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Microorganisms
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Gut Microbioma Structure and Functions in Human Health and Disease...
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Gut Microbioma Structure and Functions in Human Health and Disease 2.0

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 20281

Special Issue Editor

Dr. Francesco Di Pierro

E-Mail Website
Guest Editor
1. Medicine and Surgery Department, University of Insubria, Varese, Italy
2. UNICAM, Camerino University, Camerino, Italy
3. Scientific Department, Velleja Research, Piacenza, Italy
Interests: microbiology; probiotics; immunology; botanicals; gastroenterology; neonatology; vaccine; nutrition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent technical advances in the analysis of human colonic bacterial consortia have led to a considerable explosion of research on the gut microbiota. These advances have also generated intense interest among those clinicians motivated to apply these analyses to their patients. The gut consortium structure is driven by a number of different phenomena (type of delivery and feeding, therapies and drugs, weaning, diet, lifestyle, sport activities, probiotics and prebiotics, pathologies, environmental triggers, and so on) and is affected by many host factors (genetics, hormones, gastric and bowel pH, bile and pancreatic juice, gut carbonate release, and so on). These facts, along with the complex taxonomy by which the microbiotas are analyzed, makes it difficult to interpret the gut microbial consortium and to establish if it is responsible for an important contribution (negative or positive) to the patient’s health. Nevertheless, we are certain that there is a noticeable decrease in alfa-biodiversity of microbiota in people affected by certain pathologies, and that a strong correlation does exist between particular phylum (e.g., Proteobacteria) or taxa (e.g., Fusobacterium) with these diseases. Similarly, the positive role played in these contexts by particular taxa (e.g., Akkermansia or Faecalibacterium) cannot be denied. Therefore, despite this advance in knowledge, much remains unclear. This special issue aims to fill in some of the gaps that limit us from being able to translate this partial knowledge into everyday medicine. I kindly invite researchers or clinicians to contribute reviews or original papers having as a main focus the many aspects of the gut microbial consortium in health and disease with the unique aim to better understand the structural and taxonomic relationships, while also taking into consideration the possibilities for intervention in these processes.

Dr. Francesco Di Pierro
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

  • microbiota
  • microbiome
  • NGS analysis
  • cross-feeding
  • taxa

Published Papers (6 papers)

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Editorial

Jump to: Research, Review

3 pages, 193 KiB  
Editorial
Special Issue “Gut Microbioma Structure and Functions in Human Health and Disease 2.0”: Editorial
by Francesco Di Pierro
Microorganisms 2023, 11(3), 740; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11030740 - 14 Mar 2023
Viewed by 884
Abstract
Recent technical advances in the analysis of human colonic bacterial consortia have led to a considerable explosion of research on the gut microbiota [...] Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)

Research

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16 pages, 2107 KiB  
Article
Escherichia/Shigella, SCFAs, and Metabolic Pathways—The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico
by Tonatiuh Abimael Baltazar-Díaz, Luz Alicia González-Hernández, Juan Manuel Aldana-Ledesma, Marcela Peña-Rodríguez, Alejandra Natali Vega-Magaña, Adelaida Sara Minia Zepeda-Morales, Rocío Ivette López-Roa, Susana del Toro-Arreola, Erika Martínez-López, Adriana María Salazar-Montes and Miriam Ruth Bueno-Topete
Microorganisms 2022, 10(6), 1231; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061231 - 16 Jun 2022
Cited by 26 | Viewed by 3973
Abstract
Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples [...] Read more.
Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico. Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)
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Review

