Lubbock Medical Biofilm Research Institute

Lubbock, TX, United States

Lubbock Medical Biofilm Research Institute

Lubbock, TX, United States
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Cephas K.D.,Urbana University | Kim J.,Urbana University | Mathai R.A.,Urbana University | Barry K.A.,Urbana University | And 3 more authors.
PLoS ONE | Year: 2011

Bacterial contribution to oral disease has been studied in young children, but there is a lack of data addressing the developmental perspective in edentulous infants. Our primary objectives were to use pyrosequencing to phylogenetically characterize the salivary bacterial microbiome of edentulous infants and to make comparisons against their mothers. Saliva samples were collected from 5 edentulous infants (mean age = 4.6±1.2 mo old) and their mothers or primary care givers (mean age = 30.8±9.5 y old). Salivary DNA was extracted, used to generate DNA amplicons of the V4-V6 hypervariable region of the bacterial 16S rDNA gene, and subjected to 454-pyrosequencing. On average, over 80,000 sequences per sample were generated. High bacterial diversity was noted in the saliva of adults [1012 operational taxonomical units (OTU) at 3% divergence] and infants (578 OTU at 3% divergence). Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria were predominant bacterial phyla present in all samples. A total of 397 bacterial genera were present in our dataset. Of the 28 genera different (P<0.05) between infants and adults, 27 had a greater prevalence in adults. The exception was Streptococcus, which was the predominant genera in infant saliva (62.2% in infants vs. 20.4% in adults; P<0.05). Veillonella, Neisseria, Rothia, Haemophilus, Gemella, Granulicatella, Leptotrichia, and Fusobacterium were also predominant genera in infant samples, while Haemophilus, Neisseria, Veillonella, Fusobacterium, Oribacterium, Rothia, Treponema, and Actinomyces were predominant in adults. Our data demonstrate that although the adult saliva bacterial microbiome had a greater OTU count than infants, a rich bacterial community exists in the infant oral cavity prior to tooth eruption. Streptococcus, Veillonella, and Neisseria are the predominant bacterial genera present in infants. Further research is required to characterize the development of oral microbiota early in life and identify environmental factors that impact colonization and oral and gastrointestinal disease risk. © 2011 Cephas et al.

Swanson K.S.,Urbana University | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Suchodolski J.S.,Texas A&M University | Middelbos I.S.,Urbana University | And 9 more authors.
ISME Journal | Year: 2011

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised 35% of all sequences, followed by Proteobacteria (13-15%) and Fusobacteria (7-8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented 1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease. © 2011 International Society for Microbial Ecology All rights reserved.

Acosta-Martinez V.,U.S. Department of Agriculture | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Sun Y.,Lubbock Medical Biofilm Research Institute | Wester D.,Texas Tech University | Allen V.,Texas Tech University
Applied Soil Ecology | Year: 2010

Bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rDNA gene was used to evaluate bacterial diversity of a clay loam soil (fine, mixed, thermic Torrertic Paleustolls) after 10 years under an integrated livestock (beef)-cotton (Gossypium hirsutum L.) production system compared to continuous cotton in a semiarid region. In the integrated system, cattle alternatively grazed a perennial warm-season grass [Bothriochloa bladhii (Retz) S.T. Blake] paddock and small grains grown in two paddocks of a wheat (Triticum aestivum L.)-fallow-rye (Secale cereal L.)-cotton rotation. Areas excluded from grazing in the integrated system were also evaluated. Maximum observed number of unique sequences operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the species level) corresponded to 1200 and 1100 at 0-5 and 5-15 cm depths, respectively. Predominant phyla (up to 65% of abundance) at 0-5 and 5-15 cm in this soil were Proteobacteria, Actinobacteria and Gemmatimonadetes. Proteobacteria were predominant in soil under all components of the integrated livestock-cotton system compared to continuous cotton whereas Bacteroidetes were predominant under continuous cotton. Firmicutes (i.e., Clostridia) and Chlorofexi (i.e., Thermomicrobia) were more abundant in soil under fallow periods of the rotation compared to under cotton (Rye-Cotton-Wheat-Fallow or continuous cotton) or grass (i.e., pasture). The lowest OTUs were detected in soil under fallow periods of the rotation (Wheat-Fallow-Rye-Cotton) compared to the other treatments. Grazing effects were significant for Actinobacteria, Proteobacteria and Chlorofexi. Compared to the continuous cotton system, this study revealed significant changes in bacterial phyla distribution under integrated livestock-cotton systems for a semiarid soil after 10 years. Positive correlations were found between certain bacteria (Proteobacteria, Firmicutes, Chloroflexi, Verrucomicrobiae and Fibrobacteres) and the activities of alkaline phosphatase and β-glucosidase or β-glucosaminidase.

