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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 (30 June 2020) | Viewed by 72226

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Dr. Tomáš Hrnčíř

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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 many immune-mediated and metabolic diseases, which initially affected only wealthy Western countries, is increasing rapidly. Many of these diseases are associated with the compositional and functional alterations of gut microbiota, i.e., dysbiosis. The most typical markers of dysbiosis are a decrease in microbiota diversity, loss of beneficial microbiota, or the expansion of harmful microbiota. By the term gut microbiota, we mean all microorganisms, including not only bacteria but also fungi, protists, archaea, and viruses that reside in the gastrointestinal tract.

The main focus areas of this Special Issue are all possible triggers of gut microbiota dysbiosis, but 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, chlorinated water, 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 revealing important environmental triggers of gut microbiota dysbiosis or elucidating the role of dysbiotic microbiota in the pathogenesis of immune-mediated, metabolic, or psychiatric diseases is greatly welcomed. Additionally, the manuscripts reporting possible ways of correcting gut microbiota dysbiosis, such as the administration of pre- and probiotics or fecal microbiota transplantation, are appreciated.

Dr. Tomáš Hrnčíř
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

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Related Special Issue

Gut Microbiota Dysbiosis 2.0 in Microorganisms (10 articles)

Published Papers (12 papers)

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Editorial

Jump to: Research, Review

7 pages, 248 KiB

Open AccessEditorial

Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options

by Tomas Hrncir

Microorganisms 2022, 10(3), 578; https://doi.org/10.3390/microorganisms10030578 - 7 Mar 2022

Cited by 108 | Viewed by 10121

Abstract

The global incidence of numerous immune-mediated, metabolic, neurodegenerative, and psychiatric diseases is steadily increasing [...] Full article

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

Research

Jump to: Editorial, Review

14 pages, 2662 KiB

Open AccessArticle

A Cross-Sectional Study of the Gut Microbiota Composition in Moscow Long-Livers

by Daria A. Kashtanova, Nataliya S. Klimenko, Irina D. Strazhesko, Elizaveta V. Starikova, Oksana E. Glushchenko, Denis A. Gudkov and Olga N. Tkacheva

Microorganisms 2020, 8(8), 1162; https://doi.org/10.3390/microorganisms8081162 - 30 Jul 2020

Cited by 13 | Viewed by 3603

Abstract

The aim was to assess the gut microbiota of long-livers from Moscow. This study included two groups of patients who signed their consent to participate. The group of long-livers (LL) included 20 participants aged 97–100 years (4 men and 16 women). The second group included 22 participants aged 60–76 years (6 men) without clinical manifestations of chronic diseases (healthy elderly). Gut microbiota was studied by 16S rRNA sequencing. Long-livers underwent a complex geriatric assessment as well as expanded blood biochemistry. Gut microbiota composition in the cohorts was also compared with microbiome in long-livers from Japan and Italy. Russian long-livers’ microbiome contained more beneficial bacteria than healthy elderly including Ruminococcaceae, Christensenellaceae, Lactobacillaceae families. Conditional pathogens like Veillonellaceae, Mogibacteriaceae, Alcaligenaceae, Peptococcaceae, Peptostreptococcaceae were more abundant in the healthy elderly. Compared with Italian and Japanese microbiome LL, the Russian LL appeared to be more similar to the Italian cohort. Bifidobacterium/Coprococcus and Faecalibacterium/Coprococcus balances were associated with femoral and carotid intima–media thickness, respectively. Bifidobacterium/Coriobacteriaceae balance was assessed with the folic acid level and Faecalibacterium/Coriobacteriaceae_u the with Mini Nutritional Assessment score. Long-livers’ microbiome appeared to be unexpectedly balanced. The high representation of beneficial bacteria in long-livers may prevent them from low-grade inflammation and thus protect them from the development of atherosclerosis and other aging-associated conditions. Full article

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

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16 pages, 1213 KiB

Open AccessArticle

Effects of Maresin 1 (MaR1) on Colonic Inflammation and Gut Dysbiosis in Diet-Induced Obese Mice

by Irene C. León, Sergio Quesada-Vázquez, Neira Sáinz, Elizabeth Guruceaga, Xavier Escoté and María Jesús Moreno-Aliaga

