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PubMedDate not supplied

[The effect of products of plant and microbial origin on phagocytic function and on the release of oxygen free radicals by mouse peritoneal macrophages].

The effect of in vivo stimulation with an aqueous extract obtained from roots of Symphytum officinale and Cantastim on mouse peritoneal macrophages was investigated. The results obtained showed that these products initially activated the respiratory burst of the cells and later inhibited it, activating the synthesis of catalase, SOD etc. These data suggest that macrophages challenged by various ingested antigens destroy them initially through oxygen dependent mechanisms and later through enzymatic digestion in order to retain unimpaired their epitopes.

Adjuvants, Immunologic↗

PubMed2006

[Application of modern molecular biology techniques to study micro-ecosystem in the rumen].

The microbial community inhabiting in the rumen is characterized by its high population density, wide diversity and interactive complexity. However, until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional characterization) which probably only account for 10% to 20% of the rumen microbial population. Modem molecular biology techniques provide effective methods to study the micro-ecosystem in the rumen. The use of molecular techniques based on nucleic acid probes is likely to revolutionize the approach to microbial ecology in the rumen and provide, not simply a refinement or increased understanding but a complete description of rumen community for the first time. Modem molecular techniques based on sequence comparisons of nucleic acids may be used to explore molecular characterization and provide a classification scheme which predicts natural evolutionary relationships. Genetic fingerprinting techniques that provide a pattern or profile of genetic diversity have been applied in a variety of environmental studies for the analysis of microbial communities. Whole-cell hybridization is a powerful technique which may be used to study the structure and function of microbial communities in situ and describe the expression of key enzymes. Real-time quantitative PCR technique may be conducted to accurately quantify the target microorganisms in the rumen. Development of these procedures and techniques will result in greater insights into community structure and activity of rumen microbial communities in relation to functional interactions, spatial and temporal relationships between different microorganisms and between microorganisms and feed particles. The successful development and application of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural environment with their genetic potential and in situ activities.

Animals↗

PubMed2005

Power generation in fed-batch microbial fuel cells as a function of ionic strength, temperature, and reactor configuration.

Power density, electrode potential, coulombic efficiency, and energy recovery in single-chamber microbial fuel cells (MFCs) were examined as a function of solution ionic strength, electrode spacing and composition, and temperature. Increasing the solution ionic strength from 100 to 400 mM by adding NaCl increased power output from 720 to 1330 mW/m2. Power generation was also increased from 720 to 1210 mW/m2 by decreasing the distance between the anode and cathode from 4to 2 cm. The power increases due to ionic strength and electrode spacing resulted from a decrease in the internal resistance. Power output was also increased by 68% by replacing the cathode (purchased from a manufacturer) with our own carbon cloth cathode containing the same Pt loading. The performance of conventional anaerobic treatment processes, such as anaerobic digestion, are adversely affected by temperatures below 30 degrees C. However, decreasing the temperature from 32 to 20 degrees C reduced power output by only 9%, primarily as a result of the reduction of the cathode potential. Coulombic efficiencies and overall energy recovery varied as a function of operating conditions, but were a maximum of 61.4 and 15.1% (operating conditions of 32 degrees C, carbon paper cathode, and the solution amended with 300 mM NaCl). These results, which demonstrate that power densities can be increased to over 1 W/m2 by changing the operating conditions or electrode spacing, should lead to further improvements in power generation and energy recovery in single-chamber, air-cathode MFCs.

Bacteria, Anaerobic↗

PubMed2003

The ability of murine dendritic cell subsets to direct T helper cell differentiation is dependent on microbial signals.

