The member of program group B. Stres ia a coauthor in this work which has been till 4th March 2008 cited 6189-times (WoS). This works describes the introduction of software package Mothur aimed for the analyzes of community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, the authors used mothur to trim, screen, and align sequences, calculate distances, assign sequences to operational taxonomic units and describe the ? and ß diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
COBISS.SI-ID: 2517640
Anaerobic digestion of brewery spent grain into biogas was studied. This substrate consists of cellulose, hemicellulose and lignin, which are difficult to degrade. Therefore, a two-stage system was used. Biogas production was phase separated in a solid-state digestion phase, where microbial hydrolysis and acidogenesis occurred and granular biomass phase, where methanogenesis prevailed. The process exhibited total solids degradation efficiency between 75.9 and 83.0% and biomethane production 224 ± 34 L/kg of added total solids. Granular biomass after adaptation exhibited stable operation at substrate C/N ratios in range 0.16-4.68 and p-cresol concentrations 45 mg/L. The excellent adaptability of granular biomass was confirmed by 68.2% shift in bacterial and a 31.8% shift in archaeal community structure of granular biomass. The process exhibited stable operation for 198 days, which shows that brewery spent grain can be successfully anaerobically digested and used for biogas production.
COBISS.SI-ID: 4876283
Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5T, Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5T was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5T and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.
COBISS.SI-ID: 3534728
aim of this study was to develop and validate a community supported online infrastructure and bioresource for methane yield data and accompanying metadata collected from published literature. In total, 1164 entries described by 15749 data points were assembled. Analysis of data collection showed litle congruence in reporting of methodological approaches. The largest identifiable source of variation in reported methane yields was represented by authorship (i.e. substrate batches within particular substrate class) within which experimental scales (volumes (0.02 l to 5 l), incubation temperature (34°C to 40°C) and %VS of substrate played an important role (p(0.05, npermutations=999) as well. The largest fraction of variability, however, remained unaccounted for and thus unexplained ()63%). This calls for reconsideration of accepted approaches to reporting data in currently published literature to increase capacity to service industrial decision making to a greater extent.
COBISS.SI-ID: 7022945
In this study, the genotoxicity of TiO2 particles in the Tetrahymena thermophila micro-organism was established by a comet assay, which is a very common and modern method for assessment of DNA damage in the cell nucleus. Cells were exposed to two different concentrations of TiO2 nanoparticles and TiO2 particles larger than 100 nm in three different ways: a) cells in suspension, b) cells embedded in gel c) nuclei embedded in gel. In all three exposures, a comet assay demonstrated genotoxicity, but we did not show other cytotoxicity indicators, such as lipid peroxidation, elevated reactive oxygen species, changes in long-chain fatty acid profiles. Published reports state that, in the absence of cytotoxicity, genotoxicity does not occur directly. A possible explanation for the positive results of genotoxicity is a false positive result of the comet assay due to the interactions between TiO2 and DNA particles after the exposure of T. thermophila. In this study it was shown for the first time that the results of the comet assay in nanoparticles have to be carefully interpreted.
COBISS.SI-ID: 2573903
The Shine-Dalgarno sequence is a key element modulating the translation initiation in bacteria. Bioinformatic analysis of forty genomes from the major bacterial phylum Bacteroidetes revealed general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5'UTRs. The experiments using Prevotella bryantii TC1-1, a member of Bacteroidetes, also suggested that a functional SD interaction does not take place during the translation initiation in P. bryantii TC1-1and possibly other members of phylum Bacteroidetes. We thus propose that in the absence of the SD sequence interaction, the selection of start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5'UTR as opposed to coding region which is inaccessible due to mRNA secondary structure.
COBISS.SI-ID: 2912136
The purpose of this study was to discover differences in the human fecal microbiota composition driven by long term omnivore vs. vegan/lactovegetarian dietary pattern. In addition the possible association of demographic characteristics and dietary habits with the fecal microbiota was examined. The study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. The results of the analyses of fecal microbiome showed that vegetarian diet was associated with higher ratio of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p(0.05 and p(0.01) and decrease of Bifidobacterium with age (p(0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus ,Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4% of variance in microbial community analysed by DGGE could be explained by the vegetarian type of diet. In conclusion, long term vegetarian diet influenced the fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants’ age, gender and body mass.
COBISS.SI-ID: 3303048
Sound and timely microbial gut colonization completes newborn’s healthy metabolic programming and manifests in infant appropriate growth and weight development. Early microbial variability in fecal samples of 60 Slovenian breastfed newborns was marked by the proportion of Bacilli, but diminished and converged in later samples, as bifidobacteria started to prevail. The first month proportions of enterococci were associated with maternity hospital locality and supplementation of breastfeeding with formulae, while Enterococcus faecalis proportion reflected the mode of delivery. Group Bacteroides-Prevotella proportion was associated with infant phenotype at first month. Infant mixed feeding pattern and health issues within the first month revealed the most profound and extended microbial perturbations. Our findings raise concerns over the ability of the early feeding supplementation to emulate and support the gut microbiota in a way similar to the exclusively breastfed infants.
COBISS.SI-ID: 3954568
In the current study, the toxicity mechanism of nanosized CuO (nCuO) to the freshwater ciliated protozoa Tetrahymena thermophila was studied. Changes in fatty acid profile, lipid peroxidation metabolites and reactive oxygen species (ROS) were measured. Bulk CuO and CuSO4 served as controls for size and solubility and 3,5-dichorophenol (3,5-DCP) as a control for a chemical known to directly affect the membrane composition. Exposure to all copper compounds induced the generation of ROS, whereas nCuO was most potent. The latter effect was not solely explained by solubilized Cu-ions and was apparently particle-related. 24 h exposure of protozoa to 80 mg/L of nCuO (EC50) significantly decreased the proportion of two major unsaturated fatty acids (UFA) (C18:3 cis-6,9,12, C18:2 cis-9,12), while it increased the relative amount of two saturated fatty acids (SFA) (C18:0, C16:0). Analogous effect was not observed when protozoa were exposed to equitoxic suspensions of bulk CuO, Cu-ions or 3,5-DCP. As changes in the UFA:SFA upon exposure of protozoa to nCuO were not detected at 2 h exposure and no simultaneous dose- or time-dependent lipid peroxidation occurred, it is likely that one of the adaptation mechanisms of protozoa to nCuO was lowering membrane fluidity by the inhibition of de novo synthesis of fatty acid desaturases. This is the first study of the effects of nanoparticles on the membrane fatty acid composition.
COBISS.SI-ID: 2902920
We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment. Shotgun metagenomes, total metabolomes and intestinal metals were analyzed using standard approaches. The observed progressive decrease in defecation frequency and inflammation preceded a significant increase in the genus Bacteroides in HBR, in genes coding for proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence, defense and mucin degradation. Bayesian network analysis was used to derive the first biological hierarchical model of initial inactivity mediated deconditioning steps over time. Reintroduction of exercise resulted in stepwise amelioration of the negative physiological symptoms, indicating that exercise apparently prevented the crosstalk between the microbial physiology, mucin degradation and proinflammatory immune activities in the host.
COBISS.SI-ID: 31228455