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Lubbock, TX, United States

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. Source

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. Source

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. Source

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. Source

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. Source

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