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PubMed2002

New approaches to the study of Antarctic lithobiontic microorganisms and their inorganic traces, and their application in the detection of life in Martian rocks.

Microbial life in the harsh conditions of Antarctica's cold desert may be considered an analogue of potential life on early Mars. In order to explore the development and survival of this epilithic and endolithic form of microbial life, our most sophisticated, state-of-the-art visualization technologies have to be used to their full potential. The study of any ecosystem requires a knowledge of its components and the processes that take place within it. If we are to understand the structure and function of each component of the microecosystems that inhabit lithic substrates, we need to be able to quantify and identify the microorganisms present in each lithobiontic ecological niche and to accurately characterize the mineralogical features of these hidden microhabitats. Once we have established the techniques that will allow us to observe and identify these microorganisms and mineral substrates in situ, and have confirmed the presence of water, the following questions can be addressed: How are the microorganisms organized in the fissures or cavities? Which microorganisms are present and how many are there? Additional questions that logically follow include: What are the existing water relationships in the microhabitat and what effects do the microorganisms have on the mineral composition? Mechanical and chemical changes in minerals and mineralization of microbial cells can give rise to physical and/or chemical traces (biomarkers) and to microbial fossil formation. In this report, we describe the detection of chains of magnetite within the Martian meteorite ALH84001, as an example of the potential use of SEM-BSE in the search for plausible traces of life on early Mars.

Antarctic Regions↗

PubMed1996

DNA based typing, identification and detection systems for food spoilage microorganisms: development and implementation.

The rapid identification of spoilage microorganisms is of eminent importance to the food industry. It provides the food industry with the opportunity to reduce economical losses by designing adequate intervention measures. The use of identification systems based on biochemical and physiological characteristics resulted often in disappointing identification results and misidentifications. This will inevitably lead to inappropriate strategies to prevent spoilage. This review discusses the potential of the DNA based identification technology including the polymerase chain reaction (PCR) for the identification and specific detection of microorganisms. Fingerprinting methods based on the DNA-probe technology enable a clear insight in the identity of microorganisms on different levels, varying from genus to strain level depending on the systems used. Discrimination between subspecies and strain level is shown to be helpful for investigating routes and sources of contamination. Differentiation at the species level is demonstrated to be essential in order to design a highly specific detection system enabling to signalize a microorganism that belongs to a particular species. Also indicated in this review is the necessity and the technical approach to detect microorganisms that display a particular undesirable trait.

DNA↗

PubMed2005

Identification of probiotic microorganisms in South African products using PCR-based DGGE analysis.

Probiotic microorganisms in commercial yoghurts and other food products are currently identified by traditional methods such as growth on selective media, morphological and biochemical characteristics. In this study, PCR-based DGGE analysis was used for the rapid and accurate identification of probiotic microorganisms from South African yoghurts and lyophilized preparations in capsule and tablet form. To identify the microorganisms present in these products, the DGGE profiles obtained were compared to two reference markers (A and B) composed of five lactobacilli and seven Bifidobacterium species, respectively. The results obtained were confirmed by species-specific PCR, as well as sequence analyses of unknown bands not present in the reference markers. It was found that only 54.5% of the probiotic yoghurts contained the microorganisms stated on the label compared to only a third (33.3%) of the lyophilized probiotic products. Some Bifidobacterium species were incorrectly identified and various microorganisms were detected that were not listed on the label. Sequence analyses confirmed the presence of Streptococcus spp. other than the yoghurt starter, Streptococcus thermophilus, in some of these products and in some instances label information was vague and non-scientific. PCR-based DGGE analyses proved to be a valuable culture-independent approach for the rapid and specific identification of the microbial species present in South African probiotic products.

Bifidobacterium↗

PubMed2003

Catabolism of volatile sulfur compounds precursors by Brevibacterium linens and Geotrichum candidum, two microorganisms of the cheese ecosystem.

