Skin fungal community and its correlation with bacterial community of urban Chinese individuals

The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity

To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland's restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities' structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.

Ascomycetes yeasts: The hidden part of human microbiome

The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.

Grazing practices affect soil microbial networks but not diversity and composition in alpine meadows of northeastern Qinghai-Tibetan plateau

Livestock grazing is the primary practice in alpine meadows and can alter soil microbiomes, which is critical for ecosystem functions and services. Seasonal grazing (SG) and continuous grazing (CG) are two kinds of different grazing practices that dominate alpine meadows on the Qinghai-Tibetan Plateau (QTP), and how they affect soil microbial communities remains in-depth exploration. The present study was conducted to investigate the effects of different grazing practices (i.e., SG and CG) on the diversity, composition, and co-occurrence networks of soil bacteria and fungi in QTP alpine meadows. Soil microbial α- and β-diversity showed no obvious difference between SG and CG grasslands. Grazing practices had little impact on soil microbial composition, except that the relative abundance of Proteobacteria and Ascomycota showed significant difference between SG and CG grasslands. Soil microbial networks were more complex and less stable in SG grasslands than that in CG grasslands, and the bacterial networks were more complex than fungal networks. Soil fungal diversity was more strongly correlated with environmental factors than bacteria, whereas both fungal and bacterial structures were mainly influenced by soil pH, total nitrogen, and ammonium nitrogen. These findings indicate that microbial associations are more sensitive to grazing practices than microbial diversity and composition, and that SG may be a better grazing practice for ecological benefits in alpine meadows.

Enterotypes of the human gut mycobiome

BACKGROUND

The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS

We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS

We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.

Esophageal mycobiome landscape and interkingdom interactions in esophageal squamous cell carcinoma

Background

The study purpose was to characterize the mycobiome and its associations with the expression of pathogenic genes in esophageal squamous cell carcinoma (ESCC).

Methods

Patients with primary ESCC were recruited from two central hospitals. We performed internal transcribed spacer 1 (ITS1) ribosomal DNA sequencing analysis. We compared differential fungi and explored the ecology of fungi and the interaction of bacteria and fungi.

Results

The mycobiota diversity was significantly different between tumors and tumor-adjacent samples. We further analysed the differences between the two groups, at the species level, confirming that Rhodotorula toruloides, Malassezia dermatis, Hanseniaspora lachancei, and Spegazzinia tessarthra were excessively colonized in the tumor samples, whereas Preussia persica, Fusarium solani, Nigrospora oryzae, Acremonium furcatum, Golovinomyces artemisiae, and Tausonia pullulans were significantly more abundant in tumor-adjacent samples. The fungal co-occurrence network in tumor-adjacent samples was larger and denser than that in tumors. Similarly, the more complex bacterial-fungal interactions in tumor-adjacent samples were also detected. The expression of mechanistic target of rapamycin kinase was positively correlated with the abundance of N. oryzae and T. pullulans in tumor-adjacent samples. In tumors, the expression of MET proto-oncogene, receptor tyrosine kinase (MET) had a negative correlation and a positive correlation with the abundance of R. toruloides and S. tessarthra, respectively.

Conclusion

This study revealed the landscape of the esophageal mycobiome characterized by an altered fungal composition and bacterial and fungal ecology in ESCC.

Forgotten fungi: the importance of the skin mycobiome

The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.

