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The Role of the Gut Microbiota in Human Health and...
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The Role of the Gut Microbiota in Human Health and Disease

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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 50299

Special Issue Editor

Dr. Anisha Wijeyesekera

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Guest Editor
Department of Food & Nutritional Sciences, School of Chemistry, Food & Pharmacy, University of Reading, Reading, UK
Interests: molecular phenotyping; gut microbiota; gut microbial-host co-metabolism; gut microbiota targeted interventions; age and diet associated markers of health and disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human gastrointestinal tract is inhabited by a complex ecosystem of microorganisms that have been shown to play an important role in shaping human health. These microbes produce metabolically active compounds, some of which exert their effects throughout the body; hence, there is a growing understanding of the impact of the gut microbiota on the system as well as gut health. Analytical approaches to study the gut microbiota, such as metagenomics and metabolomics, have provided us with novel insights, particularly at a holistic level. However, there is still much to learn regarding the composition and functional capacity of microbial communities in different human health and diseased states, and how these may be targeted (for example, using dietary interventions such as prebiotics and probiotics) for therapeutic benefit.

This Special Issue of Microorganisms is focused on the latest advances in the role of gut microbiota in human health and disease. We invite researchers to submit new research and review articles focused on basic and translational research studies that further our understanding of gut microbial composition and function, host–gut microbiota interactions, and how human health outcomes may be improved through therapeutic modulation of the gut microbiota.

Dr. Anisha Wijeyesekera
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

  • gut microbiota
  • host–gut microbiota interactions
  • gut health
  • system health
  • gut microbiota targeted interventions
  • microbiomics
  • metagenomics
  • metabolomics

Published Papers (11 papers)