Two Brevibacterium linens strains and the cheese-ripening yeast Geotrichum candidum were compared with regard to their ability to produce volatile sulfur compounds (VSCs) from three different precursors namely L-methionine, 4-methylthio-2-oxobutyric acid (KMBA) and 4-methylthio-2-hydroxybutyric acid (HMBA). All microorganisms were able to convert these precursors to VSCs. However, although all were able to produce VSCs from L-methionine, only G. candidum accumulated KMBA when cultivated on this amino acid, contrary to B. linens suggesting that the transamination pathway is not active in this microorganism. Conversely, a L-methionine gamma-lyase activity--which catalyses the one step L-methionine to methanethiol (MTL) degradation route--was only found in B. linens strains. Several other enzymatic activities involved in the catabolism of the precursors tested were investigated. KMBA transiently accumulated in G. candidum cultures, and was then reduced to HMBA by a KMBA dehydrogenase (KDH) activity. This activity was not detected in B. linens. Despite no HMBA dehydrogenase (HDH) was found in G. candidum, a strong HMBA oxidase (HOX) activity was measured in this microorganism. This latter activity was weakly active in B. linens. KMBA and HMBA demethiolating activities were found in all the microorganisms. Our results illustrate the metabolic diversity between cheese-ripening microorganisms of the cheese ecosystem.

Brevibacterium↗

PubMed2005

Effect of albumin on the photodynamic inactivation of microorganisms by a cationic porphyrin.

BACKGROUND: Photodynamic inactivation (PDI) employs visible light and a photosensitizer to inactivate cells. The technique is currently clinically used for the treatment of several malignancies. However, the PDI of microorganisms still remains in the research phase. PURPOSE: To study the effect of human blood plasma and human serum albumin (HSA) on the PDI of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans. METHODS: PDI experiments were performed using white light (30 mW cm-2) and the cationic 5-phenyl-10,15,20-tris(N-methyl-4-pyridyl)porphyrin chloride (TriP[4]) as photosensitizer. RESULTS: The microorganisms could be successfully photoinactivated by TriP[4] when suspended in phosphate buffered saline (PBS). In this medium, P. aeruginosa was the most resistant microorganism. Changing the suspending medium from PBS to human blood plasma reduced the PDI of all three microorganisms. In human blood plasma C. albicans was the most resistant microorganism. The same results were obtained with 4.5% and 7% HSA/PBS suspensions. CONCLUSIONS: Albumin inhibits the PDI of S. aureus, P. aeruginosa and C. albicans in a dose dependent manner. However, our results are encouraging towards the potential future application of PDI for the treatment of superficial wound infections caused by S. aureus, P. aeruginosa and C. albicans.

Candida albicans↗

PubMed2005

Characterization of microorganisms isolated from lignite excavated from the Záhorie coal mine (southwestern Slovakia).

Microorganisms were isolated from lignite freshly excavated in the Záhorie coal mine (southwestern Slovakia) under conditions excluding contamination with either soil or air-borne microorganisms. The isolates represented both Prokarya and Eukarya (fungi). All were able to grow on standard media, although some microorganisms were unstable and became extinct during storage of coal samples. Bacteria belonged to the genera Bacillus, Staphylococcus, and Rhodococcus, according to both morphological criteria and ITS sequences. Several bacterial isolates were resistant to antibiotics. The presence of anaerobic bacteria was also documented, although they have not yet been identified. Fungal isolates were typified by using their ITS sequences. They belonged to the genera Trichoderma (Hypocrea), Penicillium, Epicoccum, Metarhizium (Cordyceps), and Cladosporium. Several fungi produced compounds with antibiotic action against standard bacterial strains. The evidence for the presence of microorganisms in native lignite was obtained by means of fluorescence microscopy, scanning electron microscopy, and electron microprobe analysis. Results demonstrated that microorganisms were able to survive in the low-rank coal over a long time period.

Anti-Bacterial Agents↗

PubMed1998

Few microorganisms associated with bacterial vaginosis may constitute the pathologic core: a population-based microbiologic study among 3596 pregnant women.