Infant Mode of Delivery Shapes the Skin Mycobiome of Prepubescent Children

Characterizing the skin mycobiome is necessary to define its association with the host immune system, particularly in children. In this study, we describe the skin mycobiome on the face, ventral forearm, and calf of 72 prepubescent children (aged 1 to 10 years) and their mothers, based on internal transcribed spacer (ITS) amplicon sequencing. The age and delivery mode at birth are the most influential factors shaping the skin mycobiome. Compared with that of the vaginally born children, the skin mycobiome of caesarean-born children is assembled by predominantly deterministic niche-based processes and exhibits a more fragile microbial network at all three sampling sites. Moreover, vaginal delivery leads to clearer intra- and interindividual specialization of fungal structures with increasing age; this phenomenon is not observed in caesarean-born children. The maternal correlation with children also differs based on the mode of delivery; specifically, the mycobiomes of vaginally born children at younger ages are more strongly correlated with vagina-associated fungal genera (Candida and Rhodotorula), whereas those of caesarean-delivered children at elder age include more skin-associated and airborne fungal genera (Malassezia and Alternaria). Based on this ecological framework, our results suggest that the delivery mode is significantly associated with maturation of the skin fungal community in children. IMPORTANCE Human skin is permanently colonized by microbes starting at birth. The hygiene hypothesis suggests that a lack of early-life immune imprinting weakens the body's resilience against atopic disorders later in life. To better understand fungal colonization following early-life periods affected by interruption, we studied the skin mycobiomes of 73 children and their mothers. Our results suggest a differentiation of the skin mycobiomes between caesarean-born and vaginally born children. Caesarean-born children exhibit a mycobiome structure with more fitted deterministic niche-based processes, a fragile network, and an unchanged microbial dissimilarity over time. In vaginally born children, this dissimilarity increases with age. The results indicate that initial microbial colonization has a long-term impact on a child's skin mycobiome. We believe that these findings will inspire further investigations of the "hygiene hypothesis" in the human microbiome, especially in providing novel insights into influences on the development of the early-life microbiome.

Surface fungal diversity and several mycotoxin-related genes' expression profiles during the Lunar Palace 365 experiment

BACKGROUND

Chinese Lunar Palace 1 (LP1) is a ground-based bio-regenerative life support system (BLSS) test bed integrating highly efficient plant cultivation, animal protein production, urine nitrogen recycling, and bioconversion of solid waste. To date, there has been no molecular method-based detailed investigation of the fungal community and mycotoxin potential in BLSS habitats. To ensure safe BLSS design for actual space missions, we analyzed the LP1 surface mycobiome and mycotoxin potential during the Lunar Palace 365 project through internal transcribed spacer region 1 (ITS1) amplicon sequencing and quantitative polymerase chain reaction (qPCR) with primers specific for idh, ver1, nor1, tri5, and ITS1.

RESULTS

The LP1 system exhibited significant differences in fungal community diversity compared to other confined habitats, with higher fungal alpha diversity and different community structures. Significant differences existed in the surface fungal communities of the LP1 habitat due to the presence of different occupant groups. However, there was no significant difference between fungal communities in the plant cabin with various occupants. Source tracker analysis shows that most of the surface fungi in LP1 originated from plants. Regardless of differences in occupants or location, there were no significant differences in mycotoxin gene copy number.

CONCLUSIONS

Our study reveals that plants are the most crucial source of the surface fungal microbiome; however, occupant turnover can induce significant perturbations in the surface fungal community in a BLSS. Growing plants reduced fungal fluctuations, maintaining a healthy balance in the surface fungal microbiome and mycotoxin potential. Moreover, our study provides data important to (i) future risk considerations in crewed space missions with long-term residency, (ii) an optimized design and planning of a space mission that incorporates crew shifts and plant growth, and (iii) the expansion of our knowledge of indoor fungal communities with plant growth, which is essential to maintain safe working and living environments. Video Abstract.

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.

Psoriasis: Interplay between dysbiosis and host immune system

With advancement in human microbiome research, an increasing number of scientific evidences have endorsed the key role of both gut and skin microbiota in the pathogenesis of psoriasis. Microbiome dysbiosis, characterized by altered diversity and composition, as well as rise of pathobionts, have been identified as possible triggers for recurrent episodes of psoriasis. Mechanistically, gut dysbiosis leads to "leaky gut syndrome" via disruption of epithelial bilayer, thereby, resulting in translocation of bacteria and other endotoxins to systemic circulation, which in turn, results in inflammatory response. Similarly, skin dysbiosis disrupts the cutaneous homeostasis, leading to invasion of bacteria and other pathogens to deeper layers of skin or even systemic circulation further enhanced by injury caused by pruritus-induced scratching, and elicit innate and adaptive inflammation. The present review explores the correlation of both skin and gut microbiota dysbiosis with psoriasis. Also, the studies highlighting the potential of bacteriotherapeutic approaches including probiotics, prebiotics, metabiotics, and fecal microbiota transplantation for the management of psoriasis have been discussed.

