbiome samples.

Dr. Huang is an assistant professor in the Department of Microbiology and Immunology. She completed her PhD at Harvard University in chemical biology, where she characterized a novel enzyme involved in anaerobic 4-hydroxyproline metabolism. During her postdoc at Lawrence Berkeley National Laboratory, she developed a new high-throughput functional genomics platform to study gut anaerobes. This approach leverages DNA barcoding to assay genes across hundreds of conditions in a cost-effective manner. Libraries are expressed in a common gut bacterium, B. theta, a physiologically relevant host instead of the distantly related model bacterium, E. coli. Throughout her scientific journey, Huang has been fascinated by microbial diversity and their ability to colonize all habitats. The gut is a nutrient-rich environment that supports a complex, densely populated microbial ecosystem. She is excited to build her research group at UB and continue to tackle key challenges in the microbiome field.

Microbiome Research Interest

The Huang Lab is using multi-disciplinary approaches, from high-throughput genetic screens to mechanistic biochemistry, to dissect molecular pathways important for bacterial colonization in the gut. Research projects currently focus on Bacteroidales, a group of anaerobes known to colonize at high abundances in the gut by metabolizing a diverse array of glycans. Bacterial viruses (phages) play critical roles in modulating the gut microbiota through bacterial predation and gene transfer. However, almost all gut phages isolated are novel and are phylogenetically distant from model phages. The researchers are also interested in studying the genetic underpinnings of bacteria-phage interactions.

Dr. Hunter is a microbial ecologist and uses a combination of microscopy, analytical biochemistry, and integrative multi-omic approaches to study the dynamics of microbial communities in chronic airway disease. The overarching goal of his lab is to define the in vivo growth environment of airway microbiota and how environmental-microbe interactions relate to disease states. The lab has a particular research interest in bioavailable carbon sources and the metabolic strategies pathogens use to obtain them. Dr. Hunter received his PhD from the University of Guelph, Canada, and pursued his postdoctoral studies at MIT and California Institute of Technology.

Microbiome Research Interest

Microbial communities in chronic airway disease, bioavailable carbon sources

Dr. Sun is a professor of bioinformatics in the Department of Microbiology and Immunology and New York State Center of Excellence in Bioinformatics and Life Sciences. He is also the associate director of AI and health science for UB’s Institute for Artificial Intelligence and Data Science. He joined UB in 2012. He has published 107 journal and 29 conference papers, many of which describe novel computational algorithms for biological and clinical applications. His research is supported by National Science Foundation, National Institutes of Health, New York State Department of Health, Bankhead-Coley Cancer Research Foundation and Susan Komen Breast Cancer Foundation. He has secured about $29 million in research funding as PI and Co-I (about $10 million as PI).

Sun earned his PhD and master’s in electrical engineering from the University of Florida, Gainesville. He holds two bachelor’s degrees, in electrical and mechanical engineering, from Shanghai Jiao Tong University, Shanghai, China.

Microbiome Research Interest

Artificial intelligence, machine learning, bioinformatics, computational genomics, and their applications to cancer genomics and metagenomics. Learn more about Dr. Sun’s lab.

Dr. Kauffman is an assistant professor in the UB School of Dental Medicine Department of Oral Biology, which she joined in 2020. Kauffman and researchers in her lab are investigating phage-bacteria interactions in the human oral microbiome, seeking to understand the underlying ecology and evolution and their impact on human health. Kauffman earned her PhD in biological oceanography through the MIT-WHOI Joint Program working in the group of Martin Polz, with whom she stayed on for her postdoctoral work. While at MIT, Kauffman established the Nahant Collection Time Series, a longitudinal study designed to enable discovery of the underpinnings of coastal microbial community dynamics, from viruses to zooplankton and phytoplankton.

Microbiome Research Interest

Kauffman’s central focus is the fundamental question of how interactions between bacteria and their viral (phage) partners and predators are shaped and how these interactions impact communities.

Dr. Kirkwood is the senior associate dean for research at the University at Buffalo School of Dental Medicine. He is also a member of the Tumor Immunology and Immunotherapy Research Program at the Roswell Park Comprehensive Cancer Center in Buffalo. Kirkwood has been the principal investigator of several grants from the National Institutes of Health/National Institute of Dental Research (NIH/NIDCR) focused on understanding immune signaling involved inflammatory periodontal bone loss and oral cancer progression.

