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PubMed2006

Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP).

Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.

Bacteria↗
PubMed1993

Deep-sea smokers: windows to a subsurface biosphere?

Since the discovery of hyperthermophilic microbial activity in hydrothermal fluids recovered from "smoker" vents on the East Pacific Rise, the widely accepted upper temperature limit for life (based on pure culture data) has risen from below the boiling point of water at atmospheric pressure to approximately 115 degrees C. Many microbiologists seem willing to speculate that the maximum may be closer to 150 degrees C. We have postulated not only higher temperatures than these (under deep-sea hydrostatic pressures), but also the existence of a biosphere subsurface to accessible seafloor vents. New geochemical information from the Endeavour Segment of the Juan de Fuca Ridge indicative of subsurface organic material caused us to re-examine both the literature on hyperthermophilic microorganisms cultured from deep-sea smoker environments and recent results of microbial sampling efforts at actively discharging smokers on the Endeavour Segment. Here we offer the case for a subsurface biosphere based on an interdisciplinary view of microbial and geochemical analyses of Endeavour smoker fluids, a case in keeping with rapidly evolving geophysical understanding of organic stability under deep-sea hydrothermal conditions.

Bacteria↗
PubMed2005

The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil.

Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil.

Bacteria↗
PubMed2006

Estimation of microbial growth using population measurements subject to a detection limit.

In this paper we develop a maximum likelihood estimation procedure for determining the mean and variance in microbial population size from microbial population measurements subject to a detection limit. Existing estimation methods generally set non-detectable measurements equal to the detection limit and are highly biased. Because changes in the mean and variance in the microbial population size are typical in industrial processes we also outline statistical tests for detecting such changes when measurements are subject to a detection limit, which is critical for process control. In an industrial process there may also potentially be variability in the microbial growth rate due to variation in the microbial strain, environment, and food characteristics. Accordingly, we also present a maximum likelihood procedure for estimating microbial growth model parameters and their variance components from microbial population measurements subject to a detection limit. Such information can be used to generate the mean and variance through time of the microbial population size, which is vital for the application of predictive microbiological models to risk assessment and food product shelf-life estimation.

Bacteria↗
PubMed2003

Use of redox potential modification by gas improves microbial quality, color retention, and ascorbic acid stability of pasteurized orange juice.

The aim of this paper was to study the effect of both redox potential (Eh) and pasteurization of orange juice on stability of color and ascorbic acid, and growth recovery of microorganisms during storage at 15 degrees C for 7 weeks. Three conditions of Eh, +360 mV (ungassed), +240 mV (gassed with N2), and -180 mV (gassed with N2-H2) were applied to orange juice. Both thermal destruction and recovery of sublethally heat-injured cells of Lactobacillus plantarum and Saccharomyces cerevisiae were investigated. While oxidizing conditions were the most effective for thermal destruction of L. plantarum and S. cerevisiae, reducing conditions decreased recovery of heated cells of S. cerevisiae. In addition, gassing the juice with N2 or N2-H2 increased color retention and ascorbic acid stability. The present study demonstrated that juice must be reduced just after the heat treatment in order, firstly, to maximize microbial destruction during pasteurization, and secondly, to prevent the development of microorganisms and stabilize color and ascorbic acid during storage.

Ascorbic Acid↗
PubMed1999

Modelling the interactions between Lactobacillus curvatus and Enterobacter cloacae. II. Mixed cultures and shelf life predictions.

The modelling approach presented in this study can be used to predict when interactions between microorganisms in homogenous systems occur. It was tested for the interaction between Lactobacillus curvatus and Enterobacter cloacae. In this binary system, L. curvatus produces lactic acid which decreases the pH in the system. The pH decrease was found to be the main limiting factor of growth of both E. cloacae and L. curvatus. This resulted in E. cloacae reaching its final concentration earlier when compared to its growth in pure culture. The models consisted of a set of first order ordinary differential equations describing the growth, consumption and production rates of both microorganisms. The parameters for these equations were obtained from pure culture studies and from literature. These equations were solved using a combination of analytical and numerical methods. The prediction of growth in mixed culture using parameters from pure culture experiments and literature were close to the experimental data. Both model predictions and experimental validation indicated that interaction occurs when the concentration of L. curvatus reaches 10(8) cfu/ml. At that moment in time, the pH had decreased to inhibiting levels. These concentrations of microorganisms (10(8) cfu/ml) do occur in fermented products where interactions obviously are important. In nonfermented foods however, this level of microorganisms indicate that spoilage has occurred or is about to start. Microbial interactions can therefore be neglected when predicting shelf life or safety of food products in most cases.