OBJECTIVE: To evaluate the association between various microorganisms isolated from the genital tract in pregnant women with bacterial vaginosis. STUDY DESIGN: A cross-sectional population-based study among pregnant women addressed at their first antenatal visit before 24 full gestational weeks from the referring area of the Department of Obstetrics and Gynecology at Odense University Hospital, Denmark, from November 1992 to February 1994. The main outcome measures were prevalence of various microorganisms and statistical estimates of interactions (crude, adjusted, and relative odds ratios) between the microorganisms isolated from the lower genital tract in pregnant women with and without clinical diagnosis of bacterial vaginosis. RESULTS: Three thousand five hundred ninety-six (3596) pregnant women were asked to participate. Of the 3596 pregnant women 3174 (88.4%) agreed to participate before 24 full gestational weeks. After controlling for the presence of other microorganisms, strong associations between Gardnerella vaginalis, anaerobic bacteria, Mycoplasma hominis, and present bacterial vaginosis were found. Similarly Lactobacillus spp. were found to be associated with the absence of bacterial vaginosis. The combination of G. vaginalis and anaerobic bacteria and/or M. hominis was found in 59.6% of the cases with bacterial vaginosis and in 3.9% of the cases without bacterial vaginosis (odds ratio 36.4, 95% confidence interval 27.8 to 47.8). The crude odds ratio was found to be as high as 74.8 (95% confidence interval 32.3 to 174.1) when the combination of G. vaginalis, M. hominis, anaerobic bacteria, and no Lactobacillus spp. was associated with bacterial vaginosis. CONCLUSION: There is a microbial foundation for bacterial vaginosis, and it is possibly due to an intermicrobial interaction in which the microorganisms G. vaginalis, anaerobic bacteria, and M. hominis are dominating, indicating that these constitute the pathologic core of bacterial vaginosis.

Adolescent↗

PubMed1997

Exposure assessment of airborne microorganisms by fluorescence microscopy and image processing.

The purpose of this study was to improve the exposure assessment of airborne microorganisms by means of image processing of fluorescence microscopy images. This technique reduces the analysis time and also offers the opportunity to measure the size distribution of the microorganisms. We developed and implemented an automatic focusing procedure in order to count and size evaluate the microorganisms in the sample. However, automatic focusing was not possible if there were any impurities such as larger particles present. Therefore, manual focusing of the microscope had to be applied in connection with automatic counting and size evaluation when assessing the exposure of workers handling materials containing microorganisms, for example. This is also an improvement as it is faster than the fully manual standard methods. The new methods developed in this study correlated (r2 > 0.85) with the standard method for samples of E. coli and for samples of generated airborne bioaerosols from household waste, although a correction factor is necessary. No correlation was found for samples of generated bioaerosols from composted waste. This work has established a possibility for improving exposure assessment of airborne microorganisms by means of image processing instead of manual counting.

Air Microbiology↗

PubMed2001

Microorganisms' activity and energy fluxes in Lake Varese (Italy): a field method.

Microorganisms are fundamental components of energy fluxes in aquatic ecosystems. Interest in plankton production and respiration has recently stimulated exploration of the use of electron transfer system (ETS) activity in oceanography and limnology. If we consider microorganism production (MP) and microorganism respiration (MR), due to aerobic and anaerobic metabolism, microorganism growth efficiency can be defined as MGE = MP/(MP + MR). In order to calculate MGE, we measured independently the two components of ETS (photosynthesis electron transfer system activity (PETS) and respiration electron transfer system activity (RETS)) during an annual cycle using a portable biosensor microorganisms amperometric detector system (MiDAS) on the site. MGE was calculated in samples collected from the photic and aphotic zones and the superficial sediment and ranged between 0.60 and 0.45 and dropped to 0.15 at the end of the summer. This substantial decrease is probably due to the prevalence of the anaerobic-heterotrophic metabolism after a pronounced state of anoxia during the summer algal bloom.

Aerobiosis↗

PubMed2004

Evaluation of dispersion methods for enumeration of microorganisms from peat and activated carbon biofilters treating volatile organic compounds.

