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PubMed2002

Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat.

The temporal variation in archaeal diversity in vent fluids from a midocean ridge subseafloor habitat was examined using PCR-amplified 16S rRNA gene sequence analysis and most-probable-number (MPN) cultivation techniques targeting hyperthermophiles. To determine how variations in temperature and chemical characteristics of subseafloor fluids affect the microbial communities, we performed molecular phylogenetic and chemical analyses on diffuse-flow vent fluids from one site shortly after a volcanic eruption in 1998 and again in 1999 and 2000. The archaeal population was divided into particle-attached (>3-microm-diameter cells) and free-living fractions to test the hypothesis that subseafloor microorganisms associated with active hydrothermal systems are adapted for a lifestyle that involves attachment to solid surfaces and formation of biofilms. To delineate between entrained seawater archaea and the indigenous subseafloor microbial community, a background seawater sample was also examined and found to consist only of Group I Crenarchaeota and Group II Euryarchaeota, both of which were also present in vent fluids. The indigenous subseafloor archaeal community consisted of clones related to both mesophilic and hyperthermophilic Methanococcales, as well as many uncultured Euryarchaeota, some of which have been identified in other vent environments. The particle-attached fraction consistently showed greater diversity than the free-living fraction. The fluid and MPN counts indicate that while culturable hyperthermophiles represent less than 1% of the total microbial community, the subseafloor at new eruption sites does support a hyperthermophilic microbial community. The temperature and chemical indicators of the degree of subseafloor mixing appear to be the most important environmental parameters affecting community diversity, and it is apparent that decreasing fluid temperatures correlated with increased entrainment of seawater, decreased concentrations of hydrothermal chemical species, and increased incidence of seawater archaeal sequences.

Archaea↗

PubMed2006

Lactobacillus delbrueckii subsp lactis strain CIDCA 133 inhibits nitrate reductase activity of Escherichia coli.

The aim of the present work was to investigate the effect of strain CIDCA 133 on the nitrate reductase activity of a non-pathogenic Escherichia coli strain. Suspensions containing different ratios of the strains under study were coincubated in MRS or MRS without glucose. In some experiments lactobacilli were killed by UV treatment. The nitrate reductase activity was determined by using a diazotization reaction for nitrite. Presence of live lactobacilli leads to a dose-response diminution in the specific nitrate reductase of E. coli even when no acidification occurred. Killing of lactobacilli by UV treatment completely abolished the anti-nitrate reductase effect. In addition, the effect was only partially observed with filtered spent culture supernatants of lactobacilli. Lactobacillus delbrueckii subsp lactis strain CIDCA 133 is able to antagonize the nitrate reductase activity of E. coli. This effect is neither due to a diminution of the viability of E. coli nor is depending on the acidification of the medium by the lactobacilli. Viability is needed for maximal anti-nitrate reductase activity. Modulation of undesirable enzymatic activities of intestinal microorganisms by means of selected microorganisms constitutes a further insight on the mechanisms by which probiotics lead to beneficial effects. Administration of probiotic strains able to modulate microbial intestinal activities could lead to a protection of the host against harmful effects of some members of the intestinal microflora.

Colony Count, Microbial↗

PubMed2002

Microbial diversity and complexity in hypersaline environments: a preliminary assessment.

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments.

Archaea↗

PubMed1992

Microbial colonization and sperm--mucus interaction: results in 1000 infertile couples.

