16: Microbiome of the Skin

Question 1

What are the most common methods to study skin microbes?

Answer 1

The most common methods to study skin microbes are based on cultivation techniques, which are especially used to help diagnose infections.

Question 2

What is the significance of Koch’s postulates in microbiome studies?

Answer 2

Koch’s postulates are a fundamental paradigm for linking a causative microbial agent to a disease, which helps in understanding host-microbial interactions.

Question 3

What challenges are associated with relying solely on cultivation methods for studying skin microbes?

Answer 3

A challenge of relying solely on cultivation methods is the difficulty in selecting the optimal culturing methods, which can skew results.

Question 4

What is the role of the Human Microbiome Project?

Answer 4

The Human Microbiome Project, launched in 2008, aims to explore the skin, gut, oral, vaginal, and nasal microbiomes in patients and healthy volunteers, developing protocols for study design, sample processing, sequencing, and analysis.

Question 5

How does sequencing microbial DNA improve skin microbiome studies?

Answer 5

By sequencing microbial DNA present within a sample, researchers can eliminate initial culturing that could skew results, allowing for a more accurate examination of the global cutaneous microbial communities.

Question 6

What distinguishes genomic studies from traditional microbiology in identifying bacterial species?

Answer 6

Genomic studies define a specific bacterial taxa based on the percent similarity of the genome, while traditional microbiology defines a distinct species based on morphologic, biochemical, and/or physiologic characteristics.

Question 7

What is the focus of investigations into the mycobiome?

Answer 7

Investigations into the mycobiome focus on its roles in human infections, production of active metabolites, and influence on bacterial growth, using specific marker genes for identification.

Question 8

What are the challenges faced in human virome studies compared to bacterial studies?

Answer 8

Human virome studies face challenges due to the heterogeneity of viral genomes, which includes single-stranded and double-stranded DNA and RNA viruses, making them less common than bacterial studies.

Question 9

What sequencing method should be used to identify bacterial taxa in a skin sample without culturing?

Answer 9

16S rRNA gene sequencing should be used because it targets all bacteria present in a sample without relying on cultivation.

Question 10

What are the implications of using genomic sequencing methods over traditional cultivation techniques in skin microbiome studies?

Answer 10

Genomic sequencing methods allow for a more comprehensive examination of skin microbes without the need for cultivation, which can skew results. They enable the identification of microbial DNA present in a sample, eliminating the reliance on live organisms and allowing for the study of both resident and transient microbes. This approach enhances the understanding of the global cutaneous microbial communities and facilitates investigations into the human microbiome.

Question 11

How does the distinction between genomic studies and traditional microbiology impact clinical microbiology?

Answer 11

Genomic studies define bacterial taxa based on genome similarity, while traditional microbiology relies on morphological, biochemical, and physiological characteristics. This distinction is crucial as it affects genus- and species-level identification, which has significant clinical implications for diagnosing and treating infections.

Question 12

What role does the 16S ribosomal RNA (rRNA) gene play in microbiome studies?

Answer 12

The 16S rRNA gene is a conserved component of the 30S ribosomal subunit in bacteria and cyanobacteria, allowing researchers to target and identify all bacteria present in a sample without needing to cultivate them. Its sufficient variation enables taxonomic identification across diverse ecosystems, making it a fundamental tool in microbiome studies.

Question 13

What challenges do human virome studies face compared to bacterial studies in microbiome research?

Answer 13

Human virome studies encounter challenges due to the heterogeneity of viral genomes, which can include both single-stranded and double-stranded DNA and RNA viruses. This complexity makes it more difficult to establish consistent marker genes and complicates the analysis compared to the more standardized approaches used in bacterial studies.

Question 14

What is shotgun metagenomic sequencing and how does it differ from traditional marker gene sequencing?

Answer 14

Shotgun metagenomic sequencing involves shearing and sequencing all DNA present in a sample, rather than focusing solely on specific marker genes like 16S or 18S rRNA genes. This method allows for the identification of microbes across multiple kingdoms and provides insights into the functional genetic potential of the resident microbes, unlike traditional methods that may only identify specific groups.

Question 15

What are the challenges associated with studying the skin microbiome?

