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Microorganisms
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Novel Strategies in the Study of the Human Gut Microbiota...
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Novel Strategies in the Study of the Human Gut Microbiota 2.0

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

Deadline for manuscript submissions: 15 July 2024 | Viewed by 1558

Special Issue Editor

Dr. Francesco Celandroni

E-Mail Website
Guest Editor
Dipartimento di Biologia, UNIPI, Università di Pisa, 56127 Pisa, Italy
Interests: bacillus subtilis; bacillus cereus; microbiology; food microbiology and safety

Special Issue Information

Dear Colleagues,

The homeostasis of the human gastrointestinal tract is strictly dependent on the resident gut microbiota, a complex and plastic community of thousands of microbial species that live permanently or more or less temporarily in the intestinal lumen or in association with the intestinal mucosa. The study of the composition and fluctuation of the intestinal microbiota in healthy humans and in particular diseases may be of great help for the comprehension of the roles that microbes play in sustaining host health as well as of the interactions between microbes and human cells. From this perspective, such studies might take advantage of animal models or in vitro systems aimed at mimicking the intestinal environment.

The aim of this Special Issue is to provide a collection of articles on microbiota composition and its effect on human health, particularly focusing on strategies that can be adopted to study this complex and plastic microbial community, in vivo or in vitro.

As the Guest Editor of this Special Issue, I invite you to submit research articles, review articles, and short communications related to “Novel Strategies in the Study of the Human Gut Microbiota”.

Dr. Francesco Celandroni
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

  • gut microbiota
  • homeostasis
  • probiotics
  • prebiotics
  • animal models
  • in vitro models

Published Papers (3 papers)