After screening a large series of infertile patients (n = 1000 couples), potentially pathogenic microorganisms were identified in genital secretions of the majority of couples. None of the patients displayed signs or symptoms of infection of the lower genital tract. In semen specimens and cervical swabs, mycoplasmas were found in 18 and 12%, potentially pathogenic aerobic bacteria in 50 and 31%, additionally commensal aerobes in 38% and 25%, respectively. The microbial pattern showed great variability with polymicrobial growth most common. The rate of cultures positive for potentially pathogenic anaerobes was markedly influenced by the transport conditions. In endocervical material, Herpes simplex virus (HSV) was identified in 4.5%. Yeasts were found in the posterior vaginal fornix in 10%. Concerning both partners, there were only 10 couples (1%) from whom microorganisms in genital secretions could not be isolated, not including lactobacilli in females. This high prevalence of microbes and the low number of leukocytes indicate colonization rather than infection. When the microbial findings from both partners were analysed with regard to the outcome of sperm-cervical mucus penetration testing in vitro, which was performed simultaneously, no significant correlation was found. Furthermore, microbial prevalence did not differ between couples with 'explained' and 'unexplained' infertility. The results of this study demonstrate that in patients without symptoms of genital tract infection, microbial colonization is of minor importance for sperm--mucus interaction and that extensive microbial screening should be preferentially performed in cases of poor sperm and/or mucus function.

Adult↗

PubMed1992

Comparative study on the antimicrobial effects of Hexomedine and Betadine on the human skin flora.

Studies were carried out to detect the modifications, if any, on the peri-umbilical flora of six healthy volunteers after two or three daily applications of Hexomedine solution (HEX) and Betadine solution (PVI) repeated for five consecutive days. A standardized scrubbing method was used for bacterial sampling. Surviving bacteria were selected with both selective and non-selective media, and then identified by gas chromatographic fatty acid analysis. Both antiseptics were highly effective, showing both immediate and residual antimicrobial activities. The use of HEX led to a slight increase in Gram-positive cocci and a small decrease in coryneforms, but PVI produced a marked increase in Gram-positive cocci and a sharp decrease in coryneforms. The two antiseptics, however, caused no major alteration in the cutaneous microbial population. Indeed, neither the overgrowth of Gram-negative bacilli nor the emergence of resistant species was observed.

Adult↗

PubMed2004

Relationship between inactivation kinetics of a Listeria monocytogenes suspension by chlorine and its chlorine demand.

AIMS: Chlorine demand by Listeria monocytogenes cells and inactivation of L. monocytogenes by chlorine (0.6-1.0 mg l(-1)) at different temperatures (4, 20 and 30 degrees C) have been investigated in a batch reactor. METHODS AND RESULTS: Chlorine demand depended on the microbial concentration and was independent on the initial chlorine concentration and temperature. Chlorine decay was modelled by the addition of two first-order decay equations. Inactivation of L. monocytogenes by chlorine depended on the initial microbial concentration, initial chlorine concentration and temperature. A mathematical model based on a biphasic inactivation properly described survival curves of L. monocytogenes and a tertiary model was developed that satisfactorily predicted the inactivation of L. monocytogenes by different concentrations of initial chlorine at different temperatures. CONCLUSIONS: Both available chlorine decay and inactivation of L. monocytogenes by chlorine were biphasic and can be modelled by a two-term exponential model. SIGNIFICANCE AND IMPACT OF THE STUDY: The biphasic nature of survival curves of L. monocytogenes did not reflect the effect of a change of available chlorine concentration during the treatment. The microbial inactivation was caused by successive reactions that occur after the consumption of the chlorine by the bacterial cell components.

Chlorine↗

PubMed1993

Microbial associations in periodontitis sites before and after treatment.

Duplicate samples from 110 periodontal sites of 6 mm or more pocket depth in 16 patients were analyzed for the presence of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Capnocytophaga spp., Campylobacter rectus, Eikenella corrodens and Fusobacterium nucleatum. The sites were sampled before and after nonsurgical periodontal treatment. No statistically significant associations were found before treatment between any of the analyzed species. After treatment, statistically significant associations were found between E. corrodens and all the other species, F. nucleatum and P. intermedia; Capnocytophaga spp. and C. rectus; P. intermedia vs Capnocytophaga spp. and P. gingivalis; and C. rectus vs Capnocytophaga spp. and A. actinomycetemcomitans. Some of these associations could be explained either by patient-related factors or site-related characteristics such as the pocket depth. The proportion of P. gingivalis seemed to be unrelated to the proportion of P. intermedia in the samples. If one of the analyzed microbes was found in one of the sampled pockets in a patient, the probability of finding that microbe in all the sampled sites in the same patient before treatment was more than 50%. This probability was reduced after treatment for many species, especially P. gingivalis, which showed a probability of zero. The probability of detecting a bacterial species on at least one additional site if it was present on one in the same individual was nearly 100%, both before and after treatment, for all species studied. This study has shown several potential microbial associations in the subgingival plaque flora of deep periodontal pockets.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2006

Cultivability of Streptococcus thermophilus in Grana Padano cheese whey starters.

