Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths
Open accessAbstract
Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.
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Results obtained from the small number of studies performed using shotgun metagenomic sequencing suggest that the oral virome may be as significant in disease pathogenesis as the oral bacteriome.
“Results obtained from the small number of studies performed using shotgun metagenomic sequencing suggest that the oral virome may be as significant in disease pathogenesis as the oral bacteriome.87, 88”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [88]
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Current Knowledge about the Impact of Microgravity on Gene Regulation
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Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation
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- Authors
- Vemuri, R., Shankar, E. M., Chieppa, M., Eri, R., & Kavanagh, K.
- Affiliations
- Wake Forest University Health Sciences (US)
- Central University of Tamil Nadu (IN)
- Gastroenterology Hospital "Saverio de Bellis" (IT)
- University of Tasmania (AU)
- Corresponding author
- Vemuri, Ravichandra
- Venue
- Microorganisms
- Publisher
- MDPI AG
- Published
- 2020-03-28
- Volume
- 8
- Issue
- 4
- Pages
- 483
- ISSN
- 2076-2607 (ISSN-L)
- PMC
- PMC7232386
- OpenAlex
- W3013399474
- Cited by
- 162
- References
- 154
- Citations by year
- 2026: 16 · 2025: 28 · 2024: 31 · 2023: 28 · 2022: 24 · 2021: 21 · 2020: 13 · 2019: 1
- FWCI
- 2.06
- Type
- journal article
- Language
- en
- Open access
- gold
- dx.doi.org
- Licence
- Locations
- Microorganisms (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UTAS Research Repository (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Figshare (submittedVersion)
- AIRUS (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, virome, fungal communities, archaeome, helminths, gut viruses, gut fungi, gut archaea, bacteriome, host-microbe interactions, prebiotics, probiotics, synbiotics, metagenomics, human health
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