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Research

17 pages, 2750 KiB  
Article
Autoprobiotics in the Treatment of Patients with Colorectal Cancer in the Early Postoperative Period
by Elena Ermolenko, Natalia Baryshnikova, Galina Alekhina, Alexander Zakharenko, Oleg Ten, Victor Kashchenko, Nadezhda Novikova, Olga Gushchina, Timofey Ovchinnikov, Anastasia Morozova, Anastasia Ilina, Alena Karaseva, Anna Tsapieva, Nikita Gladyshev, Alexander Dmitriev and Alexander Suvorov
Microorganisms 2024, 12(5), 980; https://doi.org/10.3390/microorganisms12050980 - 13 May 2024
Viewed by 336
Abstract
Despite great advances in the treatment of oncological diseases, the development of medical technologies to prevent or reduce complications of therapy, in particular, those associated with surgery and the introduction of antibiotics, remains relevant. The aim of this study is to evaluate the [...] Read more.
Despite great advances in the treatment of oncological diseases, the development of medical technologies to prevent or reduce complications of therapy, in particular, those associated with surgery and the introduction of antibiotics, remains relevant. The aim of this study is to evaluate the effectiveness of the use of autoprobiotics based on indigenous non-pathogenic strains of Enterococcus faecium and Enterococcus hirae as a personalized functional food product (PFFP) in the complex therapy of colorectal cancer (CRC) in the early postoperative period. A total of 36 patients diagnosed with CRC were enrolled in the study. Study group A comprised 24 CRC patients who received autoprobiotic therapy in the early postoperative period, while the control group C included 12 CRC patients without autoprobiotic therapy. Prior to surgery and between days 14 and 16 post-surgery, comprehensive evaluations were conducted on all patients, encompassing the following: stool and gastroenterological complaints analysis, examination of the gut microbiota (bacteriological study, quantitative polymerase chain reaction, metagenome analysis), and analysis of interleukins in the serum. Results: The use of autoprobiotics led to a decrease in dyspeptic complaints after surgery. It was also associated with the absence of postoperative complications, did not cause any side effects, and led to a decrease in the level of pro-inflammatory cytokines (IL-6 and IL-18) in the blood serum. The use of autoprobiotics led to positive changes in the structure of escherichia and enterococci populations, the elimination of Parvomonas micra and Fusobacterium nucleatum, and a decrease in the quantitative content of Clostridium perfringens and Akkermansia muciniphila. Metagenomic analysis (16S rRNA) revealed an increase in alpha diversity. Conclusion: The introduction of autoprobiotics in the postoperative period is a highly effective and safe approach in the complex treatment of CRC. Future studies will allow the discovery of additional fine mechanisms of autoprobiotic therapy and its impact on the digestive, immune, endocrine, and neural systems. Full article
(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota 2.0)
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83 pages, 403 KiB  
Article
Collider Bias Assessment in Colombian Indigenous Wiwa and Kogui Populations with Chronic Gastroenteric Disorder of Likely Infectious Etiology Suggests Complex Microbial Interactions Rather Than Clear Assignments of Etiological Relevance
by Hagen Frickmann, Joy Backhaus, Achim Hoerauf, Ralf Matthias Hagen and Simone Kann
Microorganisms 2024, 12(5), 970; https://doi.org/10.3390/microorganisms12050970 - 11 May 2024
Viewed by 281
Abstract
Multiple microbial detections in stool samples of indigenous individuals suffering from chronic gastroenteric disorder of a likely infectious origin, characterized by recurring diarrhea of variable intensity, in the rural north-east of Colombia are common findings, making the assignment of etiological relevance to individual [...] Read more.
Multiple microbial detections in stool samples of indigenous individuals suffering from chronic gastroenteric disorder of a likely infectious origin, characterized by recurring diarrhea of variable intensity, in the rural north-east of Colombia are common findings, making the assignment of etiological relevance to individual pathogens challenging. In a population of 773 indigenous people from either the tribe Wiwa or Kogui, collider bias analysis was conducted comprising 32 assessed microorganisms including 10 bacteria (Aeromonas spp., Campylobacter spp., enteroaggregative Escherichia coli (EAEC), enteropathogenic Escherichia coli (EPEC), enterotoxigenic Escherichia coli (ETEC), Salmonella spp., Shiga toxin-producing Escherichia coli (STEC), Shigella spp./enteroinvasive Escherichia coli (EIEC), Tropheryma whipplei and Yersinia spp.), 11 protozoa (Blastocystis spp., Cryptosporidium spp., Cyclospora spp., Dientamoeba fragilis, Entamoeba coli, Entamoeba bangladeshi/dispar/histolytica/moshkovskii complex, Entamoeba histolytica, Endolimax nana, Giardia duodenalis, Iodamoeba buetschlii and Pentatrichomonas hominis), 8 helminths (Ascaris spp., Enterobius vermicularis, Hymenolepis spp., Necator americanus, Schistosoma spp., Strongyloides spp., Taenia spp. and Trichuris spp.), microsporidia (Encephalocytozoon spp.) and fungal elements (microscopically observed conidia and pseudoconidia). The main results indicated that negative associations potentially pointing towards collider bias were infrequent events (n = 14), while positive associations indicating increased likelihood of co-occurrence of microorganisms quantitatively dominated (n = 88). Microorganisms showing the most frequent negative associations were EPEC (n = 6) and Blastocystis spp. (n = 3), while positive associations were most common for Trichuris spp. (n = 16), Dientamoeba fragilis (n = 15), Shigella spp./EIEC (n = 12), Ascaris spp. (n = 11) and Blastocystis spp. (n = 10). Of note, positive associations quantitively dominated for Blastocystis spp. In conclusion, collider bias assessment did not allow clear-cut assignment of etiological relevance for detected enteric microorganisms within the assessed Colombian indigenous population. Instead, the results suggested complex microbial interactions with potential summative effects. Future studies applying alternative biostatistical approaches should be considered to further delineate respective interactions. Full article
(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota 2.0)
17 pages, 5366 KiB  
Article
Innovative Biomarkers for Obesity and Type 1 Diabetes Based on Bifidobacterium and Metabolomic Profiling
by Angelica Nobili, Marco Pane, Mariya Skvortsova, Meryam Ben Salem, Stephan Morgenthaler, Emily Jamieson, Marina Di Stefano, Eirini Bathrellou, Eirini Mamalaki, Victoria Ramos-Garcia, Julia Kuligowski, Miltiadis Vasileiadis, Panagiotis Georgiadis, Marika Falcone and Paulo Refinetti
Microorganisms 2024, 12(5), 931; https://doi.org/10.3390/microorganisms12050931 - 3 May 2024
Viewed by 762
Abstract
The role of Bifidobacterium species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied in recent years. This paper discusses the [...] Read more.
The role of Bifidobacterium species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied in recent years. This paper discusses the discovery of signature biomarkers for obesity and T1D based on data from a novel test for profiling several Bifidobacterium species, combined with metabolomic analysis. Through the NUTRISHIELD clinical study, a total of 98 children were recruited: 40 healthy controls, 40 type 1 diabetics, and 18 obese children. Bifidobacterium profiles were assessed in stool samples through an innovative test allowing high taxonomic resolution and precise quantification, while SCFAs and branched amino acids were measured in urine samples through gas chromatography–mass spectrometry (GC-MS). KIDMED questionnaires were used to evaluate the children’s dietary habits and correlate them with the Bifidobacterium and metabolomic profiles. We found that B. longum subs. infantis and B. breve were higher in individuals with obesity, while B. bifidum and B. longum subs. longum were lower compared to healthy individuals. In individuals with T1D, alterations were found at the metabolic level, with an overall increase in the level of the most measured metabolites. The high taxonomic resolution of the Bifidobacterium test used meant strong correlations between the concentrations of valine and isoleucine, and the relative abundance of some Bifidobacterium species such as B. longum subs. infantis, B. breve, and B. bifidum could be observed. Full article
(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota 2.0)
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