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Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir.

Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H(2)S liter(-1) day(-1) occurred at 60 and 80 degrees C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH(4) liter(-1) day(-1). Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected.

Archaea↗

Fusidic acid vs ofloxacin prophylaxis before cataract surgery.

PURPOSE: To evaluate the safety and efficacy of two self-administrated antibiotics in eliminating conjunctival microbial flora. METHODS: A total of 133 patients operated for cataract surgery were divided into three groups. The first group (A), 55 patients, received fusidic acid drops (1%) two times per day during the 3 days before the surgery; a second group (B), 55 patients, received ofloxacin (0.3%) four times per day during the 3 days before the surgery; and the third group (C), 23 patients, did not receive any topical antibiotic before the surgery. On the day of the surgery, cultures were taken from the lower fornix. RESULTS: In Group A, 28 cultures (50.9%) were sterile, and 27 (49.1%) were positive for the presence of microbial agents. In Group B, 25 cultures (45.4%) were sterile, and 30 (54.5%) were positive for the presence of microbial agents. In Group C, 5 cultures (21.7%) were sterile, and 18 (78.2%) were not. Staphylococcus epidermidis was the most common micro-organism isolated in all the groups. Statistical analysis does not reveal a significant difference between Groups A and B for the sterile cultures (p=0.7) (chi-square test), but a statistically significant difference is present between the treated and not treated patients (p= 0.05) (chi-square test). CONCLUSIONS: A preoperative prophylaxis is useful in eliminating conjunctival micro-organism, and both antibiotics (fusidic acid and ofloxacin) are efficient.

Anti-Bacterial Agents↗

The importance of cleaning for the overall results of processing endoscopes.

Reprocessing comprises three steps: cleaning, disinfection and-if required-sterilisation. While the extents of disinfection and of sterilisation are quantitatively defined, there are only imprecise (qualitative) definitions of cleaning. There are two main reasons for accurate cleaning. First organic and inorganic materials that remain on inner and outer surfaces will interfere with the efficacy of the disinfectants. In case of endoscopes this will lead to channel blockages; they remain undisinfected. Second the bioburden found on endoscopes after use can be very high. Data available demonstrate that a bacterial burden of up to 10(9)cfu/endoscope channel can be expected. Therefore it is necessary to perform a thorough cleaning. Studies using endoscopes showed a reduction in microbial counts by a factor of approximately 10(4) by cleaning (manual and mechanical). Therefore in 2001 the German Society of Hospital Hygiene (DGKH) specified its requirements and recommendations for determining cleaning efficacy separately from those for disinfection. Cleaning and disinfecting can be done manually or mechanically, but it seems impossible to validate manual processes. However our studies in two different washer-disinfectors (WD) showed differences in cleaning efficacy. The tested cleaning processes showed different efficacies. Not all cleaning processes showed better results than water alone with regard to visible cleanliness and to a microbiological reduction E. faecium. Our results show that the evaluation of cleanliness exclusively by visible inspection is not sufficient, particular for the lumens of endoscopes. The results also show that a cleaning process may be very effective also in reducing micro-organisms present.

Colony Count, Microbial↗

[A rapid method of detecting psychrotrophic bacteria in raw milk].

Determination of the counts of psychrotrophic bacteria offers an important indicator of the technological quality of purchased raw milk, and also an indicator of the hygienic level of its production in agricultural primary production, particularly with respect to the sanitation of milking machines. The applied and published methods of determination of the counts of psychrotrophic microbial contaminants have revealed large differences, multiplied by insufficient legislation in this country, by vague and even wrong definition of the given group of bacteria, and/or by the misuse of the concepts psychrotrophic and psychrophil bacteria. Since the level of the microbial quality of raw milk should be increased, we investigated and developed convenient methods of determination of psychrotrophic bacterium counts in the last years (Urbanová et al., 1988; Urbanová, in print): these methods should facilitate the reasonable control applying an expeditious procedure. A long incubation time of standard procedure is a disadvantage complicating the practical use of the previous procedure (10 days at a temperature of 7 degrees C). An accelerated procedure of psychotrophic bacterium cultivation to determine their counts in raw milk is described in this paper. After thorough stirring, a raw milk sample is diluted with sterile physiological solution (pH 7.2) pursuant to the standard CSN 57 0101. The dilutions 10(-2), 10(-3), 10(-4) were the most convenient for inoculation when the counts of psychrotrophic contaminants were determined in raw milk. The dilutions 10(-3), 10(-4), 10(-5) were inoculated if higher milk contaminations were expected.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Rapid counting of liquid-borne microorganisms by light scattering spectrometry.

