Metabolism of Daidzein and Genistein by Gut Bacteria of the Class Coriobacteriia

The intake of isoflavones is presumed to be associated with health benefits in humans, but also potential adverse effects of isoflavones are controversially discussed. Isoflavones can be metabolized by gut bacteria leading to modulation of the bioactivity, such as estrogenic effects. Especially bacterial strains of the Eggerthellaceae, a well-known bacterial family of the human gut microbiota, are able to convert the isoflavone daidzein into equol. In addition, metabolization of genistein is also described for strains of the Eggerthellaceae. The aim of this study was to identify and investigate gut bacterial strains of the family Eggerthellaceae as well as the narrowly related family Coriobacteriaceae which are able to metabolize daidzein and genistein. This study provides a comprehensive, polyphasic approach comprising in silico analysis of the equol gene cluster, detection of genes associated with the daidzein, and genistein metabolism via PCR and fermentation of these isoflavones. The in silico search for protein sequences that are associated with daidzein metabolism identified sequences with high similarity values in already well-known equol-producing strains. Furthermore, protein sequences that are presumed to be associated with daidzein and genistein metabolism were detected in the two type strains ‘Hugonella massiliensis’ and Senegalimassilia faecalis which were not yet described to metabolize these isoflavones. An alignment of these protein sequences showed that the equol gene cluster is highly conserved. In addition, PCR amplification supported the presence of genes associated with daidzein and genistein metabolism. Furthermore, the metabolism of daidzein and genistein was investigated in fermentations of pure bacterial cultures under strictly anaerobic conditions and proofed the metabolism of daidzein and genistein by the strains ‘Hugonella massiliensis’ DSM 101782T and Senegalimassilia faecalis KGMB04484T.

Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot

Pectobacterium parmentieri is a plant-pathogenic bacterium, recently attributed as a separate species, which infects potatoes, causing soft rot in tubers. The distribution of P. parmentieri seems to be global, although the bacterium tends to be accommodated to moderate climates. Fast and accurate detection systems for this pathogen are needed to study its biology and to identify latent infection in potatoes and other plant hosts. The current paper reports on the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for P. parmentieri, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 102 cfu/mL on pure bacterial cultures and 102–103 cfu/mL on plant material. The specificity of the protocol was evaluated against P. parmentieri and more than 100 strains of potato-associated species of Pectobacterium and Dickeya. No cross-reaction with the non-target bacterial species, or loss of sensitivity, was observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range for P. parmentieri and will expand knowledge of the life cycle and environmental preferences of this pathogen.

Volatile Fatty Acids as Carbon Sources for Polyhydroxyalkanoates Production

Waste of industrial origin produced from synthetic materials are a serious threat to the natural environment. The ending resources of fossil raw materials and increasingly restrictive legal standards for the management of plastic waste have led to research on the use of biopolymers, which, due to their properties, may be an ecological alternative to currently used petrochemical polymers. Polyhydroxyalkanoates (PHAs) have gained much attention in recent years as the next generation of environmentally friendly materials. Currently, a lot of research is being done to reduce the costs of the biological process of PHA synthesis, which is the main factor limiting the production of PHAs on the industrial scale. The volatile fatty acids (VFAs) produced by anaerobic digestion from organic industrial and food waste, and various types of wastewater could be suitable carbon sources for PHA production. Thus, reusing the organic waste, while reducing the future fossil fuel, originated from plastic waste. PHA production from VFAs seem to be a good approach since VFAs composition determines the constituents of PHAs polymer and is of great influence on its properties. In order to reduce the overall costs of PHA production to a more reasonable level, it will be necessary to design a bioprocess that maximizes VFAs production, which will be beneficial for the PHA synthesis. Additionally, a very important factor that affects the profitable production of PHAs from VFAs is the selection of a microbial producer that will effectively synthesize the desired bioproduct. PHA production from VFAs has gained significant interest since VFAs composition determines the constituents of PHA polymer. Thus far, the conversion of VFAs into PHAs using pure bacterial cultures has received little attention, and the majority of studies have used mixed microbial communities for this purpose. This review discusses the current state of knowledge on PHAs synthesized by microorganisms cultured on VFAs.

