Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling

• Published in: Journal of medical microbiology Vol. 54; no. 12; pp. 1231 - 1238
• Main Authors: Dekio, Itaru, Hayashi, Hidenori, Sakamoto, Mitsuo, Kitahara, Maki, Nishikawa, Takeji, Suematsu, Makoto, Benno, Yoshimi
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.12.2005; Society for General Microbiology
• Subjects: Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria, Aerobic - isolation & purification; Bacteria, Anaerobic - isolation & purification; Bacteriology; Base Sequence; Biological and medical sciences; DNA Fingerprinting; DNA Primers; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Escherichia coli - genetics; Escherichia coli - isolation & purification; Fundamental and applied biological sciences. Psychology; Humans; Infectious diseases; Medical sciences; Methylophilus methylotrophus; Microbiology; Miscellaneous; Molecular Sequence Data; Phylogeny; Propionibacterium acnes; Reference Values; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; Skin - microbiology; Staphylococcus epidermidis; Human; Bacteria; Microflora; Skin; Microbiology; Detection
• ISSN: 0022-2615; 1473-5644
• DOI: 10.1099/jmm.0.46075-0

1,3 Department of Dermatology 1 and Department of Biochemistry and Integrative Medical Biology 3 , School of Medicine, Keio University, Tokyo 160-8582, Japan 2 Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Japan Correspondence Itaru Dekio dekio{at}1999.jukuin.keio.ac.jp Received 6 March 2005 Accepted 13 August 2005 Although the micro-organisms forming the cutaneous microbiota are considered to play important roles in the modification and prevention of skin diseases, a comprehensive analysis of their composition has not yet been carried out because of difficulties in determining yet-to-be-cultured micro-organisms in the samples. Swab-scrubbed forehead skin samples of five healthy volunteers were analysed by profiling 16S rRNA genes, as well as by conventional culture methods, to provide a profile of the cutaneous microbiota that included yet-to-be-cultured bacteria from normal human skin. Cluster analyses of the 16S rRNA gene sequences indicated a marked increase in diversity compared with that derived from the culture methods. Nineteen previously recognized species and 13 novel phylotypes were obtained from the analysis of 416 clones. In addition to well-known bacteria such as Staphylococcus epidermidis and Propionibacterium acnes , phylotype A, the 16S rRNA gene of which is 97 % similar to that of Methylophilus methylotrophus , was detected in three of the five samples, in one of which it was the predominant clone. Culture-independent genetic profiling of 16S rRNA genes for detecting human cutaneous microbiota has allowed us to detect potentially novel components of the cutaneous microbiota in humans. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of novel phylotypes (phylotypes A–M) are AB161079–AB161091.