Isolation and characterization of diverse microbial representatives from the human skin microbiome

Isolated hair bacteria reveal different isolation possibilities under various conditions

Microorganisms are assumed to inhabit various environments and organisms, including the human body. The presence of more than 700 bacterial species on scalp hair has been reported through rRNA gene amplicon analysis. However, the biological properties of bacteria on the scalp hair (hair bacteria) and their functions are poorly understood as few hair bacteria have been isolated from hair in previous studies. This study aimed to isolate hair bacteria using standard media under 24 different conditions (including medium components, component concentrations, gelling agents, and atmospheric environments). Furthermore, we evaluated the possibility of isolating strains under these isolation conditions and examined the carbon metabolic ability of several predominantly isolated strains. A total of 63 bacterial species belonging to 27 genera were isolated from hair under 24 isolation conditions. The predominant bacterial species isolated from human hair in this study showed different carbon metabolic capabilities than those of the reference strains. In addition, isolation possibility was newly proposed to systematically evaluate the number of isolation conditions that could cultivate a bacterial species. Based on isolation possibility, the isolates were categorized into groups with a high number of isolation conditions (e.g., ≥25%; such as Staphylococcus) and those with a low number (e.g., ≤25%; such as Brachybacterium). These findings indicate the existence of easily isolated microorganisms and difficultly isolated microorganism from human hair.

Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling

The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an in silico experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA.IMPORTANCESkin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.

Draft genome sequence of Bacillus safensis strain WOIS2 KX774194, a nitrile-metabolizing bacterium isolated from solid waste leachates at Olusosun dumpsite, Ojota, Lagos State, Nigeria

Bacillus safensis strain WOIS2, a nitrile-metabolizing bacterium, was isolated from solid waste leachates at the Olusosun dumpsite, Ojota, Lagos State, Nigeria. Here, we present the draft genome sequence of strain WOIS2. These data provide valuable information on the bioprospecting of B. safensis nitrilase and other intriguing genes of interest.

Unveiling genome sequence of Bacillus safensis strain WOB7 KX774196, a linamarin-utilizing bacterium (LUB) isolated from cassava wastewater (CWW) in Lagos State, Nigeria

Bacillus safensis strain WOB7 is a linamarin-utilizing bacterium (LUB) that was isolated from cassava wastewater obtained from a processing factory. We present here the draft genome sequence of the strain (WOB7). These data provide valuable information on the prospects of the linamarase and other genes of importance associated with cyanogen detoxification.

Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin

Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.

Exploring the skin microbiome in atopic dermatitis pathogenesis and disease modification

Inflammatory skin diseases such as atopic eczema (atopic dermatitis [AD]) affect children and adults globally. In AD, the skin barrier is impaired on multiple levels. Underlying factors include genetic, chemical, immunologic, and microbial components. Increased skin pH in AD is part of the altered microbial microenvironment that promotes overgrowth of the skin microbiome with Staphylococcus aureus. The secretion of virulence factors, such as toxins and proteases, by S aureus further aggravates the skin barrier deficiency and additionally disrupts the balance of an already skewed immune response. Skin commensal bacteria, however, can inhibit the growth and pathogenicity of S aureus through quorum sensing. Therefore, restoring a healthy skin microbiome could contribute to remission induction in AD. This review discusses direct and indirect approaches to targeting the skin microbiome through modulation of the skin pH; UV treatment; and use of prebiotics, probiotics, and postbiotics. Furthermore, exploratory techniques such as skin microbiome transplantation, ozone therapy, and phage therapy are discussed. Finally, we summarize the latest findings on disease and microbiome modification through targeted immunomodulatory systemic treatments and biologics. We believe that targeting the skin microbiome should be considered a crucial component of successful AD treatment in the future.

A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases

The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.

