Shareef M Dabdoub

University of Iowa | UI · College of Dentistry

Dysbiotic oral bacterial communities have a critical role in the etiology and progression of periodontal diseases. The goal of this study was to investigate the extent to which smoking increases risk for disease by influencing the composition of the subgingival microbiome in states of clinical health. Subgingival plaque samples were collected from...

Periodontally involved teeth have been implicated as 'microbial reservoirs' in the etiology of peri-implant diseases. Therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the degree of congruence between adjacent peri-implant and periodontal microbiomes in states of health and disease. Subgingival and peri-...

Accurate diagnosis and treatment of biofilm infections require iden- tification of the pathogenic organism(s) as well as determining the progress of the disease. Current tools in clinical use, including cul- turing and PCR tests, are extremely useful for identifying organ- isms, but are destructive in nature – resulting in the loss of im- portant i...

Flow Cytometry is a process by which cells, and other microscopic particles, can be identified, counted, and sorted mechanically through the use of hydrodynamic pressure and laser-activated fluorescence labeling. As immunostained cells pass individually through the flow chamber of the instrument, laser pulses cause fluorescence emissions that are r...

Background: While the microbiome is increasingly seen as a targetable contributor to atopic dermatitis (AD), questions remain as to whether the dysbiosis is secondary to diseased skin or if it predates symptom onset. Previous work has evaluated how the skin microbiome changes with age and established the influence of factors like delivery mode and...

Three years into the coronavirus disease 2019 (COVID‐19) pandemic, there are still growing concerns with the emergence of different variants, unknown long‐ and short‐term effects of the virus, and potential biological mechanisms underlying etiopathogenesis and increased risk for morbidity and mortality. The role of the microbiome in human physiolo...

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are...

Dentist participation in Iowa's Medicaid Dental program

The intersection between the human oral microbiome and oral health is an emerging area of study which has gained momentum over the last decade. This momentum has motivated a search for associations between the oral microbiome and oral cancer, in hopes of identifying possible biomarkers that facilitate earlier diagnosis and improved prognosis for pa...

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived genomes lack key information compared to isolated viruses, in particular host association. Different computational approaches are av...

One-third of postmenopausal women experience at least one osteoporotic bone fracture in their lifetime that occurs spontaneously or from low-impact events. However, osteoporosis-associated jaw bone fractures are extremely rare. It was also observed that jaw bone marrow stem cells (BMSCs) have a higher capacity to form mineralized tissues than limb...

Background: Dental implants replace missing teeth in at least 100 million people, yet over one million implants fail every year due to peri-implantitis, a bacterially induced inflammatory disease. Our ability to treat peri-implantitis is hampered by a paucity of information on host-microbiome interactions that underlie the disease. Here, we presen...

Polyamines are ubiquitous polycationic molecules that are present in all prokaryotic and eukaryotic cells, and they serve as important modulators of cell growth, stress and cell proliferation. Polyamines are present at high concentrations in the periodontal pocket and could potentially affect the stress response of periodontal bacteria to antibioti...

On March 16, 2020, 198,000 dentists in the United States closed their doors to patients, fueled by concerns that aerosols generated during dental procedures are potential vehicles for transmission of respiratory pathogens through saliva. Our knowledge of these aerosol constituents is sparse and gleaned from case reports and poorly controlled studie...

Background Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associations from those common to all three forms of periodontitis has hampered biomarker discovery. Therefore, we aimed to map the genom...

Introduction: The pediatric perineal microbiomes inhabit a dynamic environment with changes related to diet, toileting habits, and hormonal development. We hypothesized that next-generation sequencing would reveal different perineal bacterial signatures associated with developmental milestones in premenstrual females. Furthermore, we predicted that...

Our view of the periodontal microbial community has been shaped by a century or more of cultivation‐based and microscopic investigations. While these studies firmly established the infection‐mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka describ...

Background: The search for microbial biomarkers of periodontitis has been hampered by our ability to separate disease-specific associations from those that are common to all forms of periodontitis. Here, we present the first functional characterization of the microbiomes of three common clinical phenotypes of this disease: Localized aggressive peri...

Six percent of Americans, including 3 million high schoolers, use e-cigarettes, which contain potentially toxic substances, volatile organic compounds, and metals. We present the first human study on the effects of e-cigarette exposure in the oral cavity. By interrogating both immunoinflammatory responses and microbial functional dynamics, we disco...

Type 2 diabetes mellitus (T2DM) is an established risk factor for periodontitis, yet its contribution to creating host-bacterial disequilibrium in the subgingival crevice is poorly understood. The present investigation aimed to quantify the impact of hyperglycemia on host-bacterial interactions in established periodontitis and to map shifts in thes...

Aim Periodontitis is correlated with type 2 diabetes mellitus (T2DM), but little is known about glycemic status effect on subgingival microbiota associated with periodontitis. This study evaluated if periodontal microbiome of T2DM patients is affected by glycemic status. Materials and methods 21 T2DM non‐smoking patients with chronic periodontitis...

Methods: The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, prima...

Aim The goal of the present investigation was to identify site‐level factors that might allow prognostication of individual implants in partially‐dentate patients with multiple non‐splinted restorations. Methods We analyzed clinical and radiographic characteristics of 222 non‐splinted single implants in function for at least 5 years in 86 partiall...

