PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Microbial ecology”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed1977

The environment and the microbial ecology of human skin.

Microbial flora of the skin of three human population groups representing different natural environments was examined quantitatively and qualitatively to determine whether environmental differences in temperature and humidity can influence the microbial flora of normal skin. Five anatomical skin sites - hands, back, axillae, groin, and feet - were sampled from 10 subjects working in a high-humidity, high-temperature environment, 10 subjects from a low-temperature, high-humidity environment, and 10 subjects working in a moderate-temperature and low-humidity environment. Bacterial populations were significantly larger from the back, axillae, and feet in individuals from the high-temperature and high-humidity environment as compared to the moderate-temperature, low-humidity environment. High humidity and low temperature had no significant effect on total populations, but this group showed a higher frequency of isolation of fungi, and gram-negative bacteria from the back and feet. Although there was an indication that increase in the environmental humidity could result in an increased frequency of isolation of gram-negative bacteria, there was no evidence that an increase in either temperature or humidity altered the relative proportions of gram-negative bacteria in the predominantly gram-positive microbial flora found on normal skin. It was concluded that, although climatic changes may cause fluctation in microbial populations from certain sites, they are not a major influence on the ecology of the microbial flora of normal skin in the natural environment. The variables introduced by studying individuals in their natural environment and the influence of these on the results are discussed.

Journal Article↗
PubMed2001

Microorganisms with a taste for vanilla: microbial ecology of traditional Indonesian vanilla curing.

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis, and B. smithii) developed under the high temperatures (up to 65 degrees C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans.

Bacillus↗
PubMed2006

Microbial ecology of drinking water distribution systems.

The supply of clean drinking water is a major, and relatively recent, public health milestone. Control of microbial growth in drinking water distribution systems, often achieved through the addition of disinfectants, is essential to limiting waterborne illness, particularly in immunocompromised subpopulations. Recent inquiries into the microbial ecology of distribution systems have found that pathogen resistance to chlorination is affected by microbial community diversity and interspecies relationships. Research indicates that multispecies biofilms are generally more resistant to disinfection than single-species biofilms. Other recent findings are the increased survival of the bacterial pathogen Legionella pneumophila when present inside its protozoan host Hartmannella vermiformis and the depletion of chloramine disinfectant residuals by nitrifying bacteria, leading to increased overall microbial growth. Interactions such as these are unaccounted for in current disinfection models. An understanding of the microbial ecology of distribution systems is necessary to design innovative and effective control strategies that will ensure safe and high-quality drinking water.

Animals↗
PubMed2006

Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology.

Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai-Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40-70 mM) and dissolved organic carbon (1596-5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were approximately 2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 x 10(9) cells/g at the water-sediment interface to 6 x 10(7) cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the alpha-, beta-, and gamma-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water-sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but the presence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped in the Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and alpha- and gamma-proteobacterial isolates were obtained from a water sample from the lake-bottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.

Acridine Orange↗
PubMed1986

Changes in microbial ecology by therapeutic use of aminoglycosides.

Alterations in microbial ecology caused by the usage of aminoglycosides for therapy of human infections are due to their selective pressure favouring insensitive or resistant species or strains. There is a positive correlation between aminoglycoside consumption and the incidence of resistance to aminoglycosides. This correlation is, however, modified by measures of infection control. At the present time, the overall incidence of resistance to aminoglycosides does not show major changes. The ecological impacts of aminoglycoside consumption appear to be less significant as compared to other antibiotics due to factors specific for the aminoglycoside group.

Aminoglycosides↗
PubMed2006

daime, a novel image analysis program for microbial ecology and biofilm research.

Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.

Biofilms↗
PubMed2005

Culture-dependent and -independent methods to investigate the microbial ecology of Italian fermented sausages.

In this study, the microbial ecology of three naturally fermented sausages produced in northeast Italy was studied by culture-dependent and -independent methods. By plating analysis, the predominance of lactic acid bacteria populations was pointed out, as well as the importance of coagulase-negative cocci. Also in the case of one fermentation, the fecal enterocci reached significant counts, highlighting their contribution to the particular transformation process. Yeast counts were higher than the detection limit (> 100 CFU/g) in only one fermented sausage. Analysis of the denaturing gradient gel electrophoresis (DGGE) patterns and sequencing of the bands allowed profiling of the microbial populations present in the sausages during fermentation. The bacterial ecology was mainly characterized by the stable presence of Lactobacillus curvatus and Lactobacillus sakei, but Lactobacillus paracasei was also repeatedly detected. An important piece of evidence was the presence of Lactococcus garvieae, which clearly contributed in two fermentations. Several species of Staphylococcus were also detected. Regarding other bacterial groups, Bacillus sp., Ruminococcus sp., and Macrococcus caseolyticus were also identified at the beginning of the transformations. In addition, yeast species belonging to Debaryomyces hansenii, several Candida species, and Willopsis saturnus were observed in the DGGE gels. Finally, cluster analysis of the bacterial and yeast DGGE profiles highlighted the uniqueness of the fermentation processes studied.