Microorganisms 2020, 8(8), 1156; https://doi.org/10.3390/microorganisms8081156 - 30 Jul 2020

Cited by 16 | Viewed by 3149

Abstract

The aim of this study was to characterize the effects of Maresin 1 (MaR1), a DHA-derived pro-resolving lipid mediator, on obesity-related colonic inflammation and gut dysbiosis in diet-induced obese (DIO) mice. In colonic mucosa of DIO mice, the MaR1 treatment decreased the expression of inflammatory genes, such as Tnf-α and Il-1β. As expected, the DIO mice exhibited significant changes in gut microbiota composition at the phylum, genus, and species levels, with a trend to a higher Firmicutes/Bacteroidetes ratio. Deferribacteres and Synergistetes also increased in the DIO animals. In contrast, these animals exhibited a significant decrease in the content of Cyanobacteria and Actinobacteria. Treatment with MaR1 was not able to reverse the dysbiosis caused by obesity on the most abundant phyla. However, the MaR1 treatment increased the content of P. xylanivorans, which have been considered to be a promising probiotic with healthy effects on gut inflammation. Finally, a positive association was found between the Deferribacteres and Il-1β expression, suggesting that the increase in Deferribacteres observed in obesity could contribute to the overexpression of inflammatory cytokines in the colonic mucosa. In conclusion, MaR1 administration ameliorates the inflammatory state in the colonic mucosa and partially compensates changes on gut microbiota caused by obesity. Full article

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

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24 pages, 5974 KiB

Open AccessArticle

Impaired Hypothalamic Microglial Activation in Offspring of Antibiotic-Treated Pregnant/Lactating Rats Is Attenuated by Prebiotic Oligofructose Co-Administration

by Nicole A. Cho, Alissa C. Nicolucci, Teja Klancic, Weilan Wang, Keith A. Sharkey, Richelle Mychasiuk and Raylene A. Reimer

Microorganisms 2020, 8(7), 1085; https://doi.org/10.3390/microorganisms8071085 - 21 Jul 2020

Cited by 6 | Viewed by 3787

Abstract

Microbial colonization of the gut early in life is crucial for the development of the immune and nervous systems, as well as influencing metabolism and weight gain. While early life exposure to antibiotics can cause microbial dysbiosis, prebiotics are non-digestible substrates that selectively promote the growth of beneficial gut microbiota. Our objective was to examine the effects of dietary prebiotic administration on the consequences of maternal antibiotic intake on offspring body weight, behavior, and neuroimmune responses later in life. Sprague-Dawley rat dams were given low-dose penicillin (LDP), prebiotic fiber (10% oligofructose), or both, during the third week of pregnancy and throughout lactation. Anxiety-like behavior, weight gain, body composition, cecal microbiota composition, and microglial responses to lipopolysaccharide (LPS) were assessed in offspring. Male and female prebiotic offspring had lower body weight compared to antibiotic offspring. Maternal antibiotic exposure resulted in lasting effects on select offspring microbiota including a lower relative abundance of Streptococcus, Lactococcus, and Eubacterium at 10 weeks of age. Maternal antibiotic use impaired microglial response to LPS in the hypothalamus compared to control, and this phenotype was reversed with prebiotic. Prebiotic fiber warrants further investigation as an adjunct to antibiotic use during pregnancy. Full article

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

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12 pages, 2289 KiB

Open AccessArticle

The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia

by Aldian I. Amaruddin, Firdaus Hamid, Jan Pieter R. Koopman, Munawir Muhammad, Eric A.T. Brienen, Lisette van Lieshout, Anoecim R. Geelen, Sitti Wahyuni, Ed J. Kuijper, Erliyani Sartono, Maria Yazdanbakhsh and Romy D. Zwittink

Microorganisms 2020, 8(6), 961; https://doi.org/10.3390/microorganisms8060961 - 26 Jun 2020