The application of a culture-independent approach, that of reverse transcriptase-length heterogeneity-PCR coupled with epifluorescence microscopy, allowed us to observe that Streptococcus thermophilus is metabolically active, but only partially cultivable in Grana Padano cheese whey starters. A short preincubation of the starters in sterile skimmed whey was followed by cultivation in sterile skimmed whey-enriched M17. This procedure restored the cultivability of S. thermophilus and enabled us to detect S. thermophilus at ranges (10(7)-10(8) CFU mL(-1)) which have rarely been reported in these cultures. The use of cheese whey as a cultivation-revitalization substrate can be useful to obtain an unbiased picture of the microbial composition of whey starters for Grana Padano cheese, thus avoiding an underestimation of S. thermophilus in these cultures.

Bacteriological Techniques↗

PubMed2006

Characterisation of the biosand filter for E. coli reductions from household drinking water under controlled laboratory and field use conditions.

More than a billion people in the developing world lack access to safe and reliable sources of drinking water. Point of use (POU) household water treatment technology allows people to improve the quality of their water by treating it in the home. One emerging POU technology is the biosand filter (BSF), a household-scale, intermittently operated slow sand filter. Laboratory and field studies examined Escherichia coli reductions achieved by the BSF. During two laboratory studies, mean E. coli reductions were 94% and they improved over the period of filter use, reaching a maximum of 99%. Field analysis conducted on 55 household filters near Bonao, Dominican Republic averaged E. coli reductions of 93%. E. coli reductions by the BSF in laboratory and field studies were less than those typically observed for traditional slow sand filters (SSFs), although as for SSFs microbial reductions improved over the period of filter use. Further study is needed to determine the factors contributing to microbial reductions in BSFs and why reductions are lower than those of conventional SSFs.

Colony Count, Microbial↗

PubMed2001

Method for studying development of colonization and infection of dialysis catheters.

Microbial colonization and infection of dialysis catheters is the major cause of catheter failure. The present study aimed to develop a method to permit the study of microbial biofilm formation and antibiotic prophylaxis and therapy. Standard silicon rubber and silver-impregnated catheters were sectioned into 1 mm slices and placed into 1-cm x 2-cm culture slide chambers. Fresh clinical isolates were obtained from infected patients and suspended in concentrations of 10(3), 10(6), and 10(9) colony forming units (CFU) per milliliter in a variety of liquid suspending culture media, which included serum protein constituents. Antibiotics could be added to the suspending fluid to determine prophylactic activity, or at any time thereafter to determine therapeutic activity. The catheter sections were incubated with the microbial challenge for 6 hours, 12 hours, 24 hours, and 48 hours and then washed in flowing distilled water to remove unattached biofilm. They were then stained with acridine orange, which fluoresces microbial DNA, and were examined by confocal scanning laser microscopy. Biofilm formation, representing colonization and infection, were quantified by comparing the fluorescent pixel analysis of the uninoculated control with the challenged catheter. The method was reproducible and permitted quantitative analysis. Standard silicon rubber catheters demonstrated greater biofilm formation than silver-impregnated catheters. The method examines the factors involved in microbial colonization and infection, and in antibiotic prophylaxis and therapy.

Biofilms↗

PubMedDate not supplied

Clearance of biofilms from dental unit waterlines through the use of hydroperoxide ion-phase transfer catalysts.

