Identification of cutaneous fungi and mites in adult atopic dermatitis: analysis by targeted 18S rRNA amplicon sequencing

Abstract Background Atopic dermatitis (AD) patients have an altered skin bacterial community, with an abundance of Staphylococcus aureus associated with flares, highlighting that microbial organisms may be important for disease exacerbation. Despite strong evidence of association between bacterial skin colonisation and AD, very limited knowledge regarding the eukaryotic microbial community, including fungi and ectoparasites, in AD exists. In this study, we compared the skin and nasal eukaryotic microbial community between adult AD patients (n = 55) and non-AD healthy controls (n = 45) using targeted 18S rRNA amplicon sequencing. Analysis was based on the presence or absence of eukaryotic microorganisms. Results The cutaneous composition of the eukaryotic microbial community and the alpha-diversity differed significantly between AD patients and non-AD individuals, with increased species richness on AD skin. Alpha-diversity and beta-diversity were similar on lesional and non-lesional skin of patients. The ectoparasite Demodex folliculorum and the yeast Geotrichum candidum were significantly more prevalent on the skin of AD patients. The prevalence of D. folliculorum on lesional skin was greater among patients recently treated with topical corticosteroid. Malassezia was one of the most frequently detected genera at all sites, with M. globosa and M. restricta being the most prevalent. M. restricta was under represented in the anterior nares of AD patients as compared to the non-AD control population. Conclusion Significant differences in the eukaryotic microbial communities were found between AD patients and non-AD individuals, with the most striking finding being the significantly overrepresentation of D. folliculorum on AD skin. Whether D. folliculorum can contribute to skin inflammation in AD needs further investigation.

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Identification of Cutaneous Fungi and Mites in Adult Atopic Dermatitis: Analysis by Targeted 18S rRNA Amplicon Sequencing

10.21203/rs.3.rs-116456/v1 ◽

2020 ◽

Author(s):

Sofie Edslev ◽

Paal Andersen ◽

Anna Ingham ◽

Thor Johannesen ◽

Ditte Lindhardt ◽

...

Keyword(s):

Atopic Dermatitis ◽

Microbial Community ◽

18S Rrna ◽

Alpha Diversity ◽

Skin Inflammation ◽

Amplicon Sequencing ◽

Geotrichum Candidum ◽

Sequencing Analysis ◽

Lesional Skin ◽

Eukaryotic Microorganisms

Abstract Background: Atopic dermatitis (AD) patients have a changed skin bacterial community, with high abundance of Staphylococcus aureus associated with flairs, highlighting that microbial organisms may be important for disease exacerbation. Despite strong evidence of association between bacterial skin colonization and AD, very limited knowledge regarding the eukaryotic microbial community, including fungi and ectoparasites, in AD exists. In this study, we compared the skin and nasal eukaryotic microbial community between adult AD patients (n=55) and non-AD healthy controls (n=45) using targeted 18S rRNA amplicon sequencing. Analysis was based on the presence or absence of eukaryotic microorganisms. Results: The cutaneous composition of the eukaryotic microbial community and the alpha-diversity differed significantly between AD patients and non-AD individuals, with increased species richness on AD skin. Alpha-diversity and beta-diversity were similar on lesional and non-lesional skin of patients. The ectoparasite Demodex folliculorum and the yeast Geotrichum candidum were significantly more prevalent on the skin of AD patients. The prevalence of D. folliculorum on lesional skin was greater among patients recently treated with topical corticosteroid. Malassezia was one of the most frequently detected genera at all sites, with M. globosa and M. restricta being the most prevalent. M. restricta was overrepresented in the anterior nares of AD patients as compared to the non-AD control population. Conclusion: Significant differences in the eukaryotic microbial communities were found between AD patients and non-AD individuals, with the most striking finding being the significantly overrepresentation of D. folliculorum on AD skin. Whether D. folliculorum can contribute to skin inflammation in AD needs further investigation.

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Staphylococcal Communities on Skin Are Associated with Atopic Dermatitis and Disease Severity

Microorganisms ◽

10.3390/microorganisms9020432 ◽

2021 ◽

Vol 9 (2) ◽

pp. 432

Author(s):

Sofie Marie Edslev ◽

Caroline Meyer Olesen ◽

Line Brok Nørreslet ◽

Anna Cäcilia Ingham ◽

Søren Iversen ◽

...

