Scot E Dowd

Scot E Dowd
Molecular Research LP. MR DNA · next generation sequencing

Ph.D.

About

693
Publications
117,484
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
24,869
Citations
Additional affiliations
October 2011 - present
Molecular Research
Position
  • CEO, CSO
Education
January 1997 - January 2000
The University of Arizona
Field of study
  • Microbiology and Immunology

Publications

Publications (693)
Article
Full-text available
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrate the microbial and chemical microenvironment of a patient's ileal mucosa with their clinical phenotype and genotype to identify factors favoring...
Article
Full-text available
The African wild dog (AWD) (Lycaon pictus) is a critically endangered species. These animals are hypercarnivores, hunting mostly medium-sized antelope. In this study, using bacterial tag-encoded FLX-Titanium amplicon pyrosequencing (bTEFAP®), the microbiota in the fecal material of AWDs living in the Great Plains Zoo & Delbridge Museum of Natural H...
Article
Full-text available
Dermatophagoides farinae is inhabited by an intracellular bacterium, Cardinium. Using correlations between host and symbiont gene expression profiles, we identified several important molecular pathways that potentially regulate/facilitate their interactions. The expression of Cardinium genes collectively explained 95% of the variation in the expres...
Article
Full-text available
Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have...
Article
Full-text available
During laboratory cultivation of the myxobacterium Archangium violaceum strain Cb vi76, a reoccurring contaminant was isolated and sequenced. Comparative taxonomic analysis of the draft genome suggested the contaminant to be a novel species, currently designated Aneurinibacillus sp. strain BA2021, from the genus Aneurinibacillus, members of which a...
Article
Full-text available
Acinetobacter species are gram-negative, non-fermenting bacteria with coccobacilli morphology. The bacteria are found ubiquitously and have the ability to occupy niches which include environmental sites, animals, and humans. The original purpose of this study was to determine if painted turtles (Chrysemys picta) living in the wild in Western Wiscon...
Article
Full-text available
The purpose of this study was to determine if giraffes (Giraffa camelopardalis) living in captivity at the Jacksonville Zoo and Gardens, Jacksonville, FL were colonised with carbapenem-resistant bacteria and, if found, to identify underlying genetic mechanisms contributing to a carbapenem-resistant phenotype. Faecal samples from seven giraffes were...
Article
Full-text available
Apples contain bioactive compounds with the potential to alleviate clinical signs associated with obesity, a phenomenon likely related to the composition and function of the gut microbiota. The aim of this study was to investigate the effect of apple supplementation on the fecal microbiota and gut metabolites of Dawley Sprague rats fed a high-fat (...
Article
Full-text available
Saccharomyces boulardii CNCM I-745 (SB) is a probiotic yeast used to lower the incidence of antibiotic-associated Clostridium difficile (C. difficile) infection, though its mechanism of action remains unclear. Cholic acid is a primary bile acid, which triggers the germination and promotes the growth of C. difficile. The intestinal microbiota transf...
Data
First panel: the treatment received in the four groups of healthy subjects. Second panel: the number of samples available at each time of sampling.
Data
List of the 28 bile acids species measured in feces.
Data
The 2 graphs on the left shows the absence of difference in fecal conjugated bile acids, both in concentration and in %. The upper right figure shows the drop in secondary bile acids % in the antibiotics group, and the lower right figures shows the peak of CA concentration in the antibiotics group.
Preprint
Full-text available
Birds harbor diverse microorganisms in their guts, which collectively fulfill important roles in providing their hosts with nutrition and protection from pathogens. Although numerous studies have investigated the presence of certain pathogenic bacteria in the feces of wild birds, only a few have attempted to investigate the microbiota of the gut. T...
Article
Full-text available
Background The role of microbiota in Crohn’s disease (CD) is increasingly recognized. However, most of the reports are from Western populations. Considering the possible variation from other populations, the aim of this study was to describe the microbiota profile in children with CD in Saudi Arabia, a non-Western developing country population. Re...
Article
Full-text available
Gluten-related disorders (GRDs) are common chronic enteropathies and increasing evidence suggests an involvement of the gut microbiota. We examined the gut microbiota in Mexican people afflicted with GRDs. Ultra-high-throughput 16S marker sequencing was used to deeply describe the duodenal and fecal microbiota of patients with celiac disease (CD, n...
Article
Full-text available
Aim: To investigate the accuracy of fungal dysbiosis in mucosa and stool for predicting the diagnosis of Crohn's disease (CD). Methods: Children were prospectively enrolled in two medical centers: one university hospital and one private gastroenterology clinic in the city of Riyadh, Kingdom of Saudi Arabia. The children with confirmed diagnosis of...
Article
Full-text available
We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid,...
Data
Distribution in coding sequence function as identified by RAST. Subsystems with differences in the number of coding sequences in the two strains are highlighted in bold. (PDF)
Data
Minimum inhibitory concentrations for select antibiotics determined by the Sensititre system or broth microdilution method. Antibiotics displaying different MICs are highlighted in bold. (PDF)
Article
Epidemiological evidence suggests that exposure to infection during early development increases the risk for neurodevelopmental disorders associated with symptoms such as a decreased desire to engage in social interactions. This disruption in social behavior can be modelled in animals by administering bacterial mimetics such as liposaccharide (LPS)...
Article
Raspberries are polyphenol-rich fruits with the potential to reduce the severity of the clinical signs associated with obesity, a phenomenon that may be related to changes in the gut microbiota. The aim of this study was to investigate the effect of raspberry supplementation on the fecal microbiota using an in vivo model of obesity. Obese diabetic...
Article
Full-text available
Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the fecal material of seven giraffes living in captivity at the Jacksonville Zoo and Gardens, Jacksonville, FL was investigated. In all samples, the most predominant bacterial phylum was the Firmicutes followed by Bacteroidetes. The most predominant fungi...
Article
Full-text available
