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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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Comparison of microbiota differences by ethnic group, analyzed by LEfSe using baseline samples.Taxa with relative abundance ≥ 0.1% present in at least one sample in each location were included. The cladograms indicate the phylogenetic distribution of the microbial lineages associated with ethnic group, with lineages with Linear Discriminant Analysis (LDA) score ≥2.0 displayed. Significance differences for each ethnic group of the most abundant class are indicated by color, as indicated in the key. Each node’s diameter is proportional to the taxon’s abundance. The strategy of multiclass analysis is non-strict (≥ one class differential). Nodes represent phylogenetic levels from domain to genus (from inside out) (AA, n = 18 subjects; AC, n = 11; CA, n = 16; EA, n = 25; LA, n = 19; SA, n = 20).
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pone.0151990.g005: Comparison of microbiota differences by ethnic group, analyzed by LEfSe using baseline samples.Taxa with relative abundance ≥ 0.1% present in at least one sample in each location were included. The cladograms indicate the phylogenetic distribution of the microbial lineages associated with ethnic group, with lineages with Linear Discriminant Analysis (LDA) score ≥2.0 displayed. Significance differences for each ethnic group of the most abundant class are indicated by color, as indicated in the key. Each node’s diameter is proportional to the taxon’s abundance. The strategy of multiclass analysis is non-strict (≥ one class differential). Nodes represent phylogenetic levels from domain to genus (from inside out) (AA, n = 18 subjects; AC, n = 11; CA, n = 16; EA, n = 25; LA, n = 19; SA, n = 20).

Mentions: We performed comparative analyses of the relative taxa abundances in the samples at baseline across the groups studied (Fig 5). There were significant differences in the relative taxa abundances associated with both skin location and ethnic group. The largest differences in relative taxa abundances between the ethnic groups involved the scalp; the South Asian men showed the most divergent taxa compared to the other groups, but multiple differences involving diverse taxa were significant across other groups. The arm showed other major differences, with the fewest in the axilla. The East Asian men had numerous taxa that were significantly more abundant in the arm than in the other five study groups (including Class Alphaproteobacteria, as well as genus Deinococcus from phylum Deinococci-Thermi at all 5 taxonomic levels). For the axilla samples, the most significant differences involved the African-American and Caucasian-American subjects. Thus, the ethnic groups showed a number of substantial group-specific taxonomic differences.


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)

Comparison of microbiota differences by ethnic group, analyzed by LEfSe using baseline samples.Taxa with relative abundance ≥ 0.1% present in at least one sample in each location were included. The cladograms indicate the phylogenetic distribution of the microbial lineages associated with ethnic group, with lineages with Linear Discriminant Analysis (LDA) score ≥2.0 displayed. Significance differences for each ethnic group of the most abundant class are indicated by color, as indicated in the key. Each node’s diameter is proportional to the taxon’s abundance. The strategy of multiclass analysis is non-strict (≥ one class differential). Nodes represent phylogenetic levels from domain to genus (from inside out) (AA, n = 18 subjects; AC, n = 11; CA, n = 16; EA, n = 25; LA, n = 19; SA, n = 20).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4835103&req=5

pone.0151990.g005: Comparison of microbiota differences by ethnic group, analyzed by LEfSe using baseline samples.Taxa with relative abundance ≥ 0.1% present in at least one sample in each location were included. The cladograms indicate the phylogenetic distribution of the microbial lineages associated with ethnic group, with lineages with Linear Discriminant Analysis (LDA) score ≥2.0 displayed. Significance differences for each ethnic group of the most abundant class are indicated by color, as indicated in the key. Each node’s diameter is proportional to the taxon’s abundance. The strategy of multiclass analysis is non-strict (≥ one class differential). Nodes represent phylogenetic levels from domain to genus (from inside out) (AA, n = 18 subjects; AC, n = 11; CA, n = 16; EA, n = 25; LA, n = 19; SA, n = 20).
Mentions: We performed comparative analyses of the relative taxa abundances in the samples at baseline across the groups studied (Fig 5). There were significant differences in the relative taxa abundances associated with both skin location and ethnic group. The largest differences in relative taxa abundances between the ethnic groups involved the scalp; the South Asian men showed the most divergent taxa compared to the other groups, but multiple differences involving diverse taxa were significant across other groups. The arm showed other major differences, with the fewest in the axilla. The East Asian men had numerous taxa that were significantly more abundant in the arm than in the other five study groups (including Class Alphaproteobacteria, as well as genus Deinococcus from phylum Deinococci-Thermi at all 5 taxonomic levels). For the axilla samples, the most significant differences involved the African-American and Caucasian-American subjects. Thus, the ethnic groups showed a number of substantial group-specific taxonomic differences.

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