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Gut Microbiota Dysbiosis 2.0

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

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 56505

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Dr. Tomas Hrncir

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Institute of Microbiology, Czech Academy of Sciences, Czech Repulic
Interests: mucosal immunology; gut microbiota; food additives; gnotobiotic animal models; pathogenesis of immune-mediated and metabolic disorders; therapeutic modulation of gut microbiota
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Dear Colleagues,

The worldwide incidence of numerous immune-mediated, metabolic, neurodegenerative, and psychiatric diseases has been climbing rapidly. The increased morbidity of human populations leaves them more vulnerable to further complications. For example, during the COVID-19 pandemic, the mortality of people with diabetes has been three times higher than that of the overall population.

It is becoming increasingly clear that gut microbiota plays an important role in the pathogenesis of many, if not all, of these diseases. Many of these diseases, including COVID-19 infection, are associated with the compositional and functional alterations of gut microbiota, i.e., dysbiosis. The most typical dysbiosis markers are a decrease in microbiota diversity, a loss of beneficial microbiota, or the overgrowth of harmful microbiota. The term “gut microbiota” encompasses all microorganisms, including not only bacteria but also fungi, protists, archaea, and viruses, that reside within the gastrointestinal tract.

The main focus areas of this Special Issue are all of the possible triggers of gut microbiota dysbiosis. However, special attention will be paid to environmental factors, such as various categories of food and beverage additives, other processed food components, unintentional food contaminations, medications, and others. The other focus area is the interactions of dysbiotic gut microbiota with host immune and metabolic systems, both in health and disease. Any new knowledge that reveals important environmental triggers of gut microbiota dysbiosis or elucidates the role of dysbiotic microbiota in the pathogenesis of immune-mediated, metabolic, neurodegenerative, or psychiatric diseases is heartily welcomed.

This Special Issue also aims to cover the rapidly developing areas of microbiota-based diagnostics and therapies. Identifying microbiota signatures associated with human diseases and enhancing the knowledge of the specific pathways and metabolites involved in these diseases' pathogenesis will enable us to sort patients into more granular subgroups, thus increasing diagnostic and prognostic accuracy. Hopefully, better diagnoses will lead to increased therapeutic efficacy, faster recovery, and fewer therapy-related side effects. Quality contributions that describe the use of novel and promising microbiota-based treatment methods, such as the supplementation of beneficial microbes or their products (probiotics, synbiotics, or postbiotics), the elimination of harmful pathogens using bacteriophages, antibiotics, or antimycotics, or the transplantation of full microbial communities (FMT), will be greatly appreciated.

Dr. Tomas Hrncir
Guest Editor

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Keywords

gut microbiota
xenobiotics
food additives
medication
antibiotics
loss of microbiota diversity and function
dysbiosis
immune-mediated and metabolic disorders
fecal microbiota transplantation
gnotobiotic
germ-free

Related Special Issue

Gut Microbiota Dysbiosis in Microorganisms (12 articles)

Published Papers (10 papers)

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Research

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16 pages, 12662 KiB

Open AccessArticle

Transfer of Human Microbiome to Drosophila Gut Model

by Dongxu Ji, Hao Sun, Weichao Yang, Mingfu Gao and Hui Xu

Microorganisms 2022, 10(3), 553; https://doi.org/10.3390/microorganisms10030553 - 03 Mar 2022