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Research

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16 pages, 1657 KiB  
Article
Probiotic Therapy with Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis Results in Infarct Size Limitation in Rats with Obesity and Chemically Induced Colitis
by Yury Y. Borshchev, Inessa Y. Burovenko, Alena B. Karaseva, Sarkis M. Minasian, Egor S. Protsak, Victor Y. Borshchev, Natalia Y. Semenova, Olga V. Borshcheva, Alexander N. Suvorov and Michael M. Galagudza
Microorganisms 2022, 10(11), 2293; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112293 - 18 Nov 2022
Cited by 5 | Viewed by 2089
Abstract
In this study, we investigated the effect of three different probiotics, namely, a combination of Lactobacillus acidophilus (LA–5) and Bifidobacterium animalis subsp. lactis (BB–12), Saccharomyces boulardii, and Enterococcus faecium L3 on myocardial infarct size in rats with diet-induced obesity (DIO) and [...] Read more.
In this study, we investigated the effect of three different probiotics, namely, a combination of Lactobacillus acidophilus (LA–5) and Bifidobacterium animalis subsp. lactis (BB–12), Saccharomyces boulardii, and Enterococcus faecium L3 on myocardial infarct size in rats with diet-induced obesity (DIO) and chemically-induced colitis (CIC). Potential associations between the effects of probiotics on myocardial ischemia-reperfusion injury and gut microbiome patterns as well as the serum levels of pro- and anti-inflammatory cytokines, lipopolysaccharide, and short chain fatty acids were also studied. Intragastric administration of lyophilized Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis at a dose of 1.2 × 108 CFU/mL for 15 days resulted in myocardial infarct size reduction in rats with DIO, CIC, and antibiotic-induced dysbiosis. This cardioprotective effect was associated with specific changes in cytokine concentrations, namely reduced levels of IL–1β, TNF–α, IL–2, and IL–8. At the same time, the use of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis was accompanied by a significant reduction in lipopolysaccharide level, suggesting normalization of intestinal epithelial barrier permeability. However, the cardioprotective effect of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis is not secondary to improved healing of the intestinal mucosa in CIC, as evidenced by the lack of difference in histopathological scores. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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9 pages, 898 KiB  
Article
Comparative Evaluation of Luminex xTAG® Gastrointestinal Pathogen Panel and Direct-From-Stool Real-Time PCR for Detection of C. difficile Toxin tcdB in Stool Samples from a Pediatric Population
by Hannah Tyrrell, Sarah B. N. Morin, Colin D. Lloyd, Brendon Parsons, Taryn Stokowski, Jianling Xie, Ran Zhuo, Bonita E. Lee, Xiao-Li Pang, Stephen B. Freedman and Linda Chui
Microorganisms 2022, 10(11), 2214; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112214 - 09 Nov 2022
Viewed by 1575
Abstract
Detection of Clostridioides difficile toxins in patients with gastroenteritis has increasingly been accomplished through the use of enteric multiplex syndromic panels. Comparisons of the performance of these panels to both direct-from-stool (DFS) and culture-enriched stools followed by polymerase chain reaction (PCR) methods in [...] Read more.
Detection of Clostridioides difficile toxins in patients with gastroenteritis has increasingly been accomplished through the use of enteric multiplex syndromic panels. Comparisons of the performance of these panels to both direct-from-stool (DFS) and culture-enriched stools followed by polymerase chain reaction (PCR) methods in pediatric populations are limited. Here, we compare the performance of the Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) to our DFS in-house real-time PCR (DFS RT-PCR) assay for the detection of C. difficile toxin gene, tcdB, using 2641 stool specimens collected from children enrolled in the Alberta Provincial Pediatric EnTeric Infection Team (APPETITE) study in Alberta, Canada. We used culture enrichment followed by in-house RT-PCR to resolve discordant results between the two assays. We found excellent agreement (k = 0.89) between the GPP and our DFS RT-PCR assay: the positive percent agreement between the two assays was 97%, and the negative percent agreement was 99%. GPP, a multi-analyte platform can easily be implemented into a routine diagnostic laboratory for detecting enteric pathogens including C. difficile. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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15 pages, 3091 KiB  