Bacteria-based drug delivery for treating non-oncological diseases

Bacteria inhabit all over the human body, especially the skin, gastrointestinal tract, respiratory tract, urogenital tract, as well as specific lesion sites, such as wound and tumor. By leveraging their distinctive attributes including rapid proliferation, inherent abilities to colonize various biointerfaces in vivo and produce diverse biomolecules, and the flexibility to be functionalized via genetic engineering or surface modification, bacteria have been widely developed as living therapeutic agents, showing promising potential to make a great impact on the exploration of advanced drug delivery systems. In this review, we present an overview of bacteria-based drug delivery and its applications in treating non-oncological diseases. We systematically summarize the physiological positions where living bacterial therapeutic agents can be delivered to, including the skin, gastrointestinal tract, respiratory tract, and female genital tract. We discuss the success of using bacteria-based drug delivery systems in the treatment of diseases that occur in specific locations, such as skin wound healing/infection, inflammatory bowel disease, respiratory diseases, and vaginitis. We also discuss the advantages as well as the limitations of these living therapeutics and bacteria-based drug delivery, highlighting the key points that need to be considered for further translation. This review article may provide unique insights for designing next-generation bacteria-based therapeutics and developing advanced drug delivery systems.

Complete genome sequence of Cutibacterium acnes type II CCSM0331, isolated from a healthy woman's skin

The complete genome sequence of Cutibacterium acnes Type II strain CCSM0331, which was isolated from the healthy facial skin, is reported. The assembled 2.5-Mbp genome comprised a single circular chromosome. These data will provide valuable information on the beneficial role of C. acnes as a skin commensal bacteria.

Interruption of Lymph Flow Worsens the Skin Inflammation Caused by Saprophytic Staphylococcus epidermidis

Lymphedema is often complicated by chronic inflammation, leading to fibrosis, fat deposition, and inhibition of lymphangiogenesis. This study aimed to verify whether lymphedema itself or together with commensal bacterial flora infection contributes to the severity of local inflammation. Edema was induced by interruption of the lymph flow in the rat's hind limb. Immune cell infiltrates were examined by flow cytometry and immunohistochemistry. Nine-day edema alone did not affect immune cell content in the skin but resulted in a decrease in CD4+ T helper lymphocytes and monocytes in the draining popliteal lymph nodes. In turn, local saprophytic Staphylococcus epidermidis infection of the edematous limb resulted in dense infiltrates of CD68+ macrophages and monocytes, MHC class II antigen-presenting cells, CD90+ stem cells, thymocytes, and immature B cells in the skin, accompanied by a simultaneous reduction in density of CD4+ T helper lymphocytes and monocytes, OX62+ dendritic cells, CD68+ macrophages and monocytes, HiS48+ granulocytes, CD90+ stem cells, thymocytes, and immature B cells in the draining popliteal lymph nodes. These results indicate that the combination of edema and saprophytic bacteria infection induces severe inflammation in the peripheral tissues and results in a delay of antibacterial protection processes in neighboring lymphatic organs.

Heterogeneous Regulation of StaphylococcusAureus by Different StaphylococcusEpidermidisagr Types in Atopic Dermatitis

The skin commensal Staphylococcus epidermidis exhibits a protective role in skin inflammation; however, the exact functions of S. epidermidis and their mechanisms in atopic dermatitis (AD) are not fully understood. Here, whole-genome sequencing was conducted on strains of S. epidermidis isolated from pediatric patients with AD and revealed significant strain-level heterogeneity in functional genes. Specific sequence analysis of S. epidermidis identified four types of accessory gene regulator (agr) according to locus variations in the agr operon, which was consistent with the metagenomic data of the contextual microbiota. The number of S. epidermidisagr type I was slightly decreased among AD isolates, whereas agr type IV was hardly detected in AD isolates. Functional experiments showed that strains of S. epidermidisagr types I and IV, but not types II and III, inhibited the expression of S. aureusagr-mediated virulence factors in vitro, suppressed S. aureus epidermal colonization, and attenuated skin inflammation in a mouse model. The delineation of genome signatures of S. epidermidis at the strain level in AD and the quorum-sensing interference between S. epidermidisagr type IV and S. aureus provide a foundation for the modulation of the skin microbiota and the treatment of AD.

Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data

BACKGROUND

Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.

RESULTS

We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108-103 cells, 0.4-80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden's index. In the skin dataset, the Decontam prevalence filter and MicrobIEM's ratio filter effectively reduced common contaminants while keeping skin-associated genera.

CONCLUSIONS

MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.