To enumerate microorganisms having colonized biofilters treating volatile organic compounds, it is necessary firstly to evaluate dispersion methods. Crushing, shaking and sonication were then tested for the removal of microflora from biofilters packing materials (peat and activated carbon). Continuous or discontinuous procedures, and addition of glass beads had no effect on the number of microorganisms removed from peat particles. The duration of treatment also had no effect for shaking and crushing, but the number of microorganisms after 60 min of treatment with ultrasound was significantly higher than that obtained after 0.5 min. The comparison between these methods showed that crushing was the most efficient for the removal of microorganisms from both peat and activated carbon. The comparison between three chemical dispersion agents showed that 1% Na-pyrophosphate was less efficient, compared with 200 mM phosphate buffer or 1% Na-hexametaphosphate. To optimize the cultivation of microorganisms, three different agar media were compared. Tryptic soy agar tenfold diluted (TSA 1/10) was the most suitable medium for the culture of microflora from a peat biofilter. For the activated carbon biofilter, there was no significant difference between Luria Bertoni, TSA 1/10, and plate count agar. The optimized extraction and enumeration protocols were used to perform a quantitative characterization of microbial populations in an operating laboratory activated carbon biofilter and in two parallel peat biofilters.

Air Pollution↗

PubMed1999

The potential of in situ hybridization and an immunogold assay to identify Legionella associations with other microorganisms.

Based on in vitro studies, bacteria in the genus Legionella are believed to multiply within protozoa such as amoebae in aquatic environments. Current methods used for detection of Legionella species, however, are not designed to show this relationship. Thus the natural intimate association of Legionella with other microorganisms remains to be clearly documented and the extent to which protozoa might be infected with Legionella species remains undefined. In this report we describe methods based on the use of Legionella specific reagents that would prove useful in describing its associations with other microorganisms. An immunogold and in situ hybridization technique have the potential to demonstrate the natural occurrence of Legionella species in free-living amoebae. In preliminary observations, however, bacteria reactive with Legionella specific reagents were often not intimately associated with amoebae. Bacteria occurred as free single cells, as cell aggregates, in proximity to other cells and debris, and only occasionally in close proximity to amoebae. Although some Legionella species replicate within amoebae, these preliminary observations suggest the bacteria may be encountered most frequently as extracellular microorganisms, either free-floating or in association with other structures or microorganisms. The future use of these techniques will aid in the elucidation of any naturally occurring relationships between Legionella species and other microorganisms.

Acanthamoeba↗

PubMed1998

Comparison of bedside- and laboratory-inoculated Bactec high- and low-volume resin bottles for the recovery of microorganisms causing peritonitis in CAPD patients.

There is not yet a universally accepted protocol for the recovery of microorganisms causing peritonitis in patients on continuous ambulatory peritoneal dialysis (CAPD). We prospectively analyzed 343 peritoneal effluent specimens by three protocols: 1) 10 ml of effluent centrifuged and the pellet plated onto blood, MacConkey agars, and into thioglycolate broth (routine method); 2) 5 ml and 10 ml inoculated at the bedside into Bactec 16A and 26A aerobic resin-containing blood culture bottles, respectively; and 3) 5 ml and 10 ml inoculated in the laboratory into Bactec 16A and 26A media, respectively. One hundred and forty (41%) peritoneal effluent specimens had microorganisms recovered, and, of these, 101 were recovered by routine culture compared to 117 (p < .021), 125 (p < .0001), 115 (p < .047), and 116 (p < .032) for bedside-inoculated 16A and 26A and for laboratory-inoculated 16A and 26A, respectively. Bedside-inoculated bottles were not significantly better than laboratory-inoculated bottles, and high-volume bottles were not significantly better than low-volume bottles for detection of patients positive for microorganisms; however, the number of total microorganisms recovered were significantly better from all inoculated blood culture bottles compared to routine culture. Bedside- and laboratory-inoculated resin-containing blood culture bottles are superior to the routine method for recovery of microorganisms causing peritonitis in CAPD patients.

Ascitic Fluid↗

PubMed2001

L-methionine degradation potentialities of cheese-ripening microorganisms.

