Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I

Geng, Jianing; Huang, Szu-Chuan; Li, Shuangli; Hu, Songnian; Chen, Yi-Ywan M.

doi:10.1128/jb.05670-11

Cited by 14 publications

(7 citation statements)

References 18 publications

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“…However, not all S. salivarius strains possess the operon. Geng et al (2011) showed it to be absent in strain SK126, suggesting a recent loss of the operon from some strains within this species (perhaps reflecting the early stages of streamlining). The urease enzyme requires nickel to function ( Chen et al 1998 ), explaining the enrichment for nickel cation binding.…”

Section: Resultsmentioning

confidence: 97%

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Richards

Palmer

Bitar

et al. 2014

Genome Biology and Evolution

133

122

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The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.

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Section: Resultsmentioning

confidence: 97%

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Richards

Palmer

Bitar

et al. 2014

Genome Biology and Evolution

133

122

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“…Some contigs encoding dihydrofolate reductase and a mobilization element had high nucleotide identity to known commensals (e.g. F24TRSX_31, with >98% identity to Streptococcus salivarius (GenBank Accession CP002888.1)) [37] . Others were similar to pathogens: F30TRSX_13 had 99% identity to the Klebsiella pneumoniae plasmid pJIE137 (GenBank Accession EF219134), which is closely related to the p271a plasmid carrying the NDM-1 (New Delhi metallobetalactamase) that has been implicated in serious infections with carbapenem-resistant Gram-negative bacteria [38] .…”

Section: Resultsmentioning

confidence: 99%

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

et al. 2013

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Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.

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“…The complete genome sequence of S. salivarius strain 57.I reveals a chromosome and a 40,758-bp plasmid, designated YMC-2011 (27). Most of the open reading frames (ORFs) annotated from YMC-2011 share significant homology with ORFs related to phage production, suggesting that strain 57.I is lysogenically infected with a temperate phage.…”

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confidence: 99%

YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I

Chou

Huang

Chiu

et al. 2017

Appl Environ Microbiol

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Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended Ϫ10 element (p L ) and a 70 -like promoter (p R ) were mapped 5= to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5= rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.KEYWORDS Streptococcus salivarius, temperate phage, lysogeny, plasmid, Siphoviridae family P hages, prokaryotic viruses, are the most abundant biological entities on the planet (1). Although phages have been isolated from the oral cavity (2, 3), relatively little is known about the phages of oral streptococci, compared to those of other lactic acid bacteria, particularly Lactococcus lactis and Streptococcus thermophilus. To date, the better characterized phages of oral streptococci are the virulent phage M102AD of Streptococcus mutans (4) and the temperate phage SM1 of Streptococcus mitis (5). A Streptococcus salivarius-infecting phage of the family Cystoviridae wa...

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Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I

Cited by 14 publications

References 18 publications

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I

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