Keyword(s):

Atopic Dermatitis ◽

Alpha Diversity ◽

Skin Microbiota ◽

Specific Primers ◽

Staphylococcus Lugdunensis ◽

Disease Symptoms ◽

Lesional Skin ◽

Staphylococcus Capitis ◽

Staphylococcus Hominis

The skin microbiota of atopic dermatitis (AD) patients is characterized by increased Staphylococcus aureus colonization, which exacerbates disease symptoms and has been linked to reduced bacterial diversity. Skin bacterial communities in AD patients have mostly been described at family and genus levels, while species-level characterization has been limited. In this study, we investigated the role of the bacteria belonging to the Staphylococcus genus using targeted sequencing of the tuf gene with genus-specific primers. We compared staphylococcal communities on lesional and non-lesional skin of AD patients, as well as AD patients with healthy controls, and determined the absolute abundance of bacteria present at each site. We observed that the staphylococcal community, bacterial alpha diversity, and bacterial densities were similar on lesional and non-lesional skin, whereas AD severity was associated with significant changes in staphylococcal composition. Increased S. aureus, Staphylococcus capitis, and Staphylococcus lugdunensis abundances were correlated with increased severity. Conversely, Staphylococcus hominis abundance was negatively correlated with severity. Furthermore, S. hominis relative abundance was reduced on AD skin compared to healthy skin. In conclusion, various staphylococcal species appear to be important for skin health.

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Stratum corneum TARC level is a new indicator of lesional skin inflammation in atopic dermatitis

Allergy ◽

10.1111/j.1398-9995.2010.02361.x ◽

2010 ◽

Cited By ~ 12

Author(s):

E. Morita ◽

H. Takahashi ◽

H. Niihara ◽

I. Dekio ◽

Y. Sumikawa ◽

...

Keyword(s):

Atopic Dermatitis ◽

Stratum Corneum ◽

Skin Inflammation ◽

Lesional Skin

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Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline

10.1101/2019.12.17.880468 ◽

2019 ◽

Cited By ~ 3

Author(s):

Daniel Straub ◽

Nia Blackwell ◽

Adrian Langarica Fuentes ◽

Alexander Peltzer ◽

Sven Nahnsen ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Environmental Samples ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Analysis ◽

Rrna Gene Sequencing ◽

Diversity Estimates

AbstractOne of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is DNA- or RNA-based 16S rRNA (gene) amplicon sequencing. Subsequent bioinformatics analyses are required to extract valuable information from the high-throughput sequencing approach. However, manifold bioinformatics tools complicate their choice and might cause differences in data interpretation, making the selection of the pipeline a crucial step.Here, we compared the performance of most widely used 16S rRNA gene amplicon sequencing analysis tools (i.e. Mothur, QIIME1, QIIME2, and MEGAN) using mock datasets and environmental samples from contrasting terrestrial and freshwater sites. Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times less false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), while there was still room for improvement e.g. imperfect sequence recovery (recall up to 87%) or detection of additional false sequences (precision up to 72%). Furthermore, we found that microbial diversity estimates and highest abundant taxa varied among analysis pipelines (i.e. only one in five genera was shared among all analysis tools) when analyzing environmental samples, which might skew biological conclusions.Our findings were subsequently implemented in a high-performance computing conformant workflow following the FAIR (Findable, Accessible, Interoperable, and Re-usable) principle, allowing reproducible 16S rRNA gene amplicon sequence analysis starting from raw sequence files. Our presented workflow can be utilized for future studies, thereby facilitating the analysis of high-throughput DNA- or RNA-based 16S rRNA (gene) sequencing data substantially.ImportanceMicroorganisms play an essential role in biogeochemical cycling events across the globe. Phylogenetic marker gene analysis is a widely used method to explore microbial community dynamics in space and time, to predict the ecological relevance of microbial populations, or to identify microbial key players in biogeochemical cycles. Several computational analysis methods were developed to aid 16S rRNA gene analysis but choosing the best method is not trivial. In this study, we compared popular analysis methods (i.e. Mothur, QIIME1 and 2, and MEGAN) using samples with known microbial composition (i.e. mock community samples) and environmental samples from contrasting habitats (i.e. groundwater, soil, sediment, and river water). Our findings provide guidance for choosing the currently optimal 16S rRNA gene sequencing analysis method and we implemented our recommended pipeline into a reproducible workflow, which follows highest bioinformatics standards and is open source and free to use.

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Analysis of Microbial Communities in Aged Refuse Based on 16S Sequencing

Sustainability ◽

10.3390/su13084111 ◽

2021 ◽

Vol 13 (8) ◽

pp. 4111

Author(s):

Fen Hou ◽

Junjie Du ◽

Ye Yuan ◽

Xihui Wu ◽

Sai Zhao

Keyword(s):

Microbial Community ◽

Soil Fertility ◽

Community Composition ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Undisturbed Soil ◽

