Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
Among available genome relatedness indices, average nucleotide identity (ANI) is one of
the most robust measurements of genomic relatedness between strains, and has great …
the most robust measurements of genomic relatedness between strains, and has great …
Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009
The genus Listeria is currently comprised of 17 species, including 9 Listeria species newly
described since 2009. Genomic and phenotypic data clearly define a distinct group of six …
described since 2009. Genomic and phenotypic data clearly define a distinct group of six …
FEAST: fast expectation-maximization for microbial source tracking
A major challenge of analyzing the compositional structure of microbiome data is identifying
its potential origins. Here, we introduce fast expectation-maximization microbial source …
its potential origins. Here, we introduce fast expectation-maximization microbial source …
Mash: fast genome and metagenome distance estimation using MinHash
Mash extends the MinHash dimensionality-reduction technique to include a pairwise
mutation distance and P value significance test, enabling the efficient clustering and search …
mutation distance and P value significance test, enabling the efficient clustering and search …
Dynamics and stabilization of the human gut microbiome during the first year of life
F Bäckhed, J Roswall, Y Peng, Q Feng, H Jia… - Cell host & …, 2015 - cell.com
The gut microbiota is central to human health, but its establishment in early life has not been
quantitatively and functionally examined. Applying metagenomic analysis on fecal samples …
quantitatively and functionally examined. Applying metagenomic analysis on fecal samples …
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …
however existing whole-genome alignment methods are limited in their ability to perform …
Past and future species definitions for Bacteria and Archaea
Species is the basic unit of biological diversity. However, among the different microbiological
disciplines there is an important degree of disagreement as to what this unit may be. In this …
disciplines there is an important degree of disagreement as to what this unit may be. In this …
Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
The polyphasic approach used today in the taxonomy and systematics of the Bacteria and
Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of …
Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of …
Shifting the genomic gold standard for the prokaryotic species definition
DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for
prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic …
prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic …
Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome
The gut microbiota has been typically viewed as an environmental factor for human health.
Twins are well suited for investigating the concordance of their gut microbiomes and …
Twins are well suited for investigating the concordance of their gut microbiomes and …