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Microorganisms
Special Issues
Oral Microbiomes and Host Health
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Oral Microbiomes and Host Health

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 4227

Special Issue Editor

Dr. Lucinda J. Bessa

E-Mail Website
Guest Editor
Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, 2829-511 Almada, Portugal
Interests: oral microbiome; oral diseases; antimicrobial resistance; biofilms; clinical microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The oral microbiome plays a pivotal role in maintaining health and mediating disease beyond the oral cavity. This complex and dynamic microbial community influences local conditions such as dental caries, periodontitis, and oral mucosal disorders, while also contributing to systemic diseases, including cardiovascular disease, diabetes, respiratory infections, and adverse pregnancy outcomes. Recent advances in high-throughput sequencing and multi-omics are revealing intricate host–microbe and microbe–microbe interactions, uncovering mechanisms of immune modulation, microbial dysbiosis, and inflammatory signaling. This Special Issue invites original research and reviews that explore the composition, function, and clinical implications of the oral microbiome in host diseases. Topics of interest include microbial biomarkers for early disease detection, the impact of oral dysbiosis on systemic health, host genetic and immune factors shaping the oral microbiota, and novel microbiome-targeted therapies. We welcome interdisciplinary contributions that bridge microbiology, immunology, clinical sciences, and bioinformatics to advance our understanding of the oral microbiome’s role in health and disease.

Dr. Lucinda J. Bessa
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 250 words) can be sent to the Editorial Office for assessment.

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

  • oral microbiome
  • oral diseases
  • systemic diseases
  • dysbiosis
  • host–microbe interactions
  • microbial biomarkers

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Published Papers (3 papers)

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Research

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22 pages, 8251 KB  
Article
Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating
by Toru Tamahara, Atsumu Kouketsu, Satoshi Fukase, Pawat Sripodok, Tatsuru Saito, Akiko Ito, Bin Li, Kazuki Kumada, Muneaki Shimada, Masahiro Iikubo, Ritsuko Shimizu, Kensuke Yamauchi and Tsuyoshi Sugiura
Microorganisms 2026, 14(1), 2; https://doi.org/10.3390/microorganisms14010002 - 19 Dec 2025
Cited by 1 | Viewed by 1043
Abstract
The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals [...] Read more.
The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3–V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology. Full article
(This article belongs to the Special Issue Oral Microbiomes and Host Health)
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Review

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12 pages, 934 KB  
Review
Neutrophils at the Crossroads of Oral Microbiome Dysbiosis and Periodontal Disease
by João Viana, Tiago Ferro, Ricardo Pitschieller, Vanessa Machado, Naichuan Su, José João Mendes and João Botelho
Microorganisms 2025, 13(11), 2573; https://doi.org/10.3390/microorganisms13112573 - 11 Nov 2025
Cited by 1 | Viewed by 2299
Abstract
Neutrophils are the most abundant circulating leukocytes and essential components of innate immunity. Through mechanisms such as phagocytosis, reactive oxygen species (ROS) production, degranulation, and neutrophil extracellular trap (NET) formation, they play a crucial role in host defense. However, dysregulated neutrophil responses are [...] Read more.
Neutrophils are the most abundant circulating leukocytes and essential components of innate immunity. Through mechanisms such as phagocytosis, reactive oxygen species (ROS) production, degranulation, and neutrophil extracellular trap (NET) formation, they play a crucial role in host defense. However, dysregulated neutrophil responses are linked to chronic inflammatory conditions, including periodontitis. This review summarizes current evidence on neutrophil biology in periodontal health and disease, focusing on functional mechanisms, recruitment pathways, the influence of dysbiosis, and their potential as biomarkers and therapeutic targets. Neutrophils display a dual role in periodontal tissues: while protecting against microbial invasion, their excessive or impaired activity contributes to tissue destruction. Altered chemotaxis, defective phagocytosis, and uncontrolled NET release perpetuate inflammation and alveolar bone loss. Neutrophil-derived enzymes, including myeloperoxidase, elastase, and matrix metalloproteinases, emerge as promising biomarkers for early diagnosis. In parallel, therapeutic strategies targeting oxidative stress, NET regulation, or neutrophil hyperactivity are being explored to preserve periodontal tissues. Neutrophils are central players in periodontal pathophysiology. Understanding their regulation and interaction with the oral microbiome may enable the development of novel diagnostic and therapeutic approaches, ultimately improving periodontal disease management. Full article
(This article belongs to the Special Issue Oral Microbiomes and Host Health)
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Other

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47 pages, 1874 KB  
Systematic Review
Oral Microbiota and Clinical Outcomes in Allogenic Hematopoietic Stem Cell Transplantation: A Systematic Review
by Jefferson Luiz da Silva, Alexandre Soares Ferreira Junior, Danielle Amanda Niz Alvarez, Larissa da Silva Souza, Luiza Dias Machado, Sarah Cantrell, Nelson Jen An Chao and Gislane Lelis Vilela de Oliveira
Microorganisms 2026, 14(2), 308; https://doi.org/10.3390/microorganisms14020308 - 28 Jan 2026
Viewed by 584
Abstract
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), emerging evidence suggests that the oral microbiota may serve as a predictive biomarker. We conducted a systematic review to provide a critical overview of oral microbiota research in the allo-HSCT setting. We searched PubMed, [...] Read more.
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), emerging evidence suggests that the oral microbiota may serve as a predictive biomarker. We conducted a systematic review to provide a critical overview of oral microbiota research in the allo-HSCT setting. We searched PubMed, Embase, and Web of Science from inception to December 2025 to identify studies assessing the oral microbiota in allo-HSCT settings. We included all articles reporting detailed data on the oral microbiota in this context and conducted a qualitative synthesis. Risk of bias was assessed using the JBI critical appraisal tools. From 8160 initially identified records, 35 studies evaluating the oral microbiota in 1964 allo-HSCT patients were included. Of these, 27 studies (77%) assessed temporal oral microbiota dynamics and reported dysbiosis in the early post-transplantation period, followed by gradual recovery. Additionally, 27 studies (77%) evaluated the prognostic value of the oral microbiota, identifying associations with key clinical outcomes such as oral mucositis, overall survival, and graft-versus-host disease. Finally, substantial methodological heterogeneity was observed across studies, including differences in sampling techniques, sampling timepoints, and analytical strategies. This systematic review highlights the prognostic and therapeutic potential of the oral microbiota in allo-HSCT and underscores the need for standardized methodologies. Full article
(This article belongs to the Special Issue Oral Microbiomes and Host Health)
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