CoVennTree: a new method for the comparative analysis of large datasets

Lott, Steffen C.; Voß, Björn; Hess, Wolfgang R.; Steglich, Claudia

doi:10.3389/fgene.2015.00043

Cited by 8 publications

(7 citation statements)

References 14 publications

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“…Operational taxonomic units (OTUs) were assigned at 97 % similarity threshold levels, representing bacterial species (Tindall et al 2010). For visualization the distribution of the most abundant 50 OTUs among samples, CoVennTree (Lott et al 2015) was used, a tool on the Galaxy platform (Blankenberg et al 2010;Giardine et al 2005;Goecks et al 2010). The resulted output was visualized in Cytoscape 2.8.3 (Shannon et al 2003).…”

Section: S Rrna Gene Sequencingmentioning

confidence: 99%

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

et al. 2017

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Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats, therefore amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

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Section: S Rrna Gene Sequencingmentioning

confidence: 99%

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

et al. 2017

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“…Richness estimators, diversity indices and coverage percentage were calculated from randomly subsampled set of sequences (based on the smallest dataset) in mothur. To visualize the number and correlation of taxa at different taxonomic ranks among samples, CoVennTree (Lott et al, 2015) was used, a tool on the Galaxy platform (Giardine et al, 2005;Blankenberg et al, 2010;Goecks et al, 2010). The resulted output was visualized in Cytoscape 2.8.3 (Shannon et al, 2003).…”

Section: 4pyrosequencingmentioning

confidence: 99%

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Borsodi

Krett

Felföldi

et al. 2017

Microbiological Research

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Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013.Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

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“…Analyses were performed with the default settings. For normalization and selection of taxa of interest, we extracted global taxonomic tree information (number of assigned reads per taxon) from MEGAN [20]. Based on the three datasets, we computed a comparative weighted Venn tree for the Cyanobacteria phylum focusing on Prochlorococcus with CoVennTree v1.6.0 [20].…”

Section: Preprocessing and Global Read Assignmentmentioning

confidence: 99%

“…Interestingly, minD, encoding a membrane-bound ATPase, was in the top Fig. 1), the weighted Venn tree was computed using CoVennTree [20]. The numbers in parentheses refer to weighted Venn decomposition values.…”

Section: Validation and Characterization Of Predicted Srnas And Asrnamentioning

confidence: 99%

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

et al. 2020

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Small regulatory RNAs and antisense RNAs play important roles in the regulation of gene expression in bacteria but are underexplored, especially in natural populations. While environmentally relevant microbes often are not amenable to genetic manipulation or cannot be cultivated in the laboratory, extensive metagenomic and metatranscriptomic datasets for these organisms might be available. Hence, dedicated workflows for specific analyses are needed to fully benefit from this information. Here, we identified abundant sRNAs from oceanic environmental populations of the ecologically important primary producer Prochlorococcus starting from a metatranscriptomic differential RNA-Seq (mdRNA-Seq) dataset. We tracked their homologs in laboratory isolates, and we provide a framework for their further detailed characterization. Several of the experimentally validated sRNAs responded to ecologically relevant changes in cultivation conditions. The expression of the here newly discovered sRNA Yfr28 was highly stimulated in low-nitrogen conditions. Its predicted top targets include mRNAs encoding cell division proteins, a sigma factor, and several enzymes and transporters, suggesting a pivotal role of Yfr28 in the coordination of primary metabolism and cell division. A cis-encoded antisense RNA was identified as a possible positive regulator of atpF encoding subunit b' of the ATP synthase complex. The presented workflow will also be useful for other environmentally relevant microorganisms for which experimental validation abilities are frequently limiting although there is wealth of sequence information available.

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CoVennTree: a new method for the comparative analysis of large datasets

Cited by 8 publications

References 14 publications

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

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