Ishak H.D.,University of Texas at Austin | Plowes R.,University of Texas at Austin | Sen R.,University of Texas at Austin | Kellner K.,University of Texas at Austin | And 4 more authors.
Microbial Ecology | Year: 2011

Social insects harbor diverse assemblages of bacterial microbes, which may play a crucial role in the success or failure of biological invasions. The invasive fire ant Solenopsis invicta (Formicidae, Hymenoptera) is a model system for understanding the dynamics of invasive social insects and their biological control. However, little is known about microbes as biotic factors influencing the success or failure of ant invasions. This pilot study is the first attempt to characterize and compare microbial communities associated with the introduced S. invicta and the native Solenopsis geminata in the USA. Using 16S amplicon 454 pyrosequencing, bacterial communities of workers, brood, and soil from nest walls were compared between neighboring S. invicta and S. geminata colonies at Brackenridge Field Laboratory, Austin, Texas, with the aim of identifying potential pathogenic, commensal, or mutualistic microbial associates. Two samples of S. geminata workers showed high counts of Spiroplasma bacteria, a known pathogen or mutualist of other insects. A subsequent analysis using PCR and sequencing confirmed the presence of Spiroplasma in additional colonies of both Solenopsis species. Wolbachia was found in one alate sample of S. geminata, while one brood sample of S. invicta had a high count of Lactococcus. As expected, ant samples from both species showed much lower microbial diversity than the surrounding soil. Both ant species had similar overall bacterial diversities, although little overlap in specific microbes. To properly characterize a single bacterial community associated with a Solenopsis ant sample, rarefaction analyses indicate that it is necessary to obtain 5,000-10,000 sequences. Overall, 16S amplicon 454 pyrosequencing appears to be a cost-effective approach to screen whole microbial diversity associated with invasive ant species. © 2011 Springer Science+Business Media, LLC.

Bailey M.T.,Ohio State University | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Parry N.M.A.,Massachusetts Institute of Technology | Galley J.D.,Ohio State University | And 2 more authors.
Infection and Immunity | Year: 2010

The gastrointestinal tract is colonized by an enormous array of microbes that are known to have many beneficial effects on the host. Previous studies have indicated that stressor exposure can disrupt the stability of the intestinal microbiota, but the extent of these changes, as well as the effects on enteric infection, has not been well characterized. In order to examine the ability of stressors to induce changes in the gut microbiota, we exposed mice to a prolonged restraint stressor and then characterized microbial populations in the intestines using both traditional culture techniques and bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Exposure to the stressor led to an overgrowth of facultatively anaerobic microbiota while at the same time significantly reducing microbial richness and diversity in the ceca of stressed mice. Some of these effects could be explained by a stressor-induced reduction in the relative abundance of bacteria in the family Porphyromonadaceae. To determine whether these alterations would lead to increased pathogen colonization, stressed mice, as well as nonstressed controls, were challenged orally with the enteric murine pathogen Citrobacter rodentium. Exposure to the restraint stressor led to a significant increase in C. rodentium colonization over that in nonstressed control mice. The increased colonization was associated with increased tumor necrosis factor alpha (TNF-α) gene expression in colonic tissue. Together, these data demonstrate that a prolonged stressor can significantly change the composition of the intestinal microbiota and suggest that this disruption of the microbiota increases susceptibility to an enteric pathogen. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Reese B.K.,Texas A&M University | Mills H.J.,Texas A&M University | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Morse J.W.,Texas A&M University
Geomicrobiology Journal | Year: 2013

Multiple environmental mechanisms have been proposed to control bottom water hypoxia (<2 mg O2 L-1) in the northern Gulf of Mexico Louisiana shelf. Near-bottom hypoxia has been attributed to a direct consumption of oxygen through benthic microbial respiration and a secondary chemical reaction between oxygen and reduced metabolites (i.e. ferrous iron and total sulfide) from these populations. No studies to date have examined the metabolically active microbial community structure in conjunction with the geochemical profile in these sediments. Temporal and spatial differences in dissolved and solid phase geochemistry were investigated in the upper 20 cm of the sediment column. Pyrosequencing of reverse transcribed small subunit (SSU) ribosomal ribonucleic acid (rRNA) was used to determine population distribution. Results indicated that populations shallower than 10 cm below surface were temporally variable yet uniform between sites, while below this depth, populations were more site-specific. This suggests a potential interaction between the water column and the benthic microbial population limited to a shallow depth. The presence of dissolved reduced iron in the upper sediment column was indicative of low oxygen concentration, yet sulfide was at or below detection limits. Putative sulfate and iron reducing and oxidizing populations were metabolically active at similar depths suggesting potential recycling of products. Results from this study indicate low carbon concentrations in the shallow sediments limit general metabolic activity, reducing the potential for microbial respiration. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file. © 2013 Copyright Taylor and Francis Group, LLC.

