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Molecular Research in Human Microbiome 2.0
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Molecular Research in Human Microbiome 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 7596

Special Issue Editor

Dr. Maria Teresa Mascellino

E-Mail Website
Guest Editor
Department of Public Health and Infectious Diseases, Policlinico Umberto1 viale del Policlinico 155, Rome, Italy
Interests: bacterial antibiotic resistance; multidrug resistant microorganisms (MDR bacteria); probiotics; molecular laboratory methods; bacterial infections; biofilm and sonication; double carbapenem synergistic activity; association of antibiotics; enterobacterales; antimicrobial agents and resistance; relationship with the therapeutic approach; microbiota; Clostridium difficile infection; bacterial translocation and virulence factors; COVID 19 vaccines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

There are a variety of microorganisms in the human body, including fungi, bacteria and viruses, which account for about 1% to 3% of our body weight. They are usually harmless to the human body, and some can even protect our health by making vitamins, decomposing food and regulating immunity. These microorganisms form a large group called microbiome. More and more studies have shown that the changes of human microbiome are related to the occurrence of many diseases. For example alteration of the normal gut integrity is present during Clostridium difficile infections (CDI). In fact markers of microbial translocation, inflammation, and intestinal damage which are still present at clinical resolution of CDI, can be evaluated in patients with such disease. Improving microbiome may be applied to the treatment of diseases. Our microbiota plays a vital role in our health: it protects us against pathogens, promotes the development of our immune system, and helps metabolize various compounds. Maintaining a balanced microbial ecosystem is essential for defending our health. Several studies have shown significant changes in the balance of microorganisms in the host population or in the environment and this can be associated with significant changes in the balance of microorganisms in the host population. The goal of this special issue is to describe the human microbiome and analyse its role in human health and disease. In conclusion, this research topic is open in the broad subject area of microbiome and human health diseases. Welcome to submit a review of articles that study the human microbiome and analyse its role in human health and disease. The following are some recognized research cases, but not limited to the following: 

  • single group or multi group analysis of gene expression in microbiome and cell line (or animal model)
  • microbiota analysis of patients with inflammatory bowel disease
  • analyse metabolites secreted by the microbiome and their effects on patients with neuropathic diseases
  • analyse specific pathogenic organisms, their carcinogenic potential and potential mechanisms
  • changes in microbial populations in some diseases
  • Clostridium difficile infection

Dr. Maria Teresa Mascellino
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • microbiome
  • microbial population
  • inflammatory bowel disease
  • bacterial translocation
  • Clostridium difficile infection

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Published Papers (4 papers)