Establishment and Application of a Dual TaqMan Real-Time PCR Methodfor Proteus mirabilis and Proteus vulgaris

Proteus species are common opportunistic bacteria and foodborne pathogens. The proper detection of Proteus can effectively reduce the occurrence of food-borne public health events. Proteus mirabilis and Proteus vulgaris are the two most important pathogens in the Proteus genus. In this study, a dual TaqMan Real-Time PCR method was established to simultaneously detect and distinguish P. mirabilis and P. vulgaris in samples. The method exhibited good specificity, stability, and sensitivity. Specifically, the minimum detection concentrations of P. mirabilis and P. vulgaris in pure bacterial cultures were 6.08 × 102 colony forming units (CFU)/ml and 4.46 × 102 CFU/ml, respectively. Additionally, the minimum detectable number of P. mirabilis and P. vulgaris in meat and milk was 103 CFU/g. In addition, the method can be used to distinguish between strains of P. mirabilis and P. vulgaris within two hours. Overall, it is a sensitive, easy-to-use, and practical test for the identification and classification of Proteus in food.

Isolation and Molecular Characterization of Pesticide Degrading Bacteria in Polluted Soil

Pesticides are the substances for preventing, destroying, repelling any pest. Due to bulk handling or accidental release, they are accumulated in soil which leads to occasional entry into ecosystem that shows lethal effect on living system. An enrichment culture technique was used to isolate bacterial strains from organophosphate soil degrading high concentration of the selected pesticides. Five pure bacterial cultures were isolated. All five isolates were characterized on the basis of molecular and biochemical features like biodegradation test and substrate specificity, phosphate solubilization and screened for pesticide residue, pH, and extraction of DNA, quantity and quality check and salt tolerance. The organophosphate isolates were also tested for quantitative production. The screening of pesticide tolerance was done at for fungicides and insecticides.

Microflora microbiological characteristics of saline soils

The purpose of current work was isolation of halophilic bacteria from saline lands in some regions of the Krasnodar Territory, after mycological analysis, there followed the study and characterization of microorganisms with further creation on effective biocomplex basis, contributing to restoration of arid and saline irrigated areas. Soil samples were taken from saline lands of the Krasnodar Territory, the salt composition of which was studied in the work process. There were determined total titer of microorganisms and the titer of nitrogen-fixing bacteria on the Corresponding selective media in the samples. Twenty-five pure bacterial cultures were isolated from the samples and its morphophysiological and biochemical properties, as well as its nitrogenfixing activity, were studied. As a result, seven cultures with relatively high nitrogen-fixing activity were selected, as well as resistance to various environmental factors, particularly, to high concentrations of NaCl, рН alkaline values and to sharp temperature drops. After appropriate phylogenetic analysis, selected crops may become a potential target for creating a complex biological fertilizer, contributing to the restoration of dry and saline lands and increase their fertility.

Molecular bacteriology laboratory works

The training manual includes information about total nucleic acids (DNA and RNA) from pure soil water samples, genomic RNA and plasmid DNA separation from pure bacterial cultures, quantitative DNA testing, quantitative phylogenetic testing. Methods of cloning, sequencing, bioinformatics analysis of the obtained sequences are presented. The manual includes brief theoretical information covering the topic, laboratory works, as well as tasks for their implementation. This unique manual of molecular microbiology laboratory works in Armenian language is intended for students, PhD students specialized in the field of Biology.

Evaluation of the novel culture-based FAST-T system allowing selection of optimal antibiotics for critically ill patients within 4 h (for other than bloodstream infectious).

Rapid diagnostic tests are needed to improve patient care, particularly in immunocompromised hosts. Here, we describe the validation of a new phenotypic culture-based FAST-T method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. FAST-T approach, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. FAST-T-selected antibiotics are those that can completely eliminate mixed bacterial infections in specimens. The method uses a novel FASM-T medium that allows more rapid bacterial growth of gram-positive and gram-negative monoisolates compared with that achieved with conventional laboratory media. The application of the FAST-T method in 122 bacterial species demonstrated overall sensitivity, specificity, positive predictive value, and negative predictive value of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, already after 4 h. The overall category agreement with the outcome of standard testing was 98.9% with very major errors and major errors being detected in 1.2% and 0.6% of cases. The use of FASM-T medium in 20 clinical polymicrobial samples allowed culturing a more diverse set of bacteria, including fastidious species, compared with that achieved with the standard laboratory diagnostic and enabled, already within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, FAST-T system may be a valuable tool in improving phenotypic-based antibiotic selection, enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.