Malassezia: Zoonotic Implications, Parallels and Differences in Colonization and Disease in Humans and Animals

Malassezia spp. are commensals of the skin, oral/sinonasal cavity, lower respiratory and gastrointestinal tract. Eighteen species have been recovered from humans, other mammals and birds. They can also be isolated from diverse environments, suggesting an evolutionary trajectory of adaption from an ecological niche in plants and soil to the mucocutaneous ecosystem of warm-blooded vertebrates. In humans, dogs and cats, Malassezia-associated dermatological conditions share some commonalities. Otomycosis is common in companion animals but is rare in humans. Systemic infections, which are increasingly reported in humans, have yet to be recognized in animals. Malassezia species have also been identified as pathogenetic contributors to some chronic human diseases. While Malassezia species are host-adapted, some species are zoophilic and can cause fungemia, with outbreaks in neonatal intensive care wards associated with temporary colonization of healthcare worker’s hands from contact with their pets. Although standardization is lacking, susceptibility testing is usually performed using a modified broth microdilution method. Antifungal susceptibility can vary depending on Malassezia species, body location, infection type, disease duration, presence of co-morbidities and immunosuppression. Antifungal resistance mechanisms include biofilm formation, mutations or overexpression of ERG11, overexpression of efflux pumps and gene rearrangements or overexpression in chromosome 4.

Symbiosis and Dysbiosis of the Human Mycobiome

The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.

DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data

Trillions of microbes representing all kingdoms of life are resident in, and on, humans holding essential roles for the host development and physiology. The last decade over a dozen online tools and servers, accessible via public domain, have been developed for the analysis of bacterial sequences; however, the analysis of fungi is still in its infancy. Here, we present a web server dedicated to the comprehensive analysis of the human mycobiome for (i) translating raw sequencing reads to data tables and high-standard figures, (ii) integrating statistical analysis and machine learning with a manually curated relational database and (iii) comparing the user’s uploaded datasets with publicly available from the Sequence Read Archive. Using 1,266 publicly available Internal transcribed spacers (ITS) samples, we demonstrated the utility of DAnIEL web server on large scale datasets and show the differences in fungal communities between human skin and soil sites.

"Touch microbiome" as a potential tool for forensic investigation: A pilot study

Human skin hosts a variety of microbes that can be transferred to surfaces ("touch microbiome"). These microorganisms can be considered as forensic markers similarly to "touch DNA". With this pilot study, we wanted to evaluate the transferability and persistence of the "touch microbiome" on a surface after the deposition of a fingerprint and its exposure for 30 days at room temperature. Eleven volunteers were enrolled in the study. Skin microbiome samples were collected by swabbing the palm of their hands; additionally, donors were asked to touch a glass microscope slide to deposit their fingerprints, that were then swabbed. Both human and microbial DNA was isolated and quantified. Amelogenin locus and 16 human STRs were amplified, whereas the V4 region of 16 S rRNA gene was sequenced using Illumina MiSeq platform. STR profiles were successfully typed for 5 out of 22 "touch DNA" samples, while a microbiome profile was obtained for 20 out of 22 "touch microbiome" samples. Six skin core microbiome taxa were identified, as well as unique donor characterizing taxa. These unique taxa may have relevance for personal identification studies and may be useful to provide forensic intelligence information also when "touch DNA" fails. Additional future studies including greater datasets, additional time points and a greater number of surfaces may clarify the applicability of "touch microbiome" studies to real forensic contexts.

Microbiome Analysis Reveals Microecological Balance in the Emerging Rice-Crayfish Integrated Breeding Mode

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.

Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica

Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.IMPORTANCE For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium. We also show how antibiotic treatments alter microbiota diversity and function, while both features are restored after one untreated generation. Combining data from B. germanica treated with three antibiotics, we have characterized this species' resistome. It includes genes involved in resistance to several broad-spectrum antibiotics frequently used in the clinic. The presence of genetic elements involved in DNA mobilization indicates that they can be transferred among microbiota partners. Therefore, cockroaches can be considered reservoirs of antibiotic resistance genes (ARGs) and potential transmission vectors.

Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals

Dandruff is a recurrent chronic scalp disorder, affecting majority of the population worldwide. Recently a metagenomic study of the Indian scalp microbiome described an imperative role of bacterial commensals in providing essential vitamins and amino acids to the scalp. Coconut oil and its formulations are commonly applied on the scalp in several parts of the world to maintain scalp health. Thus, in this study we examined the effect of topical application of coconut oil on the scalp microbiome (bacterial and fungal) at the taxonomic and functional levels and their correlation with scalp physiological parameters. A 16-weeks-long time-course study was performed including 12-weeks of treatment and 4-weeks of relapse phase on a cohort of 140 (70 healthy and 70 dandruff) Indian women, resulting in ~ 900 metagenomic samples. After the treatment phase, an increase in the abundance of Cutibacterium acnes and Malassezia globosa in dandruff scalp was observed, which were negatively correlated to dandruff parameters. At the functional level, an enrichment of healthy scalp-related bacterial pathways, such as biotin metabolism and decrease in the fungal pathogenesis pathways was observed. The study provides novel insights on the effect of coconut oil in maintaining a healthy scalp and in modulating the scalp microbiome.