Answer 15

Challenges in studying the skin microbiome include:

1. Low microbial biomass: Limited organic matter leads to small quantities of DNA.
2. Contamination risk: Samples can easily become contaminated due to low amounts of microbial DNA.
3. Quantitative determination: It is difficult to quantitatively assess microbial bioburden.
4. Control measures: Appropriate negative and positive controls are necessary for reliable results.

Question 16

How does the anatomical location affect the composition of the skin microbiome?

Answer 16

The composition of the skin microbiome is highly specific to anatomical regions due to:

• Different microenvironments: Variations in moisture, oiliness, and exposure lead to distinct microbial communities.
• Microscopic structures: Hair follicles, eccrine/apocrine glands, and sebaceous glands are distributed differently across the skin, influencing microbial diversity and localization.

Question 17

What types of samples can be collected for skin microbiome studies?

Answer 17

Skin samples can be collected using:

1. Premoistened swab
2. Superficial scraping
3. Biopsy
4. Tape strip
5. Cup scrub

DNA isolation methods depend on whether the focus is on a specific kingdom (bacteria or fungi) or shotgun metagenomics, which requires different preparation techniques.

Question 18

What is the significance of microbial isolates in skin microbiome studies?

Answer 18

Microbial isolates are significant in skin microbiome studies as they allow researchers to:

• Investigate specific microbial functions and mechanisms.
• Understand the interactions between different microbial species.
• Explore the roles of commensals and pathogens in skin health and disease.

Question 19

What are the advantages and limitations of shotgun metagenomic sequencing?

Answer 19

Advantages: Provides information beyond identification of microbes, including functional genetic potential. Limitations: Higher costs and analytic challenges.

Question 20

What are the limitations of marker gene-based studies in skin microbiome research?

Answer 20

Marker gene-based studies typically focus on DNA-only viruses or specific groups of viruses, which limits the understanding of the full microbial diversity and functional potential present in skin samples.

Question 21

How does the anatomical specificity of skin microbiomes affect sample collection methods?

Answer 21

Skin microbiomes are highly specific to particular anatomical regions, necessitating the use of various sample collection methods such as premoistened swabs, superficial scraping, biopsies, tape strips, or cup scrubs to accurately capture the microbial diversity present in those regions.

Question 22

What challenges are associated with quantifying microbial bioburden in skin microbiome studies?

Answer 22

Quantifying microbial bioburden is challenging due to the low microbial biomass on skin, which leads to limited DNA quantities and a high risk of contamination. Culture-based studies are often used to compare relative bioburden, but they may not accurately reflect the total microbial diversity.

Question 23

What role do different anatomical regions of the skin play in the composition of the skin microbiome?

Answer 23

Different anatomical regions of the skin, such as the forehead, palm, and flexural folds, are associated with distinct bacterial and fungal communities. This topographical variation influences the biodiversity and localization of cutaneous microbes, as different microenvironments harbor specific microbial populations.

Question 24

What factors influence the composition of skin bacterial communities?

Answer 24

The composition of skin bacterial communities is influenced by several factors:

1. Site Specificity: Different skin sites harbor distinct populations of bacteria based on their microenvironments (e.g., sebaceous areas, moist skin creases).
2. Hygiene Practices: The elapsed time since the last handwashing affects bacterial communities, with some bacteria being more abundant on recently washed hands.
3. Age and Sexual Maturity: Skin bacterial communities shift based on the age or sexual maturity of individuals.
4. Host Environment: Global geographic location and individual-specific factors may also play a role in influencing skin microbiome stability.

Question 25

How do skin bacterial communities differ between neonates and older children?

Answer 25

Skin bacterial communities in neonates, infants, and young children are distinct from those in more sexually mature children and adults. Key differences include: - **Acquisition of Microbes**: Neonates acquire skin microbes quickly after birth, resembling maternal vaginal or skin communities depending on the delivery method. - **Bacterial Diversity**: The bacterial diversity of skin in infants and young children is observed to be low shortly after birth. - **Site Specificity**: By the 2nd day of life, the site specificity of skin bacteria becomes observable, indicating that skin microbiome development is influenced by age.

Question 26

What is the relationship between atopic dermatitis and Staphylococcus aureus colonization?

