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PubMed2003

The microbiological quality of drinking water sold on the streets in Kumasi, Ghana.

AIM: The aim of this study was to assess the microbiological quality of Ghanaian bottled and plastic-bagged drinking water sold on the streets of Metropolitan Kumasi, Ghana. METHODS AND RESULTS: Eight bottled, 88 factory-filled plastic sachet and 40 hand-filled hand-tied polythene-bagged drinking waters were examined for the presence of heterotrophic bacteria total viable counts (TVCs), indicators of faecal contamination (total coliforms, faecal coliforms and enterococci) and for lead, manganese and iron. Heterotrophic bacteria were found in all three types of water with TVCs per millilitre ranging from 1 to 460 for bottled water, 2-6.33 x 10(5) for factory-bagged sachet water and 2.33 x 10(3)-7.33 x 10(12) for hand-filled hand-tied bagged water. None of the microbial indicators of faecal contamination were detected in bottled water, whereas 4.5% of the factory-bagged sachets contained total coliforms and 2.3% faecal coliforms, and 42.5% of the hand-filled hand-tied bags contained total coliforms, 22.5% faecal coliforms and 5% enterococci. Iron was found in all three types of drinking water but at concentrations well within the WHO recommendations. Lead and manganese were not detected. CONCLUSION: Ghanaian bottled water is of good microbiological quality but some factory-bagged sachet and hand-filled hand-tied polythene-bagged drinking water are of doubtful quality. SIGNIFICANCE AND IMPACT OF THE STUDY: Factory-bagged sachets and hand-filled hand-tied bags of drinking water sold in Ghana should be monitored for microbiological contamination, with the aim of raising standards in the industry and re-assuring the public.

Colony Count, Microbial↗

PubMed1998

Novel screen methodologies for identification of new microbial metabolites with pharmacological activity.

Micro-organisms continue to provide an important source of chemical diversity for the discovery of compounds with new biological activities. Microbial metabolites discovered recently using assays to detect compounds with potential pharmacological utility are surveyed and found to represent an extensive range of structural types produced by a wide variety of organisms. Assays used for screening samples produced by microbial processes must be robust, sensitive and specific and able to operate above a background of potential interferences from a number of sources. Discovery assays currently in use fall into three main categories cell-based, receptor-ligand interaction and enzyme inhibition assays. Trends in the use of these assays and new developments in assay technology applicable to the screening of microbial samples are examined with particular reference to the high throughput screening environment. For microbial screening to be a competitive route to new drug leads, the disciplines involved must be engineered into a seamlessly integrated process to deliver novel compounds with the required biological properties rapidly.

Animals↗

PubMed2006

Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: implications for life detection and planetary protection.

Bacterial spores have been considered as microbial life that could survive interplanetary transport by natural impact processes or human spaceflight activity. Deposition of terrestrial microbes or their biosignature molecules onto the surface of Mars could negatively impact life detection experiments and planetary protection measures. Simulated Mars solar radiation, particularly the ultraviolet component, has been shown to reduce spore viability, but its effect on spore germination and resulting production of biosignature molecules has not been explored. We examined the survival and germinability of Bacillus subtilis spores exposed to simulated martian conditions that include solar radiation. Spores of B. subtilis that contain luciferase resulting from expression of an sspB-luxAB gene fusion were deposited on aluminum coupons to simulate deposition on spacecraft surfaces and exposed to simulated Mars atmosphere and solar radiation. The equivalent of 42 min of simulated Mars solar radiation exposure reduced spore viability by nearly 3 logs, while germination-induced bioluminescence, a measure of germination metabolism, was reduced by less than 1 log. The data indicate that spores can retain the potential to initiate germination-associated metabolic processes and produce biological signature molecules after being rendered nonviable by exposure to Mars solar radiation.

Aluminum↗

PubMed2005

Combining microarray and genomic data to predict DNA binding motifs.

