[HTML][HTML] 25 years of serving the community with ribosomal RNA gene reference databases and tools
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date,
high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria …
high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria …
The first 1000 cultured species of the human gastrointestinal microbiota
The microorganisms that inhabit the human gastrointestinal tract comprise a complex
ecosystem with functions that significantly contribute to our systemic metabolism and have …
ecosystem with functions that significantly contribute to our systemic metabolism and have …
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major …
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …
Likelihood ratios for out-of-distribution detection
Discriminative neural networks offer little or no performance guarantees when deployed on
data not generated by the same process as the training distribution. On such out-of …
data not generated by the same process as the training distribution. On such out-of …
Primer, pipelines, parameters: issues in 16S rRNA gene sequencing
Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies
investigating microbiomes. However, comparative studies on differences in procedures are …
investigating microbiomes. However, comparative studies on differences in procedures are …
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Taxonomy is an organizing principle of biology and is ideally based on evolutionary
relationships among organisms. Development of a robust bacterial taxonomy has been …
relationships among organisms. Development of a robust bacterial taxonomy has been …
Genome-Based Taxonomic Classification of the Phylum Actinobacteria
The application of phylogenetic taxonomic procedures led to improvements in the
classification of bacteria assigned to the phylum Actinobacteria but even so there remains a …
classification of bacteria assigned to the phylum Actinobacteria but even so there remains a …
Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis
N Yoshida, T Emoto, T Yamashita, H Watanabe… - Circulation, 2018 - Am Heart Assoc
Background: It is increasingly recognized that gut microbiota play a pivotal role in the
development of atherosclerotic cardiovascular disease. Previously, we have reported that …
development of atherosclerotic cardiovascular disease. Previously, we have reported that …
Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel …
The genus Mycobacterium contains 188 species including several major human pathogens
as well as numerous other environmental species. We report here comprehensive …
as well as numerous other environmental species. We report here comprehensive …
Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae …
Understanding of the phylogeny and interrelationships of the genera within the order
'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or …
'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or …