Answer 26

The relationship between atopic dermatitis and Staphylococcus aureus colonization involves: - **Increased Colonization**: Individuals with atopic dermatitis often show high frequencies of S. aureus colonization. - **Impact on Condition**: It remains unclear whether the increased presence of staphylococci contributes to the development or worsening of atopic dermatitis or if it is a consequence of the skin condition providing a conducive environment for bacterial growth. - **Research Findings**: Studies suggest that S. aureus can exacerbate skin inflammation, with topical application linked to more severe dermatitis, although human studies are challenging to conduct directly.

Question 27

What are the effects of hygiene practices on skin microbiome diversity?

Answer 27

Hygiene practices significantly affect skin microbiome diversity: - **Time Since Last Handwashing**: The elapsed time since the last handwashing can alter the composition of skin bacterial communities. - **Bacterial Abundance**: Certain bacteria, such as Staphylococcaceae, are more abundant on hands that have been recently washed, while others, like Propionibacteriaceae, are more prevalent with longer intervals since the last wash. - **Product Usage**: Changes in hygiene products can also be associated with variations in skin microbiome diversity among different populations.

Question 28

What are the common skin diseases associated with specific bacterial communities?

Answer 28

Common skin diseases and their associated bacterial communities include: | Skin Disease | Associated Bacteria | Findings | |--------------|---------------------|---------| | Acne | Cutibacterium acnes | Different strains of C. acnes are associated with various patient versions. | | Atopic Dermatitis | Staphylococcus spp. | Increased abundance of Staphylococcus correlates with different skin conditions. | | Psoriasis | S. aureus, Streptococcus | Identified cocci in skin lesions and increased Proteobacteria in psoriatic lesions. | | Diabetic Skin and Wounds | Staphylococcus | Bacterial communities are less diverse and associated with specific pathogens.

Question 29

What microbial community is most likely to dominate the skin of neonates delivered via cesarean section?

Answer 29

The skin microbiome of neonates delivered via cesarean section resembles maternal skin communities shortly after birth.

Question 30

What are the possible implications of increased colonization of Staphylococcus aureus in a patient with atopic dermatitis?

Answer 30

Increased staphylococci (S. aureus and S. epidermidis) may exacerbate skin inflammation or be a consequence of eczematous skin providing an environment conducive to staphylococcal growth.

Question 31

What microbial shifts might be observed in the skin lesions of a patient with psoriasis?

Answer 31

Psoriatic skin lesions may show increased relative abundances of the phylum Proteobacteria compared to controls.

Question 32

What role does Cutibacterium acnes play in acne?

Answer 32

C. acnes is frequently linked with acne, but its role in acne causation remains unresolved and is an active area of investigation.

Question 33

What changes might a microbiologist observe after handwashing?

Answer 33

Recently washed hands show relatively more Staphylococceae and Streptococcaceae, while Propionibacteriaceae are more abundant with longer intervals since handwashing.

Question 34

How does the mode of delivery influence the initial skin microbiome of neonates?

Answer 34

Neonates delivered vaginally have skin microbiomes resembling maternal vaginal communities, while those delivered via cesarean section resemble maternal skin communities.

Question 35

What factors influence the stability of skin bacterial communities?

Answer 35

Stability is specific to the skin site and individual, and may be influenced by the host environment, including global geographic location.

Question 36

What bacterial species are expected in the skin microbiome of healthy adults?

Answer 36

Sebaceous areas like the forehead and retroauricular crease are predominated by Cutibacterium acnes.

Question 37

How does bacterial diversity change shortly after birth in infants?

Answer 37

Bacterial diversity is low shortly after birth but site specificity of skin bacteria is observable by the second day of life.

Question 38

What dermatologic conditions might be investigated in the skin microbiome of individuals with diabetes?

Answer 38

Conditions such as diabetic wounds and ichthyosis vulgaris can be studied using microbiome methods.

Question 39

What bacterial species are likely to dominate the inguinal crease?

Answer 39

The inguinal crease, a moist fold, harbors bacterial species like Corynebacterium spp. and Staphylococcus spp. that grow favorably in humid conditions.

Question 40

How does the skin microbiome of elderly individuals differ from younger populations?

Answer 40

There are fewer studies on elderly individuals, but skin bacterial communities shift based on age and sexual maturity.

Question 41

What bacterial species are predominant in the retroauricular crease?

Answer 41

The retroauricular crease, a sebaceous site, is predominated by Cutibacterium acnes.

