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Microorganisms
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Involvement of the Gut Microbiome in Inflammatory Bowel Disease
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Involvement of the Gut Microbiome in Inflammatory Bowel Disease

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 11464

Special Issue Editor

Dr. Marcus J. Claesson

E-Mail Website
Guest Editor
APC Microbiome Institute, Biosciences Building, School of Microbiology, University College Cork, Cork, Ireland
Interests: human microbiological systems; compositional microbiota analysis; gut microbiome; inflammatory bowel disease; diet and health

Special Issue Information

Dear Colleagues,

Inflammatory Bowel Disease (IBD) is a chronic and debilitating condition that causes considerable suffering and drainage of healthcare resources worldwide. Its constituent diseases, ulcerative colitis and Crohn's disease, result from severe inflammation of the gastrointestinal tract. As genetic factors explain only a quarter of IBD cases, environmental causes, which may be more easily addressed, should be investigated. A growing body of evidence is indicating a causal link between IBD and the gut microbiome, which is generally more heterogeneous, has a lower diversity, and has a different bacterial composition. The centrality of the intestinal microbiome opens up avenues for using microbial modulation to either treat or prevent inflammation.

Technological advances over the last decade have improved the generation and study of microbiome data from large well-characterized patient cohorts. This Special Issue will present a collection of papers on the latest research on the involvement of the microbiome in the development of IBD as well as the complex interplay with the host and other environmental factors. Both original research articles and reviews are welcome.

Dr. Marcus J. Claesson
Guest Editor

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 submissions that pass pre-check are 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. Microorganisms 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 2700 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

  • Inflammatory Bowel Disease
  • ulcerative colitis
  • Crohn’s disease
  • microbiome
  • microbiota

Published Papers (4 papers)

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Research

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18 pages, 5866 KiB  
Article
Interactions between Medications and the Gut Microbiome in Inflammatory Bowel Disease
by Julia Eckenberger, James C. Butler, Charles N. Bernstein, Fergus Shanahan and Marcus J. Claesson
Microorganisms 2022, 10(10), 1963; https://doi.org/10.3390/microorganisms10101963 - 04 Oct 2022
Cited by 4 | Viewed by 2156
Abstract
In view of the increasing evidence that commonly prescribed, non-antibiotic drugs interact with the gut microbiome, we re-examined the microbiota variance in inflammatory bowel disease (IBD) to determine the degree to which medication and supplement intake might account for compositional differences between disease [...] Read more.
In view of the increasing evidence that commonly prescribed, non-antibiotic drugs interact with the gut microbiome, we re-examined the microbiota variance in inflammatory bowel disease (IBD) to determine the degree to which medication and supplement intake might account for compositional differences between disease subtypes and geographic location. We assessed the confounding effects of various treatments on the faecal microbiota composition (16S rRNA gene sequencing) in persons with Crohn’s disease (CD; n = 188) or ulcerative colitis (UC; n = 161) from either Cork (Ireland) or Manitoba (Canada) sampled at three time points. The medication profiles between persons with UC and CD and from different countries varied in number and type of drugs taken. Among Canadian participants with CD, surgical resection and overall medication and supplement usage is significantly more common than for their Irish counterparts. Treatments explained more microbiota variance (3.5%) than all other factors combined (2.4%) and 40 of the 78 tested medications and supplements showed significant associations with at least one taxon in the gut microbiota. However, while treatments accounted for a relatively small proportion of the geographic contribution to microbiome variance between Irish and Canadian participants, additive effects from multiple medications contributed significantly to microbiome differences between UC and CD. Full article
(This article belongs to the Special Issue Involvement of the Gut Microbiome in Inflammatory Bowel Disease)
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18 pages, 1600 KiB  
Article
Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa
by Gina L. Guzzo, Murthy N. Mittinty, Bastien Llamas, Jane M. Andrews and Laura S. Weyrich
Microorganisms 2022, 10(10), 1910; https://doi.org/10.3390/microorganisms10101910 - 26 Sep 2022
Cited by 3 | Viewed by 2436
Abstract
It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that [...] Read more.
It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that they may also be implicated in IBD. In our study, we characterized these often-neglected eukaryotic microbial communities by identifying fungi and protozoa in published shotgun stool metagenomes from 355 people with IBD (206 with Crohn’s disease, 126 with ulcerative colitis, and 23 with IBD-unclassified) and 471 unaffected healthy individuals. The individuals with IBD had a higher prevalence of fungi, particularly Saccharomyces cerevisiae, and a lower prevalence of protozoa, particularly Blastocystis species (subtypes 1, 2, 3, and 4). Regression analysis showed that disease state, age, and BMI were associated with the prevalence and abundance of these two genera. We also characterized the eukaryotic gut microbiome in a shotgun stool metagenomic dataset from people with IBD who received fecal transplants, with samples pre- and post-transplantation, and from their donors. We found that in some FMT recipients, a single eukaryotic species remained stable over time, while in other recipients, the eukaryotic composition varied. We conclude that the eukaryotic gut microbiome is altered and varies over time in IBD, and future studies should aim to include these microbes when characterizing the gut microbiome in IBD. Full article
(This article belongs to the Special Issue Involvement of the Gut Microbiome in Inflammatory Bowel Disease)
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19 pages, 4276 KiB  
Article
Lactobacillus salivarius UCC118™ Dampens Inflammation and Promotes Microbiota Recovery to Provide Therapeutic Benefit in a DSS-Induced Colitis Model
by Namrata Iyer, Michelle A. Williams, Amy A. O’Callaghan, Elaine Dempsey, Raul Cabrera-Rubio, Mathilde Raverdeau, Fiona Crispie, Paul D. Cotter and Sinéad C. Corr
Microorganisms 2022, 10(7), 1383; https://doi.org/10.3390/microorganisms10071383 - 09 Jul 2022
Cited by 8 | Viewed by 2625
Abstract
The use of probiotics such as Lactobacillus and Bifidobacterium spp. as a therapeutic against inflammatory bowel disease (IBD) is of significant interest. Lactobacillus salivarus strain UCC118TM is a commensal that has been shown to possess probiotic properties in vitro and anti-infective properties [...] Read more.
The use of probiotics such as Lactobacillus and Bifidobacterium spp. as a therapeutic against inflammatory bowel disease (IBD) is of significant interest. Lactobacillus salivarus strain UCC118TM is a commensal that has been shown to possess probiotic properties in vitro and anti-infective properties in vivo. However, the usefulness of UCC118 TM as a therapeutic against colitis remains unclear. This study investigates the probiotic potential of Lactobacillus salivarius, UCC118™ in a mouse model of colitis. DSS-induced colitis was coupled with pre-treatment or post-treatment with UCC118TM by daily oral gavage. In the pre-treatment model of colitis, UCC118TM reduced the severity of the disease in the early stages. Improvement in disease severity was coupled with an upregulation of tissue IL-10 levels and increased expression of macrophage M2 markers. This anti-inflammatory activity of UCC118TM was further confirmed in vitro, using a model of LPS-treated bone marrow-derived macrophages. Taken together, these results suggest that UCC118TM may promote the resolution of inflammation. This was supported in a mouse model of established DSS-induced colitis whereby UCC118TM treatment accelerated recovery, as evidenced by weight, stool, histological markers and the recovery of microbiome-associated dysbiosis with an increased abundance of beneficial commensal species. These results demonstrate the potential of Lactobacillus salivarius UCC118TM as a probiotic-based therapeutic strategy to promote health through the upregulation of anti-inflammatory IL-10 and protect against dysbiosis during IBD. Full article
(This article belongs to the Special Issue Involvement of the Gut Microbiome in Inflammatory Bowel Disease)
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Review

