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Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome.

Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ - PLoS ONE (2016)

Bottom Line: Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups.We observed an unexpected increase in α-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants.We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, New York University Langone Medical Center, New York, NY, United States of America.

ABSTRACT

Unlabelled: We studied skin microbiota present in three skin sites (forearm, axilla, scalp) in men from six ethnic groups living in New York City.

Methods: Samples were obtained at baseline and after four days following use of neutral soap and stopping regular hygiene products, including shampoos and deodorants. DNA was extracted using the MoBio Power Lyzer kit and 16S rRNA gene sequences determined on the IIlumina MiSeq platform, using QIIME for analysis.

Results: Our analysis confirmed skin swabbing as a useful method for sampling different areas of the skin because DNA concentrations and number of sequences obtained across subject libraries were similar. We confirmed that skin location was the main factor determining the composition of bacterial communities. Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups. We observed an unexpected increase in α-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants. Significant differences at phylum and genus levels were observed between subjects of the different ethnic origins at all skin sites.

Conclusions: We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

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Cutaneous microbial diversity in 645 samples from 110 subjects, based on skin location and beta diversity analysis over time, by ethnic group.The sequence depth is 3200/sample. Panel A. PCoA of clustering by sample location, based on unweighted pairwise UniFrac distances. The skin locations were Scalp [S (n = 215 samples)]; Arm [Ar (n = 215)]; Axilla [Ax (n = 215)]. Panel B. Analysis by ethnic group, including African-American [AA (n = 18 subjects/site)], East Asian [EA (n = 25)], Caucasian-American [CA (n = 16)], Latin American [LA (n = 16)], African-Continental [AC (n = 11)], and South Asian [SA (n = 19)]. PCoA of clustering of skin samples combining the three cutaneous sites, and the two time points; 1 = baseline and 2 = follow-up. Ellipses generally describe: axilla (black), scalp (yellow), and Arm (brown). Key to explain sites sampled and ethnic groups in all figures: The skin locations are colored as follows: yellow: Scalp (S); Brown: Arm (Ar); Black: Axilla (Ax). Ethnic groups are colored as: Orange: South Asian (SA); Light blue: Latin-American (LA); Purple: East Asian (EA); Red: African-American (AA); Blue: Caucasian-American (CA); Green: African-Continental (AC).
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pone.0151990.g001: Cutaneous microbial diversity in 645 samples from 110 subjects, based on skin location and beta diversity analysis over time, by ethnic group.The sequence depth is 3200/sample. Panel A. PCoA of clustering by sample location, based on unweighted pairwise UniFrac distances. The skin locations were Scalp [S (n = 215 samples)]; Arm [Ar (n = 215)]; Axilla [Ax (n = 215)]. Panel B. Analysis by ethnic group, including African-American [AA (n = 18 subjects/site)], East Asian [EA (n = 25)], Caucasian-American [CA (n = 16)], Latin American [LA (n = 16)], African-Continental [AC (n = 11)], and South Asian [SA (n = 19)]. PCoA of clustering of skin samples combining the three cutaneous sites, and the two time points; 1 = baseline and 2 = follow-up. Ellipses generally describe: axilla (black), scalp (yellow), and Arm (brown). Key to explain sites sampled and ethnic groups in all figures: The skin locations are colored as follows: yellow: Scalp (S); Brown: Arm (Ar); Black: Axilla (Ax). Ethnic groups are colored as: Orange: South Asian (SA); Light blue: Latin-American (LA); Purple: East Asian (EA); Red: African-American (AA); Blue: Caucasian-American (CA); Green: African-Continental (AC).

Mentions: Once the sequences were processed and OTUs were assigned, we analyzed the clustering of the 645 skin samples based on unweighted Unifrac distances, and visualized by Principal Coordinates Analysis (PCoA). As expected, the analysis shows that skin samples clustered according to skin location (Fig 1, Panel A).


Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome.

Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ - PLoS ONE (2016)

Cutaneous microbial diversity in 645 samples from 110 subjects, based on skin location and beta diversity analysis over time, by ethnic group.The sequence depth is 3200/sample. Panel A. PCoA of clustering by sample location, based on unweighted pairwise UniFrac distances. The skin locations were Scalp [S (n = 215 samples)]; Arm [Ar (n = 215)]; Axilla [Ax (n = 215)]. Panel B. Analysis by ethnic group, including African-American [AA (n = 18 subjects/site)], East Asian [EA (n = 25)], Caucasian-American [CA (n = 16)], Latin American [LA (n = 16)], African-Continental [AC (n = 11)], and South Asian [SA (n = 19)]. PCoA of clustering of skin samples combining the three cutaneous sites, and the two time points; 1 = baseline and 2 = follow-up. Ellipses generally describe: axilla (black), scalp (yellow), and Arm (brown). Key to explain sites sampled and ethnic groups in all figures: The skin locations are colored as follows: yellow: Scalp (S); Brown: Arm (Ar); Black: Axilla (Ax). Ethnic groups are colored as: Orange: South Asian (SA); Light blue: Latin-American (LA); Purple: East Asian (EA); Red: African-American (AA); Blue: Caucasian-American (CA); Green: African-Continental (AC).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4835103&req=5

pone.0151990.g001: Cutaneous microbial diversity in 645 samples from 110 subjects, based on skin location and beta diversity analysis over time, by ethnic group.The sequence depth is 3200/sample. Panel A. PCoA of clustering by sample location, based on unweighted pairwise UniFrac distances. The skin locations were Scalp [S (n = 215 samples)]; Arm [Ar (n = 215)]; Axilla [Ax (n = 215)]. Panel B. Analysis by ethnic group, including African-American [AA (n = 18 subjects/site)], East Asian [EA (n = 25)], Caucasian-American [CA (n = 16)], Latin American [LA (n = 16)], African-Continental [AC (n = 11)], and South Asian [SA (n = 19)]. PCoA of clustering of skin samples combining the three cutaneous sites, and the two time points; 1 = baseline and 2 = follow-up. Ellipses generally describe: axilla (black), scalp (yellow), and Arm (brown). Key to explain sites sampled and ethnic groups in all figures: The skin locations are colored as follows: yellow: Scalp (S); Brown: Arm (Ar); Black: Axilla (Ax). Ethnic groups are colored as: Orange: South Asian (SA); Light blue: Latin-American (LA); Purple: East Asian (EA); Red: African-American (AA); Blue: Caucasian-American (CA); Green: African-Continental (AC).
Mentions: Once the sequences were processed and OTUs were assigned, we analyzed the clustering of the 645 skin samples based on unweighted Unifrac distances, and visualized by Principal Coordinates Analysis (PCoA). As expected, the analysis shows that skin samples clustered according to skin location (Fig 1, Panel A).

Bottom Line: Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups.We observed an unexpected increase in α-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants.We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, New York University Langone Medical Center, New York, NY, United States of America.

ABSTRACT

Unlabelled: We studied skin microbiota present in three skin sites (forearm, axilla, scalp) in men from six ethnic groups living in New York City.

Methods: Samples were obtained at baseline and after four days following use of neutral soap and stopping regular hygiene products, including shampoos and deodorants. DNA was extracted using the MoBio Power Lyzer kit and 16S rRNA gene sequences determined on the IIlumina MiSeq platform, using QIIME for analysis.

Results: Our analysis confirmed skin swabbing as a useful method for sampling different areas of the skin because DNA concentrations and number of sequences obtained across subject libraries were similar. We confirmed that skin location was the main factor determining the composition of bacterial communities. Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups. We observed an unexpected increase in α-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants. Significant differences at phylum and genus levels were observed between subjects of the different ethnic origins at all skin sites.

Conclusions: We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

Show MeSH