Volatile sulphur compounds are major flavouring compounds in many traditional fermented foods including cheeses. These compounds are products of the catabolism of L-methionine by cheese-ripening microorganisms. The diversity of L-methionine degradation by such microorganisms, however, remains to be characterized. The objective of this work was to compare the capacities to produce volatile sulphur compounds by five yeasts, Geotrichum candidum, Yarrowia lipolytica, Kluyveromyces lactis, Debaryomyces hansenii, Saccharomyces cerevisiae and five bacteria, Brevibacterium linens, Corynebacterium glutamicum, Arthrobacter sp., Micrococcus lutens and Staphylococcus equorum of technological interest for cheese-ripening. The ability of whole cells of these microorganisms to generate volatile sulphur compounds from L-methionine was compared. The microorganisms produced a wide spectrum of sulphur compounds including methanethiol, dimethylsulfide, dimethyldisulfide, dimethyltrisulfide and also S-methylthioesters, which varied in amount and type according to strain. Most of the yeasts produced methanethiol, dimethylsulfide, dimethyldisulfide and dimethyltrisulfide but did not produce S-methylthioesters, apart from G. candidum that produced S-methyl thioacetate. Bacteria, especially Arth. sp. and Brevi. linens, produced the highest amounts and the greatest variety of volatile sulphur compounds includling methanethiol, sulfides and S-methylthioesters, e.g. S-methyl thioacetate, S-methyl thiobutyrate, S-methyl thiopropionate and S-methyl thioisovalerate. Cell-free extracts of all the yeasts and bacteria were examined for the activity of enzymes possibly involved in L-methionine catabolism, i.e. L-methionine demethiolase, L-methionine aminotransferase and L-methionine deaminase. They all possessed L-methionine demethiolase activity, while some (K. lactis, Deb. hansenii, Arth. sp., Staph. equorum) were deficient in L-methionine aminotransferase, and none produced L-methionine deaminase. The catabolism of L-methionine in these microorganisms is discussed.

Arthrobacter↗

PubMed2000

Characterization of microorganisms and biomarker development from global ESI-MS/MS analyses of cell lysates.

The capability for sensitive and accurate identification of microorganisms has potential applications that include the monitoring of industrial bioprocessing operations, food safety analyses, disease diagnosis, and detection of potential biological hazards. Efforts based upon matrix-assisted laser desorption/ionization mass spectrometry to detect and identify specific microorganisms have been actively pursued for several years. We report a new method being developed to select useful biomarkers for the identification of microorganisms based upon electrospray ionization (ESI)-ion trap mass spectrometry. Crude cell lysates are processed using a recently developed dualmicrodialysis device and then directly infused into an ion trap MS. The low ESI flow rate and precursor ion accumulation capability of the ion trap MS enables high-sensitivity MS/MS analyses. Precursor ions are automatically selected and analyzed using tandem MS (MS/MS) to produce "global" MS/MS surveys and processed to yield two-dimensional MS/MS spectral displays. Such global MS/MS surveys are demonstrated for Escherichia coli lysates. The distinctive MS/MS spectral patterns can be used to identify mass spectrometric-detected species useful as biomarkers, which then provide a basis for confident microorganism identification. The results presented demonstrate the application of this method for the identification of microorganisms, as well as for detection of bacteriophage MS2 in the presence of a large excess of E. coli.

Biomarkers↗

PubMed2002

Immunoglobulin G antibodies of children exposed to microorganisms in a water-damaged school.

The aim of this study was to determine whether exposure to fungi (molds and yeasts) among children attending a water-damaged school was reflected by the children's immunoglobulin G (IgG) response to microorganisms typical of water damage and whether the presence of these IgG antibodies was associated with respiratory symptoms and morbidity. The relationships between positive IgG antibodies and atopy, described as elevated allergen-specific immunoglobulin E (IgE) antibodies, were also examined. The study population consisted of a randomly selected group of exposed children attending a water-damaged school and a group of unexposed children of the same age. Serum samples for analyses of IgG and IgE antibodies were drawn from the children. The respiratory morbidity, the number of positive IgG antibodies to nine microorganisms indicating water damage, and IgE sensitization to common environmental allergens (Phadiatop) were studied. The mean number of positive IgG findings was significantly higher among the exposed children. The number of positive IgG antibodies did not correlate with respiratory illnesses or symptoms at the individual level even though the exposed children who had positive IgG antibodies to four or more microorganisms in the total group comparison tended to have higher respiratory morbidity. In the exposed group, a negative correlation was found between the number of positive IgG antibodies and the total value of allergen-specific IgE antibodies. As among adults exposed to microorganisms at work, IgG antibodies in children seem to be a relevant indicator of exposure to microorganisms in a water-damaged school on the group level.

