Interaction of the immune system of the organism with saprotrophic opportunistic microflora and possible coupling of the process with the metabolic status of humans

The article sets forth the concept of natural biospheric immunization of a macroorganism by opportunistic saprotrophic microflora. Immunization by opportunistic microflora and microbial control of the metabolic status (which is coupled to the immune status of the organism) may act in a concert to provide immune defense. Efficient immunization requires that normal microflora be certified and the patients, phenotyped by the type and rate of xenobiotic biotransformation (via oxidation and acetylation). Data from the literature, based on which the suggested measures to stimulating the immune defense of the organism should be taken, are analyzed.     

Interaction of the Immune System of the Organism with Saprotrophic Opportunistic Microflora and Possible Coupling of the Process with the Metabolic Status of Humans: A Scientific Discussion

The article sets forth the concept of natural biospheric immunization of a macroorganism by opportunistic saprotrophic microflora. Immunization by opportunistic microflora and microbial control of the metabolic status (which is coupled to the immune status of the organism) may act in concert to provide immune defense. Efficient immunization requires that normal microflora be certified and the patients be phenotyped by the type and rate of xenobiotic biotransformation (via oxidation and acetylation). Data from the literature, based on which the suggested measures to stimulating the immune defense of the organism should be taken, are analyzed.     

Effect of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> in feed probiotic on the digestion of fish cultured in cages

We studied the activity of the digestive enzymes, qualitative composition, and bacteria genera ratio in the intestinal chyme of carp Cyprinus carpio and sterlet Acipenser ruthenus grown on an artificial diet in cage culture. It was shown that the inclusion of live bacteria Bacillus subtilis in the probiotic ProStor had a positive impact on the size and the structure of the microbial community in intestinal chyme, on the activity of some digestive enzymes, and on the digestibility and the weight gain of carp and sterlet. The total amount of micro-organisms in the carp chyme was by 13% higher and in sterlet it was 3.5 times higher in the experimental groups compared to the control. In the studied species of fish, the increase in the activity of digestive enzymes was accompanied by the decrease in nitrogen, ammonia, and urea. Presumably, it happened because of better absorption of protein and more intensive use of nitrogen metabolites by intestinal microflora for the synthesis of their own biomass. The average daily weight gain of carp and sterlet was 25 and 35% higher, respectively, in the experimental groups than in the control.     

Microbial population and biochemical changes in fermenting finger millet (Eleusine coracana)

Natural fermentation of finger millet (Eleusine coracana) was carried out for 48 h. Microbiological and chemical analysis was performed throughout the fermentation process. The fermentation was heterolactic dominated by lactic acid bacteria accompanied by the production of lactic and acetic acids with decrease in pH and increase in titratable acidity. The microbial population increased until 18 to 24 h accompanied by a rapid decrease in total and reducing sugars. The microflora stabilized between 24 and 48 h, during which time the total and -amylase activities increased with accumulation of sugars. Total free amino acids also increased. Yeast counts were low and moulds and coliforms were absent. Repeated fermentations showed consistency in the qualitative and quantitative changes in microflora. Five predominant types of bacteria, strains belonging to Leuconostoc, Pediococcus and Lactobacillus were identified. Of these only one type, Pediococcus, dominated (>80%) in the latter half of fermentation.     

Contrasting effects of extracts from invasive Reynoutria japonica on soil microbial biomass,activity, and community structure

