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Microorganisms
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State of the Art of Gut Microbiota in Italy (2023,...
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State of the Art of Gut Microbiota in Italy (2023, 2024)

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

Deadline for manuscript submissions: closed (15 November 2024) | Viewed by 11233

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,

This Special Issue aims to provide an up-to-date and comprehensive overview of the state of the art of gut microbiota in Italy.

We encourage Italian researchers from related fields to contribute papers highlighting the latest developments in gut microbiota, or to invite relevant experts and colleagues to do so. This Special Issue will publish full research articles and comprehensive reviews. The covered topics of interest include but are not limited to the following:

  • Structure and function of the microbiota;
  • Microbial community genetics, transcriptomics, proteomics and metabolomics;
  • Interactions within the microbiota;
  • Metabolic interactions with the host;
  • Inflammatory diseases;
  • Interactions with the immune system;
  • Microbial biodegradation of nutrients and xenobiotics;
  • Microbial ecology;
  • Microbial functions in the different habitats within the gut;
  • Metabolic flux analysis;
  • Analysis of functionalities via stable isotope probing (DNA, RNA and protein);
  • Model systems for studying microbiome biology;
  • Novel technologies for the analysis of the structure and function of the microbiota.

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.

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Published Papers (5 papers)

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19 pages, 2595 KiB  
Article
Stratification of Gut Microbiota Profiling Based on Autism Neuropsychological Assessments
by Chiara Marangelo, Pamela Vernocchi, Federica Del Chierico, Matteo Scanu, Riccardo Marsiglia, Emanuela Petrolo, Elisa Fucà, Silvia Guerrera, Giovanni Valeri, Stefano Vicari and Lorenza Putignani
Microorganisms 2024, 12(10), 2041; https://doi.org/10.3390/microorganisms12102041 - 9 Oct 2024
Viewed by 2087
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation [...] Read more.
Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation Schedule-Second edition (ADOS-2), Child Behavior Checklist (CBCL) and intelligent quotient/developmental quotient (IQ/DQ) parameters. Hence, metataxonomy and PICRUSt-based KEGG predictions of fecal GM were assessed for each clinical subset. Here, 60% of ASD patients showed mild to moderate autism, while the remaining 40% showed severe symptoms; 23% showed no clinical symptoms, 21% had a risk of behavior problems and 56% had clinical symptoms based on the CBCL, which assesses internalizing problems; further, 52% had no clinical symptoms, 21% showed risk, and 26% had clinical symptoms classified by CBCL externalizing problems. Considering the total CBCL index, 34% showed no clinical symptoms, 13% showed risk, and 52% had clinical symptoms. Here, 70% of ASD patients showed cognitive impairment/developmental delay (CI/DD). The GM of ASDs with severe autism was characterized by an increase in Veillonella, a decrease in Monoglobus pectinilyticus and a higher microbial dysbiosis index (MDI) when compared to mild-moderate ASDs. Patients at risk for behavior problems and showing clinical symptoms were characterized by a GM with an increase of Clostridium, Eggerthella, Blautia, Intestinibacter, Coprococcus, Ruminococcus, Onthenecus and Bariatricus, respectively. Peptidoglycan biosynthesis and biofilm formation KEGGs characterized patients with clinical symptoms, while potential microbiota-activated PPAR-γ-signaling was seen in CI/DD patients. This evidence derived from GM profiling may be used to further improve ASD understanding, leasing to a better comprehension of the neurological phenotype. Full article
(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))
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18 pages, 1162 KiB  
Article
Effect of Bifidobacterium bifidum Supplementation in Newborns Born from Cesarean Section on Atopy, Respiratory Tract Infections, and Dyspeptic Syndromes: A Multicenter, Randomized, and Controlled Clinical Trial
by Anna Rita Bellomo, Giulia Rotondi, Prudenza Rago, Silvia Bloise, Luigi Di Ruzza, Annamaria Zingoni, Susanna Di Valerio, Eliana Valzano, Francesco Di Pierro, Massimiliano Cazzaniga, Alexander Bertuccioli, Luigina Guasti, Nicola Zerbinati and Riccardo Lubrano
Microorganisms 2024, 12(6), 1093; https://doi.org/10.3390/microorganisms12061093 - 28 May 2024