Screening and evaluation of skin potential probiotic from high-altitude Tibetans to repair ultraviolet radiation damage

Human skin microbes play critical roles in skin health and diseases. Microbes colonizing on the skin of Tibetans living in the high-altitude area for generations may have a stronger ability to resist the harsh environment, such as high ultraviolet radiation (UV). Isolation of a potential probiotic from Tibetans skin is beneficial for resistance of skin disease for humans in the world. In this study, the signature microbiota for Tibetan skin were characterized compared to low-altitude humans. Next, using culture-omics, 118 species were isolated. The culturability of high-altitude of Tibetan skin microbiome reached approximate 66.8%. Next, we found that one strain, Pantoea eucrina, had the greatest ability to repair UV damage to the skin as the lowest pathological score was observed in this group. Interestingly, another animal trial found this bacterium resisted UV rather than its metabolites. Using whole genome sequencing, this strain P. eucrina KBFS172 was confirmed, and its functions were annotated. It might involve in the metabolic pathway of carotenoid biosynthesis with anti-oxidative stress properties, which plays critical roles in UV-damage repair. In conclusion, we characterized the signature microbes of skin in high-altitude Tibetans, isolated a skin bacterium of Pantoea eucrina KBFS172 which could repair UV damage via involving the metabolic pathway of carotenoid biosynthesis. Our results provide a new potential skin probiotic for skin disease prevention or sunburn.

From gut to skin: exploring the potential of natural products targeting microorganisms for atopic dermatitis treatment

Atopic dermatitis (AD) is the most common chronic inflammatory skin disease. Recent studies have revealed that interactions between pathogenic microorganisms, which have a tendency to parasitize the skin of AD patients, play a significant role in the progression of the disease. Furthermore, specific species of commensal bacteria in the human intestinal tract can have a profound impact on the immune system by promoting inflammation and pruritogenesis in AD, while also regulating adaptive immunity. Natural products (NPs) have emerged as promising agents for the treatment of various diseases. Consequently, there is growing interest in utilizing natural products as a novel therapeutic approach for managing AD, with a focus on modulating both skin and gut microbiota. In this review, we discuss the mechanisms and interplay between the skin and gut microbiota in relation to AD. Additionally, we provide a comprehensive overview of recent clinical and fundamental research on NPs targeting the skin and gut microbiota for AD treatment. We anticipate that our work will contribute to the future development of NPs and facilitate research on microbial mechanisms, based on the efficacy of NPs in treating AD.

A systematic review of natural products for skin applications: Targeting inflammation, wound healing, and photo-aging

BACKGROUND

Every day the skin is constantly exposed to several harmful factors that induce oxidative stress. When the cells are incapable to maintain the balance between antioxidant defenses and reactive oxygen species, the skin no longer can keep its integrity and homeostasis. Chronic inflammation, premature skin aging, tissue damage, and immunosuppression are possible consequences induced by sustained exposure to environmental and endogenous reactive oxygen species. Skin immune and non-immune cells together with the microbiome are essential to efficiently trigger skin immune responses to stress. For this reason, an ever-increasing demand for novel molecules capable of modulating immune functions in the skin has risen the level of their development, particularly in the field of natural product-derived molecules.

PURPOSE

In this review, we explore different classes of molecules that showed evidence in modulate skin immune responses, as well as their target receptors and signaling pathways. Moreover, we describe the role of polyphenols, polysaccharides, fatty acids, peptides, and probiotics as possible treatments for skin conditions, including wound healing, infection, inflammation, allergies, and premature skin aging.

METHODS

Literature was searched, analyzed, and collected using databases, including PubMed, Science Direct, and Google Scholar. The search terms used included "Skin", "wound healing", "natural products", "skin microbiome", "immunomodulation", "anti-inflammatory", "antioxidant", "infection", "UV radiation", "polyphenols", "polysaccharides", "fatty acids", "plant oils", "peptides", "antimicrobial peptides", "probiotics", "atopic dermatitis", "psoriasis", "auto-immunity", "dry skin", "aging", etc., and several combinations of these keywords.