Invasive plants may modify soil properties through the release of phenolic compounds. The effects of phenolics produced by a noxious invader, Reynoutria japonica, on soil microorganisms have rarely been studied in experimental conditions. We performed a laboratory experiment to assess the influence of extracts from R. japonica on soil microbial activity, biomass, and community structure. Two types of extracts (shoots and rhizomes) were added in four concentrations (control—no extract, low—extract diluted 100 times, medium—extract diluted ten times, and high—undiluted extract) to soil collected under native plant species. Concentrations of 12 phenolic compounds, namely catechin, chlorogenic acid, emodin, epicatechin, hyperoside, quercetin, physcion, piceatannol, polydatin, procyanidin B3, resveratrol, and resveratroloside were analyzed in the extract and soil. We measured the activity of five enzymes, namely acid and alkaline phosphatases, β-glucosidase, phenoloxidase, peroxidase, the activity of bacteria on Biolog Ecoplates, as well as the biomass of bacteria, saprotrophic fungi, arbuscular mycorrhizal fungi (AMF), and microbial community structure using phospholipid (PLFA) and neutral (NLFA) fatty acid analysis. Many microbial parameters, namely phosphatase activities, total microbial, AMF, and G?+?bacterial biomass, were reduced following the addition of extracts. This was likely related to phenolics as concentrations of these compounds in soil increased with the concentration of extract added. In contrast, saprotrophic fungi and G- bacteria were largely positively affected by extract addition. Shoot and rhizome extracts had relatively similar effects on the soil properties. The changes in soil biota caused by R. japonica invasion may have implications for restoration of invaded areas.

     

The algal microflora of the salt works of Tarquinia (Italy)

The microflora and benthic microbial mats of the salt works of Tarquinia (Italy) are described. From 144 samples, 111 species and varieties of microalgae were identified. Diatoms prevailed up to 110. S. They were substituted by Cyanophyta at higher salinities. The microbial mats consisted of Cyanophyta, Beggiatoa spp., purple sulphur bacteria, and diatoms. Information on hypertonic resistance in some euryhaline species is given.     

不同地下滴灌制度下黄瓜根际微生物活性及功能多样性

采用微生物培养、BIOLOG碳素利用法和土壤酶活性测定等方法,分析了日光温室不同地下灌溉制度下黄瓜根际土壤中微生物活性及功能多样性.结果表明: 根际土壤微生物生物量C、N含量、基础呼吸、代谢熵、AWCD值、Shannon指数和McIntosh指数随灌水量的增加呈先升高后下降的趋势;在0.8E_p(E_p为20 cm标准蒸发皿蒸发量)灌溉水平下,I2处理(灌水周期8 d)根际土壤微生物生物量C、N含量、基础呼吸、代谢熵、AWCD值、Shannon指数和McIntosh指数显著高于I₁处理(灌水周期4 d).0.8E_p处理下,细菌、放线菌、自生固氮菌数量及脲酶、磷酸酶、蔗糖酶、过氧化氢酶和多酚氧化酶活性显著高于其他2个灌水量处理（0.6E_p和1.0E_p）;I₂处理的细菌和自生固氮菌数量、脲酶、磷酸酶和蔗糖酶活性显著高于I₁处理,放线菌数量、过氧化氢酶和多酚氧化酶活性与I₁处理差异不显著,而真菌数量显著低于I₁处理.I 20.8E_p处理使黄瓜根际土壤中微生物代谢活性和微生物群落功能多样性升高,微生物区系得以改善,土壤酶活性提高,促进黄瓜生长.     

Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice

Background

Intestinal bacteria are known to regulate bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulation of the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regulate the gut microbiota with their strong antimicrobial activities. It remains unclear, however, how mammalian BAs cross-talk with gut microbiome and shape microbial composition in a dynamic and interactive way.

Results

We quantitatively profiled small molecule metabolites derived from host-microbial co-metabolism in mice, demonstrating that BAs were the most significant factor correlated with microbial alterations among all types of endogenous metabolites. A high-fat diet (HFD) intervention resulted in a rapid and significant increase in the intestinal BA pool within 12 h, followed by an alteration in microbial composition at 24 h, providing supporting evidence that BAs are major dietary factors regulating gut microbiota. Feeding mice with BAs along with a normal diet induced an obese phenotype and obesity-associated gut microbial composition, similar to HFD-fed mice. Inhibition of hepatic BA biosynthesis under HFD conditions attenuated the HFD-induced gut microbiome alterations. Both inhibition of BAs and direct suppression of microbiota improved obese phenotypes.