The ability to detect regulatory elements within genome sequences is important in understanding how gene expression is controlled in biological systems. In this work, microarray data analysis is combined with genome sequence analysis to predict DNA sequences in the photosynthetic bacterium Rhodobacter sphaeroides that bind the regulators PrrA, PpsR and FnrL. These predictions were made by using hierarchical clustering to detect genes that share similar expression patterns. The DNA sequences upstream of these genes were then searched for possible transcription factor recognition motifs that may be involved in their co-regulation. The approach used promises to be widely applicable for the prediction of cis-acting DNA binding elements. Using this method the authors were independently able to detect and extend the previously described consensus sequences that have been suggested to bind FnrL and PpsR. In addition, sequences that may be recognized by the global regulator PrrA were predicted. The results support the earlier suggestions that the DNA binding sequence of PrrA may have a variable-sized gap between its conserved block elements. Using the predicted DNA binding sequences, a whole-genome-scale analysis was performed to determine the relative importance of the interplay between the three regulators PpsR, FnrL and PrrA. Results of this analysis showed that, compared to the regulation by PpsR and FnrL, a much larger number of genes are candidates to be regulated by PrrA. The study demonstrates by example that integration of multiple data types can be a powerful approach for inferring transcriptional regulatory patterns in microbial systems, and it allowed the detection of photosynthesis-related regulatory patterns in R. sphaeroides.

Bacterial Proteins↗

PubMed2025

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.

Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; 2 of these, 6-mercaptopurine by xanthine dehydrogenase and 5-fluorouracil by dihydropyrimidine dehydrogenase, have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.

Humans↗

PubMed1999

Determination of selected microbial volatile organic compounds by diffusive sampling and dual-column capillary GC-FID--a new feasible approach for the detection of an exposure to indoor mould fungi?

A new, analytically valid procedure is described to assess the exposure of human beings to the so-called microbial volatile organic compounds (MVOCs) in air. The method can be used routinely for large sample numbers and is especially valuable as a basis for further research on the correlation between single MVOCs and indoor mould growth. The procedure is based on the fact that fungi produce a variety of volatile organic compounds, such as 3-methylbutan-1-ol, 3-methylbutan-2-ol, fenchone, heptan-2-one, hexan-2-one, octan-3-one, octan-3-ol, pentan-2-ol, alpha-terpineol, and thujopsene, which they emit into the indoor environment. Using diffusive samplers, these MVOCs are adsorbed onto charcoal during a sampling interval of four weeks. The described method is thus superior to existing methods which use short-term active sampling. After desorption with carbon disulfide, the MVOCs were determined by dual-column gas chromatography with flame ionization detection using the large-volume injection technique for sample introduction. The detection limits ranged between 0.15 and 0.53 microgram m-3, within-series precision was found to range between 6.5 and 19.0%, and recovery was between 77 and 118%. The procedure has been successfully applied in the context of a large field study to measure the indoor MVOC exposure in children's rooms of 132 dwellings. The objective of the study was to examine the relation between indoor mould growth, the indoor MVOC exposure and the prevalence of adverse health effects. Information about mould formation has been obtained by a questionnaire and by the determination of colony forming units of mould fungi in mattress dust. With the exception of 3-methylbutan-2-ol, fenchone, nonan-2-one, octan-2-one, and thujopsene, indoor air concentrations of all MVOCs under investigation were significantly higher inside damp and mouldy dwellings. From the primary MVOCs under investigation, 3-methylbutan-1-ol, hexan-2-one, heptan-2-one, and octan-3-ol were found to be most reliable indicators for mould formation. A correlation was also found between selected MVOCs and the occurrence of mould species in mattress dust. Aspergillus sp. correlated with heptan-2-one, hexan-2-one, octan-3-ol, octan-3-one, and alpha-terpineol, while the occurrence of Eurotium sp. was correlated with higher indoor air concentrations of 3-methylbutan-1-ol, 3-methylbutan-2-ol, heptan-2-one, hexan-2-one, octan-3-ol, and thujopsene. Children living in dwellings with elevated MVOC levels had a higher prevalence of asthma, hay fever, wheezing, and irritations of the eyes. These positive associations persisted after controlling for confounding factors such as age, sex, body-mass index, number of siblings, social status, passive smoking, type of heating, and ventilation habits. However, they were not statistically significant. This lack of significance may be a result of the small number of investigated samples.