Article
Gut Microbiome and Its Cofactors Are Linked to Lipoprotein Distribution Profiles
by Josué L. Castro-Mejía, Bekzod Khakimov, Violetta Aru, Mads V. Lind, Eva Garne, Petronela Paulová, Elnaz Tavakkoli, Lars H. Hansen, Age K. Smilde, Lars Holm, Søren B. Engelsen and Dennis S. Nielsen
Microorganisms 2022, 10(11), 2156; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112156 - 31 Oct 2022
Cited by 5 | Viewed by 1725
Abstract
Increasing evidence indicates that the gut microbiome (GM) plays an important role in dyslipidemia. To date, however, no in-depth characterization of the associations between GM with lipoproteins distributions (LPD) among adult individuals with diverse BMI has been conducted. To determine such associations, we [...] Read more.
Increasing evidence indicates that the gut microbiome (GM) plays an important role in dyslipidemia. To date, however, no in-depth characterization of the associations between GM with lipoproteins distributions (LPD) among adult individuals with diverse BMI has been conducted. To determine such associations, we studied blood-plasma LPD, fecal short-chain fatty acids (SCFA) and GM of 262 Danes aged 19–89 years. Stratification of LPD segregated subjects into three clusters displaying recommended levels of lipoproteins and explained by age and body-mass-index. Higher levels of HDL2a and HDL2b were associated with a higher abundance of Ruminococcaceae and Christensenellaceae. Increasing levels of total cholesterol and LDL-1 and LDL-2 were positively associated with Lachnospiraceae and Coriobacteriaceae, and negatively with Bacteroidaceae and Bifidobacteriaceae. Metagenome-sequencing showed a higher abundance of biosynthesis of multiple B-vitamins and SCFA metabolism genes among healthier LPD profiles. Metagenomic-assembled genomes (MAGs) affiliated to Eggerthellaceae and Clostridiales were contributors of these genes and their relative abundance correlated positively with larger HDL subfractions. The study demonstrates that differences in composition and metabolic traits of the GM are associated with variations in LPD among the recruited subjects. These findings provide evidence for GM considerations in future research aiming to shed light on mechanisms of the GM–dyslipidemia axis. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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18 pages, 1697 KiB  
Article
Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease
by Christine Olbjørn, Milada Cvancarova Småstuen and Aina Elisabeth Fossum Moen
Microorganisms 2022, 10(7), 1273; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071273 - 22 Jun 2022
Cited by 6 | Viewed by 2236
Abstract
We explored the fecal microbiota in pediatric patients <18 years of age with treatment-naïve IBD (80 Crohn’s disease (CD), 27 ulcerative colitis (UC)), in 50 non-IBD patients with gastrointestinal symptoms without inflammation and in 75 healthy children. Using a targeted qPCR approach, the [...] Read more.
We explored the fecal microbiota in pediatric patients <18 years of age with treatment-naïve IBD (80 Crohn’s disease (CD), 27 ulcerative colitis (UC)), in 50 non-IBD patients with gastrointestinal symptoms without inflammation and in 75 healthy children. Using a targeted qPCR approach, the quantities of more than 100 different bacterial species were measured. Results: The bacterial abundance was statistically significantly reduced in the IBD and non-IBD patients compared to the healthy children for several beneficial species. The CD patients had a lower abundance of Bifidobacterium species compared to the UC patients, and the IBD patients in need of biologic therapy had a lower abundance of butyrate producing bacteria. Based on the abundance of bacterial species at diagnosis, we constructed Diagnostic, Phenotype and Prognostic Indexes. Patients with a high Diagnostic Index had 2.5 times higher odds for having IBD than those with a lower index. The CD patients had a higher Phenotype Index than the UC patients. Patients with a high Prognostic Index had 2.1 higher odds for needing biologic therapy compared to those with a lower index. Conclusions: The fecal abundance of bacterial species can aid in diagnosing IBD, in distinguishing CD from UC and in identifying children with IBD in need of biologic therapy. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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Review

