Genome sequence-based species delimitation with confidence intervals and improved distance functions
- Jan P. Meier-Kolthoff, Alexander F. Auch, H. Klenk, M. Göker
- BiologyBMC Bioinformatics
- 21 February 2013
Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty, so it is crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes.
The complete genome sequence of the gastric pathogen Helicobacter pylori
Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification, and consistent with its restricted niche, it has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity.
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
- Alexander F. Auch, M. von Jan, H. Klenk, M. Göker
- Biology, EngineeringStandards in Genomic Sciences
- 28 January 2010
This work investigates state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH and finds that some distance formulas are very robust against missing fractions of genomic information.
Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling.
- A. H. Treusch, S. Leininger, A. Kletzin, S. Schuster, H. Klenk, C. Schleper
- BiologyEnvironmental Microbiology
- 1 December 2005
These findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions.
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome…
When should a DDH experiment be mandatory in microbial taxonomy?
Whether or not, and in which situations, this threshold value might be too conservative, is investigated, which means up to half of the currently conducted DDH experiments could safely be omitted without a significant risk for wrongly differentiated species.
Taxonomy, Physiology, and Natural Products of Actinobacteria
SUMMARY Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial…
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
The genome sequence of the extreme thermophile Thermus thermophilus
The complete genome sequence of T. thermophilus HB27 is presented, the first for the genus Thermus and candidates include various proteases and key enzymes of other fundamental biological processes such as DNA replication, DNA repair and RNA maturation.
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
An overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented is provided.