Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Ciufo, Stacy; Kannan, Sivakumar; Sharma, Shobha; Badretdin, Azat; Clark, Karen; Turner, Seán; Brover, Vyacheslav; Schoch, Conrad L.; Kimchi, Avi; DiCuccio, Michael

doi:10.1099/ijsem.0.002809

Cited by 350 publications

(312 citation statements)

References 19 publications

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“…We used the ANI metric to inspect all Enterobacter genome assemblies available in Genbank (n = 1616, January 2019) for potentially misclassified genomes (see methods for details). This is an important step that is in line with the recent announcement that NCBI will use a similar strategy in a large scale [19]. This analysis allowed us to reclassify five E. cloacae and four Enterobacter spp.…”

Section: Resultssupporting

confidence: 59%

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies

Matteoli

Passarelli‐Araujo

Pedrosa-Silva

et al. 2019

Preprint

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Section: Resultssupporting

confidence: 59%

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies

Matteoli

Passarelli‐Araujo

Pedrosa-Silva

et al. 2019

Preprint

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“…In recent times the cumbersome DDR test has been replaced by various alignment-free procedures that have evolved from Chargaff's 'GC% rule' into the current ANI version with cutoff points much higher than 70% [1]. Simply stated, of 16 (= 4 2 ) possible 2-mers, a high GC% species will have a high frequency of G-rich and C-rich 2-mers (GG, GC, CC, CG).…”

Section: Ad Hoc Dna-based Classification Methodsmentioning

confidence: 99%

Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny

Forsdyke

2019

Biological Journal of the Linnean Society

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Introduction Microorganisms as species Ad hoc DNA-based classification methods Theoretical link with speciation Molecular link with speciation Nucleic acids versus proteins Concluding remarks Words: 8101 Figures and Tables: 0 References: 101 2 AbstractThe utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners. A path from the nineteenth century recognition of the informational basis of heredity to the modern era can be discerned. Crick's DNA "unpairing postulate" predicted that recombinational pairing of homologous DNAs during meiosis would be mediated by short k-mers in the loops of stem-loop structures extruded from classical duplex helices. The complementary "kissing" duplex loopslike tRNA anticodon-codon k-mer duplexeswould seed a more extensive pairing that would then extend until limited by lack of homology or other factors. Indeed, this became the principle behind alignment-based methods that assessed similarity by degree of DNA-DNA reassociation in vitro. These are now seen as less sensitive than alignment-free methods that are closely consistent, both theoretically and mechanistically, with chromosomal anti-recombination models for the initiation of divergence into new species. The analytical power of k-mer differences supports the theses that evolutionary advance sometimes serves the needs of nucleic acids (genomes) rather than proteins (genes), and that such differences have often played a role in early speciation events.

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“…In this study, we analyzed a complete SM43 genome sequence using an average nucleotide identity (ANI) calculator (50, 51). ANI values are used for molecular species definitions (52), and two bacterial strains with an ANI of ≥95% in their shared genes are considered to be the same species and with an ANI of >70% are considered to be the same genus (53, 54). We compared the SM43 genome with those of S. oralis ATCC 35037 and S. mitis ATCC 49456.…”

Section: Resultsmentioning

confidence: 99%

Phosphatidylcholine biosynthesis in Mitis group streptococci via host metabolite scavenging

Joyce¹,

Guan

Palmer³

2019

Preprint

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14The Mitis group streptococci include the major human pathogen Streptococcus 15 pneumoniae and the oral opportunistic pathogens S. mitis and S. oralis which are 16 primary colonizers in the oral cavity and agents of bacteremia and infective endocarditis 17 in immunocompromised patients. Bacterial membrane lipids play crucial roles in 18 microbe-host interactions, yet for many pathogens, the composition of the membrane is 19 poorly understood. In this study, we characterized the lipidomes of selected species of 20 Mitis group streptococci and investigated the mechanistic basis for biosynthesis of the 21 phospholipid phosphatidylcholine (PC). PC is a major lipid in eukaryotic cellular 22 membranes, but it is considered to be comparatively rare in bacterial taxa. Using liquid 23 chromatography/mass spectrometry (LC/MS) in conjunction with stable isotope tracing, 24 we determined that Mitis group streptococci synthesize PC via the rare host metabolite 25 scavenging pathway, the glycerophosphocholine (GPC) pathway, which is largely 26 uncharacterized in bacteria. Furthermore, we identify the acyltransferase, PlsC, as 27 playing a major role in the pathway by acylating lysoPC to PC. Our work demonstrates 28 that Mitis group streptococci including S. pneumoniae remodel their membrane in 29 response to the major human metabolites GPC and lysoPC. 30 31 Key words 32 33 Phosphatidylcholine, phospholipid, Streptococcus pneumoniae, Streptococcus mitis, 34 Streptococcus oralis, Mitis group streptococci, glycerophosphocholine 35 3 36 Significance 37 38We lack fundamental information about the structure of the cellular membrane even for 39 the best studied pathogens of critical significance for human health. The Mitis group 40 streptococci are closely linked to humans in health and disease. Here, we demonstrate 41 that these streptococci scavenge major human metabolites and use them to synthesize 42 the membrane phospholipid phosphatidylcholine. Our work is significant because it 43 identifies a mechanism by which the major human pathogen S. pneumoniae and the 44 primary human oral colonizers S. mitis and S. oralis remodel their membrane in 45 response to the host.46 48 The Mitis group streptococci are Gram-positive bacteria that natively inhabit the human 49 oral cavity, nasopharynx, and gastrointestinal tract (1). They include the species S. mitis 50 and S. oralis, which are among the first colonizers of the human oral cavity from birth 51 and are believed to play important roles in host-microbe-microbe interactions by 52 creating an anchor for biofilm formation with other oral microbiota (2, 3). They are also 53 opportunistic pathogens causing bacteremia and infective endocarditis (4-7). They also 54 include the major human pathogen, S. pneumoniae. S. pneumoniae has >99% 16S 55 rRNA sequence identity with S. mitis and S. oralis (8-10), and with which they 56 exchange capsule biosynthesis and antibiotic resistance genes (11, 12) and show 57 antibody cross-reactivity (13). 58 59 We, and others, recently reported that Mit...

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Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Cited by 350 publications

References 19 publications

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies

Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny

Phosphatidylcholine biosynthesis in Mitis group streptococci via host metabolite scavenging

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Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Cited by 350 publications

References 19 publications

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofblaCTX-M-55,blaNDM-5andblaIMI-1, along with sophisticated iron acquisition strategies

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofblaCTX-M-55,blaNDM-5andblaIMI-1, along with sophisticated iron acquisition strategies

Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny

Phosphatidylcholine biosynthesis in Mitis group streptococci via host metabolite scavenging

Contact Info

Product

Resources

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Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofbla_CTX-M-55,bla_NDM-5andbla_IMI-1, along with sophisticated iron acquisition strategies