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Cited by 60Gut microbiota and healthOral microbiology and periodontitis researchBacteriophages and microbial interactions

The DOI matches its Crossref record; 224 of the 224 references it cites were found in a registry or an index.

The human microbiome in clinical translation: from bench to bedside

Open access
Bautista, Jhommara, Echeverría, Carolina E., Maldonado-Noboa, Iván, Ojeda-Mosquera, Sofía, Hidalgo-Tinoco, Camila, López-Cortés, Andrés·2025·Frontiers in Microbiology
DOI 10.3389/fmicb.2025.1632435PMC PMC12479421
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Abstract

The human microbiome, once regarded as a passive passenger, is now recognized as a dynamic and essential determinant of human physiology, shaping immunity, metabolism, neurodevelopment, and therapeutic responsiveness across the lifespan. Advances in multi-omic technologies, experimental models, and computational approaches have revealed mechanistic insights into how microbial communities modulate host systems across diverse body sites, including the gut, skin, lungs, oral cavity, and reproductive tract. The clinical translation of this knowledge has begun to redefine early-life programming, cardiometabolic regulation, immune homeostasis, neuropsychiatric resilience, and cancer therapy response. Innovative strategies such as phage therapy, live biotherapeutics, precision nutrition, and microbiota transplantation illustrate the therapeutic potential of harnessing microbial functions to prevent or treat disease. In parallel, large-scale initiatives cataloging the microbiome of underexplored niches, such as the vagina and skin, are advancing health equity by broadening representation in microbial reference datasets. Yet significant challenges persist, including interindividual variability, incomplete functional annotation of microbial “dark matter,” and the absence of validated biomarkers. Addressing these gaps requires standardized methodologies, harmonized regulatory frameworks, and longitudinal studies across diverse populations. This review outlines the progress and remaining hurdles in translating microbiome science into clinical practice and concludes that the microbiome now stands at the forefront of a paradigm shift, transforming concepts of disease etiology, therapeutic design, and the future of individualized medicine.

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Figure 1 The human microbiome. Organ-specific healthy and pathogenic taxa relevant to clinical translation.
Figure 1 The human microbiome. Organ-specific healthy and pathogenic taxa relevant to clinical translation.CC BY · PubMed Central
Figure 2 Landscape of phase 2 and 3 clinical trials evaluating microbiome-based therapeutics. This Sankey plot visualizes the translational flow of microbiome-based therapies across key domains: therapeutic agent, target disease, modality of intervention, delivery route, clinical trial phase and number. Each stream illustrates the relationship between components, emphasizing the diversity of clinical applications and development strategies within the microbiome field. Data include 22 active trials representing interventions in gastrointestinal, metabolic, neurologic, oncologic, dermatologic, and pediatric disorders. CDI: Clostridioides difficile infection; GI-aGvHD: Gastrointestinal acute graft-versus-host disease; Allo-HSCT: Allogeneic hematopoietic stem cell transplantation; GERD: Gastroesophageal reflux disease; IBS-D: Irritable bowel syndrome with diarrhea; LARS: Low anterior resection syndrome; Pooled FMT: Pooled fecal microbiota transplant; GM strain: Genetically modified microbial strain. This was designed through the SankeyMATIC code available at github.com/nowthis/sankeymatic.
Figure 2 Landscape of phase 2 and 3 clinical trials evaluating microbiome-based therapeutics. This Sankey plot visualizes the translational flow of microbiome-based therapies across key domains: therapeutic agent, target disease, modality of intervention, delivery route, clinical trial phase and number. Each stream illustrates the relationship between components, emphasizing the diversity of clinical applications and development strategies within the microbiome field. Data include 22 active trials representing interventions in gastrointestinal, metabolic, neurologic, oncologic, dermatologic, and pediatric disorders. CDI: Clostridioides difficile infection; GI-aGvHD: Gastrointestinal acute graft-versus-host disease; Allo-HSCT: Allogeneic hematopoietic stem cell transplantation; GERD: Gastroesophageal reflux disease; IBS-D: Irritable bowel syndrome with diarrhea; LARS: Low anterior resection syndrome; Pooled FMT: Pooled fecal microbiota transplant; GM strain: Genetically modified microbial strain. This was designed through the SankeyMATIC code available at github.com/nowthis/sankeymatic.CC BY · PubMed Central

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Metadata

Authors
Bautista, J., Echeverría, C. E., Maldonado-Noboa, I., Ojeda-Mosquera, S., Hidalgo-Tinoco, C., & López-Cortés, A.
Affiliations
  • Universidad de Las Américas (EC)
  • New York University (US)
ORCID
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2025-09-16
Volume
16
Pages
1632435-1632435
ISSN
1664-302X (ISSN-L)
DOI
10.3389/fmicb.2025.1632435
PMC
PMC12479421
OpenAlex
W4414253972
Cited by
55
References
224
Citations by year
2026: 47 · 2025: 8
FWCI
4.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Frontiers in Microbiology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Keywords
human microbiome, clinical translation, microbiota-based therapy, phage therapy, live biotherapeutic products, personalized nutrition, microbiota transplantation, gut microbiota, skin microbiome, vaginal microbiota, early life programming, immune homeostasis, cancer therapy response, interindividual variability, microbial dark matter, health equity, regulatory framework, personalized medicine

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