Cited by 1 | Viewed by 2645

Abstract

Laboratory animals with human microbiome have increasingly been used to study the role of bacteria and host interaction. Drosophila melanogaster, as a model of microbiota-host interaction with high reproductive efficiency and high availability, has always been lacking studies of interaction with human gut microbiome. In this study, we attempted to use antibiotic therapy and human fecal exposure strategy to transfer the human microbiome to the drosophila. The method includes depleting the original intestinal bacteria using a broad-spectrum antibiotic and then introducing human microorganisms by a diet supplemented with donor’s fecal samples. The sequencing results showed that 80–87.5% of the OTUs (Operational Taxonomic Units) from donor feces were adopted by the recipient drosophila following 30 days of observation. In comparison to females, the male recipient drosophila inherited more microbiota from the donor feces and had significantly increased lifespan as well as improved vertical climbing ability. Furthermore, distinctly differential expression patterns for age and insulin-like signaling-related genes were obtained for the male vs. female recipients. Only the male drosophila offspring acquired the characteristics of the donor fecal microbiota. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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19 pages, 1906 KiB

Open AccessArticle

The Impact of a Dried Fruit and Vegetable Supplement and Fiber Rich Shake on Gut and Health Parameters in Female Healthcare Workers: A Placebo-Controlled, Double-Blind, Randomized Clinical Trial

by Marie van der Merwe, Damien Moore, Jessica L. Hill, Faith H. Keating, Randal K. Buddington, Richard J. Bloomer, Anyou Wang and Dale D. Bowman

Microorganisms 2021, 9(4), 843; https://doi.org/10.3390/microorganisms9040843 - 14 Apr 2021

Cited by 5 | Viewed by 4907

Abstract

Aim: Phytochemicals from fruits and vegetables are known to reduce inflammation and improve overall health. The objective of this study was to determine the effect of a fruit and vegetable concentrate (FVC) and high fiber component on the gut microbiome in an overweight/obese, female population. Methods: The study was a randomized, double blind, placebo-controlled trial with 57 asymptomatic, pre-menopausal, overweight/obese females between 25–50 years of age working in healthcare. Blood and fecal samples were collected before and after two, four and five months of daily supplementation. Metabolic parameters were measured, and the gut microbiome analyzed. Results: No effect was observed with FVC supplementation for blood lipids, glucose and immune parameters. There was an improvement in glucose clearance. The FVC supplement did not result in taxonomic alterations at phyla level, or changes in α or β diversity, but reduced Bacteroides abundance and increased fecal butyrate. An additional high fiber component improved levels of health associated bacteria. Conclusion: The results suggest that a dried fruit and vegetable supplement, with a high fiber meal replacement can alter the intestinal microbiota and improve glucose clearance, suggesting that this combination of supplements can improve glucose metabolism and possibly reduce the risk of insulin resistance. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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39 pages, 2208 KiB

Open AccessArticle

A Comparative Pilot Study of Bacterial and Fungal Dysbiosis in Neurodevelopmental Disorders and Gastrointestinal Disorders: Commonalities, Specificities and Correlations with Lifestyle

by Ibrahim Laswi, Ameena Shafiq, Dana Al-Ali, Zain Burney, Krishnadev Pillai, Mohammad Salameh, Nada Mhaimeed, Dalia Zakaria, Ali Chaari, Noha A. Yousri and Ghizlane Bendriss

Microorganisms 2021, 9(4), 741; https://doi.org/10.3390/microorganisms9040741 - 02 Apr 2021

Cited by 4 | Viewed by 3132

Abstract

Gastrointestinal disorders (GIDs) are a common comorbidity in patients with neurodevelopmental disorders (NDDs), while anxiety-like behaviors are common among patients with gastrointestinal diseases. It is still unclear as to which microbes differentiate these two groups. This pilot study aims at proposing an answer by exploring both the bacteriome and the mycobiome in a cohort of 55 volunteers with NDD, GID or controls, while accounting for additional variables that are not commonly included such as probiotic intake and diet. Recruited participants answered a questionnaire and provided a stool sample using the Fisherbrand collection kit. Bacterial and fungal DNA was extracted using the Qiagen Stool minikit. Sequencing (16sRNA and ITS) and phylogenetic analyses were performed using the PE300 Illumina Miseq v3 sequencing. Statistical analysis was performed using the R package. Results showed a significant decrease in bacterial alpha diversity in both NDD and GID, but an increased fungal alpha diversity in NDD. Data pointed at a significant bacterial dysbiosis between the three groups, but the mycobiome dysbiosis is more pronounced in NDD than in GID. Fungi seem to be more affected by probiotics, diet and antibiotic exposure and are proposed to be the main key player in differentiation between NDD and GID dybiosis. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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15 pages, 1550 KiB