Prior to UB, Kirkwood was a professor and founding chair of the Department Oral Health Sciences at the College of Dental Medicine at the Medical University of South Carolina, where he was also the senior associate dean for research and director for the MUSC Center for Oral Health Research. He was a tenured associate professor at the University of Michigan. Kirkwood completed a certificate in periodontology and PhD in oral biology at the University at Buffalo. He has received numerous awards and honors throughout his career, including the Tarrson Fellowship Career Development Award from the American Academy of Periodontology Foundation, the Distinguished Scientist Award from the International Associate for Dental Research, the Sunstar Fellowship Research Award from the American Academy of Periodontology Foundation, and is a two-time recipient of the IADR/GSK Innovation in Oral Care Award.

Microbiome Research Interest

Dr. Kirkwood’s lab has current interests related to mechanisms whereby the gut and oral microbiome govern myeloid cell expansion in the context of periodontal disease and oral cancer. His laboratory uses a combination of pre-clinical models along with information from human data sets to validate these pre-clinical data.

Dr. Ruhl is a professor and chair of oral biology in UB School of Dental Medicine. His research seeks to unravel the roles that saliva and microorganisms play in health, including in adhesion to teeth and surfaces of the mouth, defense against pathogens, and colonization of the oral cavity.

A fellow of the American Association for the Advancement of Science, Ruhl is an internationally renowned expert on saliva, oral bacteria and the oral microbiome. He joined UB in 2007 from the University of Regensburg, where he was a professor of operative dentistry and periodontology. He has served in various capacities in the dental school, including associate chair and acting chair of the Department of Oral Biology from 2019-21 and interim dean from 2022-23.

Ruhl is a past president of the Salivary Research Group within the International Association for Dental Research (IADR); in 2015 he was named IADR Salivary Researcher of the Year, and in 2020 he received the IADR Distinguished Scientist Award in Salivary Research, the University at Buffalo Exceptional Scholar Award for Sustained Achievement, and was elected as Fellow of the American Association for the Advancement of Science (AAAS). His scientific projects have been funded through the NIDCR since 2010. He is a member of several major professional and scientific societies, Editor in Chief of Clinical Oral Investigations, and Associate Editor of JADA Foundational Science.

Microbiome Research Interest

Ruhl’s laboratory investigates the molecular mechanisms of initial bacterial attachment to teeth, tissue or biomaterial surfaces in the mouth. Researchers try to unravel the molecular mechanisms of how glycoproteins in saliva or on host cells are recognized by glycan-binding microbial adhesins, with a long-term goal of better understanding the modulating role of saliva in supporting colonization of the human oral cavity by a benign commensal microbiota and in host defense against pathogenic microorganisms. More recently, researchers have investigated the evolutionary mechanisms that have shaped host-microbial interactions in the human mouth.

Dr. Sharma joined UB in 1994 as an assistant professor in the School of Dental Medicine's Department of Oral Biology and became professor in 2011. His research focus is on periodontal pathogens and oral bacteria. He was awarded the UB Exceptional Scholar/Teaching Innovation Award in 2021 and received the Advancement for Dental Research Award in 2012. He is a member of the American Association for the Advancement of Science (AAAS) , the American Association for Dental Research and American Society for Microbiology and AAAS. He earned his PhD, master's in biochemistry/endocrinology, and bachelor's in zoology from the University of Delhi, India. 

Microbiome Research Interest

The human oral cavity, comprising gums, cheeks, tongue, palate and teeth, is a highly diverse ecosystem harboring more than 700 bacterial species, including both cultivable and non-cultivable bacteria. An imbalance or dysbiosis of the microbiota in the subgingival niche (the space between the gum and tooth) is responsible for initiating chronic inflammation of the gums and tooth-supporting tissues. This can lead to the development of a common chronic disease in adults known as periodontitis, which if untreated, can cause tooth loss and contribute to the exacerbation of many systemic diseases, including diabetes and atherosclerosis. Colonization by a group of gram-negative anaerobes in the subgingival crevices, specifically Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola (collectively known as the "red complex") is believed to promote microbial dysbiosis, leading to periodontal inflammation and the development of periodontitis.

Our overall objectives are to gain a better understanding of the molecular mechanisms of how periodontal pathogens colonize the oral cavity, promote dental plaque formation and initiate chronic inflammation detrimental to tooth-supporting tissues. To understand the basis of inflammation, we focus on the role and interactions of innate immune system pathogen recognition receptors (PRRs), specifically Toll-like receptors (TLRs) and intracellular NOD-like receptors (NLRs), with their cognate ligands (lipopolysaccharide, lipoproteins and bacterial peptidoglycan/cell wall fragments) produced by periodontal pathogens. Additionally, we investigate the physical and metabolic basis of interbacterial interactions taking place between oral bacteria and how these interactions, in a mutualistic or antagonistic manner, impact the dental plaque microbiota to promote microbial dysbiosis.