Purpose: Crohn's disease is a chronic debilitating intestinal syndrome of unknown aetiology that is thought to result in part from an imbalance (dysbiosis) of the intestinal microbial populations, known as the microbiota. In this study we sought to compare the microbiota at the mucosal and submucosal levels at the resection margin in Crohn's disea...
Article
Full-text available
Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics) with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial compositi...
Article
Full-text available
Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of Staphylococcus species, mos...
Article
Full-text available
Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination...
Article
Full-text available
Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to dete...
Article
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilize...
Article
Full-text available
As obligate blood-feeding arthropods, ticks transmit pathogens to humans and domestic animals more often than other arthropod vectors. Livestock farming plays a vital role in the rural economy of Pakistan, and tick infestation causes serious problems with it. However, research on tick species diversity and tick-borne pathogens has rarely been condu...
Article
Full-text available
A facultatively anaerobic, Gram-stain-positive bacterium, designated ETRF1T, was found in faecal material of a timber rattlesnake (Crotalus horridus). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Enterococcus. The 16S rRNA gene sequence of strain ETRF1T showed >97 % similarity to that of the type str...
Article
Full-text available
Ticks continue to be a threat to human and animal health in Turkey, as they are considered important vectors of human and animal diseases. The objectives of this investigation are to characterize the microbial communities of two tick species, Rhipicephalus annulatus and Dermacenter marginatus, analyze patterns of co-occurrence among microbial taxa,...
Article
Full-text available
In an effort to explore myxobacterial natural product biosynthetic pathways, the draft genome sequence of Archangium sp. strain Cb G35 has been obtained. Analysis of the genome using antiSMASH predicts 49 natural product biosynthetic pathways. This genome will contribute to the investigation of myxobacterial secondary metabolite biosynthetic pathwa...
Article
Full-text available
In an effort to explore myxobacterial natural product biosynthetic pathways, the draft genome sequence of Cystobacter ferrugineus strain Cbfe23 has been obtained. Analysis of the genome using antiSMASH suggests a multitude of unique natural product biosynthetic pathways. This genome will contribute to the investigation of secondary metabolism in ot...
Article
Full-text available
Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples f...
Article
Full-text available
Probiotics are believed to be beneficial in maintaining a healthy gut microbiota whereas antibiotics are known to induce dysbiosis. This study aimed to examine the effects of the probiotic Saccharomyces boulardii CNCM I-745 (SB), the antibiotic Amoxicillin-Clavulanate (AC) and the combination on the microbiota and symptoms of healthy humans. Health...
Article
Full-text available
Haiti endures the poorest water and sanitation infrastructure in the Western Hemisphere, where waterborne diseases cause significant morbidity and mortality. Most of these diseases are reported to be caused by waterborne pathogens. In this study, we examined the overall bacterial diversity of selected source and point-of-use water from rural areas...
Data
Relative abundance of bacterial diversity at the genus level in the source and point-of-use water samples. Bacterial genus abundance less than 1% were grouped as “Others”. (TIF)
Article
Recent studies demonstrate that exposure to stress changes the composition of the intestinal microbiota, which is associated with development of stress-induced changes to social behavior, anxiety, and depression. Stress during pregnancy has also been related to the emergence of these disorders; whether commensal microbes are part of a maternal intr...
Article
Background & aims: although increasing evidence suggests a role for fungi in inflammatory bowel disease (IBD), data are scarce and mostly from adults. Our aim was to define the characteristics of fungal microbiota in newly-diagnosed treatment-naïve children with Crohn disease (CD). Methods: The children referred for colonoscopy were prospectivel...
Article
Objectives: The aim of the study was to assess the extent to which misoprostol alters mucosal or systemic immune responses following either buccal or vaginal administration. Methods: This was a prospective, crossover pilot study of 15 healthy, reproductive-age women. Women first received 800 μg misoprostol either via buccal or vaginal administra...
Article
Characterization of naturally-mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10–15th centuries using 16S rRNA gene high-throughput sequencing an...
Article
Full-text available
Crohn's disease is characterized by increased permeability of the intestinal mucosal barriers and an abnormal or dysregulated immune response to specific and/or commensal bacteria arising from the intestinal lumen. To determine the types of bacteria that are transgressing the mucosal barrier and colonizing the intestinal submucosal tissues, we perf...
Article
Full-text available
Background: The advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets,...
Article
Full-text available
Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patient...
Article
Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the faecal material of two blue whales living in the wild off the coast of California was investigated. In both samples the most predominant bacterial phylum was the Firmicutes with Clostridium spp. being the most dominant bacteria. The most predominant f...
Article
The cattle tick, Rhipicephalus (Boophilus) microplus, is a pest which causes multiple health complications in cattle. The G protein-coupled receptor (GPCR) super-family presents a candidate target for developing novel tick control methods. However, GPCRs share limited sequence similarity among orthologous family members, and there is no reference g...
Data
Full-text available
The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification a...
Article
Full-text available
Dysbiosis is a hallmark of inflammatory bowel disease (IBD), but it is unclear which specific intestinal bacteria predispose to and which protect from IBD and how they are regulated. Peptidoglycan recognition proteins (Pglyrps) are antibacterial, participate in maintaining intestinal microflora, and modulate inflammatory responses. Mice deficient i...
Article
Full-text available
The relationship between the host and its microbiota is challenging to understand because both microbial communities and their environments are highly variable. We have developed a set of techniques based on population dynamics and information theory to address this challenge. These methods identify additional bacterial taxa associated with pediatr...