Whole-genome prokaryotic phylogeny

Henz, Stefan R.; Huson, Daniel H.; Auch, Alexander F.; Nieselt, Kay; Schuster, Stephan C.

doi:10.1093/bioinformatics/bth324

Cited by 196 publications

(186 citation statements)

References 13 publications

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“…A whole-genome phylogeny (based on the proteome data) was inferred using the latest version of the Genome-BLAST Distance Phylogeny (GBDP) method 66,68 . Here, pairwise proteome comparisons (including pseudo-bootstrap replicates) were performed under the greedy-with-trimming algorithm and further recommended settings 69 .…”

Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

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Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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“…lactis. The availability of whole-genome sequences allows a more robust reconstruction of the phylogeny occurring within a particular bacterial taxon (52)(53)(54)(55) (Fig. 3).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

Milani

Duranti²,

Lugli³

et al. 2013

Appl Environ Microbiol

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Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group.

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“…Other calculations aiming at estimating global distances between all kinds of bacterial genomes have used the size of the shorter genome of the pair, L min (16,28). The use of L av instead allows a greater sensitivity to variations due to gene loss and gene acquisition (as is necessary between close relatives).…”

Section: Calculation Of Mumi (I) Principlesmentioning

confidence: 99%

“…The "gene content" (28) and "conserved-gene" (22) methods consist of creating a list of all possible orthologs between two genomes and then estimating the proximity of two strains by the ratio of orthologs to the total number of genes of the smaller or reference genome, respectively. More recently, similar methods, called DNA content and genome BLAST distance phylogeny, make use of DNA rather than genes as the starting point (10,16). Both categories of genomic methods have the advantage of being general, as they apply to all possible pairs of bacteria, irrespective of their relatedness.…”

mentioning

confidence: 99%

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Deloger¹,

Karoui²,

Petit³

2009

J Bacteriol

143

120

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The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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Whole-genome prokaryotic phylogeny

Cited by 196 publications

References 13 publications

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

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