Dendritic cells (DC) initiate T cell responses and direct the class of T cell immunity through the production of Th-polarizing cytokines. In the mouse, immunization with CD8alpha(+) DC has led to Th1 priming whereas immunization with CD8alpha(-) DC has been associated with Th2 induction. Here, we use a direct T cell priming assay in vitro to re-examine the Th-directing potential of total DC or purified CD4(+) DC, CD8alpha(+) DC or CD4(-) CD8alpha(-) (double-negative; DN) DC subsets from mouse spleen. We show that the default Th effector phenotype induced by priming with DC depends on the protocol used for T cell purification, the T cell:antigen-presenting cell ratio and the antigen dose but is only marginally affected by DC subtype. All DC subsets can direct increased Th1 development in response to microbial stimuli known to elicit IL-12 production. Similarly, all subsets can suppress Th1 development and allow Th2 cellsto expand upon exposure to IL-10-inducing microbial agents. The flexibility of DC in directing Th development in function of microbial signals argues against the notion of pre-determined "DC1" and "DC2" subsets and suggests that multiple DC subtypes can direct an appropriate Th response to different classes of infectious agents.

Animals↗

PubMed2005

Prediction of functional modules based on gene distributions in microbial genomes.

We present a computational method for prediction of functional modules that can be directly applied to the newly sequenced microbial genomes for predicting gene functions and the component genes of biological pathways. We first quantify the functional relatedness among genes based on their distribution (i.e., their existences and orders) across multiple microbial genomes, and obtain a gene network in which every pair of genes is associated with a score representing their functional relatedness. We then apply a threshold-based clustering algorithm to this gene network, and obtain modules for each of which the number of genes is bounded from above by a pre-specified value and the component genes are more strongly functionally related to each other than genes across the predicted modules. Particularly, when the module size is bounded by 130, we obtain 167 functional modules covering 813 genes for Escherichia coli K12, and 138 functional modules covering 731 genes for Bacillus subtilis subsp. subtilis str. 168. We have used the gene ontology (GO) information to assess the prediction results. The GO similarities among the genes of the same functional module are compared with the GO similarities among the genes that are randomly clustered together. This comparison reveals that our predicted functional modules are statistically and biologically significant, and the genes of the same functional module share more commonality in terms of biological process than in terms of molecular function or cellular component. We have also examined the predicted functional modules that are common to both Escherichia coli K12 and Bacillus subtilis subsp. subtilis str. 168, and provide explanations for some functional modules.

Cluster Analysis↗

PubMed2026

Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.

Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.

Particulate Matter↗

PubMed1999

Stimulation of Diesel Fuel Biodegradation by Indigenous Nitrogen Fixing Bacterial Consortia.

> Abstract Successful stimulation of N2 fixation and petroleum hydrocarbon degradation in indigenous microbial consortia may decrease exogenous N requirements and reduce environmental impacts of bioremediation following petroleum pollution. This study explored the biodegradation of petroleum pollution by indigenous N2 fixing marine microbial consortia. Particulate organic carbon (POC) in the form of ground, sterile corn-slash (post-harvest leaves and stems) was added to diesel fuel amended coastal water samples to stimulate biodegradation of petroleum hydrocarbons by native microorganisms capable of supplying a portion of their own N. It was hypothesized that addition of POC to petroleum amended water samples from N-limited coastal waters would promote the growth of N2 fixing consortia and enhance biodegradation of petroleum. Manipulative experiments were conducted using samples from coastal waters (marinas and less polluted control site) to determine the effects of POC amendment on biodegradation of petroleum pollution by native microbial consortia. Structure and function of the microbial consortia were determined by measurement of N2 fixation (acetylene reduction), hydrocarbon biodegradation (14C hexadecane mineralization), bacterial biomass (AODC), number of hydrocarbon degrading bacteria (MPN), and bacterial productivity (3H-thymidine incorporation). Throughout this study there was a consistent enhancement of petroleum hydrocarbon degradation in response to the addition of POC. Stimulation of diesel fuel biodegradation following the addition of POC was likely attributable to increases in bacterial N2 fixation, diesel fuel bioavailability, bacterial biomass, and metabolic activity. Toxicity of the bulk phase water did not appear to be a factor affecting biodegradation of diesel fuel following POC addition. These results indicate that the addition of POC to diesel-fuel-polluted systems stimulated indigenous N2 fixing microbial consortia to degrade petroleum hydrocarbons.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p69.html

Journal Article↗

PubMed2006

Microbial ecology to manage processes in environmental biotechnology.

Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.

Biotechnology↗

PubMed2004

Genome-scale models of microbial cells: evaluating the consequences of constraints.