Fast and sensitive techniques are needed to determine microorganism presence in liquid samples. In this research, the feasibility of using light scattering spectrometry for enumerating the biological particles in liquid samples was investigated. A particle size spectrometer was used to count six commonly found microbial species suspended in liquid with and without microbiological stains applied: Pseudomonas fluorescens, Micrococcus spp. vegetative cells and Bacillus subtilis var. niger endospores were stained with Acridine Orange and Crystal Violet, while Cladosporium cladosporioides, Penicillium melinii and Aspergillus versicolor fungi were stained with Acridine Orange and Lactophenol Cotton Blue. The counts obtained with the spectrometer were compared with those obtained with a phase-contrast microscope. It was found that the spectrometer counted about 32 % of non-stained B. subtilis endospores and this percentage increased to almost 90 % for stained endospores. Among the investigated species of fungi, the counting efficiency of P. melinii was the only one significantly affected by the application of the stain Lactophenol Cotton Blue: the fraction of counted fungal spores increased from 64 % (non-stained spores) to about 100 % (stained spores). The observed difference in counting efficiency may serve as a basis for differentiating biological from non-biological particles in liquid samples.

Air Microbiology↗

Effect of plants and filter materials on bacteria removal in pilot-scale constructed wetlands.

Due to the lack of testing units or appropriate experimental approaches, only little is known about the removal of bacteria in constructed wetlands. However, improved performance in terms of water sanitation requires a detailed understanding of the ongoing processes. Therefore, we analyzed the microbial diversity and the survival of Enterobacteriaceae in six pilot-scale constructed wetland systems treating domestic wastewater: two vertical sand filters, two vertical expanded clay filters and two horizontal sand filters (each planted and unplanted). Samples were taken from the in- and outflow, from the rhizosphere, and from the bulk soil at various depths. Colony-forming units of heterotrophic bacteria and coliforms were analyzed and the removal of bacteria between the in- and outflow was determined to within 1.5-2.5 orders of magnitude. To access the taxon-specific biodiversity of potential pathogens in the filters and to reduce the complexity of the analysis, specific primers for Enterobacteriaceae were developed. While performing PCR-SSCP analyses, a pronounced decrease in diversity from the inflow to the outflow of treated wastewater was observed. No differences were observed between the bulk soil of planted and unplanted vertical filters. Some bands appeared in the rhizosphere that were not present in the bulk soil, indicating the development of specific communities stimulated by the plants. The fingerprinting of the rhizosphere of plants grown on sand or expanded clay exhibited many differences, which show that different microbial communities exist depending on the soil type of the filters. The use of the taxon-specific primers enabled us to evaluate the fate of the Enterobacteriaceae entering the wetlands and to localize harboring in the rhizosphere. The most abundant bands of the profiles were sequenced: Pantoea agglomerans was found in nearly all samples from the soil but not in the effluent, whereas Citrobacter sp. could not be removed by the horizontal unplanted sand and vertical planted expanded clay filters. These results show that the community in wetland system is strongly influenced by the filtration process, the filter material and the plants.

Aluminum Silicates↗

Effect of storage time with different lens care systems on in-office hydrogel trial lens disinfection efficacy: a multi-center study.

A combined prospective and retrospective study was conducted to evaluate the efficacy of in-office disinfection methods for hydrogel trial contact lenses. Two hundred and twenty-one trial contact lenses, disinfected by four different disinfection methods, were collected from seven Study Centers and cultured for microbial contamination after various storage periods. Negative and positive control lenses were included as an additional Center in this double-masked study. There was a significant difference in the incidence of microbial contamination among the Centers for all storage times (chi 2 p < 0.001). Contamination of trial lenses in Centers using thermal disinfection with preserved saline (SoftWear Saline) was negative and thermal disinfection with nonpreserved saline (LensPlus Saline) was 8.7%. Lens contamination in Centers using chemical disinfection was 13.6% with ReNu and 40.7% with OptiFree. The degree of contamination ranged from 90 colony forming units (CFU)/ml to over 10 million CFU/ml. Among the microorganisms isolated after the different disinfection methods were Alcaligenes xylosoxidans, Serratia marcescens, Moraxella phenylpyruvica, Enterobacter agglomerans, Pseudomonas stutzeri, and various gram-positive organisms. This study suggests that practitioners should redisinfect all inventory trial lenses at least once a month to minimize the risk of patient infection.