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18 pages, 1524 KiB  
Review
Gut Microbiota, Macrophages and Diet: An Intriguing New Triangle in Intestinal Fibrosis
by Asma Amamou, Cian O’Mahony, Mathilde Leboutte, Guillaume Savoye, Subrata Ghosh and Rachel Marion-Letellier
Microorganisms 2022, 10(3), 490; https://doi.org/10.3390/microorganisms10030490 - 22 Feb 2022
Cited by 11 | Viewed by 3587
Abstract
Intestinal fibrosis is a common complication in inflammatory bowel disease (IBD) without specific treatment. As macrophages are the key actors in inflammatory responses and the wound healing process, they have been extensively studied in chronic diseases these past decades. By their exceptional ability [...] Read more.
Intestinal fibrosis is a common complication in inflammatory bowel disease (IBD) without specific treatment. As macrophages are the key actors in inflammatory responses and the wound healing process, they have been extensively studied in chronic diseases these past decades. By their exceptional ability to integrate diverse stimuli in their surrounding environment, macrophages display a multitude of phenotypes to underpin a broad spectrum of functions, from the initiation to the resolution of inflammation following injury. The hypothesis that distinct macrophage subtypes could be involved in fibrogenesis and wound healing is emerging and could open up new therapeutic perspectives in the treatment of intestinal fibrosis. Gut microbiota and diet are two key factors capable of modifying intestinal macrophage profiles, shaping their specific function. Defects in macrophage polarisation, inadequate dietary habits, and alteration of microbiota composition may contribute to the development of intestinal fibrosis. In this review, we describe the intriguing triangle between intestinal macrophages, diet, and gut microbiota in homeostasis and how the perturbation of this discreet balance may lead to a pro-fibrotic environment and influence fibrogenesis in the gut. Full article
(This article belongs to the Special Issue Involvement of the Gut Microbiome in Inflammatory Bowel Disease)
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