Air Pollution, Indoor↗

PubMed1986

Improved flotation technique for microscopy of in situ soil and sediment microorganisms.

An improved flotation method for microscopy of in situ soil and sediment microorganisms was developed. Microbial cells were released into gellike flotation films that were stripped from soil and sediment aggregates as these aggregates were submerged in 0.5% solutions of polyvinylpyrrolidone. The use of polyvinylpyrrolidone solutions instead of water facilitated the release of films from saturated samples such as aquifer sediments as well as from typical surface soils. In situ microbial morphological characteristics could then be surveyed rapidly by light microscopy of films stained with acridine orange. This method effectively determined the ranges of morphological diversity in a variety of sample types. It also detected microcolonies and other spatial relationships among microbial cells. Only a small fraction (3.4 to 10.1%) of the microflora was released into the flotation films, but plating and direct evaluations by microscopy showed that this fraction was representative of the total population.

Journal Article↗

PubMed2003

Protein microarray technology for unraveling the antibody specificity repertoire against microbial proteomes.

The genomes of microorganisms responsible for diseases of worldwide medical importance have been sequenced or will be available in the near future. Combinatorial cloning technologies for producing large numbers of proteins have been developed and high-throughput assays such as protein microarrays have been clinically validated for detecting the presence of antibodies directed against microbial antigens in human serum. These scientific and technical achievements offer the opportunity to investigate the natural immune response against the whole proteome of a variety of microorganisms. A powerful combination of genomic information, molecular tools and immunological assays are potentially available to identify the antigens that, either alone or in combination, function as targets of protective immunity, or could be used as markers for serodiagnosis.

Animals↗

PubMed2004

Microbial quality of water in dental unit reservoirs.

Microbial quality of water in a dental unit is of considerable importance since patients and dental staff are regularly exposed to water and aerosol generated by the unit. Water delivered to a dental unit by the so-called independent water system is the water coming from a reservoir which, at the same time, is an initial part of dental unit waterlines (DUWL). Thus, microbiological quality of this water is extremely important for the quality of water flowing from dental handpieces. The aim of the study was to assess microbiologically the water contained in dental unit reservoirs. Water samples were collected aseptically from the water reservoirs of 19 dental units. Results concerning microbial contamination: potable water quality indices, and detection and isolation of Legionella species bacteria, were presented. Over a half of the samples did not comply with the norms for potable water. In 63.1% of the cases, the number of colony forming units (cfu/ml) and of coliform organisms significantly exceeded acceptable values. Enterococcus was not detected in the samples of examined water. Similarly, no Legionella were found in the samples of dental unit reservoirs water. Reservoirs as water supplies and initial segment of DUWL should be subject to protocol to eliminate microbial contamination and routine monitoring to guarantee an appropriate quality of water used in dental treatment.

Dental Equipment↗

PubMed2002

Sensory, chemical and bacteriological changes in vacuum-packed pressurised squid mantle (Todaropsis eblanae) stored at 4 degrees C.

Sensory, chemical and bacteriological changes were studied in vacuum-packed squid mantles (Todaropsis eblanae) that were pressurised at 150, 200, 300 and 400 megapascal (MPa) for 15 min at ambient temperature and stored at 4 degrees C. Sensory analysis showed that the higher the pressurisation the longer the shelf-life. Thus, the lot pressurised at 400 MPa was rejected after 28 days' storage compared with 7 days for the untreated lot. The chemical results generally corresponded with the sensory ones. Furthermore, ammonia (NH3) and trimethylamine (TMA) were produced in the pressurised lots after a pressure dependent delay. Urea decreased to low levels in all lots with the exception of the 400 MPa lot. Onset of production of agmatine, the dominant amine in this species, and other biogenic amines was delayed by increasing pressure, but still, high concentrations of these amines were detected in pressurised lots of acceptable sensory quality. Microbial counts conducted after 1 day of storage showed that the bacterial load was reduced by all pressures, reaching levels below the detection limit in the lots treated with 200-400 MPa. However, growth was resumed in all lots after a pressure dependent delay. Luminous bacteria predominated initially in the lots pressurised at 300 and 400 MPa, but were outnumbered by Enterobacteriaceae and lactic acid bacteria at the time of sensory rejection of these lots. All colonies isolated prior to pressurisation were identified as Photobacterium phosphoreum. This bacterium also resumed growth faster than other members of the endogenous microflora after pressurisation. All luminous colonies were identified as P. phosphoreum. Lactic acid bacteria isolated at the final sampling point of the lot pressurised at 400 MPa were identified as Carnobacterium piscicola and Carnobacterium divergens, while Serratia liquefaciens and Proteus vulgaris make up Enterobacteriaceae.