Question 42

What variability might a clinician observe regarding hygiene products and skin microbiome diversity?

Answer 42

Alteration or usage of hygiene products is associated with changes in skin microbiome diversity in some healthy populations but not in others.

Question 43

How does the forehead respond to exposure to bacterial communities from other skin sites?

Answer 43

The forehead can revert back to its originally observed bacterial communities faster than other skin sites like the forearm.

Question 44

What bacterial species are likely to dominate the antecubital fossa?

Answer 44

The antecubital fossa, a moist fold, harbors bacterial species like Corynebacterium spp. and Staphylococcus spp. that grow favorably in humid conditions.

Question 45

What factors might a dermatologist consider when studying the effects of geographic location on skin microbiomes?

Answer 45

They might consider how the host environment, including global geographic location, influences skin microbiome stability.

Question 46

What microbiome methods might be used to study the skin microbiome of patients with melanoma?

Answer 46

They might use microbiome methods to study bacterial infections, body odor, and other dermatologic conditions.

Question 47

How does the skin microbiome of the palm differ from other skin sites?

Answer 47

The palm, a dry flat surface, demonstrates greater variability in bacterial communities compared to sebaceous or moist areas.

Question 48

How does the host environment influence skin microbiome stability?

Answer 48

The host environment, including global geographic location, influences skin microbiome stability.

Question 49

What microbiome methods might a researcher use to study the skin microbiome of patients with melanoma?

Answer 49

They might use microbiome methods to study bacterial infections, body odor, and other dermatologic conditions.

Question 50

What microbial shifts might a researcher investigate in the skin microbiome of patients with psoriasis?

Answer 50

They might investigate increased relative abundances of the phylum Proteobacteria in psoriatic skin lesions.

Question 51

How does the forearm skin microbiome respond to exposure from other skin sites?

Answer 51

The forearm reverts back to its originally observed bacterial communities slower than other skin sites like the forehead.

Question 52

What bacterial species are likely to dominate in the skin microbiome of patients with atopic dermatitis?

Answer 52

Staphylococcus aureus and Staphylococcus epidermidis are frequently observed in atopic dermatitis.

Question 53

How do skin bacterial communities differ between highly sebaceous sites and flexural, moist folds?

Answer 53

Skin bacterial communities in highly sebaceous sites, such as the forehead, are predominantly composed of Cutibacterium acnes, while flexural folds harbor species like Corynebacterium spp. and Staphylococcus spp. This difference can influence skin health, highlighting the importance of site-specific microbiome management.

Question 54

What factors influence the stability of skin bacterial communities over time?

Answer 54

Skin bacterial communities can remain stable for up to 2 years after initial sampling, influenced by the host environment, geographic location, and hygiene practices.

Question 55

What is the significance of the skin microbiome in neonates?

Answer 55

The skin microbiome in neonates is thought to be sterile prior to birth but quickly acquires microbes after delivery, resembling maternal communities. By the 2nd day of life, site specificity becomes observable.

Question 56

How do hygiene practices affect the skin microbiome?

Answer 56

Hygiene practices significantly affect skin bacterial communities, with certain bacteria being more abundant on recently washed hands, suggesting hygiene can alter microbiome diversity.

Question 57

What are the predominant species of Malassezia found on different skin areas in healthy individuals?

Answer 57

- M. restricta: Predominant on the head and facial areas. - M. globosa: Predominant on truncal areas. - Non-Malassezia fungi (e.g., Aspergillus, Cryptococcus, Epicoccum, Rhodotorula): Predominant on feet.

Question 58

How does the colonization of Malassezia fungi vary with age in individuals?

Answer 58

Younger individuals are typically colonized by Malassezia less frequently and in lower abundances than adults, with rates increasing as individuals age.

Question 59

What is the significance of lipid dependence in Malassezia species?

Answer 59

Malassezia species are lipid-dependent and generally require lipid supplements for growth, lacking the fatty synthase gene.

Question 60

What genomic differences have been identified among Malassezia species?

Answer 60

Genomic differences in lipase and phospholipase gene content have been identified among Malassezia species, influencing their growth preferences.

Question 61

What predominant fungal species are expected on the feet?

Answer 61

Non-Malassezia fungi such as Aspergillus, Cryptococcus, Epicoccum, and Rhodotorula are predominant on the feet.

