Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

40595471

DOI Digital object identifier for electronic documents.

10.1038/s41467-025-60131-7

URI Uniform resource identifier for web resources.

Authors

Durack J, Piceno Y, Vuong H, Fanelli B, Good DA, Hasan NA, Dadlani M, Weiss L, Oh J, Kostic AD, Dawson TL, Caballero-Arias H, Colwell RR

Journal

Nature communications

Year

2025

The adult skin microbiome typically exhibits low microbial complexity, particularly on sebaceous sites, where lipophilic Cutibacterium and Malassezia spp. predominate. Current understanding of healthy skin microbiome is largely based on western, industrialized populations, with limited representation of diverse cultures and lifestyles. Here, we investigate the skin microbiome of a remote indigenous Yanomami community and reveal a complex microbial ecosystem comprising 115 previously unreported bacterial genomes. The Yanomami skin microbiome includes genera common to western populations alongside diverse environmental taxa that form multiplex interactions with the dominant eukaryote Malassezia globosa. Functional profiling indicates that this microbiome supports skin homeostasis by fortifying barrier integrity through lipid metabolism and acid production and mitigating oxidative stress. Longitudinal monitoring of western expeditioner' skin demonstrates acquisition of the Yanomami microbiome following Amazonian immersion and its subsequent loss upon return to an industrialized setting. These findings reveal that diverse, environmentally enriched microbiota may confer skin benefits that are overlooked in current models of healthy skin.

Experiment 1

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Needs review

Curated date: 2025/08/10

Curator: Ese

Revision editor(s): Ese

Subjects

Location of subjects: Venezuela

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Retroarticular Retroarticular,retroarticular

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Body composition measurement Body composition measurement,body composition measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: western HMP

Group 1 name Corresponds to the case (exposed) group for case-control studies: adult Yanomami

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Group 1 sample size Number of subjects in the case (exposed) group: 5

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, Confounders controlled for: "body sites" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.body sites

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

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Curated date: 2025/08/12

Curator: Ese

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Source: Figure 2D

Description: LEfSe analysis showing most differential bacterial species on retroauricular crease (RAC) of adult Yanomami and western HMP

Abundance in Group 1: increased abundance in adult Yanomami

NCBI	Quality Control	Links
Abiotrophia
Abiotrophia defectiva
Actinomyces
Actinomyces naeslundii
Allosaccharopolyspora coralli
Arachnia propionica
Arsenicicoccus
Blastococcus
Bordetella pertussis
Brachybacterium
Brachybacterium muris
Brachybacterium paraconglomeratum
Brevibacterium ihuae
Corynebacterium
Corynebacterium appendicis
Corynebacterium durum
Corynebacterium jeddahense
Corynebacterium mucifaciens
Corynebacterium pseudogenitalium
Corynebacterium tuberculostearicum
Corynebacterium ureicelerivorans
Deinococcus wulumuqiensis
Dermacoccus
Dietzia
Dietzia cinnamea
Dietzia lutea
Dietzia maris
Dietzia timorensis
Enhydrobacter
Enhydrobacter aerosaccus
Faucicola osloensis
Janibacter indicus
Kocuria
Kocuria marina
Kocuria marina subsp. indica
Kocuria palustris
Kytococcus sedentarius
Lampadena luminosa
Mesorhizobium
Microbacterium
Micrococcaceae
Micrococcus
Micrococcus aloeverae
Micrococcus luteus
Micrococcus terreus
Micrococcus yunnanensis
Mobilicoccus
Nigerium massiliense
Paenibacillus sophorae
Paracoccus aeridis
Staphylococcus arlettae
Staphylococcus aureus
Staphylococcus haemolyticus
Staphylococcus hominis
Staphylococcus saprophyticus
Streptococcus
Yimella