Open AccessArticle

Changes in Gut Microbiota after a Four-Week Intervention with Vegan vs. Meat-Rich Diets in Healthy Participants: A Randomized Controlled Trial

by Eva Kohnert, Clemens Kreutz, Nadine Binder, Luciana Hannibal, Gregor Gorkiewicz, Alexander Müller, Maximilian Andreas Storz, Roman Huber and Ann-Kathrin Lederer

Microorganisms 2021, 9(4), 727; https://doi.org/10.3390/microorganisms9040727 - 31 Mar 2021

Cited by 15 | Viewed by 7590

Abstract

An essential role of the gut microbiota in health and disease is strongly suggested by recent research. The composition of the gut microbiota is modified by multiple internal and external factors, such as diet. A vegan diet is known to show beneficial health effects, yet the role of the gut microbiota is unclear. Within a 4-week, monocentric, randomized, controlled trial with a parallel group design (vegan (VD) vs. meat-rich (MD)) with 53 healthy, omnivore, normal-weight participants (62% female, mean 31 years of age), fecal samples were collected at the beginning and at the end of the trial and were analyzed using 16S rRNA gene amplicon sequencing (Clinical Trial register: DRKS00011963). Alpha diversity as well as beta diversity did not differ significantly between MD and VD. Plotting of baseline and end samples emphasized a highly intra-individual microbial composition. Overall, the gut microbiota was not remarkably altered between VD and MD after the trial. Coprococcus was found to be increased in VD while being decreased in MD. Roseburia and Faecalibacterium were increased in MD while being decreased in VD. Importantly, changes in genera Coprococcus, Roseburia and Faecalibacterium should be subjected to intense investigation as markers for physical and mental health. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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15 pages, 1101 KiB

Open AccessArticle

Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

by Ome Kalsoom Afridi, Johar Ali and Jeong Ho Chang

Microorganisms 2021, 9(3), 616; https://doi.org/10.3390/microorganisms9030616 - 17 Mar 2021

Cited by 5 | Viewed by 2580

Abstract

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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20 pages, 1585 KiB

Open AccessArticle

Kale Attenuates Inflammation and Modulates Gut Microbial Composition and Function in C57BL/6J Mice with Diet-Induced Obesity

by Md Shahinozzaman, Samnhita Raychaudhuri, Si Fan and Diana N. Obanda

Microorganisms 2021, 9(2), 238; https://doi.org/10.3390/microorganisms9020238 - 24 Jan 2021

Cited by 16 | Viewed by 11857

Abstract

Kale (Brassica oleracea var. acephala) is a vegetable common in most cultures but is less studied as a functional food compared to other cruciferous vegetables, such as broccoli. We investigated the effect of supplementing a high-fat diet (HFD) with kale (HFKV) in C57BL/6J mice. We particularly explored its role in metabolic parameters, gut bacterial composition and diversity using 16S rRNA sequencing, systematically compared changes under each phylum and predicted the functional potential of the altered bacterial community using PICRUSt2. Like other cruciferous vegetables, kale attenuated HFD-induced inflammation. In addition, kale modulated HFD-induced changes in cecal microbiota composition. The HFD lowered bacterial diversity, increased the Firmicutes: Bacteroidetes (F/B) ratio and altered composition. Specifically, it lowered Actinobacteria and Bacteroidetes (Bacteroidia, Rikenellaceae and Prevotellaceae) but increased Firmicutes (mainly class Bacilli). Kale supplementation lowered the F/B ratio, increased both alpha and beta diversity and reduced class Bacilli and Erysipelotrichi but had no effect on Clostridia. Within Actinobacteria, HFKV particularly increased Coriobacteriales/Coriobacteriaceae about four-fold compared to the HFD (p < 0.05). Among Bacteroidia, HFKV increased the species Bacteroides thetaiotaomicron by over two-fold (p = 0.05) compared to the HFD. This species produces plant polysaccharide digesting enzymes. Compared to the HFD, kale supplementation enhanced several bacterial metabolic functions, including glycan degradation, thiamine metabolism and xenobiotic metabolism. Our findings provide evidence that kale is a functional food that modulates the microbiota and changes in inflammation phenotype. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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13 pages, 2286 KiB