RESULTS

Natural products offer different solutions as possible treatments for several skin conditions. Significant antioxidant and anti-inflammatory activities were reported, followed by the ability to modulate immune functions in the skin. Several membrane-bound immune receptors in the skin recognize diverse types of natural-derived molecules, promoting different immune responses that can improve skin conditions.

CONCLUSION

Despite the increasing progress in drug discovery, several limiting factors need future clarification. Understanding the safety, biological activities, and precise mechanisms of action is a priority as well as the characterization of the active compounds responsible for that. This review provides directions for future studies in the development of new molecules with important pharmaceutical and cosmeceutical value.

The Skin Microbiome: Current Landscape and Future Opportunities

Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.

Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis

Objective

Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes.

Design

This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing.

Results

According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT.

Conclusion

In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals

Soil-derived microorganisms have been sampled intensively throughout the last decades in order to discover bacterial strains that produce new antibiotics. The increasing emergence of multidrug-resistant bacteria and the constant high demand for new antibiotic classes are leading to the sampling and investigation of new microbiomes that contain antimicrobial producers. Human-associated microbiomes are therefore gaining more and more attention. This chapter presents a detailed description of how human microbiomes can be sampled and how microbiota members from skin and nasal samples can be isolated. Different methods for antimicrobial compound screening are presented.

Skin Microbiome, Metabolome and Skin Phenome, from the Perspectives of Skin as an Ecosystem

Skin is a complex ecosystem colonized by millions of microorganisms, including bacteria, fungi, and viruses. Skin microbiota is believed to exert critical functions in maintaining host skin health. Profiling the structure of skin microbial community is the first step to overview the ecosystem. However, the community composition is highly individualized and extremely complex. To explore the fundamental factors driving the complexity of the ecosystem, namely the selection pressures, we review the present studies on skin microbiome from the perspectives of ecology. This review summarizes the following: (1) the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment, highlighting their proposed function on skin microbiota; (2) the features of dominant skin commensals to occupy ecological niches, through self-adaptation and microbe-microbe interactions; (3) how skin microbes, by their structures or bioactive molecules, reshape host skin phenotypes, including skin immunity, maintenance of skin physiology such as pH and hydration, ultraviolet (UV) protection, odor production, and wound healing. This review aims to re-examine the host-microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.

Twenty-four months of bacterial colonialization and infection rates in patients with transcutaneous osseointegrated prosthetic systems after lower limb amputation-A prospective analysis

BACKGROUND

Transcutaneous osseointegrated prosthesis systems (TOPS) are alternative rehabilitation methods to socket prosthetics, after limb amputation. TOPS compromise a two-step surgery: starting with the implantation of the stem which is then followed by the creation of the transcutaneous stoma through which the exoprosthesis can be connected. Immediately after surgery, this opening is permanently exposed to pathogens. This study aimed to investigate the dynamics of bacterial colonization of the stoma to analyze whether obligate bacterial colonization leads to a risk of periprosthetic infections after TOPS treatment.

METHODS

This prospective study analyzed data from 66 patients (aged 26-75 years) after TOPS treatment between 2017 and 2019. Microbiological swabs from the stoma were analyzed on the first postoperative day and 3, 6, 12, and 24 months after stoma creation. Infection rates, laboratory values (CRP, leukocyte count, hemoglobin), and body temperature were recorded at these points in time. Statistical analysis was performed using SPSS 28.

RESULTS

The results show the formation of a stable environment dominated by Gram-positive bacteria in the stoma of TOPS patients over 24 months. Staphylococcus aureus, Staphylococcus spp., and Streptococcus spp. were the most common species found. With regard to the cohort up to the 3 months follow-up, 7.9% (five patients) developed infections surrounding the TOPS procedure. In relation to the whole cohort with loss to follow-up of 80.3% at the 24 months follow-up the infection rates increased up to 38.3%.

CONCLUSION

The soft tissue inside and around the transcutaneous stoma is colonialized by multiple taxa and changes over time. A stable Gram-positive dominated bacterial taxa could be a protective factor for ascending periprosthetic infections and could possibly explain the relatively low infection rate in this study as well as in literature.

Towards standardized and reproducible research in skin microbiomes

Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.

