Special Issue "Gastrointestinal Microbiota Impacts 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: 30 April 2019

Special Issue Editor

Guest Editor
Dr. Pramod Gopal

Fonterra Co-operative Group, Auckland, New Zealand
Website | E-Mail
Interests: Human gastrointestinal microbiota;food-microbiota;health and disease

Special Issue Information

Dear Colleagues,

Enormous abundance and diversity of microorganisms that colonize different regions of the human gastrointestinal tract participate in range of metabolic activities and influence many aspects of health and disease. They play an important role in maintaining immune homeostasis, assist in energy harvest from non-digestible dietary components through fermentation in large intestine and generate many bioactive metabolites, such as short chain fatty acids. Equally, dysbiosis is associated with a number of diseases including inflammatory bowel disease, diabetes mellitus, obesity and metabolic syndrome. Gut microbiome research has been revolutionised over the past decade through development of culture independent, high throughput next generation DNA sequencing technology. We are developing much better understanding of the composition of microbial communities of the healthy human gut, defining dominant members. Application of multiple –omic technologies such metabolomics, proteomics, and transcriptomics has further enhanced our ability to decipher the function of the human gut microbiome including its interaction with human host and impact on health. It is now well known that diet is one of the major influences on both major short- and long term composition of human gut microbiome. Dietary manipulation of gut microbiome therefore offers an attractive approach to achieve a favourable health outcome.

Dr. Pramod Gopal
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 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. 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 1000 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

  • Gastrointestinal health
  • gut microbiome
  • gut-brain axis
  • probiotics
  • prebiotics
  • IBD
  • IBS
  • gut inflammation
  • gut comfort
  • gut function
  • SCFA
  • oligosaccharides

Published Papers (9 papers)

View options order results:
result details:
Displaying articles 1-9
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables
Microorganisms 2019, 7(2), 61; https://doi.org/10.3390/microorganisms7020061
Received: 27 January 2019 / Revised: 16 February 2019 / Accepted: 20 February 2019 / Published: 23 February 2019
Cited by 1 | PDF Full-text (1458 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Extra virgin olive oil (EVOO) has been reported to have a distinct influence on gut microbiota in comparison to other fats, with its physiological benefits widely studied. However, a large proportion of the population consumes olive oil after a depurative process that not [...] Read more.
Extra virgin olive oil (EVOO) has been reported to have a distinct influence on gut microbiota in comparison to other fats, with its physiological benefits widely studied. However, a large proportion of the population consumes olive oil after a depurative process that not only mellows its taste, but also deprives it of polyphenols and other minority components. In this study, we compare the influence on the intestinal microbiota of a diet high in this refined olive oil (ROO) with other fat-enriched diets. Swiss Webster mice were fed standard or a high-fat diet enriched with EVOO, ROO, or butter (BT). Physiological parameters were also evaluated. At the end of the feeding period, DNA was extracted from feces and the 16S rRNA was pyrosequenced. The group fed ROO behaved differently to the EVOO group in half the families with statistically significant differences among the diets, with higher comparative levels in three families—Desulfovibrionaceae, Spiroplasmataceae, and Helicobacteraceae—correlating with total cholesterol. These results are again indicative of a link between specific diets, certain physiological parameters and the prevalence of some taxa, but also support the possibility that polyphenols and minor components of EVOO are involved in some of the proposed effects of this fat through the modulation of the intestinal microbiota Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Graphical abstract