OBJECTIVES: The purpose of this research was to demonstrate the effectiveness of hydroperoxide ion-phase transfer catalyst (HPI-PTC) cleaners and disinfectants for maintaining dental unit waterlines free of planktonic organisms. METHOD AND MATERIALS: Water samples were taken from 117 sites, which included a variety of dental units and samples from the sink faucets of most operatories. Samples were plated on appropriate bacteriologic media and incubated. The presence or absence of biofilms was confirmed by scanning electron microscopy. Twenty-two of the dental units were retrofitted with independent water systems; the cleaning procedure involved an overnight application of an HPI-PTC cleaner followed by a 2-minute water rinse. RESULTS: Water from both the air-water syringe and the high-speed handpiece lines from all untreated units contained at least 6 x 10(2) colony-forming units per milliliter of planktonic or free-floating bacteria; the average was 1.4 x 10(5) CFU/mL. An initial 5% solution of HPI-PTC successfully cleared the lines of any apparent biofilm when applied for 3 consecutive days. Thereafter, once weekly use of the cleaner maintained the dental unit water supplies free of significant numbers of planktonic organisms. CONCLUSION: Routine weekly use of an HPI-PTC cleaner controlled dental unit waterline biofilm and reduced, with minimum effort, the microbial contamination level of water used for patient treatment to less than 200 CFU/mL.

Biofilms↗

PubMed2003

The clinical relevance of microbiologic testing. Part 2: a comparative analysis of microbiologic samples secured simultaneously from the same sites and cultured in the same laboratory.

A field study using four different private periodontal practices and two independent laboratories was conducted to compare two microbiologic cultures sampled simultaneously from the same sites in 20 individual patients. Both paired samples were submitted separately to one of the two independent laboratories for bacterial identification and antibiotic sensitivity testing. The results from the two samples were quite variable. In only two instances did both specimens reveal the presence of identical bacterial species, but these specimens differed in both threshold levels and antibiotic sensitivity. When only bacteria above threshold levels were compared, total agreement was found in 11 of 20 cases. When examining antibiotic sensitivity, using 100% kill as the ideal, agreement between the two specimens was inconsistent The use or nonuse of tetracycline was in agreement 85% of the time, amoxicillin 75% of the time, metronidazole 70% of the time, and amoxicillin-metronidazole in combination 85% of the time. The two specimens agreed on the empirical use of amoxicillin 45% of the time, tetracycline 60% of the time, and metronidazole 60% of the time. The empirical use of amoxicillin-metronidazole in combination yielded 80% agreement when the results of both specimens were combined. The empirical use of amoxicillin-metronidazole combination therapy may be more clinically sound and cost effective than culturing and antibiotic selection based on the culture from any single microbiologic testing laboratory. This supports the data from a previous study that examined specimens secured simultaneously from the same site and submitted to two different testing laboratories. The failure of microbial testing to achieve a higher level of consistency between samples leaves the clinical efficacy of microbial testing in question.

Adult↗

PubMed2006

Field released transgenic papaya effect on soil microbial communities and enzyme activities.

Soil properties, microbial communities and enzyme activities were studied in soil amended with replicase (RP)-transgenic or non-transgenic papaya under field conditions. Compared with non-transgenic papaya, significant differences (P<0.05) were observed in total nitrogen in soils grown with transgenic papaya. There were also significant differences (P<0.05) in the total number of colony forming units (CFUs) of bacteria, actinomycetes and fungi between soils amended with RP-transgenic plants and non-transgenic plants. Compared with non-transgenic papaya, the total CFUs of bacteria, actinomycetes and fungi in soil with transgenic papaya increased by 0.43-1.1, 0.21-0.80 and 0.46-0.73 times respectively. Significantly higher (P<0.05) CFUs of bacteria, actinomycetes and fungi resistant to kanamycin (Km) were obtained in soils with RP-transgenic papaya than those with non-transgenic papaya in all concentrations of Km. Higher resistance quotients for Kmr (kanamycin resistant) bacteria, actinomycetes and fungi were found in soil planted with RP-transgenic papaya, and the resistance quotients for Kmr bacteria, actinomycetes and fungi in soils with transgenic papaya increased 1.6-4.46, 0.63-2.5 and 0.75-2.30 times. RP-transgenic papaya and non-transgenic papaya produced significantly different enzyme activities in arylsulfatase (5.4-5.9x), polyphenol oxidase (0.7-1.4x), invertase (0.5-0.79x), cellulase (0.23-0.35x) and phosphodiesterase (0.16-0.2x). The former three soil enzymes appeared to be more sensitive to the transgenic papaya than the others, and could be useful parameters in assessing the effects of transgenic papaya. Transgenic papaya could alter soil chemical properties, enzyme activities and microbial communities.

