Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes
Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received...
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Published in | BMC microbiology Vol. 19; no. 1; p. 214 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
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BioMed Central Ltd
05.09.2019
BioMed Central BMC |
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Abstract | Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic.
We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method.
Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. |
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AbstractList | Background Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. Results We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Conclusion Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. Keywords: DNA purification, Bacteriophage, Skin microbiome Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. BACKGROUNDCharacterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. RESULTSWe find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. CONCLUSIONUse of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. Abstract Background Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. Results We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Conclusion Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. Background Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. Results We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Conclusion Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples. |
ArticleNumber | 214 |
Audience | Academic |
Author | Chen, Irene A Deacon, John M Kim, Colin Y Verbanic, Samuel |
Author_xml | – sequence: 1 givenname: Samuel surname: Verbanic fullname: Verbanic, Samuel organization: Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, USA – sequence: 2 givenname: Colin Y surname: Kim fullname: Kim, Colin Y organization: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA – sequence: 3 givenname: John M surname: Deacon fullname: Deacon, John M organization: Goleta Valley Cottage Hospital, Ridley-Tree Center for Wound Management, Goleta, CA, USA – sequence: 4 givenname: Irene A orcidid: 0000-0001-6040-7927 surname: Chen fullname: Chen, Irene A email: chen@chem.ucsb.edu, chen@chem.ucsb.edu, chen@chem.ucsb.edu organization: Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA. chen@chem.ucsb.edu |
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Snippet | Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample... Background Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While... BACKGROUNDCharacterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample... Abstract Background Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples.... |
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StartPage | 214 |
SubjectTerms | Bacterial genetics Bacteriophage Biomass Deoxyribonucleic acid DNA DNA purification Genomes Information management Methodology Microbiomes Microbiota (Symbiotic organisms) Microorganisms Optimization Phages Polymerase chain reaction RNA sequencing Sample preparation Skin Skin microbiome Wounds |
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Title | Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes |
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