Bacteria↗

Effect of a non-steroidal anti-inflammatory drug, naproxen, on faecal microbial flora.

Faecal Clostridium perfringens counts have been observed to be elevated in RA patients. The use of NSAIDs has been suggested as being responsible for this increase. To clarify the potential of NSAIDs to change faecal flora, 10 male volunteers were given naproxen 500 mg twice daily for 2 weeks in a randomized, placebo-controlled and double-blind study, and 10 other volunteers were given a placebo in tablets of identical appearance. Stool samples were collected and subjected to direct stool sample gas-liquid chromatography of bacterial fatty acids. The method has proved to be practical and sensitive in detecting overall changes in faecal flora. The samples were also cultured for Cl. perfringens. No significant change of faecal flora was observed by either method. The results show that naproxen given in doses and over a period in excess of the levels reported to increase intestinal permeability, does not change intestinal flora.

Anti-Inflammatory Agents, Non-Steroidal↗

The effect of sulphur dioxide and oxygen on the viability and culturability of a strain of Acetobacter pasteurianus and a strain of Brettanomyces bruxellensis isolated from wine.

AIMS: The objective of this study was to investigate the effects of free molecular and bound forms of sulphur dioxide and oxygen on the viability and culturability of a selected strain of Acetobacter pasteurianus and a selected strain of Brettanomyces bruxellensis in wine. METHODS AND RESULTS: Acetic acid bacteria and Brettanomyces/Dekkera yeasts associated with wine spoilage were isolated from bottled commercial red wines. One bacterium, A. pasteurianus strain A8, and one yeast, B. bruxellensis strain B3a, were selected for further study. The resistance to sulphur dioxide and the effect of oxygen addition on these two selected strains were determined by using plating and epifluorescence techniques for monitoring cell viability in wine. Acetobacter pasteurianus A8 was more resistant to sulphur dioxide than B. bruxellensis B3a, with the latter being rapidly affected by a short exposure time to free molecular form of sulphur dioxide. As expected, neither of these microbial strains was affected by the bound form of sulphur dioxide. The addition of oxygen negated the difference observed between plate and epifluorescence counts for A. pasteurianus A8 during storage, while it stimulated growth of B. bruxellensis B3a. CONCLUSIONS: Acetobacter pasteurianus A8 can survive under anaerobic conditions in wine in the presence of sulphur dioxide. Brettanomyces bruxellensis B3a is more sensitive to sulphur dioxide than A. pasteurianus A8, but can grow in the presence of oxygen. Care should be taken to exclude oxygen from contact with wine when it is being transferred or moved. SIGNIFICANCE AND IMPACT OF THE STUDY: Wine spoilage can be avoided by preventing growth of undesirable acetic acid bacteria and Brettanomyces/Dekkera yeasts through the effective use of sulphur dioxide and the management of oxygen throughout the winemaking process.

Acetobacter↗

The presterilization microbial load on used medical devices and the effectiveness of hydrogen peroxide gas plasma against Bacillus subtilis spores.

OBJECTIVES: To determine the microbial load found on used critical medical devices (5 spinal anesthesia needles, 21 catheters, and 28 sheaths) prior to sterilization and to evaluate the effectiveness of hydrogen peroxide gas plasma against inoculated Bacillus subtilis var globigii (American Type Culture Collection 9372) spores. METHODS: Membrane filter and pour-plate methods were applied to estimate total microbial loads (aerobic and anaerobic, mesophilic and thermophilic, vegetative and spore forms). Spinal anesthesia needles (102 units) and sheath components (61 units) were inoculated with a suspension of B. subtilis spores. After drying, the devices were sterilized with hydrogen peroxide gas plasma. RESULTS: Higher counts of aerobic, mesophilic, and fungal organisms were recovered when the drying period was insufficient. Anaerobic spores were not found in any analyzed presterilization items. The hydrogen peroxide gas plasma effected a 5 to 7 log10-fold reduction in B. subtilis spore counts in well-dried needles and sheath components. CONCLUSIONS: The success of hydrogen peroxide gas plasma sterilization depends mostly on educating the staff to assure well-cleaned and dried reusable medical devices, allowing penetration of the hydrogen peroxide gas plasma into the critical points of the items and providing a reduction in organisms.

