scholarly journals Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia

2017 ◽  
Author(s):  
Ashley A. Ross ◽  
Kirsten Müller ◽  
J. Scott Weese ◽  
Josh D. Neufeld
Keyword(s):  
Human Skin ◽  
External Environment ◽  
Geographic Location ◽  
The Body ◽  
Conservation Strategies ◽  
Body Region ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Skin Microbiota ◽  
Mammalian Skin

AbstractSkin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. The back, torso, and inner thigh regions of 177 non-human mammals were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). For reference, previously published skin microbiome data from 20 human participants, sampled using an identical protocol to the non-human mammals, were included in the analysis. Human skin was significantly less diverse than all other mammalian orders and the factor most strongly associated with community variation for all samples was whether the host was a human. Within non-human samples, host taxonomic order was the most significant factor influencing the skin community, followed by the geographic location of the habitat. By comparing the congruence between known host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing first evidence of phylosymbiosis between skin communities and their hosts.SignificanceSkin forms a critical protective barrier between a mammal and its external environment. Baseline data on the mammalian skin microbiome is crucial for making informed decisions related to veterinary research and biodiversity conservation strategies, in addition to providing insight into mammalian evolutionary history. To our knowledge, this study represents the largest mammalian skin microbiota project to date. These findings demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Using phylosymbiosis analysis, we provide the first evidence that co-evolution may be occurring between skin communities and their mammalian hosts, which warrants more in-depth future studies of the relationships between mammals and their skin microbiota.

scholarly journals Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

2018 ◽  
Vol 115 (25) ◽  
pp. E5786-E5795 ◽  
Author(s):  
Ashley A. Ross ◽  
Kirsten M. Müller ◽  
J. Scott Weese ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Human Skin ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Skin Microbiome ◽  
Skin Microbiota

Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment, yet the factors that govern skin microbial community composition among mammals are poorly understood. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. Skin from the back, torso, and inner thighs of 177 nonhuman mammals was sampled, representing individuals from 38 species and 10 mammalian orders. Animals were sampled from farms, zoos, households, and the wild. The DNA extracts from all skin swabs were amplified by PCR and sequenced, targeting the V3-V4 regions of bacterial and archaeal 16S rRNA genes. Previously published skin microbiome data from 20 human participants, sampled and sequenced using an identical protocol to the nonhuman mammals, were included to make this a comprehensive analysis. Human skin microbial communities were distinct and significantly less diverse than all other sampled mammalian orders. The factor most strongly associated with microbial community data for all samples was whether the host was a human. Within nonhuman samples, host taxonomic order was the most significant factor influencing skin microbiota, followed by the geographic location of the habitat. By comparing the congruence between host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing evidence of phylosymbiosis between skin microbial communities and their hosts.

scholarly journals Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Jiayue Yang ◽  
Tomoya Tsukimi ◽  
Mia Yoshikawa ◽  
Kenta Suzuki ◽  
Tomoki Takeda ◽  
...  
Keyword(s):  
16S Rrna ◽  
Human Skin ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Nucleotide Polymorphisms ◽  
Skin Microbiota ◽  
Content Type ◽  
Microbiome Profile ◽  
Cutibacterium Acnes ◽  
Genotype Composition

ABSTRACT The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general. IMPORTANCE Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.

scholarly journals Human Skin Microbiome: Impact of Intrinsic and Extrinsic Factors on Skin Microbiota

2021 ◽  
Vol 9 (3) ◽  
pp. 543
Author(s):  
Krzysztof Skowron ◽  
Justyna Bauza-Kaszewska ◽  
Zuzanna Kraszewska ◽  
Natalia Wiktorczyk-Kapischke ◽  
Katarzyna Grudlewska-Buda ◽  
...  
Keyword(s):  
Human Skin ◽  
Skin Diseases ◽  
The Body ◽  
Skin Microbiome ◽  
Skin Microbiota ◽  
Extrinsic Factors ◽  
Microorganism Identification ◽  
Mutual Relations ◽  
Internal And External Factors ◽  
The Impact

The skin is the largest organ of the human body and it protects the body from the external environment. It has become the topic of interest of researchers from various scientific fields. Microorganisms ensure the proper functioning of the skin. Of great importance, are the mutual relations between such microorganisms and their responses to environmental impacts, as dysbiosis may contribute to serious skin diseases. Molecular methods, used for microorganism identification, allow us to gain a better understanding of the skin microbiome. The presented article contains the latest reports on the skin microbiota in health and disease. The review discusses the relationship between a properly functioning microbiome and the body’s immune system, as well as the impact of internal and external factors on the human skin microbiome.