Cited by 16 | Viewed by 5935

Abstract

To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial communities that prevail in this population. To this end, we profiled the faecal bacterial community of 140 Indonesian schoolchildren in urban Makassar. The core microbiota of Indonesian schoolchildren consisted of Bifidobacterium, Collinsella, and multiple members of the Lachnospiraceae and Ruminicoccaceae families, but the relative abundance of these taxa varied greatly among children. Socioeconomic status (SES) was the main driver for differences in microbiota composition. Multiple bacterial genera were differentially abundant between high and low SES children, including Bifidobacterium, Lactobacillus, Prevotella, and Escherichia-Shigella. In addition, the microbiota of high SES children was less diverse and strongly associated with body mass index (BMI). In low SES children, helminth infection was prevalent and positively associated with Olsenella, Enterohabdus, Lactobacillus, and Mogibacterium abundance, while negatively associated with relative abundance of Prevotella. Protozoa infection was also prevalent, and positively associated with Rikenellaceae, while it was negatively associated with the relative abundance of Romboutsia and Prevotella. In conclusion, Indonesian schoolchildren living in urban Makassar share a core microbiota, but their microbiota varies in diversity and relative abundance of specific bacterial taxa depending on socioeconomic status, nutritional status, and intestinal parasites infection. Full article

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

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10 pages, 872 KiB

Open AccessArticle

Incidental Prophylactic Appendectomy Is Associated with a Profound Microbial Dysbiosis in the Long-Term

by Lidia Sánchez-Alcoholado, José Carlos Fernández-García, Carolina Gutiérrez-Repiso, M Rosa Bernal-López, Luis Ocaña-Wilhelmi, Eduardo García-Fuentes, Isabel Moreno-Indias and Francisco J. Tinahones

Microorganisms 2020, 8(4), 609; https://doi.org/10.3390/microorganisms8040609 - 23 Apr 2020

Cited by 19 | Viewed by 5086

Abstract

Incidental prophylactic surgeries are performed in certain situations. Incidental prophylactic appendectomies were common practice within opened bariatric surgeries. The gut microbiota has emerged as an important actor within the homeostasis of the host. A new hypothesis has been formulated about the appendix function in relation to gut microbiota. Our objective was to study the gut microbiota profiles of patients that had suffered from an incidental prophylactic appendectomy during their bariatric surgeries, while comparing them to patients whose appendixes had remained intact. A case-control observational prospective study of 40 patients who underwent bariatric surgery, with or without an incidental prophylactic appendectomy, during 2004–2008 with an evaluation of their gut microbiota populations at the end of 2016 was conducted by sequencing the 16 S rRNA gene by Next Generation Sequencing of patients’ stools and appendix tissues. Patients with their appendix removed showed lower levels of richness and diversity of their gut microbiota populations. Odoribacter, Bilophila, Butyricimonas, and Faecalibacterium levels were increased in the Intact group, while Lachnobacterium suffered an expansion in the group without the appendix. Moreover, a linear regression model introduced the concept that Butyricimonas and Odoribacter may be implicated in insulin regulation. Thus, gut microbiota should be considered in the decisions of practical surgery, regarding the appendix as a mediator of homeostasis in the host. Butyricimonas and Odoribacter require further investigation as key bacteria implicated in insulin regulation. Full article

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

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18 pages, 2924 KiB

Open AccessArticle

There is No Distinctive Gut Microbiota Signature in the Metabolic Syndrome: Contribution of Cardiovascular Disease Risk Factors and Associated Medication

by Adrián Cortés-Martín, Carlos E. Iglesias-Aguirre, Amparo Meoro, María Victoria Selma and Juan Carlos Espín

Microorganisms 2020, 8(3), 416; https://doi.org/10.3390/microorganisms8030416 - 15 Mar 2020

Cited by 19 | Viewed by 4806

Abstract

The gut microbiota (GM) has attracted attention as a new target to combat several diseases, including metabolic syndrome (MetS), a pathological condition with many factors (diabetes, obesity, dyslipidemia, hypertension, etc.) that increase cardiovascular disease (CVD) risk. However, the existence of a characteristic taxonomic signature associated with obesity-related metabolic dysfunctions is under debate. To investigate the contribution of the CVD risk factors and(or) their associated drug treatments in the composition and functionality of GM in MetS patients, we compared the GM of obese individuals (n = 69) vs. MetS patients (n = 50), as well as within patients, depending on their treatments. We also explored associations between medication, GM, clinical variables, endotoxemia, and short-chain fatty acids. Poly-drug treatments, conventional in MetS patients, prevented the accurate association between medication and GM profiles. Our results highlight the heterogeneity of taxonomic signatures in MetS patients, which mainly depend on the CVD risk factors. Hypertension and(or) its associated medication was the primary trait involved in the shaping of GM, with an overabundance of lipopolysaccharide-producing microbial groups from the Proteobacteria phylum. In the context of precision medicine, our results highlight that targeting GM to prevent and(or) treat MetS should consider MetS patients more individually, according to their CVD risk factors and associated medication. Full article