Colony Count, Microbial↗
PubMed2000

Influence of the growth rate calculation on the relationship between growth rate and temperature.

Three calculations of the growth rate (e.g. slope of a plot of the log10 of cfu ml-1 vs time, mum of the Gompertz equation and the reciprocal of time to obtain 108 cfu ml-1) were compared for Escherichia coli TG1 growing in tryptone soy broth medium at temperatures ranging from 14 to 39 degrees C. Up to now, the influence of using such different definitions on the relationship between microbial growth rate and temperature has never been investigated. In order to compare these calculation procedures, a dimensionless analysis based on the following normalized variables, mudim = mu/muopt and Tdim = [T-Tmin]/[Topt-Tmin], was used (Dantigny 1998). The influence of suboptimal temperatures on the growth rate was represented by means of a Belehràdek-type model based on a power function law: [mudim] = [Tdim]alpha. The influence of the different growth rate calculations on the model constants was assessed. Despite the great dependence of the raw growth rate values on the calculation procedure, the dimensionless analysis demonstrated that the alpha-value is independent of the growth rate definition. This result suggests that any definition for the growth rate can be utilized in studies aimed at determining the influence of temperature on microbial growth and highlights the interest of using dimensionless variables to overcome differences in the order of magnitude of the growth rate data and to avoid confusion between definitions.

Colony Count, Microbial↗
PubMedDate not supplied

Fermentation of green alga sea-lettuce (Ulva sp) and metabolism of its sulphate by human colonic microbiota in a semi-continuous culture system.

The green alga, sea-lettuce (Ulva sp), could be considered as a new source of dietary fibre. Ulva, however, contains high levels of sulphate, part of which is chemically bound in soluble polymers (ulvan). The purpose of this study was to assess the fermentation characteristics and sulphate metabolism of Ulva and ulvan by human faecal bacteria fermentation system using a semi-continuous fermenter. Ulva and ulvan were poorly fermented, even after adaptation of the microbiota. Only 16.6% and 8.9% of Ulva and ulvan organic matter, respectively, were recovered as short chain fatty acids. Nevertheless, 40% of the sulphate in Ulva was dissimilated to sulphide by sulphate-reducing bacteria. Supplementation of Ulva with more fermentable polysaccharides, such as algal xylan and resistant starch, though decreasing the ammonia production originating from Ulva protein degradation, did not significantly reduce the sulphide levels. It is postulated that unless crude Ulva is desulphated, its daily consumption at a level of 20 g of dry product could stimulate colonic microbial sulphate reduction, which may have detrimental effects for the host.

Acetates↗
PubMed2002

Maxillary sinus puncture and culture in the diagnosis of acute rhinosinusitis: the case for pursuing alternative culture methods.

OBJECTIVE: Traditional assessments of the microbial flora associated with acute bacterial rhinosinusitis have relied on maxillary sinus punctures (taps) and culture. These taps are now considered the gold standard for obtaining cultures and are used as the method of identifying bacterial pathogens in antimicrobial trials. Maxillary sinus taps are limited by discomfort to the patients and technical concerns. Because of these factors, the standard of performing taps has limited antibiotic trials and microbial surveillance. Alternatives to maxillary sinus taps have been explored. STUDY DESIGN: We conducted a retrospective, systematic review of the literature from 1950 to 2000 of articles comparing culture techniques in the nose and paranasal sinuses for acute bacterial rhinosinusitis. RESULTS: Nasal cultures have poor correlation to maxillary sinus cultures, whereas there is 60% to 85% concordance between endoscopically guided middle meatal cultures and maxillary sinus cultures. These studies, however, are all limited by small sample sizes and therefore are inadequate to make any concrete recommendations regarding the relative role of endoscopically guided middle meatal cultures as a formal method of pathogen identification in acute bacterial rhinosinusitis. CONCLUSION: A formal prospective study with sufficient sample size to assess the concordance between the microbial flora of the maxillary sinus punctures and middle meatal cultures in acute rhinosinusitis is recommended.

Acute Disease↗
PubMed1994

Microbial degradation of taurine in fecal cultures from cats given commercial and purified diets.