Long-Term In Vitro Culture Systems to Study Human Microbiome

Microbial communities are eubiotic ecosystems that interact dynamically and synergistically with the human body. Imbalances in these interactions may cause dysbiosis by enhancing the occurrence of inflammatory conditions, such as periodontal or inflammatory bowel diseases. However, the mechanisms that lie behind eubiosis-dysbiosis transitions are still unclear and constantly being redefined. While the societal impact of these diseases is steadily increasing, the lack of a clear understanding behind the onset of the inflammatory conditions prevents the proper clinical strategies from being formulated. Although preclinical and clinical models and short-term planar in vitro cultures represent superb research tools, they are still lacking human relevance and long-term use. Bioreactors and organs-on-a-chip have attracted interest because of their ability to recreate and sustain the physical, structural, and mechanical features of the native environment, as well as to support long-term coculture of mammalian cells and the microbiome through modulation of pH and oxygen gradients. Existing devices, however, are still under development to sustain the microbiome-host coculture over long periods of time. In this scenario, to understand disease triggers and develop therapeutics, research efforts should command the development of three-dimensional constructs that would allow the investigation of processes underlying the microbial community assembly and how microorganisms influence host traits in both acute and chronic conditions.

Skin Microbiota in Atopic Dermatitis

The skin microbiota represents an ecosystem composed of numerous microbial species interacting with each other, as well as with host epithelial and immune cells. The microbiota provides health benefits to the host by supporting essential functions of the skin and inhibiting colonization with pathogens. However, the disturbance of the microbial balance can result in dysbiosis and promote skin diseases, such as atopic dermatitis (AD). This review provides a current overview of the skin microbiota involvement in AD and its complex interplay with host immune response mechanisms, as well as novel therapeutic strategies for treating AD focused on restoring skin microbial homeostasis.

Environmental and Human Microbiome for Health

Microorganisms are an essential part of life on the earth and can exist in association with virtually any living thing. The environmental microbiome is much more diverse than the human microbiome. It is reported that most microbes existing in the environment are difficult to culture in the laboratory. Whereas both pathogenic and beneficial microbes may be prevailing in the environment, the human body can have three categories of microbes- beneficial, pathogenic, and opportunistic pathogenic. With at least 10-fold more cells than human cells, microbes as normal flora are critical for human survival. The microbes present in the human body play a crucial role in maintaining human health, and the environmental microbiome influences the human microbiome makeup. The interaction between the environmental and human microbiome highly influences human health, however it is poorly understood. In addition, as an established infection is associated with health-seeking behavior, a large number of studies have focused on the transmission and dynamics of infectious microorganisms than the noninfectious or beneficial ones. This review will summarize how the interaction between the environmental and human microbiome affects human health and identify approaches that might be beneficial for humans to improve health by being exposed to the natural environment.

The Gut-Skin Microbiota Axis and Its Role in Diabetic Wound Healing-A Review Based on Current Literature

Diabetic foot ulcers (DFU) are a growing concern worldwide as they pose complications in routine clinical practices such as diagnosis and management. Bacterial interactions on the skin surface are vital to the pathophysiology of DFU and may control delayed wound healing. The microbiota from our skin directly regulates cutaneous health and disease by interacting with the numerous cells involved in the wound healing mechanism. Commensal microbiota, in particular, interact with wound-repairing skin cells to enhance barrier regeneration. The observed microbes in DFU include Staphylococcus, Streptococcus, Corynebacterium, Pseudomonas, and several anaerobes. Skin commensal microbes, namely S. epidermidis, can regulate the gamma delta T cells and induce Perforin-2 expression. The increased expression of Perforin-2 by skin cells destroyed S. aureus within the cells, facilitating wound healing. Possible crosstalk between the human commensal microbiome and different cell types involved in cutaneous wound healing promotes the immune response and helps to maintain the barrier function in humans. Wound healing is a highly well-coordinated, complex mechanism; it can be devastating if interrupted. Skin microbiomes are being studied in relation to the gut-skin axis along with their effects on dermatologic conditions. The gut-skin axis illustrates the connection wherein the gut can impact skin health due to its immunological and metabolic properties. The precise mechanism underlying gut-skin microbial interactions is still unidentified, but the immune and endocrine systems are likely to be involved. Next-generation sequencing and the development of bioinformatics pipelines may considerably improve the understanding of the microbiome-skin axis involved in diabetic wound healing in a much more sophisticated way. We endeavor to shed light on the importance of these pathways in the pathomechanisms of the most prevalent inflammatory conditions including the diabetes wound healing, as well as how probiotics may intervene in the gut-skin axis.

Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768)

Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.

Characterization of the microbiome in the infant diapered area: Insights from healthy and damaged skin

It has been recognized for nearly a century that human beings are inhabited by a remarkably dense and diverse microbial ecosystem, yet we are only just beginning to understand and appreciate the many roles that these microbes play in human health and development. Establishment of the microbiome begins at birth, but many previous studies on infant skin health have focused on Candida species. Little is known on the full microbial composition across different areas and even less is known on how these communities change during disease/inflammatory states. In this clinical study, infants were recruited during periods of diaper dermatitis (DD) and health to characterize the skin microbiome in these two states. Substantial shifts in the skin microbiome were observed across four sites in the diapered area (genitals, intertriginous, buttocks and perianal), as well as during periods of DD. As DD scores increased, there was a shift in relative abundance that demonstrated higher community percentages of faecal coliforms, such as Enterococcus, and lower percentages of Staphylococcus strains. In high-rash samples, the predominant Staphylococcus species is S aureus, potentially implicating S aureus as a DD aetiological agent. This study provides new information related to the microbiome on infant skin in the diapered area and provides insights into the role of the microbiome in the development of DD.

A Journey on the Skin Microbiome: Pitfalls and Opportunities

The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.

Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome

Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin “archaeomes” dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome.

IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.

Challenges in exploring and manipulating the human skin microbiome

The 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. Video abstract.

Insight Into Microbial Community Aerosols Associated With Electronic Waste Handling Facilities by Culture-Dependent and Culture-Independent Methods

Airborne microorganisms in the waste associated environments are more active and complex compared to other places. However, the diversity and structure of airborne bacteria in waste-associated environments are still not clearly understood. The purpose of this study was to assess airborne bacterial community in electronic waste dismantling site and a waste transfer station based on culture-dependent and culture-independent methods. A total of 229 isolates were obtained from four airborne sites collected from residential area, electronic industrial park, and office area in or near an electronic waste dismantling site and a waste transfer station in Southern China in the morning, afternoon, and evening. Most of the isolates were isolated from air for the first time and 14 potentially novel species were identified by Sanger sequencing. Bacterial communities in waste-associated bioaerosols were predominated by Proteobacteria and Bacteroidetes. Abundant genera (>1%) included Paracaedibacteraceae (uncultured EF667926), Ralstonia, Chroococcidiopsis, Chitinophagaceae (uncultured FN428761), Sphingobium, and Heliimonas. One-third of the species in these genera were uncultured approximately. Differences community structure existed in airborne bacterial diversity among different sampling sites. These results showed that waste-associated environments have unique bacterial diversity. Further studies on such environments could provide new insights into bacterial community.

A mixed community of skin microbiome representatives influences cutaneous processes more than individual members

BACKGROUND

Skin, the largest organ of the human body by weight, hosts a diversity of microorganisms that can influence health. The microbial residents of the skin are now appreciated for their roles in host immune interactions, wound healing, colonization resistance, and various skin disorders. Still, much remains to be discovered in terms of the host pathways influenced by skin microorganisms, as well as the higher-level skin properties impacted through these microbe-host interactions. Towards this direction, recent efforts using mouse models point to pronounced changes in the transcriptional profiles of the skin in response to the presence of a microbial community. However, there is a need to quantify the roles of microorganisms at both the individual and community-level in healthy human skin. In this study, we utilize human skin equivalents to study the effects of individual taxa and a microbial community in a precisely controlled context. Through transcriptomics analysis, we identify key genes and pathways influenced by skin microbes, and we also characterize higher-level impacts on skin processes and properties through histological analyses.