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19 pages, 1069 KiB  
Review
Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions
by Mikhail Syromyatnikov, Ekaterina Nesterova, Maria Gladkikh, Yuliya Smirnova, Mariya Gryaznova and Vasily Popov
Microorganisms 2022, 10(9), 1866; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10091866 - 18 Sep 2022
Cited by 17 | Viewed by 5628
Abstract
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality [...] Read more.
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn’s disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities. Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)
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19 pages, 373 KiB  
Review
Nutraceuticals and Herbal Food Supplements for Weight Loss: Is There a Prebiotic Role in the Mechanism of Action?
by Alexander Bertuccioli, Marco Cardinali, Marco Biagi, Sara Moricoli, Ilaria Morganti, Giordano Bruno Zonzini and Giovanna Rigillo
Microorganisms 2021, 9(12), 2427; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122427 - 25 Nov 2021
Cited by 5 | Viewed by 2846
Abstract
Numerous nutraceuticals and botanical food supplements are used with the intention of modulating body weight. A recent review examined the main food supplements used in weight loss, dividing them according to the main effects for which they were investigated. The direct or indirect [...] Read more.
Numerous nutraceuticals and botanical food supplements are used with the intention of modulating body weight. A recent review examined the main food supplements used in weight loss, dividing them according to the main effects for which they were investigated. The direct or indirect effects exerted on the intestinal microbiota can also contribute to the effectiveness of these substances. The aim of this review is to evaluate whether any prebiotic effects, which could help to explain their efficacy or ineffectiveness, are documented in the recent literature for the main nutraceuticals and herbal food supplements used for weight loss management. Several prebiotic effects have been reported for various nutraceutical substances, which have shown activity on Bifidobacterium spp., Lactobacillus spp., Akkermansia muciniphila, Faecalibacterium prausnitzi, Roseburia spp., and the Firmicutes/Bacteroidetes ratio. Different prebiotics have beneficial effects on weight and the related metabolic profile, in some cases even acting on the microbiota with mechanisms that are completely independent from those nutraceuticals for which certain products are normally used. Further studies are necessary to clarify the different levels at which a nutraceutical substance can exert its action. Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)
20 pages, 1402 KiB  
Review
Gut Microbiota Parameters Potentially Useful in Clinical Perspective
by Francesco Di Pierro
Microorganisms 2021, 9(11), 2402; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112402 - 22 Nov 2021
Cited by 23 | Viewed by 3465
Abstract
Interest in gut microbiota analyses is at an all-time high. Gut microbiota is thought to relate to an increasing range of diseases of interest to physicians and nutritionists. Overweight, obesity, response to diet, metabolic syndrome, low grade inflammation, diabetes and colon neoplasms could [...] Read more.
Interest in gut microbiota analyses is at an all-time high. Gut microbiota is thought to relate to an increasing range of diseases of interest to physicians and nutritionists. Overweight, obesity, response to diet, metabolic syndrome, low grade inflammation, diabetes and colon neoplasms could maybe be observed in microbiota if affordable markers were available. Possible biomarkers like the Firmicutes/Bacteroidetes ratio, the Gram-positive/Gram-negative ratio, the Prevotella/Bacteroides ratio, and the Fusobacterium nucleatum/Faecalibacterium prausnitzii ratio are here reviewed in a narrative way in the attempt to highlight their possible future role in routine practice and clinically relevant diagnostics. Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)
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17 pages, 1552 KiB  
Review
A Possible Perspective about the Compositional Models, Evolution, and Clinical Meaning of Human Enterotypes
by Francesco Di Pierro
Microorganisms 2021, 9(11), 2341; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112341 - 12 Nov 2021
Cited by 11 | Viewed by 2677
Abstract
Among the various parameters obtainable through the analysis of the human gut microbiota, the enterotype is one of the first classifications of the bacterial consortia, which tried to obtain, at the same time, as much information as possible to be applied in clinical [...] Read more.
Among the various parameters obtainable through the analysis of the human gut microbiota, the enterotype is one of the first classifications of the bacterial consortia, which tried to obtain, at the same time, as much information as possible to be applied in clinical medicine. Although some authors observed the existence not of clusters, but only of a real continuous gradient, enterotypes are commonly described according to various models. The first model predicted either clustering into enterotypes 1 and 2 based on two specific dominances, Bacteroides and Prevotella, respectively, with the Ruminococcus dominance blurred within the Bacteroides dominance, or it predicted a threedominant condition, in which the Ruminococcus driver constituted enterotype 3, separated from enterotype 1. A second model envisaged three possible ways to cluster gut microbiota, respectively centred on two, three, and four dominances. In the first case, enterotypes 1 and 2 coincided with the two original enterotypes, with the dominance of Bacteroides and Prevotella, respectively. In the second case, the existence of enterotype 3 was evident and whose dominance was not centred on Ruminococcus but extended more towards the entire Firmicutes phylum. In the third case, the presence of the phylum Firmicutes was split into two different enterotypes generating the clusters defined and named as Mixtures 1 and 2. Subsequently, the analysis of the water content (hydration) in the stool allowed the splitting of the Bacteroides enterotype into two sub-enterotype, respectively known as B1 and B2. All these models have allowed us to highlight some correlations between a specific enterotype, or cluster, and some characteristics, such as the greater predisposition of the respective hosts towards certain pathologies. These observations, coupled with the attempt to derive the different microbiota on an evolutionary basis, can help to shed new light on this topic and demonstrate the possible utility that the different ways of clustering the gut microbiota can have in a clinical application perspective and in preventive medicine. Full article
(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)
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