Dr. Visser is an associate professor in oral biology at the University at Buffalo School of Dental Medicine. She joined UB in 2013; prior to UB, she was a research technician at the University of Calgary, where she focused on the pathogensis of bacteria associated with cystic fibrosis. 

Visser earned her PhD from the University of Queensland, Australia, and holds a BSc from the University of Calgary, Canada. She completed her post-doc training at the University of Toronto under Dr. Richard Ellen, focusing on spirochete-neutrophil interactions, and Dr. Michael Glogauer, where she focused on neutrophil biology. 

Microbiome Research Interest 

Visser's research interests focus on bacterial pathogenesis and host-pathogen interactions within the oral cavity and in the oral-systemic health axis. One of her major interests is to understand how novel bacteria including spirochete species can manipulate both neutrophil response and tissue resident cell signaling and functions. 

Dr. Wactawski-Wende is an epidemiologist who has been conducting research on women’s health for the past three decades. Her work includes identifying and understanding risk factors for chronic disease in postmenopausal women, conduct of prevention clinical trials and studies of reproductive aged women. She has been a study investigator, and later PI, of the Buffalo center for the NIH funded Women’s Health Initiative (WHI) study since it was funded as a Vanguard center in 1993 (Current: Wactawski-Wende PI, NHLBI 75N92021D00002; 2020-2027). She currently leads the Northeast regional center and serves as a member of the Steering Committee of WHI. Originally a study of 162,000 US.. women, it continues to follow nearly 55,000 women still living and active in the study over 30 years later. These data, and data from the many ancillary studies that have been funded in Buffalo and elsewhere. WHI does have questions on periodontal disease at two time points. It has served as a valuable training resource for many graduate students, post docs and young faculty. Wactawski-Wende's personal research focus in WHI has been in cancer, osteoporosis, periodontal disease and the oral microbiome.

Microbiome Research Interest

The Buffalo WHI Observational Study has been the source of participants for her work in periodontal disease and osteoporosis that has been ongoing for the past 27 years. The “OsteoPerio” study enrolled women participating in the WHI Observational Study (OS) at the University at Buffalo clinic. The team has been funded to conduct ancillary studies in periodontal disease, including work in the oral microbiome. Originally funded to determine the relationship between periodontal disease, osteoporosis and oral bone loss (Wactawski-Wende (PI), DoD #OS950077, 1997-2001) and later funding from NIDCR to explore the longitudinal (5-year) relationship between osteoporosis and oral bone loss with periodontal disease (Wactawski-Wende (PI), NIDCR R01 DE13505, 2002-2007), OsteoPerio has expanded over time. Several mechanistic grants have been funded since OsteoPerio began in 1997 that have expanded and extended our understanding of periodontal disease, including knowledge of biomarkers in participant samples. These include a study of the relationship between periodontal disease and metabolic syndrome (measured glucose, insulin and lipids in baseline samples) (LaMonte (PI), NIDCR R03 DE022654-2, 2012-2015), a study of the relationship between plasma Vitamin D levels and periodontal disease in these same women – measured at baseline and year-5 (Millen (PI), R21 DE020918-02, 2010-2013) and NIH ARRA funding to explore Serum and Salivary Biomarkers in Periodontal Disease using baseline samples where cytokines and other biomarkers were measured in stored serum and saliva samples in these women (Wactawski-Wende (PI), NIDCR RC1 DE020404-02, 2009-2012). Researchers have also obtained university funding to measure sex steroid hormones in these same women. Currently, in addition to our most recent R01 exploring the oral microbiome and periodontal disease (Wactawski-Wende PI, R01 DE024523, 08/2014-08/2020) in 1300 women at 3 time points 17 years apart. We have also had a grant to explore novel AI approaches and algorithms for use of microbiome data (Sun PI, NIAID, R01 AI125982, 2016-2019). The OsteoPerio study includes 1,300 women at baseline, 1,000 women five-years post baseline, and 500 women 17-years post baseline. These women have also have stored blood and saliva. At the 17-year visit, in addition to plaque samples, we collected samples of skin, nares, vagina and feces in the participants. All the women are also participants of WHI, so they have follow-up of all chronic disease and health updates annually.

Design paper:

Banack H, Genco RJ, LaMonte MJ, Millen AE, Buck MJ, Sun Y, Andrews CA, Hovey KM, Tsompana M, McSkimming DI, Zhao J, Wactawski-Wende J for the OsteoPerio Study Group. Cohort Profile: The Buffalo OsteoPerio Microbiome Prospective Cohort Study. BMJ Open. 2018 Dec 4;8(12):e024263. doi: 10.1136/bmjopen-2018-024263. PMID: 30518590

A complete list of published work of over 450 publications can be found in MyBibliography.