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

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14 pages, 3083 KiB

Open AccessArticle

SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs

by Sheila Connelly, Brian Fanelli, Nur A. Hasan, Rita R. Colwell and Michael Kaleko

Microorganisms 2020, 8(2), 152; https://doi.org/10.3390/microorganisms8020152 - 22 Jan 2020

Cited by 10 | Viewed by 3654

Abstract

Beta-lactamases, enzymes produced by bacteria to degrade beta-lactam antibiotics, have been harnessed as therapeutics to protect the gut microbiome from damage caused by antibiotics. Proof-of-concept of this approach using SYN-004 (ribaxamase), a beta-lactamase formulated for oral delivery with intravenous (IV) penicillins and cephalosporins, was demonstrated with animal models and in humans. Ribaxamase degraded ceftriaxone in the gastrointestinal tract, protected the gut microbiome, significantly reduced the incidence of Clostridioides difficile disease and attenuated emergence of antibiotic resistant organisms. SYN-007 is a delayed release formulation of ribaxamase intended for use with oral beta-lactams. In dogs treated with oral amoxicillin, SYN-007 diminished antibiotic-mediated microbiome disruption and reduced the emergence of antibiotic resistance without altering amoxicillin systemic absorption. Here, SYN-007 function in the presence of clavulanate, a beta-lactamase inhibitor, was investigated. Dogs received amoxicillin (40 mg/kg, orally (PO), three times a day (TID)) or the combined antibiotic/beta-lactamase inhibitor, amoxicillin/clavulanate (40 mg/kg amoxicillin, 5.7 mg/kg clavulanate, PO, TID) +/™ SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were not significantly different +/™ SYN-007 compared to amoxicillin alone or amoxicillin/clavulanate alone as controls for both first and last doses, indicating SYN-007 did not interfere with systemic absorption of the antibiotic. Whole genome shotgun metagenomics analyses of the fecal microbiomes demonstrated both amoxicillin and amoxicillin/clavulanate significantly reduced diversity and increased the frequency of antibiotic resistance genes. Microbiome damage appeared more severe with amoxicillin/clavulanate. In contrast, with SYN-007, microbiome diversity was not significantly altered, and frequency of antibiotic resistance genes did not increase. Importantly, SYN-007 functioned in the presence of clavulanate to protect the gut microbiome indicating that SYN-007 activity was not inhibited by clavulanate in the dog gastrointestinal tract. SYN-007 has the potential to expand microbiome protection to beta-lactam/beta-lactamase inhibitor combinations delivered orally or systemically. Full article

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

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Review

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16 pages, 2556 KiB

Open AccessReview

Disease, Drugs and Dysbiosis: Understanding Microbial Signatures in Metabolic Disease and Medical Interventions

by Ceri Proffitt, Gholamreza Bidkhori, David Moyes and Saeed Shoaie

Microorganisms 2020, 8(9), 1381; https://doi.org/10.3390/microorganisms8091381 - 9 Sep 2020

Cited by 13 | Viewed by 5155

Abstract

Since the discovery of the potential role for the gut microbiota in health and disease, many studies have gone on to report its impact in various pathologies. These studies have fuelled interest in the microbiome as a potential new target for treating disease Here, we reviewed the key metabolic diseases, obesity, type 2 diabetes and atherosclerosis and the role of the microbiome in their pathogenesis. In particular, we will discuss disease associated microbial dysbiosis; the shift in the microbiome caused by medical interventions and the altered metabolite levels between diseases and interventions. The microbial dysbiosis seen was compared between diseases including Crohn’s disease and ulcerative colitis, non-alcoholic fatty liver disease, liver cirrhosis and neurodegenerative diseases, Alzheimer’s and Parkinson’s. This review highlights the commonalities and differences in dysbiosis of the gut between diseases, along with metabolite levels in metabolic disease vs. the levels reported after an intervention. We identify the need for further analysis using systems biology approaches and discuss the potential need for treatments to consider their impact on the microbiome. Full article