Bacillus subtilis↗

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments.

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Bacteria↗

[The possibility of preserving the causative agent of plague in soil in resting (nonculturable) form].

The parallel study of soil specimens from the burrows of great gerbils, taken in the natural focus of infection at the period between epidemics, by the bacteriological method and with the use of polymerase chain reaction (PCR) demonstrated that, simultaneously with the negative results of inoculations into nutrient media, PCR revealed the presence of Y. pestis in 4 out of 72 soil specimens. The serological study (in the indirect hemagglutination test) revealed the presence of Y. pestis capsular antigen (fraction l) in 16 out of 75 soil specimens. The transition of Y. pestis (strain EV) into the nonculturable state was experimentally shown in sterile soil extract and in association with protozoa, algae and Euglena. Bacteriologically detected Y. pestis disappeared or were represented by a few cells after day 7, while PCR could register the presence of Y. pestis at a concentration of 10(4)-10(5) microbial cells per ml until the end of the term of observation (30 days). After the enrichment of the nutrient medium with fetal serum the complete reversion of Y. pestis nonculturable forms was observed: the concentration of bacteria grown on agar was 10(5) colony-forming units per ml. Transition into the nonculturable state was also observed in distilled water. The results of this investigation are discussed with special emphasis to the possibility of the preservation of Y. pestis in the nonculturable from during the period between epidemics as applied to the problem of plague epizootic.

Animals↗

Comparison between cultured small-intestinal and fecal microbiotas in beagle dogs.

The microbiota of the small intestine is poorly known because of difficulties in sampling. In this study, we examined whether the organisms cultured from the jejunum and feces resemble each other. Small-intestinal fluid samples were collected from 22 beagle dogs with a permanent jejunal fistula in parallel with fecal samples. In addition, corresponding samples from seven of the dogs were collected during a 4-week period (days 4, 10, 14, and 28) to examine the stability of the microbiota. In the jejunal samples, aerobic/facultative and anaerobic bacteria were equally represented, whereas anaerobes dominated in the fecal samples. Despite lower numbers of bacteria in the jejunum (range, 10(2) to 10(6) CFU/g) than in feces (range, 10(8) to 10(11) CFU/g), some microbial groups were more prevalent in the small intestine: staphylococci, 64% versus 36%; nonfermentative gram-negative rods, 27% versus 9%; and yeasts, 27% versus 5%, respectively. In contrast, part of the fecal dominant microbiota (bile-resistant Bacteroides spp., Clostridium hiranonis-like organisms, and lactobacilli) was practically absent in the jejunum. Many species were seldom isolated simultaneously from both sample types, regardless of their overall prevalence. In conclusion, the small intestine contains a few bacterial species at a time with vastly fluctuating counts, opposite to the results obtained for the colon, where the major bacterial groups remain relatively constant over time. Qualitative and quantitative differences between the corresponding jejunal and fecal samples indicate the inability of fecal samples to represent the microbiotas present in the upper gut.

Animals↗

The use of direct epifluorescent microscopy (DEM) and the direct epifluorescent filter technique (DEFT) to assess microbial populations on food contact surfaces.

Two rapid methods, direct epifluorescent microscopy (DEM) and the direct epifluorescent filter technique (DEFT) on swab resuspension fluids, were compared with the traditional total viable count (TVC) on swab resuspension fluids for their ability to enumerate surface populations of attached bacteria. The degree of error in estimating surface populations was shown to be significantly less with DEM than DEFT followed by TVC. DEM estimated populations in the range 3 x 10(3) to 5 x 10(7) colonies/cm2 whilst DEFT enumerated populations above 3 x 10(4) colonies/cm2 and TVC above 3 x 10(5) colonies/cm2 (as measured by DEM). Swabbing was shown to remove a constant proportion of organisms from the surface populations tested, although below 3 x 10(5) colonies/cm2 most of the organisms remained in the cotton matrix and were difficult to resuspend. DEFT was more able to enumerate swab resuspension fluids obtained from surface populations below 3 x 10(5) colonies/cm2 than was TVC.

Acinetobacter↗

Mutans streptococci and lactobacilli in saliva after the application of fissure sealants.