Freshly passed feces were collected from cats (n = 5-7) given cooked and uncooked commercial canned-type diets, casein and soy protein containing purified diets and a commercial extruded diet. The feces were anaerobically cultured in medium containing either taurine, taurocholic acid or [2-3H]taurine for 24 h at 37 degrees C. Taurine degradation in cultures was greatest for cultures from cats receiving diets reputed to cause taurine depletion. Diaminopimelic acid in feces indicated that differences in taurine degradation rate among groups was associated with differences in bacterial numbers in feces. After 6 h of incubation, < 10% of taurocholate and > 60% of taurine remained. Nearly all the tritium on the labeled taurine was recovered as water. These results indicate that deconjugation and deamination are the initial steps in microbial catabolism of taurocholic acid and that enteric microbial growth may be a major determinant of dietary taurine requirement of cats.

Animal Feed↗
PubMed2004

Application of a vital fluorescent staining method for simultaneous, near-real-time concentration monitoring of two bacterial strains in an Atlantic coastal plain aquifer in Oyster, Virginia.

Two differentially labeled bacterial strains were monitored in near-real time during two field-scale bacterial transport experiments in a shallow aquifer in July 2000 and July 2001. Comamonas sp. strain DA001 and Acidovorax sp. strain OY-107 were grown and labeled with the vital fluorescent stain TAMRA/SE (5 [and -6]-carboxytetramethylrhodamine, succinimidyl ester) or CFDA/SE (5 [and -6]-carboxyfluorescein diacetate, succinimidyl ester). Fluorescently labeled cells and a conservative bromide tracer were introduced into a suboxic superficial aquifer, followed by groundwater collection from down-gradient multilevel samplers. Cells were enumerated in the field by microplate spectrofluorometry, with confirmatory analyses for selected samples done in the laboratory by epifluorescence microscopy, flow cytometry, and ferrographic capture. There was general agreement in the results from all of the vital-stain-based enumeration methods, with differences ranging from <10% up to 40% for the analysis of identical samples between different tracking methods. Field analysis by microplate spectrofluorometry was robust and efficient, allowing thousands of samples to be analyzed in quadruplicate for both of the injected strains. The near-real-time data acquisition allowed adjustments to the predetermined sampling schedule to be made. The microplate spectrofluorometry data sets for the July 2000 and July 2001 experiments allowed the transport of the injected cells to be related to the site hydrogeology and injection conditions and enabled the assessment of differences in the transport of the two strains. This near-real-time method should prove effective for a number of microbial ecology applications.

Biodegradation, Environmental↗
PubMed2002

Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR.

The use of real-time quantitative PCR (5' nuclease PCR assay) as a tool to study the gastrointestinal microflora that adheres to the colonic mucosa was evaluated. We developed primers and probes based on the 16S ribosomal DNA gene sequences for the detection of Escherichia coli and Bacteroides vulgatus. DNA was isolated from pure cultures and from gut biopsy specimens and quantified by the 5' nuclease PCR assay. The assay showed a very high sensitivity: as little as 1 CFU of E. coli and 9 CFU of B. vulgatus could be detected. The specificities of the primer-probe combinations were evaluated with samples that were spiked with the species most closely related to E. coli and B. vulgatus and with eight other gut microflora species. Mucosal samples spiked with known amounts of E. coli or B. vulgatus DNA showed no PCR inhibition. We conclude that the 5' nuclease PCR assay may be a useful alternative to conventional culture techniques to study the actual in vivo composition of a complex microbial community like the gut microflora.

Bacterial Adhesion↗
PubMed2001

Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems.

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.

Adenosine Triphosphate↗
PubMed2005

Combined efficacy of nisin and pediocin with sodium lactate, citric acid, phytic acid, and potassium sorbate and EDTA in reducing the Listeria monocytogenes population of inoculated fresh-cut produce.