Ammonia↗

PubMedDate not supplied

Comparison of the microbicidal activities of superoxidized and ozonated water in the disinfection of endoscopes.

The microbicidal activities of superoxidized water (electrolysed strong acid water [ESAW] or electrolysed weak acid water [EWAW]), ozonated water, 0.05% chlorhexidine and 2% glutaraldehyde were tested against seven strains of clinical micro-organism isolates. Following incubation of bacterial suspensions in ESAW and EWAW for 10 s, the number of micro-organisms was reduced below the detection limit. The microbicidal activities of ESAW and EWAW were similar to that of glutaraldehyde, and superior to ozonated water and 0.05% chlorhexidine. The microbicidal activities of ESAW, EWAW and ozonated water were markedly diminished in the presence of albumin. Microbial contamination of upper gastrointestinal endoscopes was detected after 90 endoscopic procedures, but treatment of the endoscope with ESAW, EWAW or ozonated water eradicated the microbes. These results indicate that ESAW and EWAW are effective disinfectants after mechanical cleaning of upper gastrointestinal endoscopes, and can, therefore, be used in the endoscopy unit.

Acids↗

PubMed2005

Bacterial communities associated with benthic organic matter in headwater stream microhabitats.

Bacterial communities associated with a variety of benthic detritus types were studied in three streams in the context of the chemical characteristics of the sediment material and the stream water. A cell purification assay was developed for a quantitative microscopic evaluation of bacterial community structure in detritus samples by fluorescence in situ hybridization (FISH). The efficiency of FISH with fluorescently monolabelled probes was compared with FISH with signal amplification by catalysed reporter deposition (CARD-FISH). In detritus types poor in organic carbon and nitrogen, the numbers of prokaryotes were related to the chemical characteristics of the stream water column, whereas no such relationship was found for detritus types rich in organic carbon and nitrogen. These results might help to provide criteria for the selection of detritus types for river ecosystem assessment and monitoring. The percentage of bacteria detected by FISH with monolabelled probes was correlated with the detritus total organic matter (OM). This is likely attributed to a higher ribosome content of microbial cells on substrates rich in OM. Cell detection by CARD-FISH did not show any correlation with OM content, indicating that this technique renders the results more independent from the activity state of cells. Fluorescence in situ hybridization with four group-specific probes suggested a relationship between substrate quality and the composition of the microbial assemblages on the various types of detritus. The improved protocol for cell purification and CARD-FISH may facilitate future investigations on the relationship between the riverine benthic detritus quality and microbial community composition.

Bacteria↗

PubMed1997

A low molecular weight artificial RNA of unique size with multiple probe target regions.

Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

Base Sequence↗

PubMed2003

Peptidoglycan molecular requirements allowing detection by Nod1 and Nod2.

Nod1 and Nod2 are mammalian proteins implicated in the intracellular detection of pathogen-associated molecular patterns. Recently, naturally occurring peptidoglycan (PG) fragments were identified as the microbial motifs sensed by Nod1 and Nod2. Whereas Nod2 detects GlcNAc-MurNAc dipeptide (GM-Di), Nod1 senses a unique diaminopimelate-containing GlcNAc-MurNAc tripeptide muropeptide (GM-TriDAP) found mostly in Gram-negative bacterial PGs. Because Nod1 and Nod2 detect similar yet distinct muropeptides, we further analyzed the molecular sensing specificity of Nod1 and Nod2 toward PG fragments. Using a wide array of natural or modified muramyl peptides, we show here that Nod1 and Nod2 have evolved divergent strategies to achieve PG sensing. By defining the PG structural requirements for Nod1 and Nod2 sensing, this study reveals how PG processing and modifications, either by host or bacterial enzymes, may affect innate immune responses.