Conclusions

Our study highlights a liver–BA–gut microbiome metabolic axis that drives significant modifications of BA and microbiota compositions capable of triggering metabolic disorders, suggesting new therapeutic strategies targeting BA metabolism for metabolic diseases.

     

Infection of ‘Candidatus Phytoplasma ulmi’ reduces the protein content and alters the activity of detoxifying enzymes in Amplicephalus curtulus

It has been reported that insecticide‐detoxifying enzymes such as glutathione S‐transferases (GST) and esterases are affected by microbial infections in hemipteran insect vectors. The total protein content, and GST and α‐ and β‐esterase activities were quantified in ‘Candidatus Phytoplasma ulmi’‐infected and uninfected adults of Amplicephalus curtulus Linnavuori & DeLong (Hemiptera: Cicadellidae) at 25, 35, and 45 days after the acquisition access period (AAP) in the head‐thorax and abdomen sections. The total protein content was lower in phytoplasma‐infected leafhoppers 25, 35, and 45 days after the AAP. Thirty‐five days after the AAP, the GST and β‐esterase activities had increased (26 and 69%, respectively) compared to the control. However, 45 days after the AAP, the phytoplasma‐infected leafhoppers displayed lower GST (87%) and β‐esterase (253%) activities than the uninfected individuals. On the other hand, the α‐esterase activity proved to be unaffected by the phytoplasma infection. Forty‐five days after the AAP, females had a higher phytoplasma titer (46%) in their head‐thorax than in their abdomen sections, whereas males showed a higher titer in their abdomens (75%). In addition, the GST and β‐esterase activities in the abdomen were affected negatively by 96–98% as a result of the increasing ‘Ca. Phytoplasma ulmi’ titer. These results indicate that an infection of ‘Ca. Phytoplasma ulmi’ alters the metabolic activities of A. curtulus.     

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences

Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/.     

Phylogenetic Diversity of Aerobic Saprotrophic Bacteria Isolated from the Daqing Oil Field

A diverse and active microbial community in the stratal waters of the Daqing oil field (China), which is exploited with the use of water-flooding, was found to contain aerobic chemoheterotrophic bacteria (including hydrocarbon-oxidizing ones) and anaerobic fermentative, sulfate-reducing, and methanogenic bacteria. The aerobic bacteria were most abundant in the near-bottom zones of injection wells. Twenty pure cultures of aerobic saprotrophic bacteria were isolated from the stratal waters. Under laboratory conditions, they grew at temperatures, pH, and salinity values typical of the stratal water from which they were isolated. These isolates were found to be able to utilize crude oil and a wide range of hydrocarbons, fatty acids, and alcohols. Phylogenetic analysis carried out with the use of complete 16S rRNA sequences showed that the isolates could be divided into three major groups: gram-positive bacteria with a high and a low G+C content of DNA and gram-negative bacteria of the -subclass of the Proteobacteria. Gram-positive isolates belonged to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, and Clavibacter. Gram-negative isolates belonged to the genera Pseudomonas and Acinetobacter. In their 16S rRNA sequences, many isolates were similar to the known microbial species and some probably represented new species.     

Functional genomics and enzyme evolution

Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses — the area of research often referred to as functional genomics — aims at deciphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function. This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution. Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed. A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at http://www.ncbi.nlm.nih.gov/COG). This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism. Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size-parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives. Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function. An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle.This revised version was published online in October 2005 with corrections to the Cover Date.     