Actinomyces↗

PubMed2002

Numbers and types of microorganisms in vacuum-packed cold-smoked freshwater fish at the retail level.

Fifty-four packages (each one belonging to a different lot) of vacuum-packed cold-smoked salmon (30) and trout (24) produced by six Spanish smokehouses were obtained at retail level after 3 weeks storage at 2+/-1 degrees C. Sensorial, chemical, physicochemical and microbiological characteristics were examined. Overall, pH, a(w), salt content in water phase, aerobic plate counts at 30 and 25 degrees C. levels of Enterobacteriaceae, lactic acid bacteria (LAB), fungi and presumptive aeromonads and staphylococci are in agreement with available data on lightly preserved fish products. Psychrotrophic clostridia ranged between 1.71 and 2.21 log CFU/g. Levels of ethanol were highly variable and not significantly related (p > 0.05) to sensory scores or to microbial numbers. Salmonella, Escherichia coli and Listeria monocytogenes were not detected in any sample. Listeriae other than L. monocytogenes were isolated from three packages. Levels of Staphylococcus aureus lower than 4 log CFU/g were also found in three packages. Among 377 bacteria randomly isolated from aerobic 25 degrees C plate counts, LAB predominated, with Carnobacterium (C. piscicola) and Lactobacillus (eight species) being the genera most frequently found. The second and third major groups were Enterobacteriaceae and Micrococcaceae, respectively. Proteus vulgaris, P. mirabilis and Serratia liquefaciens were dominant among Enterobacteriaceae and coagulase-negative staphylococci among Micrococcaceae. Minor microbial groups such as aerobic gram-negative bacilli (Acinetobacter; Moraxella and Pseudomonas), Brochothrix, Aeromonas, Bacillus and Vibrio constituted less than 17% of the total flora.

Animals↗

PubMed1997

The diagnosis of ventilator-associated pneumonia: a comparison of histologic, microbiologic, and clinical criteria.

STUDY OBJECTIVE: To evaluate histologic, microbiological, and clinical criteria in the recognition of ventilator-associated pneumonia (VAP) in patients who died while mechanically ventilated. METHODS: The study group consisted of 39 patients who died after a mean of 14 days of mechanical ventilation. Postmortem fiberoptic bronchoscopy (FOB) and open lung biopsy were performed with collection of specimens initiated <1 h after death. The microbiological specimens included suction catheter aspirate of tracheal secretions, FOB-guided protected specimen brush (PSB) of tracheal secretions, blindly placed PSB in a distal airway, FOB-guided PSB in a distal airway, and FOB-guided BAL fluid (BALF) in a distal airway. Qualitative bacteriologic study was performed on all specimens, and quantitative bacteriologic study was performed on all but the suction catheter aspirate of the trachea. A biopsy specimen of peripheral lung parenchyma from the same region sampled by FOB was sent for quantitative culture and histologic analysis. The BALF was analyzed for cell population and percent of neutrophils containing intracellular organisms. The clinical criteria selected for comparison with histologic and microbiological results included a temperature > or =38.5 degrees C during the 48 h prior to death, a WBC count > or =15,000/mm3 in the 48 h prior to death, presence of a bacterial or fungal pathogen on the last sputum culture, radiographic worsening in the week prior to death, and worsening gas exchange defined as a 15% decrease in the PaO2/fraction of inspired oxygen ratio in the 72 h prior to death. RESULTS: None of the quantitative cultures had a reliable positive predictive value for histologic pneumonia. None of the five clinical criteria tested showed agreement with the presence or absence of histologic pneumonia. There was a significant correlation between qualitative and quantitative microbiological results from the distal airway/FOB-guided PSB, distal airway/BALF, and quantitative culture of the lung parenchyma. Also, suction catheter aspirate of the trachea had a sensitivity of 87% in recognizing the bacterial species simultaneously present in lung parenchyma. None of the patients with histologic pneumonia had <50% neutrophils in the BALF. CONCLUSIONS: Neither the bacterial, density from the four airway quantitative cultures, nor the bacterial density from quantitative culture of lung parenchyma accurately separated the histologic pneumonia and nonpneumonia groups. No clinical criteria or combination of clinical criteria correlated with the presence or absence of histologic pneumonia. A BALF with <50% neutrophils had a 100% negative predictive value for histologic pneumonia. A BALF quantitative culture had a sensitivity of 63%, specificity of 96%, and positive predictive value of 91% in recognizing sterile lung parenchyma. Thus, BALF may have a role in excluding pneumonia/infection in the ventilated patient. Antibiotic choice for the empiric therapy of VAP can be accurately guided by the microbial population recognized through culture of a tracheal suction catheter aspirate.

