scholarly journals Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification

2021 ◽  
Author(s):  
Hemanoel Passarelli-Araujo ◽  
Gloria Regina Franco ◽  
Thiago Motta Venancio
Keyword(s):  
Network Analysis ◽  
Microbial Diversity ◽  
Genomic Diversity ◽  
Biotechnological Applications ◽  
Genomic Distance ◽  
Bacterial Genomes ◽  
Community Identification ◽  
Type Strains ◽  
Shed Light ◽  
High Diversity

The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, comprising isolates associated with processes from pathogenesis to biotechnological applications. However, this high diversity led to historical taxonomic inconsistencies. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified inconsistencies with several type strains and found that 25.65% of the Pseudomonas genomes deposited on Genbank are misclassified. We retrieved the 13 main Pseudomonas groups and proposed P. alcaligenes as a new group. Finally, this work provides new insights on the phylogenetic boundaries of Pseudomonas and highlights that the Pseudomonas diversity has been hitherto overlooked.

What´s driving dermatology: Contribution title analysis of the largest German Dermatology Congress 2019 (Preprint)

2020 ◽  
Author(s):  
Robert Kaczmarczyk ◽  
Felix Bauerdorf ◽  
Alexander Zink
Keyword(s):  
Network Analysis ◽  
Annual Meeting ◽  
Research Network ◽  
Graph Analysis ◽  
Network Graph ◽  
Research Topics ◽  
German Speaking ◽  
Specialist Groups ◽  
Community Meeting ◽  
High Diversity

BACKGROUND Every two years, German-speaking dermatologic specialist groups gather in Berlin to share the latest developments at Germany´s largest dermatologic conference, the Annual Meeting of the Germany Society of Dermatology (DDG). Because this conference has a lasting effect on dermatologic practice and research, understanding what is moving the specialist groups means understanding what is driving dermatology in Germany. OBJECTIVE The objective of the article is to introduce the medical scientific community to a data visualization method, which will help understand more sophisticated data analysis and processing approaches in the future. METHODS We used word network analysis to compile and visualize the information embedded in the contribution titles to the DDG Annual Meeting in 2019. We extracted words, contributing cities and inter-connections. The data was standardized, visualized using network graphs and analyzed using common network analysis parameters. RESULTS A total of 5509 words were extracted from 1150 contribution titles. The most frequently used words were “therapy”, “patients”, and “psoriasis”. The highest number of contributions came from Hamburg, Berlin and Munich. High diversity in research topics was found, as well as a well-connected research network. CONCLUSIONS Focus of the well-connected German-speaking dermatology community meeting 2019 was patient and therapy centered and lies especially on the diseases psoriasis and melanoma. Network graph analysis can provide helpful insights and help planning future congresses. It can facilitate the choice which contributors to include as imbalances become apparent. Moreover, it can help distributing the topics more evenly across the whole dermatologic spectrum.

scholarly journals Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danijela Šantić ◽  
Kasia Piwosz ◽  
Frano Matić ◽  
Ana Vrdoljak Tomaš ◽  
Jasna Arapov ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Analysis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Adriatic Sea ◽  
Bacterial Community Composition ◽  
Environmental Data ◽  
Large Contribution ◽  
Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals The Communication of Ideas across Subfields in Political Science

2014 ◽  
Vol 47 (02) ◽  
pp. 468-476 ◽  
Author(s):  
Erin R. Graham ◽  
Charles R. Shipan ◽  
Craig Volden
Keyword(s):  
Network Analysis ◽  
International Relations ◽  
Political Science ◽  
Comparative Politics ◽  
Diffusion Processes ◽  
Methodological Approach ◽  
Journal Articles ◽  
Insight Into ◽  
Shed Light ◽  
Levels Of Integration

ABSTRACTWhat factors inhibit or facilitate cross-subfield conversations in political science? This article draws on diffusion scholarship to gain insight into cross-subfield communication. Diffusion scholarship represents a case where such communication might be expected, given that similar diffusion processes are analyzed in American politics, comparative politics, and international relations. We identify nearly 800 journal articles published on diffusion within political science between 1958 and 2008. Using network analysis we investigate the degree to which three “common culprits”—terminology, methodological approach, and journal type—influence levels of integration. We find the highest levels of integration among scholars using similar terms to describe diffusion processes, sharing a methodological approach (especially in quantitative scholarship), and publishing in a common set of subfield journals. These findings shed light on when cross-subfield communication is likely to occur with ease and when barriers may prove prohibitive.

scholarly journals Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification

2021 ◽  
pp. 126919
Author(s):  
Hemanoel Passarelli-Araujo ◽  
Glória Regina Franco ◽  
Thiago M. Venancio
Keyword(s):  
Network Analysis ◽  
Shed Light

Complete Mitogenome of Threespot Flounder Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae) and Study on the Mechanism of Gene Rearrangement in 13 Bothids

2019 ◽  
Author(s):  
Hairong Luo ◽  
Xiaoyu Kong ◽  
Shixi Chen ◽  
Wei Shi
Keyword(s):  
Gene Rearrangement ◽  
Structural Diversity ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Significant Evidence ◽  
Rearrangement Process ◽  
Genomic Scale ◽  
Complete Mitogenome ◽  
Shed Light ◽  
High Diversity