Cited by 7 | Viewed by 2662
Abstract
Cesarean section is considered a possible trigger of atopy and gut dysbiosis in newborns. Bifidobacteria, and specifically B. bifidum, are thought to play a central role in reducing the risk of atopy and in favoring gut eubiosis in children. Nonetheless, no trial [...] Read more.
Cesarean section is considered a possible trigger of atopy and gut dysbiosis in newborns. Bifidobacteria, and specifically B. bifidum, are thought to play a central role in reducing the risk of atopy and in favoring gut eubiosis in children. Nonetheless, no trial has ever prospectively investigated the role played by this single bacterial species in preventing atopic manifestations in children born by cesarean section, and all the results published so far refer to mixtures of probiotics. We have therefore evaluated the impact of 6 months of supplementation with B. bifidum PRL2010 on the incidence, in the first year of life, of atopy, respiratory tract infections, and dyspeptic syndromes in 164 children born by cesarean (versus 249 untreated controls). The results of our multicenter, randomized, and controlled trial have shown that the probiotic supplementation significantly reduced the incidence of atopic dermatitis, upper and lower respiratory tract infections, and signs and symptoms of dyspeptic syndromes. Concerning the gut microbiota, B. bifidum supplementation significantly increased α-biodiversity and the relative values of the phyla Bacteroidota and Actinomycetota, of the genus Bacteroides, Bifidobacterium and of the species B. bifidum and reduced the relative content of Escherichia/Shigella and Haemophilus. A 6-month supplementation with B. bifidum in children born by cesarean section reduces the risk of gut dysbiosis and has a positive clinical impact that remains observable in the following 6 months of follow-up. Full article
(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))
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10 pages, 2533 KiB  
Communication
Intestinal Emphysema and Gut Bacterial Microbiota Composition
by Jasmine Hattab, Alfonso Rosamilia, Chiara Guarnieri, Domenico Sciota, Giuseppe Marruchella and Pietro Giorgio Tiscar
Microorganisms 2024, 12(5), 981; https://doi.org/10.3390/microorganisms12050981 - 13 May 2024
Viewed by 1229
Abstract
Pneumatosis cystoides intestinalis, or intestinal emphysema, is a condition characterized by the presence of multiple cystic structures within the gut wall and on the serosal surface of the intestine. Intestinal emphysema represents an accidental finding in swine, although it can be clinically [...] Read more.
Pneumatosis cystoides intestinalis, or intestinal emphysema, is a condition characterized by the presence of multiple cystic structures within the gut wall and on the serosal surface of the intestine. Intestinal emphysema represents an accidental finding in swine, although it can be clinically relevant in humans. Its etiology is unknown, and many theories have been proposed. Among them, a bacterial etiology is considered the most likely. Therefore, in this study, the V3-V4 region of the 16S rRNA gene was sequenced from 19 swine ileal tracts, 12 with intestinal emphysema and 7 without lesions, to detect a possible bacterial agent. In parallel, prevalence was estimated. Escherichia–Shigella (13.15%), Clostridium_sensu_stricto_1; s__uncultured_bacterium (7.09%), and Fusobacterium; s_uncultured bacterium (6.60%) were the most abundant species identified. No statistically relevant differences were observed between the pathological and physiological groups. Prevalence ranged from 1.25 to 5.12% depending on the batch. Our results suggest that the gut wall bacterial microbiota greatly match the normal gut microbiota, and that the etiological agent of intestinal emphysema may be (1) undetectable due to the chronicity of the lesions, (2) not considered statistically relevant in comparing the two groups (p < 0.05) and likewise in causing lesions, and (3) undetectable due to contamination. Regarding prevalence, the condition is moderately frequent. Full article
(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))
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18 pages, 2388 KiB  
Article
Gut Microbiota Ecological and Functional Modulation in Post-Stroke Recovery Patients: An Italian Study
by Riccardo Marsiglia, Chiara Marangelo, Pamela Vernocchi, Matteo Scanu, Stefania Pane, Alessandra Russo, Eleonora Guanziroli, Federica Del Chierico, Massimiliano Valeriani, Franco Molteni and Lorenza Putignani
Microorganisms 2024, 12(1), 37; https://doi.org/10.3390/microorganisms12010037 - 25 Dec 2023
Cited by 7 | Viewed by 2608
Abstract