Open AccessArticle

The Gut Microbiota Profile According to Glycemic Control in Type 1 Diabetes Patients Treated with Personal Insulin Pumps

by Sandra Mrozinska, Przemysław Kapusta, Tomasz Gosiewski, Agnieszka Sroka-Oleksiak, Agnieszka H. Ludwig-Słomczyńska, Bartłomiej Matejko, Beata Kiec-Wilk, Malgorzata Bulanda, Maciej T. Malecki, Pawel P. Wolkow and Tomasz Klupa

Microorganisms 2021, 9(1), 155; https://doi.org/10.3390/microorganisms9010155 - 12 Jan 2021

Cited by 15 | Viewed by 3013

Abstract

Recently, several studies explored associations between type 1 diabetes (T1DM) and microbiota. The aim of our study was to assess the colonic microbiota structure according to the metabolic control in T1DM patients treated with insulin pumps. We studied 89 T1DM patients (50.6% women) at the median age of 25 (IQR, 22–29) years. Pielou’s evenness (p = 0.02), and Shannon’s (p = 0.04) and Simpson’s diversity indexes (p = 0.01), were higher in patients with glycosylated hemoglobin (HbA1c) ≥ 53 mmol/mol (7%). There were no differences in beta diversity between groups. A linear discriminant analysis effect size (LEfSe) algorithm showed that one family (Ruminococcaceae) was enriched in patients with HbA1c < 53 mmol/mol, whereas one family (Streptococcaceae) and four species (Ruminococcus torques, unclassified species of Lactococcus, Eubacteroim dolichum, and Coprobacillus cateniformis) were enriched in patients with HbA1c ≥ 53 mmol/mol. We found that at class level, the following pathways according to Kyoto Encyclopedia of Genes and Genomes were enriched in patients with HbA1c < 53 mmol/mol: bacterial motility proteins, secretion system, bacterial secretion system, ribosome biogenesis, translation proteins, and lipid biosynthesis, whereas in patients with HbA1c ≥ 53 mmol/mol, the galactose metabolism, oxidative phosphorylation, phosphotransferase system, fructose, and mannose metabolism were enriched. Observed differences in alpha diversity, metabolic pathways, and associations between bacteria and HbA1c in colonic flora need further investigation. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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Review

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18 pages, 608 KiB

Open AccessReview

Gut Microbiota and NAFLD: Pathogenetic Mechanisms, Microbiota Signatures, and Therapeutic Interventions

by Tomas Hrncir, Lucia Hrncirova, Miloslav Kverka, Robert Hromadka, Vladimira Machova, Eva Trckova, Klara Kostovcikova, Pavlina Kralickova, Jan Krejsek and Helena Tlaskalova-Hogenova

Microorganisms 2021, 9(5), 957; https://doi.org/10.3390/microorganisms9050957 - 29 Apr 2021