Tobacco: How smoking promotes harmful biofilms Tobacco smoke inhibits the metabolism of beneficial bacteria in biofilms, while activating specific genes in pathogenic bacteria. This suggests a mechanism to explain how smoking quickly leads to the formation of damaging biofilms in the mouth and respiratory tract. Purnima Kumar and colleagues at Ohio...

Although smoking and diabetes have been established as the only two risk factors for periodontitis, their individual and synergistic impacts on the periodontal microbiome are not well studied. The present investigation analyzed 2.7 million 16S sequences from 175 non-smoking normoglycemic individuals (controls), smokers, diabetics and diabetic smoke...

Background: Although enamel matrix derivative (EMD) has been used to promote periodontal regeneration, little is known of its effect on the microbiome. Therefore, this investigation aimed to identify the changes in periodontal microbiome following treatment with EMD using a deep-sequencing approach. Methods: Thirty-nine patients having mandibula...

The phylogenetic characteristics of microbial communities associated with periodontitis have been well studied, however, little is known about the functional endowments of this ecosystem. The present study examined 73 microbial assemblages from 25 individuals with generalized chronic periodontitis and 25 periodontally healthy individuals using whol...

The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations...

Current visualizations of molecular motion use a Timeline-analogous representation that conveys "first the molecule was shaped like this, then like this...". This scheme is orthogonal to the Pathline-like human understanding of motion "this part of the molecule moved from here to here along this path". We present MoFlow, a system for visualizing mo...

Smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. Therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. Peri-implant biofilm samples were collected from 80 partial...

Objectives: Smoking and diabetes are known risk factors for periodontitis, and their effect on the subgingival biofilm have been independently studied. However the combined effect of these periodontitis risk factors is unknown. The aim of the current study is to analyze and compare the microbial composition of the subgingival biofilm in diabetics,...

Objective: It is known that smoking alters the composition of the oral microbiome, leading to pathogen-rich, commensal-poor communities. However, little is known about the genome signatures of these complex microbial communities. Therefore, the purpose of the present investigation was to use whole-genome shotgun sequencing to compare the functional...

Objectives: Understanding oral microbial ecology is essential for insight into health, as well as identifying disease states, risk factors, and etiology. The 16S ribosomal RNA gene is the most common genetic marker for taxonomic identification due to its near universal presence and static function over time, and a wide variety of tools exist for qu...

Objective: It is known that bacteria are the primary etiological agents of periodontal diseases and that the composition of disease-associated microbiome is significantly different from a health-compatible community. However, little is known about the genome signatures of these complex microbial communities. Therefore, the purpose of the present in...

Objectives: Biofilms play a critical role in maintaining immune homeostasis on all mucosal surfaces; and loss of commensal protection is an important determinant of risk for disease. It has been established that smoking alters microbial communities in several ecological niches; however, the effect of smoking on gene expression in biofilms is not kn...

Objective: Smoking has been established as a substantial risk factor for the development of periodontal disease. With 1.2 billion smokers worldwide, periodontitis in smokers is an enormous health burden. Subgingival biofilms are important for maintaining periodontal health, however disruptions in this community play an integral role in the suscepti...

Objective: Peri-implantitis is a biofilm-induced disease that leads to destruction of implant-supporting structures and may result in loss of the implant. It is known that smokers are at higher risk for implant failure than non-smokers. We have previously demonstrated that even in states of clinical health, smokers have a pathogen-enriched period...

Objectives: It is established that bacterial biofilms play an important role in the etiology of peri-implant diseases. Although early studies indicated that peri-implant microbiota may be similar to subgingival microbiota, evidence is emerging, that the microbial profiles of peri-implant health and peri-implantitis are different from periodontal he...

Objective: Over 50% of patients with periodontitis are current or former smokers. With 1.2 billion smokers worldwide, periodontitis in smokers is an enormous health burden. Successful treatment of periodontitis requires re-establishing healthy oral biofilms, and current treatment protocols assume that the composition of health-associated biofilms i...

Uropathogenic Escherichia coli (UPEC) utilizes a complex community-based developmental pathway for growth within superficial epithelial cells of the bladder during cystitis. Extracellular DNA (eDNA) is a common matrix component of organized bacterial communities. Integration host factor (IHF) is a heterodimeric protein that binds to double-stranded...

Urinary tract infections (UTIs) represent one of the most commonly acquired diseases among the general population as well as hospital in-patients, yet remain difficult to effectively and consistently treat. High rates of recurrence, anatomic abnormalities, and functional disturbances of the urinary tract all contribute to the difficulty in manageme...

FIND User and Developer Documentation. This document provides a complete introduction and tutorial for the FIND end-user as well as a complete description, tutorial, and code examples on developing plugins for the FIND platform. This material is also available online at the project website.

One of the most commonly applied image filtering algorithms is the Gaussian blur. An image is convolved with the radially symmetric Gaussian kernel, and each pixel is replaced by a weighted average of all its surrounding neighbors. While this performs admirably for general smoothing of local intensity variation, it has no awareness of important str...

The current state of biological science is such that many sources of data are simply too large to be analyzed by hand. Furthermore, given the amazing breadth of investigation into the natural world, the potential for serious investigation from just mining heterogenous data sets is too rich to ignore. These two factors combined with the amount of co...