Open AccessArticle Effects of Bifidobacterium bifidum in Mice Infected with Citrobacter rodentium
Microorganisms 2019, 7(2), 51; https://doi.org/10.3390/microorganisms7020051
Received: 12 December 2018 / Revised: 7 February 2019 / Accepted: 11 February 2019 / Published: 14 February 2019
PDF Full-text (3537 KB) | HTML Full-text | XML Full-text
Abstract
In vitro and in vivo studies suggest that selected Bifidobacterium bifidum strains sustain intestinal homeostasis. This study aimed to examine whether the administration of B. bifidum MIMBb75 (BB75) attenuates Citrobacter rodentium infection, a murine model for enteric infection and inflammatory bowel disease in [...] Read more.
In vitro and in vivo studies suggest that selected Bifidobacterium bifidum strains sustain intestinal homeostasis. This study aimed to examine whether the administration of B. bifidum MIMBb75 (BB75) attenuates Citrobacter rodentium infection, a murine model for enteric infection and inflammatory bowel disease in humans. C57Bl6/J mice were randomized to receive BB75 daily starting before or after C. rodentium infection. BB75 load and infection kinetics were monitored. On day 10 post-infection (p.i.), histological parameters of the large intestine were assessed. Barrier integrity was evaluated by pathogen translocation to secondary organs and in vivo permeability test. Fecal C. rodentium load peaked at 1010 CFU/g at day 10 p.i., with clearance at day 24 p.i., regardless of probiotic treatment. BB75 administration resulted in 107 cells/g of feces with no effect of timing of administration. BB75 treatment did not attenuate C. rodentium-induced crypt hyperplasia nor inflammation. C. rodentium and BB75 can co-exist in the gut with no mutual displacement. However, BB75 cannot counteract C. rodentium pathology. Our findings provide insight for the understanding of probiotics behavior and their clinical relevance in intestinal inflammation. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Open AccessArticle Identification, Characterization, and Formulation of a Novel Carbapenemase Intended to Prevent Antibiotic-Mediated Gut Dysbiosis
Microorganisms 2019, 7(1), 22; https://doi.org/10.3390/microorganisms7010022
Received: 3 December 2018 / Revised: 6 January 2019 / Accepted: 15 January 2019 / Published: 16 January 2019
Cited by 1 | PDF Full-text (2308 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Antibiotics can damage the gut microbiome leading to opportunistic infections and the emergence of antibiotic resistance. Microbiome protection via antibiotic inactivation in the gastrointestinal (GI) tract represents a strategy to limit antibiotic exposure of the colonic microbiota. Proof of concept for this approach [...] Read more.
Antibiotics can damage the gut microbiome leading to opportunistic infections and the emergence of antibiotic resistance. Microbiome protection via antibiotic inactivation in the gastrointestinal (GI) tract represents a strategy to limit antibiotic exposure of the colonic microbiota. Proof of concept for this approach was achieved with an orally-administered beta-lactamase enzyme, SYN-004 (ribaxamase), that was demonstrated to degrade ceftriaxone excreted into the GI tract and protect the gut microbiome from antibiotic-mediated dysbiosis. Ribaxamase efficiently degrades penicillin and cephalosporin beta-lactam antibiotics, but is not active against carbapenems. To expand this microbiome protection strategy to include all classes of beta-lactams, three distinct carbapenemases were evaluated for manufacturability, antibiotic degradation spectrum, and stability in human intestinal fluid. E. coli production strains were generated for P2A, a novel metallo-enzyme isolated from B. cereus, New Delhi metallo-beta-lactamase (NDM), and Klebsiella pneumoniae carbapenemase (KPC). While all three enzymes effectively inactivated a broad range of antibiotics, including penicillins, most cephalosporins, and carbapenems in vitro, only P2A retained biological activity when incubated with human chyme. As functional stability in the intestinal tract is a key requirement for an orally-delivered enzyme, P2A was chosen as a potential clinical candidate. An enteric formulation of P2A was developed, called SYN-006, that was inert under high acid conditions, with enzyme dissolution occurring at pH > 5.5. SYN-006 has the potential to expand microbiome protection via antibiotic inactivation to include all classes of beta-lactam antibiotics. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Open AccessArticle A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice
Microorganisms 2018, 6(4), 101; https://doi.org/10.3390/microorganisms6040101
Received: 30 June 2018 / Revised: 12 September 2018 / Accepted: 26 September 2018 / Published: 29 September 2018
PDF Full-text (1439 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It [...] Read more.
Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It has been reported that the composition of intestinal luminal metabolites between the small and large intestine are different; however, comprehensive metabolomic and commensal microbiota profiles specific to each part of the gastrointestinal lumen remain obscure. In this study, by using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome and 16S rRNA gene-based microbiome analyses of specific pathogen-free (SPF) and germ-free (GF) murine gastrointestinal luminal profiles, we observed the different roles of commensal microbiota in each part of the gastrointestinal tract involved in carbohydrate metabolism and nutrient production. We found that the concentrations of most amino acids in the SPF small intestine were higher than those in the GF small intestine. Furthermore, sugar alcohols such as mannitol and sorbitol accumulated only in the GF large intestine, but not in the SPF large intestine. On the other hand, pentoses, such as arabinose and xylose, gradually accumulated from the cecum to the colon only in SPF mice, but were undetected in GF mice. Correlation network analysis between the gastrointestinal microbes and metabolites showed that niacin metabolism might be correlated to Methylobacteriaceae. Collectively, commensal microbiota partially affects the gastrointestinal luminal metabolite composition based on their metabolic dynamics, in cooperation with host digestion and absorption. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Review

