Journal ArticleDOI
Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria.
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TLDR
The order Acidithiobacillales was previously assigned to the class Gammaproteobacteria, but it is now confirmed that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes BetaproteOBacteria and GammAProteob bacteria.Abstract:
The order Acidithiobacillales was previously assigned to the class Gammaproteobacteria. Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes Betaproteobacteria and Gammaproteobacteria. We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order Acidithiobacillales and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia, with the type order Acidithiobacillales, comprising the families Acidithiobacillaceae and Thermithiobacillaceae with the type genus Acidithiobacillus.read more
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Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
Jan P. Meier-Kolthoff,Richard L. Hahnke,Jörn Petersen,Carmen Scheuner,Victoria Michael,Anne Fiebig,Christine Rohde,Manfred Rohde,Berthold Fartmann,Lynne Goodwin,Olga Chertkov,T. B. K. Reddy,Amrita Pati,Natalia Ivanova,Victor Markowitz,Nikos C. Kyrpides,Nikos C. Kyrpides,Tanja Woyke,Markus Göker,Hans-Peter Klenk +19 more
TL;DR: Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies withinE.
Journal ArticleDOI
Microbial diversity and metabolic networks in acid mine drainage habitats.
Celia Méndez-García,Ana Isabel Pelaez,Victoria Mesa,Jesús Sánchez,Olga V. Golyshina,Manuel Ferrer +5 more
TL;DR: A complete overview of the bacterial, archaeal, and eukaryotic diversity in these ecosystems are presented, and a thorough depiction of the metabolism and element cycling in AMD habitats is included.
Journal ArticleDOI
Microbial communities, processes and functions in acid mine drainage ecosystems
Lin-Xing Chen,Li-Nan Huang,Celia Méndez-García,Jialiang Kuang,Zheng-Shuang Hua,Jun Liu,Wen-Sheng Shu +6 more
TL;DR: The diversity of microorganisms and their functions in AMD ecosystems are described, and their biotechnological applications in biomining and AMD bioremediation according to their capabilities are discussed.
Journal ArticleDOI
Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp.
Rui Wang,Jianqiang Lin,Xiangmei Liu,Xin Pang,Chengjia Zhang,Chun-Long Yang,Xue-Yan Gao,Chun-Mao Lin,Ya-Qing Li,Yang Li,Jianqun Lin,Linxu Chen +11 more
TL;DR: The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp.
Journal ArticleDOI
Extreme environments: microbiology leading to specialized metabolites.
Ahmed M. Sayed,Marwa H.A. Hassan,Hani A. Alhadrami,Hossam M. Hassan,Hossam M. Hassan,Michael Goodfellow,Mostafa E. Rateb +6 more
TL;DR: This review explores the premise that harsh environmental conditions in extreme biomes select for micro‐organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules, and provides an overview of microbial‐derived molecules and their biological activities.
References
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Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
TL;DR: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.
Journal ArticleDOI
A Rapid Bootstrap Algorithm for the RAxML Web Servers
TL;DR: This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
Journal ArticleDOI
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
TL;DR: OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs.
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