Genes detected in class I integrons in carriage water microbiota of ornamental fish. Numbers show percentages out of a total of 18,806 reads.

<p>*QAC-quaternary ammonium compounds, Tp-trimethoprim, Str-streptomycin, AG-aminoglycosides, Cm-chloramphenicol, Ery-erythromycin, Kan–kanamycin, Rif–rifampicin, Enr–enrofloxacin.</p

Prevalence of antibiotic resistance genes in ornamental fish carriage water.

<p>Antibiotic resistance gene prevalence is presented with the median, 25% and 75% percentiles (box) and the whiskers indicating the minimum and maximum values recorded.</p

Heat map showing the correlation coefficients of the presence of individual families and particular antibiotic resistance genes.

<p>Three main clusters according to their positive and negative correlation with the prevalence of antibiotic resistance genes tested in this study are indicated by red, blue and green color.</p

Distribution of selected genes in integron structures determined by pyrosequencing and real-time PCR.

<p>Average values calculated from data available for 48 samples were used for both real-time PCR based pie charts. Quantification of genes in integrons by pyrosequencing and real-time PCR resulted in similar results whereas the comparison of these results with the results from carriage water DNA indicated that <i>dfrA</i> was associated with integrons as its representation decreased when total carriage water was used as a template in real-time PCR. On the other hand, <i>aacA</i> and <i>ereA</i> must have been common in genetic elements different from integrons.</p

List of primers used in this study.

<p>List of primers used in this study.</p

Data_Sheet_1_Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.).docx

BackgroundThis paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.MethodsP. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.Results and discussionThe typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.</p

Composition of ornamental fish carriage water microbiota at class level.

<p>1 – <i>Sphingobacteria</i>, 2 – <i>Gammaproteobacteria</i>, 3 – <i>Fusobacteria</i>, 4 – <i>Flavobacteria</i>, 5 – <i>Clostridia</i>, 6 – <i>Betaproteobacteria</i>, 7 – <i>Bacteroidia</i>, 8 – <i>Alphaproteobacteria</i>, 9 – <i>Bacilli</i>, 10 – <i>Actinobacteria</i>. For the full data set see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103865#pone.0103865.s001" target="_blank">table S1</a>.</p

Additional file 3: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Putative active genes misidentified as pseudogenes due to assembly errors. (PDF 210 kb

Correlation of bacterial families forming the microbiota in the chicken caecum.

<p>Correlation of bacterial families forming the caecal microbiota of chickens and hens is presented as a heat map based on correlation coefficients calculated across all time points and all samples. The correlation coefficients were also used for the calculation of dendrogram trees. Two main clusters, cluster I and cluster II, with 2 subclusters within cluster II could be distinguished. Families within cluster I formed microbiota of mainly adult hens whilst families within cluster IIb were characteristic of young chickens. Dark brown color represents a positive correlation between particular families. Dark blue color represents a negative correlation between particular families.</p

Unweighted and weighted BiPlot PCoA analysis of chicken caecal microbiota.

<p>Red spots, pooled samples from the long-term on-farm experiment. Blue spots, individual chicken samples from the short-term animal house experiment. Yellow spots, individual samples from chicken and hens of particular age. “d” stands for age in days, “w” stands for age in weeks. Size and location of the bacterial spots represent their amount and association with microbiota of chickens and hens of a particular age.</p