Insights into the effects of heavy metal pressure driven by long-term treated wastewater irrigation on bacterial communities and nitrogen-transforming genes along vertical soil profiles

Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss.

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait

Kuwait is a country with a very high dust loading; in fact it bears the world's highest particulate matter concentration in the outdoor air. The airborne dust often has associated biological materials, including pathogenic microbes that pose a serious risk to the urban ecosystem and public health. This study has established the baseline taxonomic characterization of microbes associated with dust transported into Kuwait from different trajectories. A high volume air sampler with six-stage cascade impactor was deployed for sample collection at a remote as well as an urban site. Samples from three different seasons (autumn, spring and summer) were subjected to targeted amplicon sequencing. A set of ~ 50 and 60 bacterial and fungal genera, respectively, established the core air microbiome. The predominant bacterial genera (relative abundance ≥ 1%) were Brevundimonas (12.5%), Sphingobium (3.3%), Sphingopyxis (2.7%), Pseudomonas (2.5%), Sphingomonas (2.4%), Massilia (2.3%), Acidovorax (2.0%), Allorhizobium (1.8%), Halomonas (1.3%), and Mesorhizobium (1.1%), and the fungal taxa were Cryptococcus (12%) followed by Alternaria (9%), Aspergillus (7%), Candida (3%), Cladosporium (2.9%), Schizophyllum (1.6%), Fusarium (1.4%), Gleotinia (1.3%) and Penicillium (1.15%). Significant spatio-temporal variations were recorded in terms of relative abundances, α-diversities, and β-diversities of bacterial communities. The dissimilarities were less pronounced and instead the communities were fairly homogenous. Linear discrimant analysis revealed three fungal genera known to be significantly differentially abundant with respect to different size fractions of dust. Our results shed light on the spatio-temporal distribution of airborne microbes and their implications in general health.

New Insights Into the Skin Microbial Communities and Skin Aging

Although it is well-known that human skin aging is accompanied by an alteration in the skin microbiota, we know little about how the composition of these changes during the course of aging and the effects of age-related skin microbes on aging. Using 16S ribosomal DNA and internal transcribed spacer ribosomal DNA sequencing to profile the microbiomes of 160 skin samples from two anatomical sites, the cheek and the abdomen, on 80 individuals of varying ages, we developed age-related microbiota profiles for both intrinsic skin aging and photoaging to provide an improved understanding of the age-dependent variation in skin microbial composition. According to the landscape, the microbial composition in the Children group was significantly different from that in the other age groups. Further correlation analysis with clinical parameters and functional prediction in each group revealed that high enrichment of nine microbial communities (i.e., Cyanobacteria, Staphylococcus, Cutibacterium, Lactobacillus, Corynebacterium, Streptococcus, Neisseria, Candida, and Malassezia) and 18 pathways (such as biosynthesis of antibiotics) potentially affected skin aging, implying that skin microbiomes may perform key functions in skin aging by regulating the immune response, resistance to ultraviolet light, and biosynthesis and metabolism of age-related substances. Our work re-establishes that skin microbiomes play an important regulatory role in the aging process and opens a new approach for targeted microbial therapy for skin aging.

Biology, diagnosis and treatment of Malassezia dermatitis in dogs and cats Clinical Consensus Guidelines of the World Association for Veterinary Dermatology

BACKGROUND

The genus Malassezia is comprised of a group of lipophilic yeasts that have evolved as skin commensals and opportunistic cutaneous pathogens of a variety of mammals and birds.

OBJECTIVES

The objective of this document is to provide the veterinary community and other interested parties with current information on the ecology, pathophysiology, diagnosis, treatment and prevention of skin diseases associated with Malassezia yeasts in dogs and cats.