Ischemic stroke (IS) can be caused by perturbations of the gut–brain axis. An imbalance in the gut microbiota (GM), or dysbiosis, may be linked to several IS risk factors and can influence the brain through the production of different metabolites, such as short-chain [...] Read more.
Ischemic stroke (IS) can be caused by perturbations of the gut–brain axis. An imbalance in the gut microbiota (GM), or dysbiosis, may be linked to several IS risk factors and can influence the brain through the production of different metabolites, such as short-chain fatty acids (SCFAs), indole and derivatives. This study examines ecological changes in the GM and its metabolic activities after stroke. Fecal samples of 10 IS patients were compared to 21 healthy controls (CTRLs). GM ecological profiles were generated via 16S rRNA taxonomy as functional profiles using metabolomics analysis performed with a gas chromatograph coupled to a mass spectrometer (GC-MS). Additionally fecal zonulin, a marker of gut permeability, was measured using an enzyme-linked immuno assay (ELISA). Data were analyzed using univariate and multivariate statistical analyses and correlated with clinical features and biochemical variables using correlation and nonparametric tests. Metabolomic analyses, carried out on a subject subgroup, revealed a high concentration of fecal metabolites, such as SCFAs, in the GM of IS patients, which was corroborated by the enrichment of SCFA-producing bacterial genera such as Bacteroides, Christensellaceae, Alistipes and Akkermansia. Conversely, indole and 3-methyl indole (skatole) decreased compared to a subset of six CTRLs. This study illustrates how IS might affect the gut microbial milieu and may suggest potential microbial and metabolic biomarkers of IS. Expanded populations of Akkermansia and enrichment of acetic acid could be considered potential disease phenotype signatures. Full article
(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))
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11 pages, 2321 KiB  
Case Report
Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infections in a Cystic Fibrosis Child Previously Screen Positive, Inconclusive Diagnosis (CFSPID): A Case Report
by Riccardo Marsiglia, Stefania Pane, Federica Del Chierico, Alessandra Russo, Pamela Vernocchi, Lorenza Romani, Sabrina Cardile, Antonella Diamanti, Luisa Galli, Agnese Tamborino, Vito Terlizzi, Paola De Angelis, Giulia Angelino and Lorenza Putignani
Microorganisms 2024, 12(10), 2059; https://doi.org/10.3390/microorganisms12102059 - 12 Oct 2024
Viewed by 1729
Abstract
Clostridioides difficile infection (CDI) is generally treated with vancomycin, metronidazole or fidaxomicin, although fecal microbiota transplantation (FMT) represents a promising therapeutic option for antibiotic-resistant recurrent C. difficile infections (rCDIs) in adults. In pediatric cystic fibrosis (CF) patients, CDIs are generally asymptomatic and respond [...] Read more.
Clostridioides difficile infection (CDI) is generally treated with vancomycin, metronidazole or fidaxomicin, although fecal microbiota transplantation (FMT) represents a promising therapeutic option for antibiotic-resistant recurrent C. difficile infections (rCDIs) in adults. In pediatric cystic fibrosis (CF) patients, CDIs are generally asymptomatic and respond to treatment. Here, we present the case of an 8-year-old female, initially diagnosed as “CFTR-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis” (CMRS/CFSPID), who then progressed to CF at 12 months. In the absence of CF-related symptoms, she presented multiple and disabling episodes of bloody diarrhoea with positive tests for C. difficile antigen and A/B toxin. After conventional treatments failed and several CDI relapses, FMT was proposed. Donor screening and GM donor–receiver matching identified her mother as a donor. Metataxonomy and targeted metabolomics provided, through a pre- and post-FMT time course, gut microbiota (GM) profiling to assess GM engraftment. At first, the GM map revealed severe dysbiosis, with a prevalence of Bacteroidetes and Proteobacteria (i.e., Klebsiella spp., Escherichia coli), a reduction in Firmicutes, a GM nearly entirely composed of Enterococcaceae (i.e., Enterococcus) and an almost complete depletion of Verrucomicrobia and Actinobacteria, mostly represented by Veillonella dispar. Post FMT, an increment in Bifidobacterium spp. and Collinsella spp. with a decrease in V. dispar restored intestinal eubiosis. Consistently, four weeks after FMT treatment, the child’s gut symptoms cleared, without CDI recurrence. Full article
(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))
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