Microbial cells operate under governing constraints that limit their range of possible functions. With the availability of annotated genome sequences, it has become possible to reconstruct genome-scale biochemical reaction networks for microorganisms. The imposition of governing constraints on a reconstructed biochemical network leads to the definition of achievable cellular functions. In recent years, a substantial and growing toolbox of computational analysis methods has been developed to study the characteristics and capabilities of microorganisms using a constraint-based reconstruction and analysis (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.

Bacterial Physiological Phenomena↗

PubMed2005

Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment.

Detailed studies on the relation of structure and function of microbial communities in a sediment depth profile scarcely exist. We determined as functional aspect the vertical distribution of the acetotrophic and hydrogenotrophic CH4 production activity by measuring production rates and stable 13C/12C-isotopic signatures of CH4 in the profundal sediment of Lake Dagow. The structural aspect was determined by the composition of the methanogenic community by quantifying the abundance of different archaeal groups using 'real-time' polymerase chain reaction and analysis of terminal restriction fragment length polymorphism (T-RFLP). Methane production rates in the surface sediment (0-3 cm depth) were higher in August than in May, but strongly decreased with depth (down to 20 cm). The delta13C of the produced CH4 and CO2 indicated an increase in isotopic fractionation with sediment depth. The relative contribution of hydrogenotrophic to total methanogenesis, which was calculated from the isotopic signatures, increased with depth from about 22% to 38%. Total numbers of microorganisms were higher in August than in May, but strongly decreased with depth. The increase of microorganisms from May to August mainly resulted from Bacteria. The Archaea, on the other hand, exhibited a rather constant abundance, but also decreased with depth from about 1 x 10(8) copies of the archaeal 16S rRNA gene per gram of dry sediment at the surface to 4 x 10(7) copies per gram at 15-20 cm depth. T-RFLP analysis combined with phylogenetic analysis of cloned sequences of the archaeal 16S rRNA genes showed that the methanogenic community consisted mainly of Methanomicrobiales and Methanosaetaceae. The relative abundance of Methanosaetaceae decreased with depth, whereas that of Methanomicrobiales slightly increased. Hence, the vertical distribution of the functional characteristics (CH4 production from acetate versus H2/CO2) was reflected in the structure of the community consisting of acetotrophic (Methanosaetaceae) versus hydrogenotrophic (Methanomicrobiales) phenotypes.

Archaea↗

PubMed2005

Fungal community composition and metabolism under elevated CO(2) and O(3).

Atmospheric CO(2) and O(3) concentrations are increasing due to human activity and both trace gases have the potential to alter C cycling in forest ecosystems. Because soil microorganisms depend on plant litter as a source of energy for metabolism, changes in the amount or the biochemistry of plant litter produced under elevated CO(2) and O(3) could alter microbial community function and composition. Previously, we have observed that elevated CO(2) increased the microbial metabolism of cellulose and chitin, whereas elevated O(3) dampened this response. We hypothesized that this change in metabolism under CO(2) and O(3) enrichment would be accompanied by a concomitant change in fungal community composition. We tested our hypothesis at the free-air CO(2) and O(3) enrichment (FACE) experiment at Rhinelander, Wisconsin, in which Populus tremuloides, Betula papyrifera, and Acer saccharum were grown under factorial CO(2) and O(3) treatments. We employed extracellular enzyme analysis to assay microbial metabolism, phospholipid fatty acid (PLFA) analysis to determine changes in microbial community composition, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to analyze the fungal community composition. The activities of 1,4-beta-glucosidase (+37%) and 1,4,-beta-N-acetylglucosaminidase (+84%) were significantly increased under elevated CO(2), whereas 1,4-beta-glucosidase activity (-25%) was significantly suppressed by elevated O(3). There was no significant main effect of elevated CO(2) or O(3) on fungal relative abundance, as measured by PLFA. We identified 39 fungal taxonomic units from soil using DGGE, and found that O(3) enrichment significantly altered fungal community composition. We conclude that fungal metabolism is altered under elevated CO(2) and O(3), and that there was a concomitant change in fungal community composition under elevated O(3). Thus, changes in plant inputs to soil under elevated CO(2) and O(3) can propagate through the microbial food web to alter the cycling of C in soil.