Aged↗

PubMed1991

Diversity of micro-fungi in an Antarctic dry valley.

The fungal microflora of a dry valley in Southern Victoria Land near McMurdo Sound, Antarctica, was investigated. Samples were collected from introduced objects such as a mummified penguin and spent chewing tobacco in addition to the sparse soil found in rock fissures, isolated moss colonies, shoreline deposit materials, CaCO3 precipitates, and microbial mat debris obtained from the frozen surface of the lake in the basin of Taylor Valley. Using conventional media and techniques, all collection sites yielded populations of yeasts and filamentous fungi. Water samples and live microbial mats from beneath the lake ice yielded species of fungi along with an abundance of bacteria.

Antarctic Regions↗

PubMed2005

PAH degradation capacity of soil microbial communities--does it depend on PAH exposure?

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of the environment. But is their microbial degradation equally wide in distribution? We estimated the PAH degradation capacity of 13 soils ranging from pristine locations (total PAHs approximately 0.1 mg kg(-1)) to heavily polluted industrial sites (total PAHs approximately 400 mg kg(-1)). The size of the pyrene- and phenanthrene-degrading bacterial populations was determined by most probable number (MPN) enumeration. Densities of phenanthrene degraders reflected previous PAH exposure, whereas pyrene degraders were detected only in the most polluted soils. The potentials for phenanthrene and pyrene degradation were measured as the mineralization of (14)C-labeled spikes. The time to 10% mineralization of added (14)C phenanthrene and (14)C pyrene was inversely correlated with the PAH content of the soils. Substantial (14)C phenanthrene mineralization in all soils tested, including seven unpolluted soils, demonstrated that phenanthrene is not a suitable model compound for predicting PAH degradation in soils. (14)C pyrene was mineralized by all Danish soil samples tested, regardless of whether they were from contaminated sites or not, suggesting that in industrialized areas the background level of pyrene is sufficient to maintain pyrene degradation traits in the gene pool of soil microorganisms. In contrast, two pristine forest soils from northern Norway and Ghana mineralized little (14)C pyrene within the 140-day test period. Mineralization of phenanthrene and pyrene by all Danish soils suggests that soil microbial communities of inhabited areas possess a sufficiently high PAH degradation capacity to question the value of bioaugmentation with specific PAH degraders for bioremediation.

Bacteria↗

PubMed1990

Effect of ionization on microbial air pollution in the dental clinic.

The use of spray-producing instruments in the dental clinic continuously creates a potentially harmful contamination of the room environment. In the present study a 13.5-kV corona discharge ionizing generator was used in order to investigate the effect of ions on the microbial air pollution of the dental clinic. Samples of microbial air population were collected in 9-cm-diameter plates containing either Bacto-Brain Heart Infusion Agar or Bacto-Mitis Salivarius Agar and exposed to different time periods in various locations of an active dental clinic. Microbial air levels in the dental clinic were significantly reduced with the generator (by 40-50%). The data suggest that the ionizing generator can be used to reduce the microbial air pollution within the dental clinic, thus reducing the environmental hazard of infections to the staff.

Air Ionization↗