16S Sequencing ◽

Bacterial Phyla ◽

Aged Refuse

Aged refuse is widely considered to have certain soil fertility. 16S rRNA amplicon sequencing is used to investigate the microbial community of aged refuse. The aged refuse is found to contain higher soil fertility elements (total nitrogen, total phosphorus, total potassium, etc.) and higher concentrations of heavy metals (Pb, Cd, Zn, and Hg). Taxonomy based on operational taxonomic units (OTUs) shows that Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes are the main bacterial phyla in the two soils and there is a palpable difference in the microbial community composition between the two groups of samples. The genera Paramaledivibacter, Limnochorda, Marinobacter, Pseudaminobacter, Kocuria, Bdellovibrio, Halomonas, Gillisia, and Membranicola are enriched in the aged refuse. Functional predictive analysis shows that both the control soil and aged refuse have a high abundance of “carbohydrate metabolism” and “amino acid metabolism”, and show differences in the abundance of several metabolism pathways, such as “xenobiotics biodegradation and metabolism” and “lipid metabolism”. Aged refuse and undisturbed soil show significant differences in alpha diversity and microbial community composition. Multiple environmental factors (Hg, TN, Cr, Cd, etc.) significantly impact microorganisms’ abundance (Marinobacter, Halomonas, Blastococcus, etc.). Our study provides valuable knowledge for the ecological restoration of closed landfills.

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Shotgun Metagenomic Analysis Reveals New Insights into Bacterial Community Profiles in Tempeh

10.21203/rs.3.rs-42618/v3 ◽

2020 ◽

Author(s):

Adi Yulandi ◽

Antonius Suwanto ◽

Diana Elizabeth Waturangi ◽

Aris Tri Wahyudi

Keyword(s):

Microbial Community ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Food Samples ◽

Iron Complex ◽

Fermented Food ◽

Metagenomic Analysis ◽

Whole Genome Sequence ◽

Sequencing Analysis ◽

Functional Profiling

Abstract Objective: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.Results: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.

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Shotgun Metagenomic Analysis Reveals New Insights into Bacterial Community Profiles in Tempeh

10.21203/rs.3.rs-42618/v2 ◽

2020 ◽

Author(s):

Adi Yulandi ◽

Antonius Suwanto ◽

Diana Elizabeth Waturangi ◽

Aris Tri Wahyudi

Keyword(s):

Microbial Community ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Food Samples ◽

Iron Complex ◽

Fermented Food ◽

Metagenomic Analysis ◽

Whole Genome Sequence ◽

Sequencing Analysis ◽

Functional Profiling

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Shotgun Metagenomic Analysis Reveals New Insights into Bacterial Community Profiles in Tempeh

10.21203/rs.3.rs-42618/v1 ◽

2020 ◽

Author(s):

Adi Yulandi ◽

Antonius Suwanto ◽

Diana Elizabeth Waturangi ◽

Aris Tri Wahyudi

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Iron Complex ◽

Metagenomic Analysis ◽

Whole Genome Sequence ◽

Sequencing Analysis ◽

16S Rrna Analysis ◽

Functional Profiling

Abstract Objective: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used for the profile analysis of the microbial community from fermented food samples. Previous results of 16S rRNA analysis metagenome showed that Firmicutes was the dominant phylum in tempeh. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in the estimation of microbial community composition. An alternative approach known as shotgun metagenomic might be able to avoid this limitation. In this study, we employed total metagenomic DNA fragments that were sequenced directly for taxonomic dan functional profiling analysis.Results: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the direct shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed genes based in this metagenomic analysis. The binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.

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Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh

BMC Research Notes ◽

10.1186/s13104-020-05406-6 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Adi Yulandi ◽

Antonius Suwanto ◽

Diana Elizabeth Waturangi ◽

Aris Tri Wahyudi

Keyword(s):

Microbial Community ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Food Samples ◽

Iron Complex ◽

Fermented Food ◽

Metagenomic Analysis ◽

Whole Genome Sequence ◽

Sequencing Analysis ◽

Functional Profiling

Abstract Objective Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis. Results Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.

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Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh

10.1101/2020.03.12.988444 ◽

2020 ◽

Author(s):

Adi Yulandi ◽

Diana Elizabeth Waturangi ◽

Aris Tri Wahyudi ◽

Antonius Suwanto

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Iron Complex ◽

Fermented Food ◽

Metagenomic Analysis ◽

Sequencing Analysis ◽

16S Rrna Analysis ◽

Functional Profiling

AbstractObjectiveAmplicon sequencing targeted 16S ribosomal RNA (rRNA) has been widely used for the analysis profile of the microbial community from fermented food samples. Previous results of 16S rRNA analysis metagenome showed that Firmicutes was the dominant phylum in tempeh. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in the estimation of microbial community composition. An alternative approach known as shotgun metagenomic might be able to avoid this limitation. In this study, we employed total metagenomic DNA fragments sequenced directly for taxonomic dan functional profiling analysis.ResultTaxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from direct shotgun metagenomic analysis in all tempeh samples. In terms of composition, the shotgun metagenomic study revealed that Proteobacteria was the most relatively abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed genes based on metagenome from tempeh samples.

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