METHODS AND MATERIAL

The authors served as a Guideline Panel (GP) and reviewed the literature available prior to October 2018. The GP prepared a detailed literature review and made recommendations on selected topics. The World Association of Veterinary Dermatology (WAVD) Clinical Consensus Guideline committee provided guidance and oversight for this process. The document was presented at two international meetings of veterinary dermatology societies and one international mycology workshop; it was made available for comment on the WAVD website for a period of six months. Comments were shared with the GP electronically and responses incorporated into the final document.

CONCLUSIONS AND CLINICAL IMPORTANCE

There has been a remarkable expansion of knowledge on Malassezia yeasts and their role in animal disease, particularly since the early 1990's. Malassezia dermatitis in dogs and cats has evolved from a disease of obscurity and controversy on its existence, to now being a routine diagnosis in general veterinary practice. Clinical signs are well recognised and diagnostic approaches are well developed. A range of topical and systemic therapies is known to be effective, especially when predisposing factors are identified and corrected.

The gut mycobiota of rural and urban individuals is shaped by geography

BACKGROUND

Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota.

RESULTS

Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers.

CONCLUSIONS

Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

Dynamics of Skin Mycobiome in Infants

Understanding the microbial community structure of the human skin is important for treating cutaneous diseases; however, little is known regarding skin fungal communities (mycobiomes). The aim of the present study was to investigate the features of and variations in skin fungal communities during infancy in 110 subjects less than 6 months of age. Skin samples were obtained from the back, antecubital fossa, and volar forearm, while physiological parameters including transepidermal water loss, pH, surface moisture, and deep layer hydration were evaluated. Skin fungal diversity decreased after the first three months of life. Differences in fungal community composition were greater among individual infants than among the three skin sites in the same individual. Inter- and intra-individual variation were similar and lower, respectively, than the variability between two samples obtained 12 weeks apart, from the same site in the same subject, suggesting low stability of fungal communities on infant skin. Skin physiological parameters showed little correlation with skin fungal community structure. Additionally, Malassezia was the most represented genus (36.43%) and M. globosa was the most abundant species in Malassezia with its abundance decreasing from 54.06% at 0–2 months to 34.54% at 5–6 months. These findings provide a basis for investigating the causative fungi-skin interactions associated with skin diseases.

Structures of the Skin Microbiome and Mycobiome Depending on Skin Sensitivity

Sensitive skin (SS) syndrome is a globally widespread, self-diagnosed discomfort characterized by subjective complaints. Although the skin microbiome is considered important in skin health, the relationship between the skin microbiome and skin sensitivity is still unknown. Here, we aimed to (i) investigate whether the microbiome and mycobiome of SS are distinct from those of non-sensitive skin (NS), and (ii) define the characteristics of the skin microbiome associated with skin sensitivity. A total of 42 Korean women subjects were recruited (SS, n = 23; NS, n = 19) and the microbiome/mycobiome of their right facial cheeks were analyzed. We identified the differential microbiome and mycobiome structures between SS and NS. The mycobiome of SS was more phylogenetically diverse than that of NS. Lactobacillus and Mucor racemosus were more abundant on SS than NS, whereas Malassezia restricta was less abundant. Interestingly, both skin microbiome and mycobiome varied according to the perceived skin sensitivities of the subjects. This study suggests that the skin microbiome and mycobiome are associated with skin sensitivity. Accordingly, it lays the foundation for developing microbiome-based cosmetics or remedies for individuals suffering from SS syndrome.

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

RESULTS

Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

CONCLUSIONS

The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.

Microbiome and antibiotic resistome in household dust from Beijing, China

We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia

Human body microbes interact with the host, forming microbial communities that are in continual flux during the aging process. Previous studies have mostly focused on surveying a single body habitat to determine the age-related variation in the bacterial and fungal communities. A more comprehensive understanding of the variation in the human microbiota and mycobiota across multiple body habitats related to aging is still unclear. To obtain an integrated view of the spatial distribution of microbes in a specific Mediterranean population across a wide age range, we surveyed the bacterial and fungal communities in the skin, oral cavity, and gut in the young, elderly, and centenarians in Sardinia using 16S rRNA gene and internal transcribed spacer 1 (ITS1) sequencing. We found that the distribution and correlation of bacterial and fungal communities in Sardinians were largely determined by body site. In each age group, the bacterial and fungal communities found in the skin were significantly different in structure. In the oral cavity, age had a marginal impact on the structures of the bacterial and fungal communities. Furthermore, the gut bacterial communities in centenarians clustered separately from those of the young and elderly, while the fungal communities in the gut habitat could not be separated by host age.IMPORTANCE Site-specific microbial communities are recognized as important factors in host health and disease. To better understand how the human microbiota potentially affects and is affected by its host during the aging process, the fundamental issue to address is the distribution of microbiota related to age. Here, we show an integrated view of the spatial distribution of microbes in a specific Mediterranean population (Sardinians) across a wide age range. Our study indicates that age plays a critical role in shaping the human microbiota in a habitat-dependent manner. The dynamic age-related microbiota changes we observed across multiple body sites may provide possibilities for modulating microbe communities to maintain or improve health during aging.

Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals

Impaired immunity and changes in the microenvironment in patients with diabetes might influence the composition of the cutaneous microbiome. However, data on the cutaneous microbiome of these patients are scarce. This study compared the fungal and bacterial components of the skin microbiome between patients with type 2 diabetes mellitus (DM) and healthy individuals. We obtained skin swab samples from the plantar forefoot of 17 patients with DM and 18 healthy individuals to conduct a cross-sectional study. The samples were profiled with culture-independent sequencing of the V3 to V4 regions of the bacterial 16S rRNA gene and the fungal ITS2 region, followed by direct DNA extraction and molecular polymerase chain reaction (PCR). We observed a differential cutaneous microbiome, especially for fungi, in patients with type 2 diabetes compared to that in healthy controls. Trichophyton rubrum was more abundant in DM samples. The Shannon diversity index for fungi was lower in the DM patients. Principal coordinate analysis plots and permutational multivariate analysis of variance (PERMANOVA) tests based on Bray-Curtis distances between samples supported the association of the fungal microbiome with DM at the species level. The results suggest that clinicians should pay attention to both fungi and bacteria and provide appropriate prevention and therapeutic strategies for diabetic cutaneous complications including diabetic foot ulcers. These data also contribute to future research associated with diabetes and cutaneous microbiomes.

The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges

Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.

The Impact of Microbial Communities on Wound Healing: A Review

Chronic, nonhealing wounds place an enormous burden on both the health care system and patients, with no definitive treatments available. There has been increasing evidence that the microbial composition of wounds may play an important role in wound healing. Culture-independent methods for bacterial detection and analysis have revealed the wound microbiome to be much more diverse and complex than culture alone. Such methods primarily rely on targeted amplification and sequencing of various hypervariable regions of the bacterial 16S rRNA for phylogenetic analysis. To date, there have been several studies utilizing culture-independent methods to investigate the microbiome of a variety of chronic wounds, including venous insufficiency ulcers, pressure ulcers, and diabetic foot ulcers. Major bacteria found include Staphylococcus, Streptococcus, Corynebacterium, Pseudomonas, and various anaerobes. Current studies suggest that improved healing and outcomes may be correlated with increased bacterial diversity and instability of the microbiome composition of a wound. However, the exact role of the microbiome in wound healing remains poorly understood. While the current research is promising, studies are very heterogeneous, hindering comparisons of findings across different research groups. In addition, more studies are needed to correlate microbiome findings with clinical factors, as well as in the relatively unexplored fields of acute wounds and nonbacterial microbiomes, such as the wound mycobiome and virome. Better understanding of the various aspects of the microorganisms present in wounds may eventually allow for the manipulation of the wound microbiota in such a way as to promote healing, such as through bacteriophage therapies or probiotics.

The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites

Background

The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition.

Methods

Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS.

Results

A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome.

Conclusion

Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction.

Electronic supplementary material

The online version of this article (10.1186/s12985-019-1211-z) contains supplementary material, which is available to authorized users.

[Role of the microbiome in chronic wounds]

BACKGROUND

The microbiome, collective microbial life in defined areas of the body, is of great importance.

OBJECTIVE

What is the significance of the wound microbiome in the treatment of chronic wounds? Which interactions exist with other microbiomes and which conclusions can be drawn for wound management?

MATERIALS AND METHODS

Swabs or debridement samples from wounds were analysed for microbial growth by culture or gene-based techniques. The genetic results are used to determine the wound microbiome. The pathogens were evaluated according to proportion of different species and related to different factors like type and location of wound, disease and underlying illnesses and to define the wound microbiome.

RESULTS

In comparison with conventional microbiological detection methods the wound microbiome comprises many more types and quantities of species. The wound microbiome is related to skin microbiome showing complex and time-dependent composition, as well as inter- and intraindividual differences. Diabetic wounds exhibit disease-related changes, e.g. staphylococcal species dominate whereas streptococcal species dominate in nondiabetic wounds.