Allergens↗

PubMed1990

16S rRNA sequences reveal numerous uncultured microorganisms in a natural community.

Microbiologists have been constrained in their efforts to describe the compositions of natural microbial communities using traditional methods. Few microorganisms have sufficiently distinctive morphology to be recognized by microscopy. Culture-dependent methods are biased, as a microorganism can be cultivated only after its physiological niche is perceived and duplicated experimentally. It is therefore widely believed that fewer than 20% of the extant microorganisms have been discovered, and that culture methods are inadequate for studying microbial community composition. In view of the physiological and phylogenetic diversity among microorganisms, speculation that 80% or more of microbes remain undiscovered raises the question of how well we know the Earth's biota and its biochemical potential. We have performed a culture-independent analysis of the composition of a well-studied hot spring microbial community, using a common but distinctive cellular component, 16S ribosomal RNA. Our results confirm speculations about the diversity of uncultured microorganisms it contains.

Base Sequence↗

PubMed1990

Microorganisms associated with chromosome destruction and reproductive isolation between two insect species.

Microorganisms have been implicated in causing cytoplasmic incompatibility in a variety of insect species, including mosquitoes, fruitflies, beetles and wasps. The effect is typically unidirectional: incompatible crosses produce no progeny or sterile males, whereas the reciprocal crosses produce normal progeny. The parasitic wasp Nasonia vitripennis is one of the few species in which the cytogenetic mechanism of incompatibility is known. In this species the paternal chromosome set forms a tangled mass in a fertilized egg and is eventually lost. Here we report that cytoplasmic microorganisms are associated with complete bidirectional incompatibility between N. vitripennis and a closely related sympatric species, N. giraulti. Microorganisms can be seen in the eggs of both species. Hybrid offspring are normally not produced in crosses between the two species, but do occur after elimination of the microorganisms by antibiotic treatment. A cytogenetic and genetic study shows that bidirectional interspecific incompatibility is due to improper condensation of the paternal chromosomes. Microorganism-mediated reproductive isolation is of interest because it could provide a rapid mode of speciation. The mechanism of incompatibility in Nasonia is also of interest as a potential tool for studying chromosome imprinting and chromosome condensation.

Animals↗

PubMed1993

Molecular identification of microorganisms associated with parthenogenesis.

Cytoplasmically interited microorganisms are widespread in insects and have been implicated as causes of female parthenogenesis (females developing from unfertilized eggs) and cytoplasmic incompatibility. Normal sexual reproduction can be restored by treatment with antibiotics. Sequence analysis of the DNA encoding 16S ribosomal RNA has shown that cytoplasmic incompatibility bacteria from diverse insect taxa are closely related (they share >95% sequence sililarity) and belong to the alpha subdivision of Proteobacteria. Here we show that parthenogenesis-associated bacteria from parasitoid Hymenoptera also fall into this bacterial group, having up to 99% sequence similarity to some incompatibility microorganisms. Both incompatibility and parthenogenesis microorganisms alter host chromosome behaviour during early mitotic divisions of the egg. Incompatibility bacteria act by interfering with paternal chromosome incorporation in fertilized eggs, whereas parthenogenesis bacteria prevent segregation of chromosomes in unfertilized eggs. These traits are adaptive for the microorganisms. On the basis of their sequence similarities, we conclude that parthenogenesis bacteria and cytoplasmic incompatibility bacteria form a monophyletic group of microorganisms that 'specialize' in manipulating chromosome behaviour and reproduction of insects.

Animals↗