Because dental fissures may serve as reservoirs for mutans streptococci, preventive measures should be taken to control microbial concentrations at these sites. This study estimated the influence that sealing permanent first molars would have on the levels of mutans streptococci and lactobacilli in saliva of healthy seven-year-old schoolchildren. Permanent first molars were sealed in 31 children without caries (NC group) and in 32 children with caries (C group). None of the children had caries in their permanent first molars. Conventional methods were used to count mutans streptococci and lactobacilli in saliva before applying the sealant and again at 4 and 12 weeks after application. Baseline counts of lactobacilli and mutans streptococci were significantly higher in the C group. A significant reduction in mutans streptococci was observed in the NC group at 4 and 12 weeks. It was concluded that fissure sealants in permanent first molars can help reduce salivary levels of mutans streptococci in children without caries.

Child↗

Nematode-enhanced microbial colonization of the wheat rhizosphere.

The mechanisms by which seed-applied bacteria colonize the rhizosphere in the absence of percolating water are poorly understood. Without mass flow, transport of bacteria by growing roots or soil animals, particularly nematodes may be important. We used a sand-based microcosm system to investigate the ability of three species of nematodes (Caenorhabditis elegans, Acrobeloides thornei and a Cruznema sp.) to promote rhizosphere colonization by four strains of beneficial rhizobacteria. In nearly all cases, rhizosphere colonization was substantially increased by the presence of nematodes, irrespective of bacterial or nematode species. Our results suggest that nematodes are important vectors for bacteria rhizosphere colonization in the absence of percolating water.

Animals↗

Strains and species of lactic acid bacteria in fermented milks (yogurts): effect on in vivo lactose digestion.

Lactose in yogurt with live bacteria is better tolerated than lactose in other dairy foods, partly because of the activity of microbial beta-galactosidase (beta-gal), which digests lactose in vivo. To evaluate the ability of different strains and species of lactic acid bacteria to digest lactose in vivo, yogurts (containing mixtures of strains of Streptococcus salivarius subsp thermophilus and Lactobacillus delbrueckii subsp bulgaricus) and fermented milks (containing individual species of S thermophilus, L bulgaricus, L acidophilus, or Bifidobacterium bifidus) that varied in microbial beta-gal activity were produced. Selected products were fed to healthy people who cannot digest lactose, and breath hydrogen production was monitored. All yogurts dramatically and similarly improved lactose digestion, regardless of their total or specific beta-gal activity. The response to fermented milks varied from marginal improvement with B bifidus milk to nearly complete lactose digestion with L bulgaricus milk. The results suggest that total beta-gal was not the limiting factor in promoting lactose digestion, perhaps because of a limited rate of intracellular substrate transport.

Adult↗

Killing of Fusobacterium nucleatum, Porphyromonas gingivalis and Prevotella intermedia by protegrins.

Protegrins are broad spectrum antibiotic peptides isolated from porcine leukocytes. In this study, we (i) examine the sensitivity of Gram-negative, anaerobic periodontal pathogens to synthetic protegrins; (ii) determine the relative potencies of protegrin congeners against these bacteria; and (iii) compare the potency of protegrins with other antibiotic peptides, including magainin MSI-78, tachyplesin I, cecropin P1, human defensins HNP-1-3, and clavanin A. Synthetic L- and D-enantiomers of protegrin 1 (PG-1 and D-PG-1, respectively), and L-enantiomers of protegrins 2, 3 and 5 (PG-2, PG-3 and PG-5) were tested against Fusobacterium nucleatum, and black-pigmented organisms including Porphyromonas gingivalis and Prevotella intermedia. Strains of both F. nucleatum and the black-pigmented organisms were sensitive to PG-1, and exhibited mean ED99 of 2.2-2.3 micrograms/ml and 3.4-9.9 micrograms/ml, respectively. The D-form was statistically more potent than the L-form against these oral anaerobes, and although this difference in potency is unlikely to be of decisive therapeutic significance, the D-form may be of value given ability to resist microbial and host-derived proteases. PG-1 was more potent than magainin, tachyplesin, cecropin, defensins and clavanin under test conditions. Hypertonic salt concentrations and heat-inactivated serum were found to be inhibitory to the bactericidal activity of PG-1. PG-1 was found to induce morphologic alterations in the ultrastructural appearance of F. nucleatum consistent with damage to the bacterial membranes. We conclude that protegrins may be useful antimicrobial agents in therapy against Gram-negative anaerobic bacteria believed to be involved in chronic, adult forms of periodontal infections.

Amino Acid Sequence↗