CONCLUSIONS

The analysis of wound microbiome is still at an early stage; however it has already been shown that in hemodynamic disorders there are disease-specific relationships with the wound microbiome, which can also provide clues about the course of the disease. Phenomena from the skin microbiome should also be effective in wounds. In this context modern antimicrobial treatment options beyond conventional chemotherapy like colonization modulation become possible.

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome

The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. IMPORTANCE Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.

Cross-Domain and Viral Interactions in the Microbiome

The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.

The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection

Background

Microbial flora in several organs of HIV-infected individuals have been characterized; however, the palatine tonsil bacteriome and mycobiome and their relationship with each other remain unclear. Determining the palatine tonsil microbiome may provide a better understanding of the pathogenesis of oral and systemic complications in HIV-infected individuals. We conducted a cross-sectional study to characterize the palatine tonsil microbiome in HIV-infected individuals.

Results

Palatine tonsillar swabs were collected from 46 HIV-infected and 20 HIV-uninfected individuals. The bacteriome and mycobiome were analyzed by amplicon sequencing using Illumina MiSeq. The palatine tonsil bacteriome of the HIV-infected individuals differed from that of HIV-uninfected individuals in terms of the decreased relative abundances of the commensal genera Neisseria and Haemophilus. At the species level, the relative abundances and presence of Capnocytophaga ochracea, Neisseria cinerea, and Selenomonas noxia were higher in the HIV-infected group than those in the HIV-uninfected group. In contrast, fungal diversity and composition did not differ significantly between the two groups. Microbial intercorrelation analysis revealed that Candida and Neisseria were negatively correlated with each other in the HIV-infected group. HIV immune status did not influence the palatine tonsil microbiome in the HIV-infected individuals.

Conclusions

HIV-infected individuals exhibit dysbiotic changes in their palatine tonsil bacteriome, independent of immunological status.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1274-9) contains supplementary material, which is available to authorized users.

Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health

Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. However, the functional role of scalp microbiota in scalp disorders and health remains scarcely explored. Here, we examined the bacterial and fungal diversity of the scalp microbiome and their potential functional role in the healthy and dandruff scalp of 140 Indian women. Propionibacterium acnes and Staphylococcus epidermidis emerged as the core bacterial species, where the former was associated with a healthy scalp and the latter with dandruff scalp. Along with the commonly occurring Malassezia species (M. restricta and M. globosa) on the scalp, a strikingly high association of dandruff with yet uncharacterized Malassezia species was observed in the core mycobiome. Functional analysis showed that the fungal microbiome was enriched in pathways majorly implicated in cell-host adhesion in the dandruff scalp, while the bacterial microbiome showed a conspicuous enrichment of pathways related to the synthesis and metabolism of amino acids, biotin, and other B-vitamins, which are reported as essential nutrients for hair growth. A systematic measurement of scalp clinical and physiological parameters was also carried out, which showed significant correlations with the microbiome and their associated functional pathways. The results point toward a new potential role of bacterial commensals in maintaining the scalp nutrient homoeostasis and highlights an important and yet unknown role of the scalp microbiome, similar to the gut microbiome. This study, therefore, provides new perspectives on the better understanding of the pathophysiology of dandruff.

Development of the Human Mycobiome over the First Month of Life and across Body Sites

With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life (n = 17) and the anal and vaginal mycobiomes of mothers (n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing. We found that infant mycobiomes differed by body site, with the infant mycobiomes at the anal sites being different from those at the skin and oral sites. The relative abundances of body site-specific taxa differed by birth mode, with significantly more Candida albicans fungi present on the skin of vaginally born infants on day 30 and significantly more Candida orthopsilosis fungi present in the oral cavity of caesarean section-born infants throughout the first month of life. We found the mycobiomes within individual infants to be variable over the first month of life, and vaginal birth did not result in infant mycobiomes that were more similar to the mother's vaginal mycobiome. Therefore, although vertical transmission of specific fungal isolates from mother to infant has been reported, it is likely that other sources (environment, other caregivers) also contribute to early-life mycobiome establishment. Thus, future longitudinal studies of mycobiome and bacterial microbiome codevelopment, with dense sampling from birth to beyond the first month of life, are warranted. IMPORTANCE Humans are colonized by diverse fungi (mycobiome), which have received much less study to date than colonizing bacteria. We know very little about the succession of fungal colonization in early life and whether it may relate to long-term health. To better understand fungal colonization and its sources, we studied the skin, oral, and anal mycobiomes of healthy term infants and the vaginal and anal mycobiomes of their mothers. Generally, infants were colonized by few fungal taxa, and fungal alpha diversity did not increase over the first month of life. There was no clear community maturation over the first month of life, regardless of body site. Key body-site-specific taxa, but not overall fungal community structures, were impacted by birth mode. Thus, additional studies to characterize mycobiome acquisition and succession throughout early life are needed to form a foundation for research into the relationship between mycobiome development and human disease.