Acetylglucosamine↗

PubMed2003

Evaluation of simple microbiol tests for detection of fecal coliforms directly at 44.5 degrees C.

Simple microbial test comprising H2S paper strip test, presence-absence (PA) test, and fluorogenic brila broth (BB) test performed directly at 44.5 degrees C were evaluated and compared with the standard most probable number (MPN) method for detection of fecal coliforms in 173 drinking water sources. BB and PA test were comparable with standard MPN method, whereas, poor compliance was noted for H2S test. PA test when compared with standard MPN test only 15% disagreement was detected, whereas, highest disagreement of 40% was observed in case of H2S test. BB test was found to be highly sensitive as only 7.8% disagreement with that of standard MPN test was found. Three hundred cultures obtained from positive tests were identified in order to evaluate the specificities of test used in detection of fecal indicator Escherichia coli. BB test was also found highly specific in detection of indicator organism as compared to PA and H2S test. Among the organisms isolated from BB test 84.4% of them were identified as E. coli as compared to 43.4 and 33.3 in PA and H2S test, respectively. The low incidence of recovery of E. coli (18.1%) for the standard MPN method places doubt on the validity of its application in tropical areas. The result of this investigation suggest that BB performed directly at 44.5 degrees C could be suitable cost effective test to assess the microbiological quality of drinking water in India and other tropical countries.

Developing Countries↗

PubMed2005

Computational detection of prokaryotic core promoters in genomic sequences.

The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non-adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.

Base Sequence↗

PubMed1996

New cineromycins and musacins obtained by metabolite pattern analysis of Streptomyces griseoviridis (FH-S 1832). I. Taxonomy, fermentation, isolation and biological activity.

Chemical screening using thin layer chromatography and various staining reagents offers the opportunity to visualize a nearly complete picture of a microbial secondary metabolite pattern (metabolic finger-print). This approach can be used advantageously for both, the detection of so-called "talented" strains, and for qualifying microbial strain collections, especially as a fundamental step of efficiently applied biological high-throughput assays. Based on their metabolic finger-print, microbial isolates can be classified in: (i) non-producing organisms, which gave no indication of the formation of secondary metabolites up to a defined detection limit, (ii) organisms of narrow productivity, which produce one or two secondary metabolites as main products with a restricted dependence to alteration of the culture conditions, and (iii) talented organisms, which are able to synthesize an array of structurally different secondary metabolites. As an example, the talented strain, Streptomyces griseoviridis (FH-S 1832), was studied in detail. Investigations in its taxonomical characterization, fermentation, as well as the isolation and purification procedures leading to 14-membered macrocyclic lactones of the cineromycin-type (cineromycin B and three new congeners) and to the musacins A to F are reported. Musacin C exhibits anthelminthic and weak antiviral activities.

Antiviral Agents↗

PubMed2006

Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules.

Microbial ecologists have used direct RT-PCR amplification of 16S rRNA molecules for the detection of active species of bacteria and archaea, and 18S rRNA molecules for the detection of active fungi. The drawback to this approach for fungi is that 18S rRNA sequences often do not provide sufficient taxonomic resolution to allow identification of taxa in mixed communities to genus or species level. Internal transcribed spacer (ITS) sequences are known to be more taxonomically informative than 18S rRNA sequences and are the common target in DNA based studies but are thought to be absent from RNA pools as they are cleaved after transcription of the large rRNA precursor molecule to leave the mature rRNA's for ribosome synthesis. Here we show, however, that fungal ITS regions can be detected in RNA pools by RT-PCR amplification of fungal precursor rRNA molecules. This suggests that precursor rRNA molecules reside in the cells of active fungi for sufficient time to allow RT-PCR amplification of ITS regions prior to their removal by post-transcriptional cleavage. The RT-PCR conditions for this approach were initially optimised using a range of fungi grown in pure culture prior to applying the approach to complex fungal communities in two contrasting soil types.

Cloning, Molecular↗