Special Issue "Interplay of Gene Expression Regulation and Microbiome"

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: 30 November 2021.

Special Issue Editors

Dr. Axel Künstner
E-Mail Website
Guest Editor
Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
Interests: Microbiome; (Meta-) Genomics; (Meta-) Transcriptomics; Mutational Landscape of Tumors; Rare Diseases; Machine Learning; Biomarker; Multi-Omics
Dr. Philipp Rausch
E-Mail Website
Guest Editor
Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Germany Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen Ø, Denmark
Interests: Microbiome; Microbial ecology; Metagenomics; Co-evolution; Multi-Omics; Biostatistics

Special Issue Information

Dear Colleagues,

Genes do not function as single entities but work in concert in gene-interaction-networks with some genes interacting physically via their products or by functioning as regulators. These interactions have a key function to maintain stable gene expression and, more generally, this regulation of gene expression is a fundamental process to maintain cellular homeostasis and pleiotropy shaping the organism's phenotype. Besides these internal mechanisms, external factors and environmental factors influence or even regulate gene expression as well. One highly influential set of environmental factors is the diverse assembly of microbes surrounding and interacting with the organisms, the microbiome.

During the past 10-15 years, the microbiome was diligently investigated and a plethora of studies have contributed to our understanding of its role and effects on host organisms. The host not only provides an ecosystem for the microbiota but in return, the host derives beneficial effects from the diverse communities of bacteria, archaea, fungi, and viruses that live on and in the host (e.g., metabolites, developmental cues). However, we still lack a detailed understanding of the complex microbial interactions with its host. Particularly knowledge to which extend and through which mechanisms the microbiome acts as a regulator of gene expression is still mostly unknown. The expression of genes in the host and the microbiota has to be closely regulated as both sides continuously interact and shape each other's environment.

Thanks to advances in sequencing techniques over the past 15 years, we are able to study gene expression of model and non-model organisms in an almost unbiased manner. Furthermore, the development of high-throughput sequencing made it feasible to study the highly diverse and mainly uncultured microbiome on a large scale including many different host organisms and experimental setups. Commonly, the microbiome is described by using 16S amplicon sequencing but untargeted shotgun metagenomic approaches are getting more popular as sequencing costs drop. Furthermore, the use of naturally tractable host-microbiota associations and the continuous improvement of gnotobiotic and organoid model systems have additionally brought methods of experimental validation to the field of microbiome research.

This Special Issue should serve as a platform to bring together recent advances in the understanding of the dynamic interplay between gene regulation and host-microbiome interaction. We invite researchers to share their results on gene regulation by microbiome interactions. Besides experimental work, we would like to encourage researchers with a strong theoretical and modeling background to share their ideas and theories on interindividual and interspecies gene regulatory dynamics.

We are looking forward to your contributions to this Special Issue.

Dr. Axel Künstner
Dr. Philipp Rausch
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Microbiome/Microbiota
  • Gene expression
  • Symbiosis
  • Dysbiosis
  • Signaling Pathways
  • Regulation of Gene Expression

Published Papers (2 papers)

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Research

Article
Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cells 2021, 10(6), 1292; https://doi.org/10.3390/cells10061292 - 23 May 2021
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Abstract
CYP17A1 is a cytochrome P450 enzyme that has 17-alpha-hydroxylase and C17,20-lyase activities. Cyp17a11 deficiency is associated with high body mass and visceral fat deposition in atherosclerotic female ApoE knockout (KO, d/d or −/−) mice. In the present study, we aimed to investigate the [...] Read more.
CYP17A1 is a cytochrome P450 enzyme that has 17-alpha-hydroxylase and C17,20-lyase activities. Cyp17a11 deficiency is associated with high body mass and visceral fat deposition in atherosclerotic female ApoE knockout (KO, d/d or −/−) mice. In the present study, we aimed to investigate the effects of diet and Cyp17a1 genotype on the gut microbiome. Female Cyp17a1 (d/d) × ApoE (d/d) (DKO) and ApoE (d/d) (controls) were fed either standard chow or a Western-type diet (WTD), and we demonstrated the effects of genetics and diet on the body mass of the mice and composition of their gut microbiome. We found a significantly lower alpha diversity after accounting for the ecological network structure in DKO mice and WTD-fed mice compared with chow-fed ApoE(d/d). Furthermore, we found a strong significant positive association of the Firmicutes vs. Bacteroidota ratio with body mass and the circulating total cholesterol and triglyceride concentrations of the mice when feeding the WTD, independent of the Cyp17a1 genotype. Further pathway enrichment and network analyses revealed a substantial effect of Cyp17a1 genotype on associated cardiovascular and obesity-related pathways involving aspartate and L-arginine. Future studies are required to validate these findings and further investigate the role of aspartate/L-arginine pathways in the obesity and body fat distribution in our mouse model. Full article
(This article belongs to the Special Issue Interplay of Gene Expression Regulation and Microbiome)
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Article
Oral Administration of Lactobacillus rhamnosus Ameliorates the Progression of Osteoarthritis by Inhibiting Joint Pain and Inflammation
Cells 2021, 10(5), 1057; https://doi.org/10.3390/cells10051057 - 29 Apr 2021
Viewed by 594
Abstract
Osteoarthritis (OA) is the most common form of arthritis and age-related degenerative joint disorder, which adversely affects quality of life and causes disability. However, the pathogenesis of OA remains unclear. This study was performed to examine the effects of Lactobacillus rhamnosus in OA [...] Read more.
Osteoarthritis (OA) is the most common form of arthritis and age-related degenerative joint disorder, which adversely affects quality of life and causes disability. However, the pathogenesis of OA remains unclear. This study was performed to examine the effects of Lactobacillus rhamnosus in OA progression. OA was induced in 6-week-old male Wistar rats by monosodium iodoacetate (MIA) injection, and the effects of oral administration of L. rhamnosus were examined in this OA rat model. Pain severity, cartilage destruction, and inflammation were measured in MIA-induced OA rats. The small intestines were isolated from OA rats, and the intestinal structure and inflammation were measured. Protein expression in the dorsal root ganglion was analyzed by immunohistochemistry. The effects of L. rhamnosus on mRNA and protein expression in chondrocytes stimulated with interleukin (IL)-1β and lipopolysaccharide (LPS) were analyzed by real-time polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Pain severity was decreased in L. rhamnosus-treated MIA-induced OA rats. The levels of expression of MCP-1, a potential inflammatory cytokine, and its receptor, CCR2, were decreased, and GABA and PPAR-γ expression were increased in L. rhamnosus-treated OA rats. The inflammation, as determined by IL-1β, and cartilage destruction, as determined by MMP3, were also significantly decreased by L. rhamnosus in OA rats. Additionally, intestinal damage and inflammation were improved by L. rhamnosus. In human OA chondrocytes, TIMP1, TIMP3, SOX9, and COL2A1 which are tissue inhibitors of MMP, and IL-10, an anti-inflammatory cytokine, were increased by L. rhamnosus. L. rhamnosus treatment led to decreased pain severity and cartilage destruction in a rat model of OA. Intestinal damage and inflammation were also decreased by L. rhamnosus treatment. Our findings suggested the therapeutic potential of L. rhamnosus in OA. Full article
(This article belongs to the Special Issue Interplay of Gene Expression Regulation and Microbiome)
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