Bailey M.T.,Ohio State University | Walton J.C.,Ohio State University | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Weil Z.M.,Ohio State University | Nelson R.J.,Ohio State University
Brain, Behavior, and Immunity | Year: 2010

Seasonal changes in day length (i.e., photoperiod) provide animals with a reliable environmental cue to determine time of year, and many physiological changes occur in laboratory animals simply by extending or shortening day length. Male Siberian hamsters (Phodopus sungorus) housed in long summer-like day lengths have significantly elevated body and fat masses compared to short-day hamsters. Because others have demonstrated that the intestinal microbiota of humans and rodents promotes host adiposity, we hypothesized that photoperiod-induced changes in body and fat masses could be associated with changes in the microbial composition in the intestines. We used bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) to assess microbial diversity in the cecal contents of hamsters; long days significantly increased the relative abundance of bacteria in the phylum Proteobacteria. This effect was primarily due to a significant increase in the abundance of the genus Citrobacter, with both the abundance of Proteobacteria and Citrobacter spp. significantly correlated with body mass and with inguinal fat mass. In general, the abundance of the Firmicutes phylum was inversely associated with body mass. These data indicate that the intestinal microbiota are responsive to changes in photoperiod and suggest that these changes may in part influence photoperiodic changes in body and fat masses. © 2009 Elsevier Inc.

Ammons M.C.B.,Montana State University | Ward L.S.,Glanbia Research and Development Center | Dowd S.,Lubbock Medical Biofilm Research Institute | James G.A.,Montana State University
International Journal of Antimicrobial Agents | Year: 2011

With an ageing and ever more obese population, chronic wounds such as diabetic ulcers, pressure ulcers and venous leg ulcers are an increasingly relevant medical concern. Identification of bacterial biofilm contamination as a major contributor to non-healing wounds demands biofilm-targeted strategies to manage chronic wounds. Pseudomonas aeruginosa has been identified as a principal biofilm-forming opportunistic pathogen in chronic wounds. The innate immune molecule lactoferrin and the rare sugar alcohol xylitol have been demonstrated to be co-operatively efficacious against P. aeruginosa biofilms in vitro. Data presented here propose a model for the molecular mechanism behind this co-operative antimicrobial effect. Lactoferrin iron chelation was identified as the primary means by which lactoferrin destabilises the bacterial membrane. By microarray analysis, 183 differentially expressed genes of ≥1.5-fold difference were detected. Interestingly, differentially expressed transcripts included the operon encoding components of the pyochelin biosynthesis pathway. Furthermore, siderophore detection verified that xylitol is the component of this novel synergistic treatment that inhibits the ability of the bacteria to produce siderophores under conditions of iron restriction. The findings presented here demonstrate that whilst lactoferrin treatment of P. aeruginosa biofilms results in destabilisation of the bacterial cell membrane though iron chelation, combined treatment with lactoferrin and xylitol inhibits the ability of P. aeruginosa biofilms to respond to environmental iron restriction. © 2011 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Sibley C.D.,University of Calgary | Grinwis M.E.,University of Calgary | Field T.R.,University of Calgary | Eshaghurshan C.S.,University of Calgary | And 7 more authors.
PLoS ONE | Year: 2011

The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured. © 2011 Sibley et al.

Ghosh A.,Kansas State University | Dowd S.E.,Lubbock Medical Biofilm Research Institute | Zurek L.,Kansas State University
PLoS ONE | Year: 2011

The enterococcal community from feces of seven dogs treated with antibiotics for 2-9 days in the veterinary intensive care unit (ICU) was characterized. Both, culture-based approach and culture-independent 16S rDNA amplicon 454 pyrosequencing, revealed an abnormally large enterococcal community: 1.4±0.8×10 8 CFU gram -1 of feces and 48.9±11.5% of the total 16,228 sequences, respectively. The diversity of the overall microbial community was very low which likely reflects a high selective antibiotic pressure. The enterococcal diversity based on 210 isolates was also low as represented by Enterococcus faecium (54.6%) and Enterococcus faecalis (45.4%). E. faecium was frequently resistant to enrofloxacin (97.3%), ampicillin (96.5%), tetracycline (84.1%), doxycycline (60.2%), erythromycin (53.1%), gentamicin (48.7%), streptomycin (42.5%), and nitrofurantoin (26.5%). In E. faecalis, resistance was common to tetracycline (59.6%), erythromycin (56.4%), doxycycline (53.2%), and enrofloxacin (31.9%). No resistance was detected to vancomycin, tigecycline, linezolid, and quinupristin/dalfopristin in either species. Many isolates carried virulence traits including gelatinase, aggregation substance, cytolysin, and enterococcal surface protein. All E. faecalis strains were biofilm formers in vitro and this phenotype correlated with the presence of gelE and/or esp. In vitro intra-species conjugation assays demonstrated that E. faecium were capable of transferring tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin resistance traits to human clinical strains. Multi-locus variable number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) of E. faecium strains showed very low genotypic diversity. Interestingly, three E. faecium clones were shared among four dogs suggesting their nosocomial origin. Furthermore, multi-locus sequence typing (MLST) of nine representative MLVA types revealed that six sequence types (STs) originating from five dogs were identical or closely related to STs of human clinical isolates and isolates from hospital outbreaks. It is recommended to restrict close physical contact between pets released from the ICU and their owners to avoid potential health risks. © 2011 Ghosh et al.

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