Cited by 83 | Viewed by 6169

Abstract

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease. Its worldwide prevalence is rapidly increasing and is currently estimated at 24%. NAFLD is highly associated with many features of the metabolic syndrome, including obesity, insulin resistance, hyperlipidaemia, and hypertension. The pathogenesis of NAFLD is complex and not fully understood, but there is increasing evidence that the gut microbiota is strongly implicated in the development of NAFLD. In this review, we discuss the major factors that induce dysbiosis of the gut microbiota and disrupt intestinal permeability, as well as possible mechanisms leading to the development of NAFLD. We also discuss the most consistent NAFLD-associated gut microbiota signatures and immunological mechanisms involved in maintaining the gut barrier and liver tolerance to gut-derived factors. Gut-derived factors, including microbial, dietary, and host-derived factors involved in NAFLD pathogenesis, are discussed in detail. Finally, we review currently available diagnostic and prognostic methods, summarise latest knowledge on promising microbiota-based biomarkers, and discuss therapeutic strategies to manipulate the microbiota, including faecal microbiota transplantation, probiotics and prebiotics, deletions of individual strains with bacteriophages, and blocking the production of harmful metabolites. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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19 pages, 371 KiB

Open AccessReview

Obesity, Early Life Gut Microbiota, and Antibiotics

by Alyssa T. Wilkins and Raylene A. Reimer

Microorganisms 2021, 9(2), 413; https://doi.org/10.3390/microorganisms9020413 - 17 Feb 2021

Cited by 26 | Viewed by 3822

Abstract

Obesity is a major public health problem that continues to be one of the leading risk factors for premature death. Early life is a critical period of time when the gut microbiota and host metabolism are developing in tandem and significantly contribute to long-term health outcomes. Dysbiosis of the gut microbiota, particularly in early life, can have detrimental effects on host health and increase the susceptibility of developing obesity later in life. Antibiotics are an essential lifesaving treatment; however, their use in early life may not be without risk. Antibiotics are a leading cause of intestinal dysbiosis, and early life administration is associated with obesity risk. The following review explores the relevant literature that simultaneously examines antibiotic-induced dysbiosis and obesity risk. Current evidence suggests that disruptions to the composition and maturation of the gut microbiota caused by antibiotic use in early life are a key mechanism linking the association between antibiotics and obesity. Without compromising clinical practice, increased consideration of the long-term adverse effects of antibiotic treatment on host health, particularly when used in early life is warranted. Novel adjunct interventions should be investigated (e.g., prebiotics) to help mitigate metabolic risk when antibiotic treatment is clinically necessary. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

29 pages, 709 KiB

Open AccessReview

Gut Microbiota Dysbiosis–Immune Hyperresponse–Inflammation Triad in Coronavirus Disease 2019 (COVID-19): Impact of Pharmacological and Nutraceutical Approaches

by Carolina Ferreira, Sofia D. Viana and Flávio Reis

Microorganisms 2020, 8(10), 1514; https://doi.org/10.3390/microorganisms8101514 - 01 Oct 2020

Cited by 48 | Viewed by 9675

Abstract

Coronavirus Disease 2019 (COVID-19) is a pandemic infection caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients present a complex clinical picture that, in severe cases, evolves to respiratory, hepatic, gastrointestinal, and neurological complications, and eventually death. The underlying pathophysiological mechanisms are complex and multifactorial and have been summarized as a hyperresponse of the immune system that originates an inflammatory/cytokine storm. In elderly patients, particularly in those with pre-existing cardiovascular, metabolic, renal, and pulmonary disorders, the disease is particularly severe, causing prolonged hospitalization at intensive care units (ICU) and an increased mortality rate. Curiously, the same populations have been described as more prone to a gut microbiota (GM) dysbiosis profile. Intestinal microflora plays a major role in many metabolic and immune functions of the host, including to educate and strengthen the immune system to fight infections, namely of viral origin. Notably, recent studies suggest the existence of GM dysbiosis in COVID-19 patients. This review article highlights the interplay between the triad GM dysbiosis–immune hyperresponse–inflammation in the individual resilience/fragility to SARS-CoV-2 infection and presents the putative impact of pharmacological and nutraceutical approaches on the triumvirate, with focus on GM. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis 2.0)

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