scholarly journals Rhodomyrtus tomentosa Fruit Extract and Skin Microbiota: A Focus on C. acnes Phylotypes in Acne Subjects

Cosmetics ◽  
2020 ◽  
Vol 7 (3) ◽  
pp. 53 ◽  
Author(s):  
Sandie Gervason ◽  
Isabelle Metton ◽  
Elodie Gemrot ◽  
Edwige Ranouille ◽  
Gilbert Skorski ◽  
...  
Keyword(s):  
Active Ingredient ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Skin Microbiota ◽  
Cutibacterium Acnes ◽  
Culture Independent ◽  
Rrna Gene Sequencing ◽  
Abundant Genus ◽  
Rhodomyrtus Tomentosa

Knowing that Rhodomyrtus tomentosa is known to have antibacterial effects, this study investigated the skin microbiota with a focus on Cutibacterium acnes (C. acnes) phylotypes in subjects with acne, and determined microbiota changes after 28 days of treatment with berries Rhodomyrtus tomentosa as an active ingredient (RT). Skin swabs from seventeen acne subjects were collected and the skin microbiome was analyzed using 16S rRNA gene sequencing. A culture-independent next-generation sequencing (NGS)-based SLST (single-locus sequence typing) approach was aimed at evaluating RT extract effects on C. acnes phylotype repartition. Clinical evaluations (lesion counts) were performed at baseline (D0) and after 28 days (D28) of twice-daily application of the RT active ingredient. We determined: (1) the skin microbiota at D0 was dominated by Actinobacteria followed by Firmicutes and Proteobacteria; (2) at the genus level, Cutibacterium was the most abundant genus followed by Staphylococcus and Corynebacterium; (3) C. acnes was the major species in terms of mean abundance, followed by Staphylococcus epidermidis (S. epidermidis) and Staphylococcus hominis (S. hominis); and (4) phylotype IA1 was most represented, with a predominance of SLST type A1, followed by phylotypes II, IB, IA2, IC, and III. After 28 days of RT extract treatment, phylotype repartition were modified with a decrease in abundance (approximately 4%) of phylotype IA1 and an increase in phylotype II and III. Cutibacterium granulosum (C. granulosum) abundance also decreased. Reduction of retentional and inflammatory lesions was also noted only after RT treatment; thus, RT extract acts as a microbiota-regulating agent.

scholarly journals Leprous lesion reveals disturbed skin-resident microbiota

2014 ◽  
Author(s):  
Andréa Nascimento ◽  
Paulo Silva ◽  
Patrícia Costa ◽  
Mariana Reis ◽  
Marcelo Ávila ◽  
...  
Keyword(s):  
Human Skin ◽  
Pathogenic Bacteria ◽  
Massively Parallel ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Healthy Skin ◽  
Skin Microbiota ◽  
Cutaneous Lesions ◽  
Taxonomic Analysis ◽  
Rrna Gene Sequencing

Leprosy is a chronic infectious disease that remains a major challenge to public health in endemic countries. Increasing evidence has highlighted the importance of microbiota for human general health and, as such, the study of skin microbiota is of interest. But while studies are continuously revealing the complexity of human skin microbiota, the microbiota of leprous cutaneous lesions has not yet been characterized. Here we used Sanger and massively parallel SSU rRNA gene sequencing to characterize the microbiota of leprous lesions, and studied how it differs from the bacterial skin composition of healthy individuals previously described in the literature. Taxonomic analysis of leprous lesions revealed main four phyla: Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with Proteobacteria presenting the highest diversity. There were considerable differences in the distribution of Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with the first two phyla enriched and the other markedly diminished in the leprous lesions, when compared with healthy skin. Propionibacterium, Corynebacterium and Staphylococcus, resident and abundant in healthy skin, were underrepresented in skin from leprous lesions. Most of the taxa found in skin from leprous lesions are not typical of human skin and potentially pathogenic, with the Bulkorderia, Pseudomonas and Bacillus genera being overrepresented. Our data suggest significant shifts of the microbiota with emergence and competitive advantage of potentially pathogenic bacteria over skin resident taxa.