Bacteria↗
PubMed2006

Effect of hypochloride on microbial ecology of bulking and foaming activated sludge treatment for tannery wastewater.

This study investigates the effect of hypochloride application for controlling bulking and foaming on the microbial ecology of an activated sludge system treating tannery wastewater. Detailed characterization of the wastewater treatment influent and effluent is also reported for the study period. During the study, bulking and foaming are first monitored with a sudden burst in the sludge volume index over 250 mL g(-1), creating a significant deterioration of the effluent quality. The corresponding upset in the microbial ecology is the combined excessive proliferation of M. parvicella, N. limicola II and Gordona (Nocardia) spp., but mainly triggered by Gordona contamination of the floc structure and the rapid outward growth of this filamentous microorganism extending to adjacent flocs. Chlorine application at an average rate of 3 g Cl(-1)(kg MLSS.day)(-1) for 12 days provide an effective solution for bulking and foaming, restoring the effluent quality. It destroys filamentous texture between the flocs, leaving only a lot of loose and chopped filament fragments and, totally removes the Gordona spp. from solution which retrieves back into the flocs. Therefore, chlorine remediation of bulking and foaming, although temporarily effective, is only superficial as the Gordona seeding inside the floc remains intact and potentially available for excessive growth in the next favorable conditions.

Actinobacteria↗
PubMed2006

Wastewater treatment: a model system for microbial ecology.

Biological wastewater treatment is among the most important biotechnological applications and, as drivers of the key processes, microorganisms are central to its success. Therefore, the study of wastewater microorganisms has obvious applied significance; however, the importance of wastewater treatment reactors as model systems for microbial ecology is often overlooked. Modern molecular techniques, including environmental genomics, have identified unexpected microbial key players for nutrient removal and sludge bulking and/or foaming, and provided many exciting insights into the diversity, functions and niche differentiations of these predominantly uncultivated microorganisms. It is now time for wastewater microbiology to be recognized as a mature and dynamic discipline in its own right, offering much toward a deeper understanding of life in complex microbial communities. Here, we consider selected key findings to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology.

Bacteria↗
PubMed2006

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

Bacteria↗
PubMed1998

Manipulating ruminal fermentation: a microbial ecological perspective.

The essential role of ruminal microflora in ruminant nutrition provides the potential for improvement in animal production via altering the numbers or activities of specific classes of microorganisms. Successful alterations will be facilitated by an understanding of the microbial ecology of the rumen based on its mechanistic underpinnings. Demonstrated improvements in ruminal fermentation can be traced to their consonance with well-established principles of microbial ecology (niche occupancy, selective pressure, adaptation, and interactions) and the thermodynamics and kinetics of substrate utilization. Application of these principles to several proposed alterations of the ruminal bacterial population allows a prediction of their relative feasibility. Improving fiber digestion, decreasing protein degradation, and detoxifying feed components that are present in low concentrations will be difficult to achieve in the rumen and are best approached by altering the feed, either genetically or with postharvest treatment. By contrast, the detoxification of feed components present in high concentration, and redirection of electron disposal away from methanogenesis, are more productive targets for microbiological research.

Animals↗
PubMedDate not supplied

[Microbial ecology and the state of the gastrointestinal mucosa in patients with allergic diseases].

Patients with allergic diseases of the skin and the respiratory system were found to have a high rate of disturbances in the microbial ecology of the gastrointestinal tract and the involvement of all its sections into the pathological process. On the mucous membrane of different sections of the digestive tract spiral-like bacteria were detected in a large percentage of cases. The possibility of the fact that the development and maintenance of the allergic process were evidently linked with the detected changes in the microbial ecology and pathomorphological features of the gastrointestinal mucosa could hardly be excluded, which made it necessary to make corrections in the therapeutic process.

Adult↗
PubMed1985

Microbial ecology of plaque in rats with naturally occurring gingivitis.