The inability of chlorine to completely inactivate human bacterial pathogens on whole and fresh-cut produce suggests a need for other antimicrobial washing treatments. Nisin (50 microg/ml) and pediocin (100 AU/ml) individually or in combination with sodium lactate (2%), potassium sorbate (0.02%), phytic acid (0.02%), and citric acid (10 mM) were tested as possible sanitizer treatments for reducing the population of Listeria monocytogenes on cabbage, broccoli, and mung bean sprouts. Cabbage, broccoli, and mung bean sprouts were inoculated with a five-strain cocktail of L. monocytogenes at 4.61, 4.34, and 4.67 log CFU/g, respectively. Inoculated produce was left at room temperature (25 degrees C) for up to 4 h before antimicrobial treatment. Washing treatments were applied to inoculated produce for 1 min, and surviving bacterial populations were determined. When tested alone, all compounds resulted in 2.20- to 4.35-log reductions of L. monocytogenes on mung bean, cabbage, and broccoli, respectively. The combination treatments nisin-phytic acid and nisin-pediocin-phytic acid caused significant (P < 0.05) reductions of L. monocytogenes on cabbage and broccoli but not on mung bean sprouts. Pediocin treatment alone or in combination with any of the organic acid tested was more effective in reducing L. monocytogenes populations than the nisin treatment alone. Although none of the combination treatments completely eliminated the pathogen on the produce, the results suggest that some of the treatments evaluated in this study can be used to improve the microbial safety of fresh-cut cabbage, broccoli, and mung bean sprouts.

Anti-Bacterial Agents↗
PubMed1999

Current and future approaches for diagnosis of periodontal diseases.

Our understanding of the etiology and pathogenesis of periodontal diseases has grown in the recent past, and new findings have led to advances in patient management. This article summarizes important new knowledge and offers a description of traditional and novel diagnostic approaches. These include clinical and radiographic assessments of the periodontal tissues, evaluation of the microbial challenge and the host response, and certain elements of the host genotype that may confer susceptibility to destructive periodontal diseases.

Bacterial Typing Techniques↗
PubMed2001

Chemical, microbiological, and AromaScan evaluation of mahi-mahi fillets under various storage conditions.

The quality for mahi-mahi stored at 1.7, 7.2, and 12.8 degrees C for 0, 1, 3, and 5 days was determined using biogenic amine analysis, microbial counts, and sensory evaluation (by a sensory test panel and an AromaScan). Biogenic amines in methanol extracts from mahi-mahi samples were analyzed using capillary electrophoresis (CE) with ultraviolet detection at 210 nm and a gas chromatography (GC) method that can simultaneously determine the contents of putrescine, cadaverine, histamine, spermidine, and spermine within 20 min after pentafluoropropionic anhydride derivatization. A good correlation R2= 0.99) was found between CE and GC methods for detecting histamine in mahi-mahi. Fish quality deteriorated and correlated with increasing microbial numbers. Biogenic amines may be useful indicators for mahi-mahi quality and safety. AromaScan was able to correlate quality changes for mahi-mahi in microbiological and sensory analyses.

Animals↗
PubMed1989

Microbiological profile of selected samples of "Al-Kohl" eye cosmetics in northern Jordanian provinces before and after use.

Fifty items of Al-Kohl collected from northern Jordanian provinces representing: 20 unopened ready to use samples purchased from retail outlets, 20 in-use samples obtained from ladies of different socioeconomic standards and 10 samples of the original stones (used for Al-Kohl preparation) were examined for their microbial contents. Ready to use and in-use samples were much more contaminated than the original stones. On sterility testing, more than 85% of the unused and in-use samples were contaminated with bacteria and or fungi comparing to 50% of the original stone samples. Quantitatively, 90% of the original stones contained less than 100 bacterial or fungal cells/g and the other remaining 10% were in the range of 10(2)-10(3) cfu/g either for bacterial or fungal counts. The level and distribution of the viable microbial counts in unused and in-use samples were comparable and much higher than original stones. More than 70% and 20% of those items contained more than 100 cfu/g of bacteria and fungi respectively. Among those samples 20% and 5% were heavily contaminated (contain more than 10(4) cfu/g) with bacteria and fungi respectively. Coliform bacteria in a number of 100 cfu/g or more were recovered from 10% of the unused and 20% of the in-use samples, none were recovered from original stones. The results of qualitative tests for identification of isolated microorganisms showed that 7 different species of Bacillus were found in the 50 examined samples. Approximately 50% of the examined samples contained Bacillus spp., Staphylococcus spp., Pseudomonas spp., P. vulgaris, S. marcescens were recovered from unused and in-use samples in different percentages, none from original stones, some of the detected Staphylococcus were aureus type and also one isolate of P. aeruginosa was detected in one of the in-use samples. The relationship between the detected level of microbial contamination in the tested samples with the proposed allowable international limits of contamination as well as the possible sources of contamination and the hygienic implications of using such products by the public were discussed.

Bacillus↗