RESULTS

The presence of a microbiome on a 3D skin tissue model led to significantly altered patterns of gene expression, influencing genes involved in the regulation of apoptosis, proliferation, and the extracellular matrix (among others). Moreover, microbiome treatment influenced the thickness of the epidermal layer, reduced the number of actively proliferating cells, and increased filaggrin expression. Many of these findings were evident upon treatment with the mixed community, but either not detected or less pronounced in treatments by single microorganisms, underscoring the impact that a diverse skin microbiome has on the host.

CONCLUSIONS

This work contributes to the understanding of how microbiome constituents individually and collectively influence human skin processes and properties. The results show that, while it is important to understand the effect of individual microbes on the host, a full community of microbes has unique and pronounced effects on the skin. Thus, in its impacts on the host, the skin microbiome is more than the sum of its parts. Video abstract.

SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics

In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolize molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop “SkinBug.” It integrates machine learning, neural networks, and chemoinformatics methods, and displays a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harboring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome and will find applications in exposome and microbiome studies, dermatology, and skin cancer research.

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SkinBug is AI/ML-based tool to predict metabolism of molecules by Skin microbiome

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Database of 1,094,153 metabolic enzymes from 897 pangenomes of skin microbiome

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Predicts enzymes, bacterial species, and skin sites for the predicted reactions

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82.4% multilabel and 90.0% binary accuracy, and validated on 28 diverse real cases

The Composition and Concordance of Lactobacillus Populations of Infant Gut and the Corresponding Breast-Milk and Maternal Gut

The maternal gut is the principal source of commensal bacteria in the infant gut during the lactation stage, where breast milk acts as an intermediary for the transfer of potential probiotic bacteria consortia, including Lactobacillus. This study aimed to characterize the bacterial communities in human milk, maternal, and infant feces in a small yet very homogeneous cohort of 25 healthy mother–infant pairs in northwestern China (n = 25, infant age from 7 days to 2 years), with special emphasis on the cooccurrence and vertical transfer of Lactobacillus phylotypes at the species or strain level in mother-breast milk-infant triads. Accurate sequencing analysis revealed that among 73 Lactobacillus zero-radius operational classification units (ZOTUs) identified, 58 belonging to 18 recognized species or species groups were distributed in all three types of samples. Lactobacillus ruminis, L. mucosae and L. gasseri-johnsonii as true residents were the most represented in all three ecosystems, whereas the content of Lactobacillus phylotypes commonly developed as probiotics was not dominant. While the numbers of Lactobacillus species in breast milk and infant feces were greater than that in maternal feces, principal coordinates analysis (PCoA) based on beta diversity, coupled with the frequency of isolates determined by culture methods, showed that the Lactobacillus community in the infant gut was more similar to that in the maternal gut than to that in breast milk, suggesting that the gut is niche selective for Lactobacillus populations. In addition, identical strains of L. ruminis, L. paracasei, L. mucosae and L. salivarius were isolated from multiple mother–infant pairs, supporting the hypothesis that vertical transfer of bacteria via breastfeeding contributes to the initial establishment of the microbiota in the developing infant intestine.

Microbial Biosurfactants in Cosmetic and Personal Skincare Pharmaceutical Formulations

Cosmetic and personal care products are globally used and often applied directly on the human skin. According to a recent survey in Europe, the market value of cosmetic and personal care products in Western Europe reached about 84 billion euros in 2018 and are predicted to increase by approximately 6% by the end of 2020. With these significant sums of money spent annually on cosmetic and personal care products, along with chemical surfactants being the main ingredient in a number of their formulations, of which many have been reported to have the potential to cause detrimental effects such as allergic reactions and skin irritations to the human skin; hence, the need for the replacement of chemical surfactants with other compounds that would have less or no negative effects on skin health. Biosurfactants (surfactants of biological origin) have exhibited great potential such as lower toxicity, skin compatibility, protection and surface moisturizing effects which are key components for an effective skincare routine. This review discusses the antimicrobial, skin surface moisturizing and low toxicity properties of glycolipid and lipopeptide biosurfactants which could make them suitable substitutes for chemical surfactants in current cosmetic and personal skincare pharmaceutical formulations. Finally, we discuss some challenges and possible solutions for biosurfactant applications.