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

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16 pages, 371 KiB

Open AccessReview

Gallstone Disease and Microbiome

by Irina N. Grigor’eva and Tatyana I. Romanova

Microorganisms 2020, 8(6), 835; https://doi.org/10.3390/microorganisms8060835 - 2 Jun 2020

Cited by 79 | Viewed by 9301

Abstract

Gallstone disease (GSD) has, for many years, remained a high-cost, socially significant public health problem. Over the past decade, a number of studies have been carried out—both in humans and in animal models—confirming the role of the microbiota in various sections of the gastrointestinal tract as a new link in the etiopathogenesis of GSD. The microbiome of bile correlates with the bacterial composition of saliva, and the microbiome of the biliary tract has a high similarity with the microbiota of the duodenum. Pathogenic microflora of the oral cavity, through mechanisms of immunomodulation, can affect the motility of the gallbladder and the expression of mucin genes (MUC1, Muc3, MUC4), and represent one of the promoters of stone formation in the gallbladder. The presence of H. pylori infection contributes to the formation of gallstones and affects the occurrence of complications of GSD, including acute and chronic cholecystitis, cholangitis, pancreatitis. Intestinal bacteria (Clostridium, Bifidobacterium, Peptostreptococcus, Bacteroides, Eubacterium, and Escherichia coli) participating in the oxidation and epimerization of bile acids can disrupt enterohepatic circulation and lead to the formation of gallstones. At the same time, cholecystectomy due to GSD leads to the further transformation of the composition of the microbiota in various parts of the gastrointestinal tract, increasing the risk of developing stomach cancer and colorectal cancer. Further research is required to determine the possibility of using the evaluation of the composition of the microbiota of the gastrointestinal and biliary tracts as an early diagnostic marker of various gastroenterological diseases. Full article

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

12 pages, 891 KiB

Open AccessReview

Gut Microbiota Dysbiosis in Functional Dyspepsia

by Georgios Tziatzios, Paraskevas Gkolfakis, Ioannis S. Papanikolaou, Ruchi Mathur, Mark Pimentel, Evangelos J. Giamarellos-Bourboulis and Konstantinos Triantafyllou

Microorganisms 2020, 8(5), 691; https://doi.org/10.3390/microorganisms8050691 - 8 May 2020

Cited by 47 | Viewed by 10039

Abstract

Functional dyspepsia (FD) is one of the most prevalent chronic functional gastrointestinal disorders. Several distinct pathophysiological mechanisms, including gastro duodenal motor disorders, visceral hypersensitivity, brain-gut interactions, duodenal subtle inflammation, and genetic susceptibility, have been implicated in the pathogenesis of the disease, so far. However, emerging evidence suggests that both quantitative and qualitative disturbances of the gastrointestinal microbiota may also be implicated. In this context, several studies have demonstrated differences of the commensal bacterial community between patients with FD and healthy controls, while others have shown that intestinal dysbiosis might associate with disease’s symptoms severity. Elucidating these complex interactions constituting the microbiota and host crosstalk, may eventually lead to the discovery of novel, targeted therapeutic approaches that may be efficacious in treating the multiple aspects of the disorder. In this review, we summarize the data of the latest research with focus on the association between gut microbiota alterations and host regarding the pathogenesis of FD. Full article

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

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11 pages, 225 KiB

Open AccessReview

Dietary Carbohydrate Constituents Related to Gut Dysbiosis and Health

by Ye Seul Seo, Hye-Bin Lee, Yoonsook Kim and Ho-Young Park

Microorganisms 2020, 8(3), 427; https://doi.org/10.3390/microorganisms8030427 - 18 Mar 2020

Cited by 38 | Viewed by 6323

Abstract

Recent studies report that microbiota in the human intestine play an important role in host health and that both long- and short-term diets influence gut microbiota. These findings have fueled interest in the potential of food to promote health by shaping the intestinal microbiota. Despite the fact that large populations in Asia consume high quantities of carbohydrates, such diets have been ignored in comparison to the attention received by Western diets containing high quantities of fat and animal protein. We gathered data that suggest an association between imbalanced high-carbohydrate intake and gut microbiota and host health. In this review, we identify not only the effect of total carbohydrates on the intestinal microbiota specifically and the health of their hosts in general, but also how specific types of carbohydrates influence both factors. Full article

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