Significant Differences in the Bacterial Microbiome of the Pharynx and Skin in Patients with Psoriasis Compared with Healthy Controls

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Abstract

Studies have shown differences in the skin and gut bacterial microbiomes in patients with psoriasis, but the pharyngeal microbiome has not been studied previously. The aim of this study was to investigate differences in the bacterial microbiome of the pharynx and skin of patients with psoriasis compared with healthy controls. Swabs were taken from the pharynx and elbow skin of 39 patients with psoriasis and 70 controls. Microbiomes were characterized by sequencing 16S rRNA genes on the Illumina MiSeq platform. Significant differences were found in alpha and beta diversity in the skin, but not in the pharynx. Significant differences were also found between several phyla and genera in both skin and pharynx. The severity of psoriasis did not correlate with any genera in the pharynx, but with Capnocytophaga, Leptotrichia, Abiotrophia and Tannerella in the skin. The composition of the pharyngeal and skin microbiome may be of importance in the pathogenesis of psoriasis.

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Most cited references 45

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Microbial ecology: human gut microbes associated with obesity.

Ruth E Ley, Peter J Turnbaugh, Samuel Klein … (2006)

Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.

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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

Davis J. McCarthy, Yunshun Chen, Gordon K. Smyth (2012)

A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and blocking variables while still taking full account of biological variation. Biological variation between RNA samples is estimated separately from the technical variation associated with sequencing technologies. Novel empirical Bayes methods allow each gene to have its own specific variability, even when there are relatively few biological replicates from which to estimate such variability. The pipeline is implemented in the edgeR package of the Bioconductor project. A case study analysis of carcinoma data demonstrates the ability of generalized linear model methods (GLMs) to detect differential expression in a paired design, and even to detect tumour-specific expression changes. The case study demonstrates the need to allow for gene-specific variability, rather than assuming a common dispersion across genes or a fixed relationship between abundance and variability. Genewise dispersions de-prioritize genes with inconsistent results and allow the main analysis to focus on changes that are consistent between biological replicates. Parallel computational approaches are developed to make non-linear model fitting faster and more reliable, making the application of GLMs to genomic data more convenient and practical. Simulations demonstrate the ability of adjusted profile likelihood estimators to return accurate estimators of biological variability in complex situations. When variation is gene-specific, empirical Bayes estimators provide an advantageous compromise between the extremes of assuming common dispersion or separate genewise dispersion. The methods developed here can also be applied to count data arising from DNA-Seq applications, including ChIP-Seq for epigenetic marks and DNA methylation analyses.

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MUSCLE: a multiple sequence alignment method with reduced time and space complexity

Robert Edgar (2004)

Background In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. Results We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. Conclusions MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at .

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Author and article information

Journal

Journal ID (nlm-ta): Acta Derm Venereol

Journal ID (iso-abbrev): Acta Derm Venereol

Journal ID (publisher-id): ActaDV

Title: Acta Dermato-Venereologica

Publisher: Society for Publication of Acta Dermato-Venereologica

ISSN (Print): 0001-5555

ISSN (Electronic): 1651-2057

Publication date (Electronic): 30 September 2020

Publication date Collection: 2020

Volume: 100

Issue: 16

Electronic Location Identifier: 5868

Affiliations

[1 ]Division of Dermatology and Venereology, Region Jönköping County

[2 ]Division of Medical Diagnostics, Region Jönköping County, Jönköping

[3 ]Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden

Author notes

Corr: Malin Assarsson, Division of Dermatology, Ryhov Hospital, SE-551 85 Jönköping, Sweden. E-mail: malin.assarsson@ 123456rjl.se

Article

Publisher ID: ActaDV-100-16-5868

DOI: 10.2340/00015555-3619

PMC ID: 9234991

PubMed ID: 32852562

SO-VID: 2b1a037b-be8f-4e2f-93fd-f56829d2c736

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This is an open access article under the CC BY-NC license

History

Date accepted : 21 August 2020

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Significant Differences in the Bacterial Microbiome of the Pharynx and Skin in Patients with Psoriasis Compared with Healthy Controls

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Tick microbiome

Most cited references 45

Microbial ecology: human gut microbes associated with obesity.

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

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