Bootstrap methods in phylogenetics

V posledních desetiletích zaznamenala fylogenetická rekonstrukce velký rozvoj. Použitím nově získaných molekulárních znaků a počítačového zpracování bylo dosaženo toho, že začala být brána jako objektivní věda. Rychlý vývoj však ukázal, že je potřeba výsledky vyhodnotit, neboť nové techniky vytvořily fylogramy i z nespolehlivých dat. Pro tyto účely byly do fylogenetiky aplikovány vzorkovací statistické metody, z nichž později začal převládat bootstrapping. I ten má však omezení, se kterými je nutno počítat při interpretaci výsledků, které nám poskytl. Spojením principů bootstrappingu a konsenzuálních stromů však lze získat fylogramy, jejichž vlastnosti jsou lepší než vlastnosti klasických fylogramů jak prokazuje tato práce.In recent decades, phylogenetic reconstruction has noted great development. It was achieved by using newly acquired molecular characteristics and processing that it began to be taken as an objective science. Rapid development showed that it is necessary to evaluate the results because new techniques provided phylograms from unreliable data. For these purposes, statistical sampling methods have been applied to the phylogeny, of which bootstrapping began later to dominate. However, it also has limitations, which should be considered during interpreting the results it provided to us. This work demonstrates by combining the principles of bootstrapping and consensus trees we can obtain phylograms with better properties than those of conventional phylograms.

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing

The aims of this study were to determine the microbial community in five rivers in the proximity of a city in the Czech Republic using 454-pyrosequencing, as well as to assess seasonal variability over the course of 1 year and to identify the factors influencing the structure of bacterial communities. Samples from five rivers around the city of Brno were obtained during four seasons and analysed using 454 pyrosequencing of the 16S rRNA gene. The core composition of bacterial communities consisted of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, TM7 and others. Our approach enabled us to more closely study the correlation between the abundance of different families and environmental factors. Overall, Actinobacteria negatively correlated with phosphorus, sulphate, dissolved particle and chloride levels. In contrast, Proteobacteria positively correlated with sulphate, dissolved particle, chloride, dissolved oxygen and nitrite levels. Future work should focus on the dynamics of bacterial communities present in river water and their relation to the overall stability of the water ecosystem

Bipartite Graphs for Visualization Analysis of Microbiome Data

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts

Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410

Clostridium diolis DSM 15410 is a type strain of solventogenic clostridium capable of conducting isopropanol-butanol-ethanol fermentation. By studying its growth on different carbohydrates, we verified its ability to utilize glycerol and produce 1,3-propanediol and discovered its ability to produced isopropanol. Complete genome sequencing showed that its genome is a single circular chromosome and belongs to the cluster I (sensu scricto) of the genus Clostridium. By cultivation analysis we highlighted its specific behavior in comparison to two selected closely related strains. Despite the fact that several CRISPR loci were found, 16 putative prophages showed the ability to receive foreign DNA. Thus, the strain has the necessary features for future engineering of its 1,3-propanediol biosynthetic pathway and for the possible industrial utilization in the production of biofuels

Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping

Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g. local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also noncoding regions are examined

Free-Living Enterobacterium Pragia fontium 24613: Complete Genome Sequence and Metabolic Profiling

Pragia fontium is one of the few species that belongs to the group of atypical hydrogen sulfide-producing enterobacteria. Unlike other members of this closely related group, P. fontium is not associated with any known host and has been reported as a free-living bacterium. Whole genome sequencing and metabolic fingerprinting confirmed the phylogenetic position of P. fontium inside the group of atypical H2S producers. Genomic data have revealed that P. fontium 24613 has limited pathogenic potential, although there are signs of genome decay. Although the lack of specific virulence factors and no association with a host species suggest a free-living style, the signs of genome decay suggest a process of adaptation to an as-yet-unknown host