scholarly journals Effects of sampling strategy and DNA extraction on human skin microbiome investigations

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rie Dybboe Bjerre ◽  
Luisa Warchavchik Hugerth ◽  
Fredrik Boulund ◽  
Maike Seifert ◽  
Jeanne Duus Johansen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Extraction ◽  
Human Skin ◽  
Alpha Diversity ◽  
Sampling Strategy ◽  
Sampling Technique ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Library Preparation ◽  
Reliable Technique

AbstractThe human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.

scholarly journals Challenges in exploring and manipulating the human skin microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Manon Boxberger ◽  
Valérie Cenizo ◽  
Nadim Cassir ◽  
Bernard La Scola
Keyword(s):  
Human Skin ◽  
Human Body ◽  
Skin Aging ◽  
Microbial Populations ◽  
Skin Microbiome ◽  
Microbiota Composition ◽  
Skin Microbiota ◽  
Extrinsic Factors ◽  
Health And Disease ◽  
Intrinsic And Extrinsic Factors

AbstractThe skin is the exterior interface of the human body with the environment. Despite its harsh physical landscape, the skin is colonized by diverse commensal microbes. In this review, we discuss recent insights into skin microbial populations, including their composition and role in health and disease and their modulation by intrinsic and extrinsic factors, with a focus on the pathobiological basis of skin aging. We also describe the most recent tools for investigating the skin microbiota composition and microbe-skin relationships and perspectives regarding the challenges of skin microbiome manipulation.

scholarly journals Charting host-microbe co-metabolism in skin aging and application to metagenomics data

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258960
Author(s):  
Wynand Alkema ◽  
Jos Boekhorst ◽  
Robyn T. Eijlander ◽  
Steve Schnittger ◽  
Fini De Gruyter ◽  
...  
Keyword(s):  
Human Skin ◽  
Molecular Mechanisms ◽  
Markov Models ◽  
Age Groups ◽  
Skin Aging ◽  
Protein Glycation ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Sequencing Data ◽  
Extrinsic Factors

During aging of human skin, a number of intrinsic and extrinsic factors cause the alteration of the skin’s structure, function and cutaneous physiology. Many studies have investigated the influence of the skin microbiome on these alterations, but the molecular mechanisms that dictate the interplay between these factors and the skin microbiome are still not fully understood. To obtain more insight into the connection between the skin microbiome and the human physiological processes involved in skin aging, we performed a systematic study on interconnected pathways of human and bacterial metabolic processes that are known to play a role in skin aging. The bacterial genes in these pathways were subsequently used to create Hidden Markov Models (HMMs), which were applied to screen for presence of defined functionalities in both genomic and metagenomic datasets of skin-associated bacteria. These models were further applied on 16S rRNA gene sequencing data from skin microbiota samples derived from female volunteers of two different age groups (25–28 years (‘young’) and 59–68 years (‘old’)). The results show that the main bacterial pathways associated with aging skin are those involved in the production of pigmentation intermediates, fatty acids and ceramides. This study furthermore provides evidence for a relation between skin aging and bacterial enzymes involved in protein glycation. Taken together, the results and insights described in this paper provide new leads for intervening with bacterial processes that are associated with aging of human skin.

scholarly journals The Bovine Foot Skin Microbiota is Associated with Host Genotype and the Development of Infectious Digital Dermatitis Lesions

2021 ◽  
Author(s):  
V. Bay ◽  
A. Gillespie ◽  
E.K. Ganda ◽  
Nicholas Evans ◽  
Stuart Carter ◽  
...  
Keyword(s):  
Bovine Genome ◽  
Bacterial Species ◽  
Significant Proportion ◽  
Subsequent Development ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Metagenomic Sequencing ◽  
Skin Microbiota ◽  
Host Genotype ◽  
Digital Dermatitis

Abstract Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. The polymicrobial nature of this disease has led to the hypothesis that the foot skin microbiota may be associated with occurrence and progression of lesions. We describe herein the bovine foot skin microbiota using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. We show differences in the foot skin microbiome profiles of clinically healthy animals that were associated with subsequent development of BDD. We also present the first co-occurrence analysis of the bovine foot skin microbiome showing ecological relationships among bacterial species. Taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and the foot skin microbiota profiles. We show the existence of genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.

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