Jump to: Research

Open AccessReview Microbial Population Changes and Their Relationship with Human Health and Disease
Microorganisms 2019, 7(3), 68; https://doi.org/10.3390/microorganisms7030068
Received: 30 January 2019 / Revised: 26 February 2019 / Accepted: 27 February 2019 / Published: 3 March 2019
PDF Full-text (9890 KB) | HTML Full-text | XML Full-text
Abstract
Specific microbial profiles and changes in intestinal microbiota have been widely demonstrated to be associated with the pathogenesis of a number of extra-intestinal (obesity and metabolic syndrome) and intestinal (inflammatory bowel disease) diseases as well as other metabolic disorders, such as non-alcoholic fatty [...] Read more.
Specific microbial profiles and changes in intestinal microbiota have been widely demonstrated to be associated with the pathogenesis of a number of extra-intestinal (obesity and metabolic syndrome) and intestinal (inflammatory bowel disease) diseases as well as other metabolic disorders, such as non-alcoholic fatty liver disease and type 2 diabetes. Thus, maintaining a healthy gut ecosystem could aid in avoiding the early onset and development of these diseases. Furthermore, it is mandatory to evaluate the alterations in the microbiota associated with pathophysiological conditions and how to counteract them to restore intestinal homeostasis. This review highlights and critically discusses recent literature focused on identifying changes in and developing gut microbiota-targeted interventions (probiotics, prebiotics, diet, and fecal microbiota transplantation, among others) for the above-mentioned pathologies. We also discuss future directions and promising approaches to counteract unhealthy alterations in the gut microbiota. Altogether, we conclude that research in this field is currently in its infancy, which may be due to the large number of factors that can elicit such alterations, the variety of related pathologies, and the heterogeneity of the population involved. Further research on the effects of probiotics, prebiotics, or fecal transplantations on the composition of the human gut microbiome is necessary. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Open AccessReview Probiotics and Colon Cancer
Microorganisms 2019, 7(3), 66; https://doi.org/10.3390/microorganisms7030066
Received: 4 January 2019 / Revised: 10 February 2019 / Accepted: 23 February 2019 / Published: 28 February 2019
PDF Full-text (426 KB) | HTML Full-text | XML Full-text
Abstract
Literature has recently highlighted the enormous scientific interest on the relationship between the gut microbiota and colon cancer, and how the use of some selected probiotics can have a future impact on the adverse events which occur during this disease. Although there is [...] Read more.
Literature has recently highlighted the enormous scientific interest on the relationship between the gut microbiota and colon cancer, and how the use of some selected probiotics can have a future impact on the adverse events which occur during this disease. Although there is no clear evidence to claim that probiotics are effective in people with cancer, recent reviews have found that probiotics can significantly reduce the incidence of diarrhea and the average frequency of daily bowel movements. However, most of this evidence needs to be more clinically convincing and further discussed. Undoubtedly, some probiotics, when properly dosed and administered, can have a strong rebalance effect on the gut microbiota and as a consequence a possible positive action on immune modulation of the gastrointestinal tract and on inflammation of the intestinal mucosa. Many recent findings indeed support the hypothesis that the daily use of some selected probiotics can be a feasible approach to effectively protect patients against the risk of some severe consequences due to radiation therapy or chemotherapy. This paper aims to review the most recent articles in order to consider a possible adjuvant approach for the use of certain well-balanced probiotics to help prevent colon cancer and the adverse effects caused by related therapies. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Graphical abstract

