Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using ...Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.
•Microbiome profiles obtained from QIIME2 showed higher alpha-diversity and lower beta-diversity than from MG-RAST.•Whole taxonomic compositions generated in MG-RAST led to more accurate discrimination between sample collection sites.•Removing low abundance taxa from QIIME2 compositions let to higher discrimination accuracy between sample collection sites.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
An investigation of the adsorption equilibrium of carbon dioxide (CO2) and nitrogen (N2) and their mixtures on zeolites ZSM-5 and 13X is presented. Pure component isotherms are measured at five ...different temperatures in the range of 25 °C and pressures up to 10 bar, and the resulting data are described with an appropriate isotherm equation. Adsorption equilibrium of CO2/N2 mixtures was measured at two temperatures (25 °C and 45 °C) and three pressure levels (1.2 bar, 3 bar and 10 bar) using three feed gas compositions on both materials tested. The isotherms obtained from the pure component measurements are used to predict the binary data using two approaches: An empirical extension of the Sips isotherm and the application of ideal adsorbed solution theory (IAST). In the context of the binary CO2/N2 adsorption, it was found that for ZSM-5 the system behaves close to ideal over the whole range of pressure and temperature investigated here and thus is well described by the IAST prediction. On the other hand, our results demonstrate non-ideal behavior in the adsorbed phase with increasing pressure for zeolite 13X, thus motivating the use of real adsorbed solution theory (RAST) to accurately describe the binary adsorption data.
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•Pure component adsorption data of CO2 and N2 on ZSM-5 and 13X.•Binary adsorption equilibria of the CO2 and N2 mixture.•Non-ideal behavior of the CO2/N2 mixture in the adsorbed phase of 13X.•Proper description by ideal and real adsorbed solution theory.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA ...sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.
Istraživana je dinamika rasta ploda sorti: Springold, Redhaven, Suncrest i Fayette u ekološkim uvjetima Ravnih kotara. Breskve su uzgajane u obliku vretenastog grma na podlozi GF 677. Rezultati ...istraživanja predočeni su u tablicama i grafikonima. Rast ploda slijedi dvostruku sigmoidnu krivulju na kojoj su istaknute dvije faze bržeg rasta i jedna faza vrlo usporenog rasta. Prva faza brzog rasta traje oko 65 dana za sve četiri sorte. Druga faza rasta traje u sorte Springold 5 do 7 dana, u sorata Redhaven i Suncrest 28 dana, a u sorte Fayette 35 dana. Treća faza ponovnog bržeg rasta traje u sorata Springold i Redhaven 14 dana, u sorte Suncrest 21 dan, a u sorte Fayette 10 dana.
The dynamics of fruit growth of the varieties: Springold, Redhaven, Suncrest and Fayette in the ecological conditions of Ravni kotari were investigated. Peaches were grown in the form of a spindly bush on the rootstock GF 677. The results of the research are presented in tables and graphs. Fruit growth follows a double sigmoid curve, where two phases of faster growth and one phase of very slow growth are highlighted. The first phase of rapid growth lasts about 65 days for all four varieties. The second growth phase lasts 5 to 7 days in the Springold variety, 28 days in the Redhaven and Suncrest varieties, and 35 days in the Fayette varieties. The third phase of faster growth again lasts 14 days in the Springold and Redhaven varieties, 21 days in the Suncrest variety, and 10 days in the Fayette variety.
The purpose of the research is to reveal in the diachronic aspect some principles of development of the mugham genre tasnif. The research aims also to study some features of the musical language of ...tasnifs and investigate the role of singers and performers of folk instruments in the development of the mugham of Azerbaijan. The research methodology is aimed at using the methods of historical musicology and the application of certain methodological principles of ethnomusicology in the study of the musical language of Tasnif. The scientific novelty of the research. The article presents some new facts related to the creation and implementation of tariffs. Conclusions. Tasnifs are vocal-instrumental musical works with a certain point basis, melodic and formal structure. Outstanding Azerbaijani singers played an important role in the development of this genre. In the Soviet period, tasnifs created by singers were presented under the name of folk songs.
We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and ...observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses.
The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages.
The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.
Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this ...premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of
Bos taurus
(cow) and
Bubalus bubalis
(buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90–96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera
Fibrobacter
,
Bacteroides
,
Clostridium
,
Prevotella
and
Ruminococcus
involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation ...sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
After the Styrian composer Anselm Hüttenbrenner had largely withdrawn from public life, he spent most of his time between the autumn of 1853 and the autumn of 1858 in Maribor (Marburg). In Maribor ...and its surroundings he found peace of mind and a closeness to nature, devoting himself intensively to compositional and pedagogical activities. He composed numerous lieder on texts by his host Ferdinand von Rast (Hilarius) plus many piano pieces, in addition to orchestral overtures and church music. The article attempts to shed light on this period in Hüttenbrenner’s life, which has not been previously studied.
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