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Research

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11 pages, 2269 KiB  
Article
Microbiota of Healthy Dental Pulp Under the Omics Loupe
by Alan Bérard, Florian Mauffrey, Nadia Gaïa, Alexandre Perez, Chiraz Chaabane, Jacques Schrenzel, Julian Grégoire Leprince, Serge Bouillaguet and Vladimir Lazarevic
Int. J. Mol. Sci. 2025, 26(7), 3232; https://doi.org/10.3390/ijms26073232 - 31 Mar 2025
Viewed by 319
Abstract
This study aims to contribute to the understanding of the dental pulp microbiome through metataxonomic analysis of pulp tissues from clinically healthy impacted third molars in 17 patients. Samples from coronal pulp, outer radicular dentin, and negative controls were included. Each sample was [...] Read more.
This study aims to contribute to the understanding of the dental pulp microbiome through metataxonomic analysis of pulp tissues from clinically healthy impacted third molars in 17 patients. Samples from coronal pulp, outer radicular dentin, and negative controls were included. Each sample was spiked with a known bacterial standard. Sequencing of the 16S rRNA V3–V4 region revealed similarity in bacterial taxonomic profiles. The bacterial DNA was detected in all pulp samples, primarily originating from reagent contaminants. Although some oral taxa appeared more abundant in pulp than in dentin or controls, contaminant species overwhelmingly dominated. Most of the extracted DNA was of human origin, rather than bacterial. Our findings question the concept of a core microbiome in healthy pulp and highlight the critical need for rigorous controls in pulpal microbiome studies. Full article
(This article belongs to the Special Issue Molecular Research in Human Microbiome 2.0)
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16 pages, 1838 KiB  
Article
Relationship Between the Presence of Red Complex Species and the Distribution of Other Oral Bacteria, Including Major Periodontal Pathogens in Older Japanese Individuals
by Mariko Kametani, Yasuyuki Nagasawa, Momoko Usuda, Ami Kaneki, Masashi Ogawa, Kensaku Shojima, Hiromitsu Yamazaki, Kana Tokumoto, Daiki Matsuoka, Kana Suehara, Yuto Suehiro, Tatsuya Akitomo, Chieko Mitsuhata, Taro Misaki, Seigo Ito, Shuhei Naka, Michiyo Matsumoto-Nakano, Kazuhiko Nakano, Hiromitsu Kishimoto, Ken Shinmura and Ryota Nomuraadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2024, 25(22), 12243; https://doi.org/10.3390/ijms252212243 - 14 Nov 2024
Cited by 1 | Viewed by 1574
Abstract
Red complex bacteria (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) have high virulence in periodontal disease. In the present study, we aimed to elucidate the detailed symbiotic relationships between the red complex and other oral bacteria in older Japanese [...] Read more.
Red complex bacteria (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) have high virulence in periodontal disease. In the present study, we aimed to elucidate the detailed symbiotic relationships between the red complex and other oral bacteria in older Japanese individuals. Polymerase chain reaction was performed using dental plaque from 116 subjects and specific primers for ten periodontal pathogens. The detection rate of Prevotella intermedia and Capnocytophaga sputigena was significantly higher in P. gingivalis-positive subjects than in P. gingivalis-negative subjects (p < 0.05). The detection rate of Campylobacter rectus, Prevotella nigrescens, Capnocytophaga ochracea, and Eikenella corrodens was significantly higher in T. forsythia-positive subjects than in T. forsythia-negative subjects (p < 0.01). In a comprehensive analysis of oral microbiomes, three red complex species-positive subjects had significantly higher α-diversity than only P. gingivalis-positive subjects (p < 0.05) and had significantly lower β-diversity than only T. forsythia-positive subjects (p < 0.01). In the taxonomy analysis, Porphyromonas was significantly higher in three red complex species-positive subjects than in only P. gingivalis-positive and only T. forsythia-positive subjects (p < 0.01). These results suggest that each red complex species forms a unique oral microbiome and individuals positive for all red complex bacteria may harbor oral bacteria that confer a significant advantage in developing periodontal disease. Full article
(This article belongs to the Special Issue Molecular Research in Human Microbiome 2.0)
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27 pages, 3818 KiB  
Article
Mechanistic Insights into the Anti-Proliferative Action of Gut Microbial Metabolites against Breast Adenocarcinoma Cells
by Kayla Jaye, Muhammad A. Alsherbiny, Dennis Chang, Chun-Guang Li and Deep Jyoti Bhuyan
Int. J. Mol. Sci. 2023, 24(20), 15053; https://doi.org/10.3390/ijms242015053 - 10 Oct 2023
Cited by 6 | Viewed by 2542
Abstract
The gut microbiota undergoes metabolic processes to produce by-products (gut metabolites), which play a vital role in the overall maintenance of health and prevention of disease within the body. However, the use of gut metabolites as anticancer agents and their molecular mechanisms of [...] Read more.
The gut microbiota undergoes metabolic processes to produce by-products (gut metabolites), which play a vital role in the overall maintenance of health and prevention of disease within the body. However, the use of gut metabolites as anticancer agents and their molecular mechanisms of action are largely unknown. Therefore, this study evaluated the anti-proliferative effects of three key gut microbial metabolites—sodium butyrate, inosine, and nisin, against MCF7 and MDA-MB-231 breast adenocarcinoma cell lines. To determine the potential mechanistic action of these gut metabolites, flow cytometric assessments of apoptotic potential, reactive oxygen species (ROS) production measurements and proteomics analyses were performed. Sodium butyrate exhibited promising cytotoxicity, with IC50 values of 5.23 mM and 5.06 mM against MCF7 and MDA-MB-231 cells, respectively. All three metabolites were found to induce apoptotic cell death and inhibit the production of ROS in both cell lines. Nisin and inosine indicated a potential activation of cell cycle processes. Sodium butyrate indicated the possible initiation of signal transduction processes and cellular responses to stimuli. Further investigations are necessary to ascertain the effective therapeutic dose of these metabolites, and future research on patient-derived tumour spheroids will provide insights into the potential use of these gut metabolites in cancer therapy. Full article
(This article belongs to the Special Issue Molecular Research in Human Microbiome 2.0)
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Review

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16 pages, 1057 KiB  
Review
An Update on Microbial Interventions in Autism Spectrum Disorder with Gastrointestinal Symptoms
by Rachel J. Moreno and Paul Ashwood
Int. J. Mol. Sci. 2024, 25(23), 13078; https://doi.org/10.3390/ijms252313078 - 5 Dec 2024
Viewed by 2387
Abstract
In the United States, autism spectrum disorder (ASD) affects 1 in 33 children and is characterized by atypical social interactions, communication difficulties, and intense, restricted interests. Microbial dysbiosis in the gastrointestinal (GI) tract is frequently observed in individuals with ASD, potentially contributing to [...] Read more.
In the United States, autism spectrum disorder (ASD) affects 1 in 33 children and is characterized by atypical social interactions, communication difficulties, and intense, restricted interests. Microbial dysbiosis in the gastrointestinal (GI) tract is frequently observed in individuals with ASD, potentially contributing to behavioral manifestations and correlating with worsening severity. Moreover, dysbiosis may contribute to the increased prevalence of GI comorbidities in the ASD population and exacerbate immune dysregulation, further worsening dysbiosis. Over the past 25 years, research on the impact of microbial manipulation on ASD outcomes has gained substantial interest. Various approaches to microbial manipulation have been preclinically and clinically tested, including antibiotic treatment, dietary modifications, prebiotics, probiotics, and fecal microbiota transplantation. Each method has shown varying degrees of success in reducing the severity of ASD behaviors and/or GI symptoms and varying long-term efficacy. In this review, we discuss these microbiome manipulation methods and their outcomes. We also discuss potential microbiome manipulation early in life, as this is a critical period for neurodevelopment. Full article
(This article belongs to the Special Issue Molecular Research in Human Microbiome 2.0)
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