Comparative skin mucus and serum humoral defence mechanisms in the teleost gilthead seabream (Sparus aurata)

Mucosal surfaces of fish, including skin, gill and gut, contain numerous immune substances poorly studied that act as the first line of defence against a broad spectrum of pathogens. This study aimed to identify and characterize for the first time different constitutive humoral defence mechanisms of the skin mucus of gilthead seabream (Sparus aurata). To do this, the levels of total immunoglobulin M, several enzymes and proteins (peroxidase, lysozyme, alkaline phosphatase, esterases, proteases and antiproteases), as well as the bactericidal activity against opportunist fish pathogens (Vibrio harveyi, Vibrio angillarum, Photobacterium damselae) and non-pathogenic bacteria (Escherichia coli, Bacillus subtilis) were measured in the skin mucus and compared with those found in the serum. This study demonstrates that gilthead seabream skin mucus contains lower levels of IgM, similar levels of lysozyme, alkaline phosphatase and proteases, and higher esterase, peroxidase and antiprotease activities than serum. In addition, skin mucus revealed stronger bactericidal activity against tested fish pathogen bacteria compared to the serum activity, while human bacteria can even grow more in the presence of mucus. The results could be useful for better understanding the role of the skin mucus as a key component of the innate immune system with potential application for the aquaculture.     

A cytochemical study of acid phosphatases and esterases during the induction of crown gall in the tomatoLycopersicon esculentum

Synopsis A cytochemical study has been made of acid -glycerophosphatase, acid naphthol-AS-BI-phosphatase and naphthol esterase activities during the induction of crown gall inLycopersicon esculentum byAgrobacterium tumefaciens. There was an increased activity of these enzymes with time after infection, being more marked for the phosphatases than the esterases. It is suggested that the esterase activities may play a part in cell wall development of the maturing gall.     

Control and regulation of metabolic fluxes in microbes by substrates and enzymes

The control of enzymes and substrates on the flux through microbial metabolic pathways can be quantified in terms of flux control coefficients. In pathways involving group transfer, the summation theorem for flux control by the enzymes has to be modified: the sum of control by all enzymes is between 1 and 2. The phosphoenolpyruvate:glucose phosphotransferase system is such a pathway. Experimental determination of the control by the enzymes in this pathway is under way. The control of the enzymes on the glycolytic flux in yeast is low, with the possible exception of the uptake step. InKlebsiella pneumoniae potassium and ammonium ions can simultaneously be limiting, (i.e. have significant control on growth) at pH 6, but not at pH 8. This may be due to the fact that at pH 8 the high-affinity potassium uptake system is absent.     

Wood-inhabiting ligninolytic basidiomycetes in soils: Ecology and constraints for applicability in bioremediation

Ligninolytic basidiomycetes associated with wood decay are a physiologically distinct group of saprotrophic fungi capable of decomposition of all major components of wood. Although wood is their natural substrate, several species can survive in soil if suitable substrates are available, the soil-colonizing ability of species in the genera Phanerochaete, Pleurotus and Trametes being comparable to that of the soil-inhabiting basidiomycetes utilizing plant litter. Wood-inhabiting ligninolytic basidiomycetes (WLB) in soil interact with soil microflora, and some species are very efficient competitors affecting both the soil microbial biomass and the composition of the indigenous microbial community. The extracellular enzymes utilized by saprotrophic basidiomycetes for nutrient acquisition participate in the interspecific interactions with other soil biota but are also involved in the transformation of soil organic matter – lignocellulose and humic compounds. Bioremediation research has significantly enriched our knowledge of the ecology of basidiomycetes, but it has also identified several limitations for practical applicability of WLB at a field scale, and has led to the conclusion that natural attenuation or bioaugmentation are todays methods of choice for on site treatment.     

Small enzymes with esterase activities from two thermophilic fungi, Emericella nidulans and Talaromyces emersonii

Extracellular esterase activities in Emericella nidulans and Talaromyces emersonii are attributed to small enzymes with molecular weights less than 10 kDa (microenzymes). A 1.6 kDa esterase accounted for most of the esterase activity observed in both organisms and one of them also contained a 4.1 kDa microenzyme with weaker esterase activity. These esterases were growth-associated and active towards fluorescein dibutyrate and -naphthyl acetate as well as tributyrin.     