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16 pages, 938 KiB  
Review
The Role of Gut Bacteriome in Asthma, Chronic Obstructive Pulmonary Disease and Obstructive Sleep Apnoea
by Andras Bikov, Silvano Dragonieri, Balazs Csoma, Carmen Mazzuca, Panaiotis Finamore, Giulia Rocchi, Lorenza Putignani, Michele Guarino and Simone Scarlata
Microorganisms 2022, 10(12), 2457; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122457 - 13 Dec 2022
Cited by 3 | Viewed by 4121
Abstract
The human body contains a very complex and dynamic ecosystem of bacteria. The bacteriome interacts with the host bi-directionally, and changes in either factor impact the entire system. It has long been known that chronic airway diseases are associated with disturbances in the [...] Read more.
The human body contains a very complex and dynamic ecosystem of bacteria. The bacteriome interacts with the host bi-directionally, and changes in either factor impact the entire system. It has long been known that chronic airway diseases are associated with disturbances in the lung bacteriome. However, less is known about the role of gut bacteriome in the most common respiratory diseases. Here, we aim to summarise the evidence concerning the role of the intestinal bacteriome in the pathogenesis and disease course of bronchial asthma, chronic obstructive pulmonary disease, and obstructive sleep apnea. Furthermore, we discuss the consequences of an altered gut bacteriome on the most common comorbidities of these lung diseases. Lastly, we also reflect on the therapeutic potential of influencing the gut microbiome to improve disease outcomes. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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17 pages, 1590 KiB  
Review
The Potential Role of Human Milk Oligosaccharides in Irritable Bowel Syndrome
by Patricia Sanz Morales, Anisha Wijeyesekera, Margaret Denise Robertson, Peter P. J. Jackson and Glenn R. Gibson
Microorganisms 2022, 10(12), 2338; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122338 - 25 Nov 2022
Cited by 2 | Viewed by 2318
Abstract
Irritable Bowel Syndrome (IBS) is the most common gastrointestinal (GI) disorder in Western populations and therefore a major public health/economic concern. However, despite extensive research, psychological and physiological factors that contribute to the aetiology of IBS remain poorly understood. Consequently, clinical management of [...] Read more.
Irritable Bowel Syndrome (IBS) is the most common gastrointestinal (GI) disorder in Western populations and therefore a major public health/economic concern. However, despite extensive research, psychological and physiological factors that contribute to the aetiology of IBS remain poorly understood. Consequently, clinical management of IBS is reduced to symptom management through various suboptimal options. Recent evidence has suggested human milk oligosaccharides (HMOs) as a potential therapeutic option for IBS. Here, we review literature concerning the role of HMOs in IBS, including data from intervention and in vitro trials. HMO supplementation shows promising results in altering the gut microbiota and improving IBS symptoms, for instance by stimulating bifidobacteria. Further research in adults is required into HMO mechanisms, to confirm the preliminary results available to date and recommendations of HMO use in IBS. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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22 pages, 725 KiB  
Review
Functional Gastrointestinal Disorders with Psychiatric Symptoms: Involvement of the Microbiome–Gut–Brain Axis in the Pathophysiology and Case Management
by Cristina Gabriela Șchiopu, Cristinel Ștefănescu, Alexandra Boloș, Smaranda Diaconescu, Georgiana-Emmanuela Gilca-Blanariu and Gabriela Ștefănescu
Microorganisms 2022, 10(11), 2199; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112199 - 07 Nov 2022
Cited by 7 | Viewed by 3357
Abstract
Functional Gastrointestinal Disorders have been an important cause of poor life quality in affected populations. The unclear etiology and pathophysiological mechanism alter the clinical evolution of the patient. Although a strong connection with psychological stress has been observed, it was not until recently [...] Read more.
Functional Gastrointestinal Disorders have been an important cause of poor life quality in affected populations. The unclear etiology and pathophysiological mechanism alter the clinical evolution of the patient. Although a strong connection with psychological stress has been observed, it was not until recently that the gut–brain axis involvement has been revealed. Furthermore, the current literature not only promotes the gut–brain axis modulation as a therapeutical target for functional digestive disorders but also states that the gut microbiome has a main role in this bi-directional mechanism. Psychiatric symptoms are currently recognized as an equally important aspect of the clinical manifestation and modulation of both the digestive and central nervous systems and could be the best approach in restoring the balance. As such, this article proposes a detailed description of the physiology of the microbiome–gut–brain axis, the pathophysiology of the functional gastrointestinal disorders with psychiatric symptoms and current perspectives for therapeutical management, as revealed by the latest studies in the scientific literature. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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13 pages, 1013 KiB  
Review
B Vitamins and Their Roles in Gut Health
by Khandkar Shaharina Hossain, Sathya Amarasena and Shyamchand Mayengbam
Microorganisms 2022, 10(6), 1168; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061168 - 07 Jun 2022
Cited by 38 | Viewed by 21890
Abstract
B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B [...] Read more.
B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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18 pages, 838 KiB  
Review
Gut Microbiota Regulation and Their Implication in the Development of Neurodegenerative Disease
by Peilin Sun, Lei Su, Hua Zhu, Xue Li, Yaxi Guo, Xiaopeng Du, Ling Zhang and Chuan Qin
Microorganisms 2021, 9(11), 2281; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112281 - 02 Nov 2021
Cited by 28 | Viewed by 4111
Abstract
In recent years, human gut microbiota have become one of the most promising areas of microorganism research; meanwhile, the inter-relation between the gut microbiota and various human diseases is a primary focus. As is demonstrated by the accumulating evidence, the gastrointestinal tract and [...] Read more.
In recent years, human gut microbiota have become one of the most promising areas of microorganism research; meanwhile, the inter-relation between the gut microbiota and various human diseases is a primary focus. As is demonstrated by the accumulating evidence, the gastrointestinal tract and central nervous system interact through the gut–brain axis, which includes neuronal, immune-mediated and metabolite-mediated pathways. Additionally, recent progress from both preclinical and clinical studies indicated that gut microbiota play a pivotal role in gut–brain interactions, whereas the imbalance of the gut microbiota composition may be associated with the pathogenesis of neurological diseases (particularly neurodegenerative diseases), the underlying mechanism of which is insufficiently studied. This review aims to highlight the relationship between gut microbiota and neurodegenerative diseases, and to contribute to our understanding of the function of gut microbiota in neurodegeneration, as well as their relevant mechanisms. Furthermore, we also discuss the current application and future prospects of microbiota-associated therapy, including probiotics and fecal microbiota transplantation (FMT), potentially shedding new light on the research of neurodegeneration. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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Other