Open AccessReview Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health
Microorganisms 2019, 7(2), 41; https://doi.org/10.3390/microorganisms7020041
Received: 17 January 2019 / Revised: 26 January 2019 / Accepted: 28 January 2019 / Published: 31 January 2019
PDF Full-text (1047 KB) | HTML Full-text | XML Full-text
Abstract
This article reviews the current evidence associating gut microbiota with factors that impact host circadian-metabolic axis, such as light/dark cycles, sleep/wake cycles, diet, and eating patterns. We examine how gut bacteria possess their own daily rhythmicity in terms of composition, their localization to [...] Read more.
This article reviews the current evidence associating gut microbiota with factors that impact host circadian-metabolic axis, such as light/dark cycles, sleep/wake cycles, diet, and eating patterns. We examine how gut bacteria possess their own daily rhythmicity in terms of composition, their localization to intestinal niches, and functions. We review evidence that gut bacteria modulate host rhythms via microbial metabolites such as butyrate, polyphenolic derivatives, vitamins, and amines. Lifestyle stressors such as altered sleep and eating patterns that may disturb the host circadian system also influence the gut microbiome. The consequent disruptions to microbiota-mediated functions such as decreased conjugation of bile acids or increased production of hydrogen sulfide and the resultant decreased production of butyrate, in turn affect substrate oxidation and energy regulation in the host. Thus, disturbances in microbiome rhythms may at least partially contribute to an increased risk of obesity and metabolic syndrome associated with insufficient sleep and circadian misalignment. Good sleep and a healthy diet appear to be essential for maintaining gut microbial balance. Manipulating daily rhythms of gut microbial abundance and activity may therefore hold promise for a chrononutrition-based approach to consolidate host circadian rhythms and metabolic homeorhesis. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Graphical abstract

Open AccessReview Microbial Fermentation of Dietary Protein: An Important Factor in Diet–Microbe–Host Interaction
Microorganisms 2019, 7(1), 19; https://doi.org/10.3390/microorganisms7010019
Received: 20 December 2018 / Revised: 8 January 2019 / Accepted: 9 January 2019 / Published: 13 January 2019
Cited by 2 | PDF Full-text (1667 KB) | HTML Full-text | XML Full-text
Abstract
Protein fermentation by gut microbiota contributes significantly to the metabolite pool in the large intestine and may contribute to host amino acid balance. However, we have a limited understanding of the role that proteolytic metabolites have, both in the gut and in systemic [...] Read more.
Protein fermentation by gut microbiota contributes significantly to the metabolite pool in the large intestine and may contribute to host amino acid balance. However, we have a limited understanding of the role that proteolytic metabolites have, both in the gut and in systemic circulation. A review of recent studies paired with findings from previous culture-based experiments suggests an important role for microbial protein fermentation in altering the gut microbiota and generating a diverse range of bioactive molecules which exert wide-ranging host effects. These metabolic products have been shown to increase inflammatory response, tissue permeability, and colitis severity in the gut. They are also implicated in the development of metabolic disease, including obesity, diabetes, and non-alcoholic fatty liver disease (NAFLD). Specific products of proteolytic fermentation such as hydrogen sulfide, ammonia, and p-Cresol may also contribute to the development of colorectal cancer. These findings are in conflict with other studies showing that tryptophan metabolites may improve gut barrier function and attenuate severity in a multiple sclerosis model. Further research examining proteolytic fermentation in the gut may be key to our understanding of how microbial and host metabolism interact affecting health. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Open AccessReview What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases
Microorganisms 2019, 7(1), 14; https://doi.org/10.3390/microorganisms7010014
Received: 29 November 2018 / Revised: 15 December 2018 / Accepted: 9 January 2019 / Published: 10 January 2019
Cited by 1 | PDF Full-text (876 KB) | HTML Full-text | XML Full-text
Abstract
Each individual is provided with a unique gut microbiota profile that plays many specific functions in host nutrient metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Gut microbiota are composed of different bacteria species taxonomically classified [...] Read more.
Each individual is provided with a unique gut microbiota profile that plays many specific functions in host nutrient metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Gut microbiota are composed of different bacteria species taxonomically classified by genus, family, order, and phyla. Each human’s gut microbiota are shaped in early life as their composition depends on infant transitions (birth gestational date, type of delivery, methods of milk feeding, weaning period) and external factors such as antibiotic use. These personal and healthy core native microbiota remain relatively stable in adulthood but differ between individuals due to enterotypes, body mass index (BMI) level, exercise frequency, lifestyle, and cultural and dietary habits. Accordingly, there is not a unique optimal gut microbiota composition since it is different for each individual. However, a healthy host–microorganism balance must be respected in order to optimally perform metabolic and immune functions and prevent disease development. This review will provide an overview of the studies that focus on gut microbiota balances in the same individual and between individuals and highlight the close mutualistic relationship between gut microbiota variations and diseases. Indeed, dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extra-intestinal diseases such as metabolic and neurological disorders. Understanding the cause or consequence of these gut microbiota balances in health and disease and how to maintain or restore a healthy gut microbiota composition should be useful in developing promising therapeutic interventions. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
Figures

Figure 1

Microorganisms EISSN 2076-2607 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top