Acetylglucosaminidase↗

PubMed2005

Human gut microbial degradation of flavonoids: structure-function relationships.

The relationship between chemical structure and gut microbial degradation rates of 14 flavonoids, flavone, apigenin, chrysin, naringenin, kaempferol, genistein, daidzein, daidzin, puerarin, 7,4'-dihydroxyflavone, 6,4'-dihydroxyflavone, 5,4'-dihydroxyflavone, 5,3'-dihydroxyflavone, and 4'-hydroxyflavone, was investigated by anaerobically fermenting the flavonoids with human gut microflora (n = 11 subjects). Degradation rates for the 5,7,4'-trihydroxyl flavonoids, apigenin, genistein, naringenin, and kaempferol, were significantly faster than the other structural motifs. Puerarin was resistant to degradation by the gut microflora. Extensive degradation of flavonoids by gut microflora may result in lower overall bioavailability than those flavonoids that are slowly degraded because rapidly degrading flavonoids are less likely to be absorbed intact.

Adult↗

PubMed2006

Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system.

Microorganisms will be an integral part of biologically based waste processing systems used for water purification or nutrient recycling on long-term space missions planned by the National Aeronautics and Space Administration. In this study, the function and stability of microbial inocula of different diversities were evaluated after inoculation into plant-based waste processing systems. The microbial inocula were from a constructed community of plant rhizosphere-associated bacteria and a complexity gradient of communities derived from industrial wastewater treatment plant-activated sludge. Community stability and community function were defined as the ability of the community to resist invasion by a competitor (Pseudomonas fluorescens 5RL) and the ability to degrade surfactant, respectively. Carbon source utilization was evaluated by measuring surfactant degradation and through Biolog and BD oxygen biosensor community level physiological profiling. Community profiles were obtained from a 16S-23S rDNA intergenic spacer region array. A wastewater treatment plant-derived community with the greatest species richness was the least susceptible to invasion and was able to degrade surfactant to a greater extent than the other complexity gradient communities. All communities resisted invasion by a competitor to a greater extent than the plant rhizosphere isolate constructed community. However, the constructed community degraded surfactant to a greater extent than any of the other communities and utilized the same number of carbon sources as many of the other communities. These results demonstrate that community function (carbon source utilization) and community stability (resistance to invasion) are a function of the structural composition of the community irrespective of species richness or functional richness.

Bacteria↗

PubMed2026

Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.

Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.

Antibiotic resistance genes↗

PubMed2026

Evaluation of Indigenous Bacillus Strains from Asian Fermented Foods for Probiotic Properties.

Bacillus species hold particular importance due to their versatile enzymatic repertoire and ability to synthesize diverse bioactive metabolites. In this study, two fermented food-derived strains, Bacillus siamensis BB3 (from douchi) and Bacillus velezensis TMA10 (from tapai) were evaluated for their probiotic, anti-microbial and functional potentials. Both strains exhibited desirable probiotic characteristics, including desirable tolerance to simulated gastric and intestinal conditions, with BB3 showing greater acid tolerance than TMA10. Safety assessments confirmed the absence of hemolytic activity, virulence factors and antibiotic resistance genes. Whole genome sequencing showed that the strains harbored genomic sequences for a wide range of metabolites, including non-ribosomal peptides and polyketides. Ethyl acetate (EtOAc) extracts from both strains demonstrated broad-spectrum anti-microbial activity against several indicator microorganisms, including Listeria grayi, Bacillus cereus, Serratia marcescens, Escherichia coli, and Pseudomonas aeruginosa, with TMA10 additionally inhibiting MRSA and Streptococcus mutans. Liquid Chromatography-Mass Spectrometry profiling identified key anti-microbial compounds, namely surfactins, macrolactins, bacillaene from BB3 and TMA10. In addition, difficidins were also detected from TMA10. Genomic analysis further indicated diverse carbohydrate utilization capacities; both strains encoded pathways for sucrose, raffinose-family oligosaccharides and lactose metabolism, while TMA10 possessed pathways for trehalose, glucomannan and arabinoxylan degradation. Both strains also showed anti-oxidant activity, with enhanced effects observed in their cell-free supernatants and heat-killed preparations. Overall, these findings highlight BB3 and TMA10 as promising candidates for the development of fermented food-derived Bacillus probiotics and functional cultures with anti-microbial, anti-oxidant, and broad carbohydrate-utilization capabilities.

