Limits...
A novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo.

Scholz CF, Jensen A, Lomholt HB, Brüggemann H, Kilian M - PLoS ONE (2014)

Bottom Line: Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease.Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences.We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark.

ABSTRACT
The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST) scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.

Show MeSH

Related in: MedlinePlus

The SLST scheme discriminates the phylogenetic clusters of P. acnes.Minimum Evolution phylogenetic tree based on 86 complete and draft P. acnes genomes, generated in MEGA v. 5.22 and based on a 1,964,522-bp concatemer of core sequences. Only bootstrap values of 100% are shown. The leftmost column depicts the identified SLST type. Type designations according to MLST9 and MLST8 schemes and ribotyping are also given, in addition to the traditional type assignments based on recA and tly sequence analysis. * indicates unknown types.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4128656&req=5

pone-0104199-g001: The SLST scheme discriminates the phylogenetic clusters of P. acnes.Minimum Evolution phylogenetic tree based on 86 complete and draft P. acnes genomes, generated in MEGA v. 5.22 and based on a 1,964,522-bp concatemer of core sequences. Only bootstrap values of 100% are shown. The leftmost column depicts the identified SLST type. Type designations according to MLST9 and MLST8 schemes and ribotyping are also given, in addition to the traditional type assignments based on recA and tly sequence analysis. * indicates unknown types.

Mentions: A phylogenetic reference tree was constructed using shared core sequences of 86 P. acnes genomes of the 188 strains used in this study (Table S1). The core of the 86 genomes was obtained by splitting the genome sequence of the reference strain P. acnes KPA171202 into 500 bp fragments and aligning each fragment against all other genomes using blastn v. 2.2.28+ [21] with the following cut-off parameters: coverage > 90% and identity > 80%. Any fragment that did not yield a hit from all genomes was discarded, and the rest were aligned using Muscle v. 3.8.31[22] and concatenated into a 1,964,522 bp-sequence, hereafter referred to as the core genome. Using MEGA v. 5.2.2[23] we identified 107,397 single nucleotide polymorphisms (SNPs) and 8,100 gaps. A reference phylogenetic tree (Figure 1) was built in MEGA [23] using the Minimal evolution algorithm and 500 replication in the bootstrap test with the “complete deletion” option to exclude gaps from the analysis.


A novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo.

Scholz CF, Jensen A, Lomholt HB, Brüggemann H, Kilian M - PLoS ONE (2014)

The SLST scheme discriminates the phylogenetic clusters of P. acnes.Minimum Evolution phylogenetic tree based on 86 complete and draft P. acnes genomes, generated in MEGA v. 5.22 and based on a 1,964,522-bp concatemer of core sequences. Only bootstrap values of 100% are shown. The leftmost column depicts the identified SLST type. Type designations according to MLST9 and MLST8 schemes and ribotyping are also given, in addition to the traditional type assignments based on recA and tly sequence analysis. * indicates unknown types.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128656&req=5

pone-0104199-g001: The SLST scheme discriminates the phylogenetic clusters of P. acnes.Minimum Evolution phylogenetic tree based on 86 complete and draft P. acnes genomes, generated in MEGA v. 5.22 and based on a 1,964,522-bp concatemer of core sequences. Only bootstrap values of 100% are shown. The leftmost column depicts the identified SLST type. Type designations according to MLST9 and MLST8 schemes and ribotyping are also given, in addition to the traditional type assignments based on recA and tly sequence analysis. * indicates unknown types.
Mentions: A phylogenetic reference tree was constructed using shared core sequences of 86 P. acnes genomes of the 188 strains used in this study (Table S1). The core of the 86 genomes was obtained by splitting the genome sequence of the reference strain P. acnes KPA171202 into 500 bp fragments and aligning each fragment against all other genomes using blastn v. 2.2.28+ [21] with the following cut-off parameters: coverage > 90% and identity > 80%. Any fragment that did not yield a hit from all genomes was discarded, and the rest were aligned using Muscle v. 3.8.31[22] and concatenated into a 1,964,522 bp-sequence, hereafter referred to as the core genome. Using MEGA v. 5.2.2[23] we identified 107,397 single nucleotide polymorphisms (SNPs) and 8,100 gaps. A reference phylogenetic tree (Figure 1) was built in MEGA [23] using the Minimal evolution algorithm and 500 replication in the bootstrap test with the “complete deletion” option to exclude gaps from the analysis.

Bottom Line: Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease.Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences.We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark.

ABSTRACT
The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST) scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.

Show MeSH
Related in: MedlinePlus