Question 62

What species of Malassezia is predominant on the trunk?

Answer 62

Malassezia globosa is predominant on the trunk.

Question 63

What changes are expected in younger individuals regarding Malassezia colonization?

Answer 63

Younger individuals are colonized by Malassezia less frequently and in lower abundances than adults.

Question 64

What are the differences in the relative abundances of Malassezia species between adults and children?

Answer 64

Adults have lower relative abundances of M. globosa and higher relative abundances of M. restricta, while children typically have higher relative abundances of M. restricta.

Question 65

What is the significance of the high relative abundance of Malassezia spp. in postpubertal individuals?

Answer 65

The high relative abundance of Malassezia spp. in postpubertal individuals corresponds to the higher frequency of tinea versicolor in adults.

Question 66

How do the relative abundances of non-Malassezia fungi in prepubertal children relate to skin conditions?

Answer 66

The higher relative abundances of non-Malassezia fungi in prepubertal children correspond to the higher prevalence of tinea capitis and tinea corporis.

Question 67

What are the common DNA viruses associated with dermatologic diseases?

Answer 67

The most common DNA viruses associated with dermatologic diseases include bacteriophages, papillomaviruses, polyomaviruses, and circoviruses.

Question 68

What challenges exist in studying cultured viruses in dermatologic diseases?

Answer 68

A major challenge is the lack of a marker gene common to all viruses, complicating the study of cultured viruses.

Question 69

What is the relationship between gut bacteria and skin diseases?

Answer 69

There may be instances where gut bacteria affect skin diseases, indicating a potential link between the gut microbiome and skin health.

Question 70

What are the goals of investigating the skin microbiome?

Answer 70

The goals include determining how microbes influence human health and disease and developing preventive or therapeutic interventions.

Question 71

What gaps exist in the understanding of a 'healthy' skin microbiome?

Answer 71

There remain significant gaps in defining what constitutes a 'healthy' skin microbiome and understanding the biological links between skin microbes and health.

Question 72

What microbial shift is likely associated with tinea versicolor in postpubertal individuals?

Answer 72

Postpubertal individuals have a high relative abundance of Malassezia spp., which corresponds to the higher frequency of tinea versicolor.

Question 73

What differences in fungal communities are expected when comparing prepubertal children and adults?

Answer 73

Prepubertal children have higher relative abundances of non-Malassezia fungi, while adults have higher Malassezia spp.

Question 74

What challenges might a researcher studying the skin virome face?

Answer 74

Challenges include the lack of a common marker gene for all viruses and the heterogeneity of viral genomes.

Question 75

What virus is likely implicated in Merkel cell carcinoma?

Answer 75

Merkel cell polyomavirus is associated with Merkel cell carcinoma.

Question 76

What changes are expected in fungal communities during puberty?

Answer 76

Increased sebum production during puberty leads to higher colonization rates of Malassezia spp.

Question 77

What fungal diversity is expected in healthy preadolescent subjects?

Answer 77

Healthy preadolescent subjects have low relative abundances of Malassezia and higher fungal diversity compared to adults.

Question 78

What systemic links might be investigated in patients with vitiligo?

Answer 78

They might investigate links between gut bacteria and skin diseases or how skin bacteria affect distal body sites.

Question 79

What systemic links might be investigated in patients with pyoderma gangrenosum?

Answer 79

They might investigate links between skin bacteria and inflammatory bowel disease.

Question 80

What changes are expected in skin fungal communities due to puberty?

Answer 80

Puberty leads to increased colonization rates of Malassezia spp. due to increased sebaceous gland activity.

Question 81

What viral associations might be investigated in patients with herpes labialis?

Answer 81

They might investigate herpes simplex viruses, which are associated with herpes labialis.

Question 82

What are the differences in the relative abundances of Malassezia species between adults and children?

Answer 82

Adults have lower relative abundances of M. globosa and higher relative abundances of M. restricta, while children have higher relative abundances of M. restricta.

Question 83

What challenges are faced in studying skin viral communities?

Answer 83

A major challenge is the lack of a marker gene common to all viruses, complicating the study of viral communities.

Question 84

How might the gut microbiome influence skin diseases?

Answer 84

There may be instances where gut bacteria affect skin diseases, indicating a potential gut-skin axis.