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Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths

1
Department of Pathology, Section of Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
2
School of Basic and Applied Sciences, Central University of Tamil Nadu, Thiruvarur 610005, India
3
National Institute of Gastroenterology “S. de Bellis”, Research Hospital, 70013 Castellana Grotte (Bari), Italy
4
School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston 7248, Australia
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(4), 483; https://doi.org/10.3390/microorganisms8040483
Received: 6 March 2020 / Revised: 26 March 2020 / Accepted: 26 March 2020 / Published: 28 March 2020
(This article belongs to the Special Issue Gut Microbiome and Aging)
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. View Full-Text
Keywords: gut microbiota; virome; fecal virome transplants; mycobiome; archaeome; helminths gut microbiota; virome; fecal virome transplants; mycobiome; archaeome; helminths
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MDPI and ACS Style

Vemuri, R.; Shankar, E.M.; Chieppa, M.; Eri, R.; Kavanagh, K. Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms 2020, 8, 483. https://doi.org/10.3390/microorganisms8040483

AMA Style

Vemuri R, Shankar EM, Chieppa M, Eri R, Kavanagh K. Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms. 2020; 8(4):483. https://doi.org/10.3390/microorganisms8040483

Chicago/Turabian Style

Vemuri, Ravichandra; Shankar, Esaki M.; Chieppa, Marcello; Eri, Rajaraman; Kavanagh, Kylie. 2020. "Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths" Microorganisms 8, no. 4: 483. https://doi.org/10.3390/microorganisms8040483

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