Microbiomes in Human Health and Diseases

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

Deadline for manuscript submissions: 31 October 2026 | Viewed by 2976

Special Issue Editor


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Guest Editor
1. Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, 0372 Oslo, Norway
2. Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden
Interests: genomics and metagenomics; microbiome; infectious diseases; Shiga toxin-producing Escherichia coli
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Special Issue Information

Dear Colleagues,

The human microbiome—the collective microorganisms inhabiting in and on the human body and their genes/products—is a pivotal determinant of health and disease through various mechanisms, including influencing digestion, immunity, metabolism, production of hormones, neurotransmitters, etc. Consequently, the human microbiome has been linked to diverse conditions, including metabolic, gastrointestinal, autoimmune, neurological, and infectious diseases. However, significant knowledge gaps persist in the field. Current research predominantly focuses on bacterial communities (bacteriome), particularly in the gut, while microbiome in other niches (e.g., skin, respiratory tract, and urogenital) and other microbial kingdoms beyond bacteria (e.g., viruses, archaea, and fungi) remain understudied. Furthermore, the mechanisms of microbial communications across body sites and their integrated roles in host physiology are poorly understood so far.

The aim of this Special Issue is to showcase cutting-edge research advancing our understanding of how resident microbial communities influence host physiological functions and contribute to health and disease pathogenesis. We welcome original research and reviews providing insights into the microbiome and its role in human health and disease conditions, with emphasis on host–microbiome interactions, multi-kingdom microbial dynamics, and cross-niche microbiome communications, highlighting the translational potential for microbiome-based diagnostics and therapeutics.

Dr. Xiangning Bai
Guest Editor

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Keywords

  • microbiome
  • health and disease
  • immunity
  • metabolism
  • microbiome-directed diagnostics and therapeutics

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Published Papers (2 papers)

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Review

18 pages, 642 KB  
Review
Tobacco-Induced Oral Dysbiosis and Microbial Shifts: A Narrative Review of Their Role in Systemic Inflammation and Disease
by Glenda M. Davison, Tandi Matsha, Shanel Raghubeer, Stanton Hector, Saarah Davids and Yvonne Prince
Microorganisms 2026, 14(5), 1104; https://doi.org/10.3390/microorganisms14051104 - 13 May 2026
Viewed by 234
Abstract
The oral cavity is home to a diverse community of microbiota comprising bacteria, viruses, protozoa, and fungi. These microorganisms inhabit several oral niches and play a significant role in supporting both oral and systemic health. The fine balance between the microbial communities can [...] Read more.
The oral cavity is home to a diverse community of microbiota comprising bacteria, viruses, protozoa, and fungi. These microorganisms inhabit several oral niches and play a significant role in supporting both oral and systemic health. The fine balance between the microbial communities can be influenced by genetics and environmental factors, potentially leading to dysbiosis. Alterations in the oral microbiota have been implicated in periodontitis, chronic inflammation, and systemic disease. Tobacco has been identified as a major player in altering the oral microenvironment and disturbing the balance between potentially pathogenic and beneficial commensals. The resulting dysbiosis promotes inflammation and assists in the passage of pathogenic microorganisms into the blood system. This narrative review examines current evidence linking the use of tobacco with the dominance of pathogenic oral bacteria and a dysfunctional immune response. We explore how the chemicals and toxins in cigarettes promote a reduction in oxygen and cause changes in the abundance of anaerobic bacteria. After discussing the mechanistic pathways leading to periodontitis and the entry of microorganisms into the circulation, the review will interrogate previous studies and identify opportunities and priorities for future research. Full article
(This article belongs to the Special Issue Microbiomes in Human Health and Diseases)
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Graphical abstract

22 pages, 1294 KB  
Review
Early-Life Gut Microbiota: Education of the Immune System and Links to Autoimmune Diseases
by Pleun de Groen, Samantha C. Gouw, Nordin M. J. Hanssen, Max Nieuwdorp and Elena Rampanelli
Microorganisms 2026, 14(1), 210; https://doi.org/10.3390/microorganisms14010210 - 16 Jan 2026
Cited by 5 | Viewed by 2376
Abstract
Early life is a critical window for immune system development, during which the gut microbiome shapes innate immunity, antigen presentation, and adaptive immune maturation. Disruptions in microbial colonization—driven by factors such as cesarean delivery, antibiotic exposure, and formula feeding—deplete beneficial early-life taxa (e.g., [...] Read more.
Early life is a critical window for immune system development, during which the gut microbiome shapes innate immunity, antigen presentation, and adaptive immune maturation. Disruptions in microbial colonization—driven by factors such as cesarean delivery, antibiotic exposure, and formula feeding—deplete beneficial early-life taxa (e.g., Bifidobacterium, Bacteroides, and Enterococcus) and impair key microbial functions, including short-chain fatty acid (SCFA) production by these keystone species, alongside regulatory T cell induction. These dysbiosis patterns are associated with an increased risk of pediatric autoimmune diseases, notably type 1 diabetes, inflammatory bowel disease, celiac disease, and juvenile idiopathic arthritis. This review synthesizes current evidence on how the early-life microbiota influences immune maturation, with potential effects on the development of autoimmune diseases later in life. We specifically focus on human observational and intervention studies, where treatments with probiotics, synbiotics, vaginal microbial transfer, or maternal fecal microbiota transplantations have been shown to partially restore a disrupted microbiome. While restoration of the gut microbiome composition and function is the main reported outcome of these studies, to date, no reports have disclosed direct prevention of autoimmune disease development by targeting the early-life gut microbiome. In this regard, a better understanding of the early-life microbiome–immune axis is essential for developing targeted preventive strategies. Future research must prioritize longitudinal evaluation of autoimmune outcomes after microbiome modulation to reduce the burden of chronic immune-mediated diseases. Full article
(This article belongs to the Special Issue Microbiomes in Human Health and Diseases)
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