Origin of enzymes involved in detoxification and root softening during cassava retting

The origin of root softening during cassava retting was investigated in a natural retting and in a sterile fermentation. Softening only occurred in the natural retting. Although high activities of endogenous pectin methyl esterase were found in cassava extracts from both fermentations, the depolymerizing enzymes polygalacturonase, active at low pH, and pectate lyase were only found in the non-sterile retting. No cellulase or xylanase activity was observed. The role of pectinases in the softening of cassava roots was confirmedin vitro using commericial enzymes. Root softening is therefore due to the combined action of endogenous pectin methyl esterase and exogenous bacterial depolymerizing enzymes. Detoxification occurred in both fermentations, confirming that the linamarase responsible for the destruction of cassava cyanide glycosides was mainly endogenous, even though microbial -glucosidases may help in the detoxication.F. Ampe is and A. Brauman was with the Laboratoire de Microbiologie et de Biotechnologie, ORSTOM, BP 181-Brazzaville, Congo. A. Brauman is now with the Laboratoire d'Ecophysiologie des Invertébrés, Université Paris XII, Avenue du Général De Gaulle, 94 010 Créteil, France     

A glimpse of the diversity of complex polysaccharide-degrading culturable bacteria from Kongsfjorden,Arctic Ocean

Cold-adapted, complex polysaccharide-degrading marine bacteria have important implications in biogeochemical processes and biotechnological applications. Bacteria capable of degrading complex polysaccharide substrates, mainly starch, have been isolated from various cold environments, such as sea ice, glaciers, subglacial lakes, and marine sediments. However, the total diversity of polysaccharide-degrading culturable bacteria in Kongsfjorden, Arctic Ocean, remains unexplored. In the study reported here, we tested 215 cold-adapted heterotrophic bacterial cultures (incubated at 4 and 20 °C, respectively) isolated from Kongsfjorden, for the production of cold-active extracellular polysaccharide-degrading enzymes, including amylase, pectinase, alginase, xylanase, and carboxymethyl (CM)-cellulase. Our results show that 52 and 41% of the bacterial isolates tested positive for extracellular enzyme activities at 4 and 20 °C, respectively. A large fraction of the bacterial isolates (37% of the positive isolates) showed multiple extracellular enzyme activities. Alginase and pectinase were the most predominantly active enzymes, followed by amylase, xylanase, and CM-cellulase. All isolates which tested positive for extracellular enzyme activities were affiliated to microbial class Gammaproteobacteria. The four genera with the highest number of isolates were Pseudomonas, followed by Psychrobacter, Pseudoalteromonas, and Shewanella. The prevalence of complex polysaccharide-degrading enzymes among the isolates indicates the availability of complex polysaccharide substrates in the Kongsfjorden, likely as a result of glacial melting and/or macroalgal load. In addition, the observed high functional/phenotypic diversity in terms of extracellular enzyme activities within the bacterial genera indicates a role in regulating carbon/carbohydrate turnover in the Kongsfjorden, especially by reducing recalcitrance.     

Impact of histamine treatment and feeding on the hydrolytic enzyme level of Tetrahymena in culture and in conditions of starvation

• 1.1. The unicellular Tetrahymena pyriformis contains and also produces hydrolytic enzymes, such as glucosidase, phosphatase and glucosaminidase.
• 2.2. Return of Tetrahymena to plain medium after treatment with bacteria alone, histamine alone or bacteria plus histamine was equally followed by persistence of the hydrolytic enzyme activity around the control value and an activity increase at about 60 min.
• 3.3. Incubation of Tetrahymena in salt (Losina-Losinsky) solution after the applied treatment accounted for reduction to practically zero of the glucosidase and glucosaminidase activities, whereas the phosphatase activity tended to increase rather than to decrease in both the bacterium-treated and histamine-treated cultures.
• 4.4. The enzyme activity patterns of the Tetrahymena cells pretreated (imprinted) with histamine did not differ from the control pattern either after re-exposure to histamine or after feeding with bacteria, but showed a uniformization of the activity pattern and a considerable decrease in enzyme activity on incubation (starvation) in salt (Losina-Losinsky) solution.