The microbial ecology of adherent plaque was investigated in relation to the pathological findings of gingivitis in plaque-susceptible rats. Plaque developed in the gingiva of the lower incisor in plaque-susceptible rats, but not in plaque-resistant rats, after they were fed a commercial powder diet. With increase in plaque volume, the total counts of bacteria increased 10(9) to 10(11)/g. In the first 3 months, Bacteroides species increased and became the predominant population. Streptococcus species also increased at the same time. After 9 months, Fusobacterium species and oral Treponema species were recognized in increasing numbers. The anaerobic bacteria increased in proportion with the progression of plaque development. Bacteroides intermedius, Fusobacterium nucleatum, Streptococcus salivarius, and other species were isolated. Acute gingivitis was observed within 3 months, and subacute-chronic gingivitis was observed between 2 and 12 months. These findings suggest that proportional changes in the gingival plaque flora may uniquely contribute to the development of gingival inflammation in this experimental model.

Animals↗
PubMed2006

The maturing of microbial ecology.

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

Archaea↗
PubMed1988

Microbial ecology of the terrestrial subsurface.

We have presented a current view of the microbial ecology of the terrestrial subsurface by considering primarily the ecology of shallow aquifer sediments. The properties of the aquifer sediments and groundwater determine their ability to support microbial life and control the abundance and activities of microorganisms. Pore size, nutrient limitations, availability of electron acceptors, and large surface area for attachment all may have major effects on microbial abundance and activities in aquifer material. Microorganisms are the predominant forms of life in the subsurface. They will be found wherever enough space, nutrients, and water are available for them to live. Environmental factors such as pH, temperature, hydrostatic pressure, and dissolved salts also may influence subsurface microbial populations, but these factors do not exhibit great extremes in shallow water table aquifers, and thus only in very deep formations might they limit diversity or preclude the existence of microorganisms. Although the presence and activity of microorganisms in most subsurface environments are predictable, only recently have subsurface microbial populations in shallow subsurface zones been characterized. Aseptic sampling methods have been employed and microbiological and biochemical methods have been adapted to determine the types, abundance, and metabolic activities of microorganisms in subsurface material. Bacteria dominate, but eukaryotic microorganisms also are present. Vertical profile studies of a shallow aquifer in Oklahoma showed that active microbial biomass declined with depth to the unsaturated zone, but was variable in saturated sediments. Such a distribution of active biomass may be common in shallow aquifers. Studies on the lateral distribution of microorganisms in shallow and deep aquifers suggest that microorganisms are transported or migrate over fairly long distances in aquifer sediments. Surficial aquifers may be colonized by vertical or lateral transport and migration of surface microorganisms from recharge areas, but microorganisms could also have colonized when sediments were originally deposited. The biological and physical mechanisms controlling the migration of microorganisms in aquifers are not well understood. The function of shallow aquifers was considered with regard to nutritional ecology. Most pristine aquifers are oligotrophic. Heterotrophic life in these unique ecosystems is supported by secondary organic compounds that filter down from the soil above. The quantity and quality of organic nutrients depend on the age of water and rate of recharge of the aquifer.(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteria↗
PubMed2000

Microbial ecology of the leach bed anaerobic digestion of unsorted municipal solid waste.

The microbial ecology of the sequential, leach-bed, mesophilic anaerobic digestion of unsorted, coarse municipal solid waste (MSW) was examined over 80 days. The methane yield was approximately 75% of the ultimate biochemical methane potential (BMP) of the waste loaded into the digesters. The operational strategy involved a sequence of two digesters containing fresh and anaerobically stabilised MSW respectively. Cell wall phospholipid fatty acid (PLFA) and ether lipid (PLEL) analysis was used to monitor changes in microbial biomass. Both Bacterial and Archaeal biomass were heavily influenced by pH during the two-week start up period. Archaeal biomass peaked just before the methane production rate reached a maximum whereas Bacterial biomass peaked at a later stage. Changes in the phylogenetic diversity of the population were monitored by denaturing gradient gel electrophoresis (DGGE). An analysis of the changes in DGGE banding patterns suggested that rapid start-up of a new reactor was effected by inoculation as well as the provision of buffering capacity from the mature reactor leachate.

Archaea↗
PubMed2000

Dental caries and the microbial ecology of dental plaque: a review of recent advances.

Our understanding of the microbial ecology of dental plaque has rapidly grown with recent developments in the techniques of molecular biology. In particular, knowledge of the mechanisms underlying the acquisition, establishment, pathogenicity, and evolution of the group of organisms responsible for dental caries--the mutans streptococci--has expanded to the point that we can now contemplate new opportunities for caries prevention. These advances reinforce developing concepts of dental plaque as an interdependent, interacting community of specialised organisms with an ability to rapidly adapt conferred by gene structures that facilitate the expeditious modular rearrangement of protein components.

Adaptation, Biological↗