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network

BACKGROUND

Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association network properties. Also, there is little understanding of how living conditions, specifically cohabitation and household occupancy, may be associated with the nature and extent (or degree) of cutaneous microbiota change within individuals over time. In this study, the dynamics of the skin microbiota, and its association networks, on the skin of urban residents over four seasons were characterized.

RESULTS

Similar to western cohorts, the individuals of this cohort show different extents of variations in relative abundance of common skin colonizers, concomitant with individual- and household-associated changes in differential abundances of bacterial taxa. Interestingly, the individualized nature of the skin microbiota extends to various aspects of microbial association networks, including co-occurring and excluding taxa, as well as overall network structural properties. Household occupancy is correlated with the extent of variations in relative abundance of Propionibacterium, Acinetobacter, and Bacillus over multiple skin sites. In addition, household occupancy is also associated with the extent of temporal changes in microbial diversity and composition within a resident's skin.

CONCLUSIONS

This is the first study investigating the potential roles household occupancy has on the extent of change in one's cutaneous microbiota and its association network structures. In particular, we show that relationships between the skin microbiota of a resident, his/her cohabitants, and those of non-cohabitants over time are highly personal and are possibly governed by living conditions and nature of interactions between cohabitants within households over 1 year. This study calls for increased awareness to personal and lifestyle factors that may govern relationships between the skin microbiota of one individual and those of cohabitants, and changes in the microbial association network structures within a person over time. The current study will act as a baseline for future assessments in comparing against temporal dynamics of microbiota from individuals with different skin conditions and for identifying residential factors that are beneficial in promoting the dynamics of the skin microbiota associated with health.

The Mycobiome: Impact on Health and Disease States

The term "microbiome" refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term "second genome" to underscore the importance of the microbiota and its collective metagenome on their host's health and/or disease. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. In recognition, projects were launched nationally and internationally to unify efforts to characterize the microbiome and elucidate the functional role of the microbiota and the mechanism(s) by which these organisms and their metabolites (metabolome) may affect health and disease states. In this article, we will highlight the role of the fungal community as an indispensable component of the microbiome.

The gut mycobiome of the Human Microbiome Project healthy cohort

BACKGROUND

Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.

RESULTS

Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.

CONCLUSIONS

Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.

City-scale distribution and dispersal routes of mycobiome in residences

BACKGROUND

Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hong Kong as well as the skin surfaces of the occupants. As a complementary study, here, we investigated the fungal communities (mycobiome) in the same residences and occupants and identified factors that are important in shaping their diversity, composition, distribution, and dispersal patterns.

RESULTS

We observed that common skin and environmental fungal taxa dominated air, surface, and skin samples. Individual and touch frequency strongly and respectively shaped the fungal community structure on occupant skin and residential surfaces. Cross-domain analysis revealed positive correlations between bacterial and fungal community diversity and composition, especially for skin samples. SourceTracker prediction suggested that some fungi can be transferred bidirectionally between surfaces and skin sites, but bacteria showed a stronger dispersal potential. In addition, we detected a modest but significant association between indoor airborne bacterial composition and geographic distance on a city-wide scale, a pattern not observed for fungi. However, the distance-decay effects were more pronounced at shorter local scale for both communities, and airflow might play a prominent role in driving the spatial variation of the indoor airborne mycobiome.

CONCLUSIONS

Our study suggests that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and local environmental factors, including air currents, appear to be stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.

Infant fungal communities: current knowledge and research opportunities

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research, including longitudinal studies of mother-infant pairs while monitoring long-term health outcomes, further exploration of bacterium-fungus interactions, and improved methods and databases for mycobiome quantitation.

Topographical and physiological differences of the skin mycobiome in health and disease

Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities - the mycobiome - in health and disease, and challenges associated with sequencing-based mycobiome research.