Bacillus↗

PubMed2002

[Selection of a composite microbial system MC1 with efficient and stability cellulose degradation bacteria and its function].

Four groups of microbial mix culture with considerable capability of cellulose degradation were selected from four compost heaps, by combining the four groups, a composite microbial system MC1 with highly efficient cellulose degradation was obtained. It was found that 0.48 g of filter paper, 0.49 g of absorbent cotton, 0.19 g of wheat straw, or 0.08 g of wood residue can be degraded by 100 mL of MC1 at 50 degrees C with in 72 hours under static culture. The CM1 saccharification activity was much higher at 24th hours when degrading filter paper that was 122.3 U.mL-1. This capability of degradation maintained more than 20 days when the substrates were continually added. MC1 could be inoculated in a wide pH rang, from 4 to 10; however, the final pH would be changed to neutrality after incubation. The pH would be stability with filter paper between 6.0 and 6.5, and between 8.0 and 8.5 without the filter paper.

Bacteria↗

PubMedDate not supplied

[Influence of chemical analogues of microbial autoregulators on the sensitivity of DNA to UV radiation].

We established that chemical analogues of alkylhydroxybenzenes (AHB), belonging to alkylresorcinols and functioning as microbial autoregulatory d1 factors, enhance the UV resistance of various DNA molecules of different origin and conformation. These include the linear DNA of the lambda phage, bovine spleen DNA, and the DNA of the pUC19 plasmid that is composed of a number of annular (supercoiled and relaxed) and linearized molecules. Irradiating DNA with UV light (lambda = 254 nm) in the presence of methylresorcinol (MR) or hexylresorcinol (HR) results in comparatively insignificant DNA destruction as evidenced by our data on the electrophoretic mobility pattern in agarose gel. Using the linear Hind III restricts of the lambda phage DNA, we revealed that the protective effect of AHB varies depending on their chemical structure (it is more manifest with HR than MR) and concentration. Importantly, the effect of HR on bovine spleen DNA was based on its protective activity and manifested itself after a long incubation period. Studies using the pUC19 plasmid demonstrated that AHB, apart from increasing the resistance of linearized DNA molecules to UV irradiation, prevented both the supercoiled annular-supercoiled relaxed and the supercoiled relaxed-linearized transitions. The possible mechanisms of the UV-protective effect of AHB on DNA and their contributions to the resistance of dormant microbial forms to environmental factors are discussed.

Animals↗

PubMed1999

An automated comparative analysis of 17 complete microbial genomes.

MOTIVATION: As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality; identification of enzymes, putative operons and metabolic pathways; and to derive phylogenetic classification of microbes. RESULTS: This paper extends an automated pair-wise genome comparison technique (Bansal et al., Math. Model. Sci. Comput., 9, 1-23, 1998, Bansal and Bork, in First International Workshop of Declarative Languages, Springer, pp. 275-289, 1999) used to identify orthologs and gene groups to derive orthologous genes in a group of genomes and to identify genes with conserved functionality. Seventeen microbial genomes archived at ftp://ncbi.nlm.nih.gov/genbank/genomes have been compared using the automated technique. Data related to orthologs, gene groups, gene duplication, gene fusion, orthologs with conserved functionality, and genes specifically orthologous to Escherichia coli and pathogens has been presented and analyzed. AVAILABILITY: A prototype database is available at ftp://www.mcs.kent.edu/arvind/intellibio / orthos.html. The software is free for academic research under an academic license. The detailed database for every microbial genome in NCBI is commercially available through intellibio software and consultancy corporation (Web site: http://www.mcs.kent.edu/årvind/intellibio . html). CONTACT: arvind@mcs.kent.edu.

Algorithms↗