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18 pages, 2085 KiB  
Systematic Review
Efficacy and Safety of Fecal Microbiota Transplantation in Treatment of Clostridioides difficile Infection among Pediatric Patients: A Systematic Review and Meta-Analysis
by Kyaw Min Tun, Mark Hsu, Kavita Batra, Chun-Han Lo, Tooba Laeeq, Tahne Vongsavath, Salman Mohammed and Annie S. Hong
Microorganisms 2022, 10(12), 2450; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122450 - 12 Dec 2022
Cited by 4 | Viewed by 2038
Abstract
Background and Aims: Cases of Clostridioides difficile infection have been rising among the pediatric and adolescent population. Fecal microbiota transplantation (FMT) has emerged as an alternative therapy for recurrent C. difficile infection. We aim to perform the first systematic review and meta-analysis investigating [...] Read more.
Background and Aims: Cases of Clostridioides difficile infection have been rising among the pediatric and adolescent population. Fecal microbiota transplantation (FMT) has emerged as an alternative therapy for recurrent C. difficile infection. We aim to perform the first systematic review and meta-analysis investigating the safety and efficacy of fecal microbiota transplantation for C. difficile infection in children and adolescents. Methods: A literature search was performed using variations of the keywords “pediatrics”, “C. difficile infection”, and “fecal microbiota transplantation” in PubMed, EMBASE, CINAHL, Cochrane, and Google Scholar from inception to 30 June 2022. The resulting 575 articles were independently screened by three authors. Fourteen studies that satisfied the eligibility criteria were included in the meta-analysis. Results: The pooled success rate of FMT in the overall cohort was 86% (95% confidence interval: 77–95%; p < 0.001; I2 = 70%). There were 38 serious adverse events in 36 patients with a pooled rate of 2.0% (95% confidence interval: 0.0–3.0%; p = 0.1; I2 = 0.0%) and 47 adverse events in 45 patients with a pooled rate of 15% (95% confidence interval: 5.0–25.0%; p = 0.02; I2 = 54.0%). There was no death associated with FMT. Conclusions: FMT was concluded to be an effective and safe therapy in pediatric and adolescent patients with C. difficile infection. Underlying comorbidities may impede the efficacy. A rigorous screening process of the donors is recommended prior to embarking on FMT. There is no universal and cost-effective way to monitor the long-term outcomes of FMT. While promising, metagenomic sequencing may not be available in settings with limited resources. Robust data from randomized clinical trials is warranted. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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6 pages, 1329 KiB  
Brief Report
Stool Microbiota Diversity Analysis of Blastocystis-Positive and Blastocystis-Negative Individuals
by Christen Rune Stensvold, Brede Aksdal Sørland, Rebecca P. K. D. Berg, Lee O’Brien Andersen, Mark van der Giezen, Joanna L. Bowtell, Ayman A. El-Badry, Salem Belkessa, Özgür Kurt and Henrik Vedel Nielsen
Microorganisms 2022, 10(2), 326; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020326 - 31 Jan 2022
Cited by 19 | Viewed by 3376
Abstract
Blastocystis is a unicellular eukaryote found in the gastrointestinal tract of both human and other animal hosts. The clinical significance of colonic Blastocystis colonization remains obscure. In this study, we used metabarcoding and bioinformatics analyses to identify differences in stool microbiota diversity between [...] Read more.
Blastocystis is a unicellular eukaryote found in the gastrointestinal tract of both human and other animal hosts. The clinical significance of colonic Blastocystis colonization remains obscure. In this study, we used metabarcoding and bioinformatics analyses to identify differences in stool microbiota diversity between Blastocystis-positive and Blastocystis-negative individuals (n = 1285). Alpha diversity was significantly higher in Blastocystis carriers. At phylum level, Firmicutes and Bacteroidetes were enriched in carriers, while Proteobacteria were enriched in non-carriers. The genera Prevotella, Faecalibacterium, Flavonifracter, Clostridium, Succinivibrio, and Oscillibacter were enriched in carriers, whereas Escherichia, Bacteroides, Klebsiella, and Pseudomonas were enriched in non-carriers. No difference in beta diversity was observed. Individuals with Blastocystis-positive stools appear to have gut microbiomes associated with eubiosis unlike those with Blastocystis-negative stools, whose gut microbiomes are similar to those associated with dysbiosis. The role of Blastocystis as an indicator organism and potential modulator of the gut microbiota warrants further scrutiny. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)
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