Abstract Background: The mitochondrial genomes (mitogenomes) of 12 bothids (Pleuronectiformes) from eight genera have been obtained. From the data, the genomic-scale and various gene rearrangements revealed the high diversity of variation in these mitogenomes. Results: A total of 18170 bp of Grammatobothus polyophthalmus mitogenome was determined including 37 genes and two control regions (CRs). Genes encoded by L-strand were grouped to an eight-genes cluster (Q-A-C-Y-S1-ND6-E-P) except for the tRNA-N, other genes encoded by H-strand were grouped together (F-12S … CytB-T) except for the tRNA-D that was translocated to inside of the eight-genes cluster. The mitogenome of G. polyophthalmus and that of 12 known bothids possessed the similar genomic-scale rearrangements with the only differences in the various combinations of CR, tRNA-D and eight-genes cluster, and the shuffling of tRNA-V. Based on the structure character of all 13 bothid mitogenomes, the Dimer-Mitogenome and Non-Random Loss (DMNR) model was fitted to account for all these rearrangements. And the translocation of tRNA-D occurring after the DMNR process in 10 of 13 bothid mitogenomes was confirmed. The striking finding was that each of degenerated genes existing in the gene rearrangement process in 13 bothids had their counterparts of intergenic spaces. Conclusions: The result of corresponding relationship between degenerated genes and intergenic spaces provided the significant evidence to support the possibility of the DMNR model, as well as, the existing of dimeric mitogenome in mitochondrion. The findings of this study were rare phenomenona in teleost fish, which not only promoted the understanding of mitogenome structural diversity, but also shed light on studying of mitochondrial rearrangement and replication.

scholarly journals Putative Transposases Conserved in Exiguobacterium Isolates from Ancient Siberian Permafrost and from Contemporary Surface Habitats

2005 ◽  
Vol 71 (11) ◽  
pp. 6954-6962 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Sophia Kathariou
Keyword(s):  
Surface Water ◽  
High Resolution ◽  
Food Processing ◽  
Microbial Mats ◽  
Genomic Diversity ◽  
Insertion Sequences ◽  
Gram Positive Bacteria ◽  
Lake Fryxell ◽  
Siberian Permafrost ◽  
Type Strains

ABSTRACT Gram-positive bacteria of the genus Exiguobacterium have been repeatedly isolated from Siberian permafrost ranging in age from 20,000 to 2 to 3 million years and have been sporadically recovered from markedly diverse habitats, including microbial mats in Lake Fryxell (Antarctic), surface water, and food-processing environments. However, there is currently no information on genomic diversity of this microorganism or on the physiological strategies that have allowed its survival under prolonged freezing in the permafrost. Analysis of the genome sequence of the most ancient available Exiguobacterium isolate (Exiguobacterium sp. strain 255-15, from 2 to 3 million-year-old Siberian permafrost) revealed numerous putative transposase sequences, primarily of the IS200/IS605, IS30, and IS3 families, with four transposase families identified. Several of the transposase genes appeared to be part of insertion sequences. Southern blots with different transposase probes yielded high-resolution genomic fingerprints which differentiated the different permafrost isolates from each other and from the Exiguobacterium spp. type strains which have been derived from diverse surface habitats. Each of the Exiguobacterium sp. strain 255-15 transposases that were used as probes had highly conserved homologs in the genome of other Exiguobacterium strains, both from permafrost and from modern sites. These findings suggest that, prior to their entrapment in permafrost, Exiguobacterium isolates had acquired transposases and that conserved transposases are present in Exiguobacterium spp., which now can be isolated from various modern surface habitats.

Genomic diversity and relationship of Bacillus thuringiensis and Bacillus cereus by multi-REP-PCR fingerprinting

2007 ◽  
Vol 53 (3) ◽  
pp. 343-350 ◽  
Author(s):  
Ameur Cherif ◽  
Besma Ettoumi ◽  
Noura Raddadi ◽  
Daniele Daffonchio ◽  
Abdellatif Boudabous
Keyword(s):  
Bacillus Thuringiensis ◽  
Bacillus Cereus ◽  
Genetic Relationship ◽  
Genomic Diversity ◽  
Consensus Sequences ◽  
Pcr Fingerprinting ◽  
Polymorphic Bands ◽  
Relationship Of ◽  
Type Strains ◽  
Group Similarity

The genomic diversity and relationship among 56 Bacillus thuringiensis and Bacillus cereus type strains were investigated by multi-REP-PCR fingerprinting consisting of three PCR reactions targeting the enterobacterial ERIC1 and ERIC2 and the streptococcal BOXA1R consensus sequences. A total of 113 polymorphic bands were generated in the REP-PCR profiles that allowed tracing of a single dendrogram with three major groups. Bacillus cereus strains clustered together in the A and B groups. Most of the B. thuringiensis strains clustered in group C, which included groups of serovars with a within-group similarity higher than 40% as follows: darmstadiensis, israelensis, and morrisoni; aizawai, kenyae, pakistani, and thompsoni; canadensis, entomocidus, galleriae, kurstaki, and tolworthi; alesti, dendrolimus, and kurstaki; and finitimus, sotto, and thuringiensis. Multi-REP-PCR fingerprinting clustered B. thuringiensis serovars in agreement with previously developed multilocus sequence typing schemes, indicating that it represents a rapid shortcut for addressing the genetic relationship of unknown strains with the major known serovars.

Sign in / Sign up

Export Citation Format

Share Document