Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities

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Abstract

Bacteria, viruses, protozoa, and fungi establish a complex ecosystem in the gut. Like other microbiota, gut mycobiota plays an indispensable role in modulating intestinal physiology. Notably, the most striking characteristics of intestinal fungi are their extraintestinal functions. Here, we provide a comprehensive review of the importance of gut fungi in the regulation of intestinal, pulmonary, hepatic, renal, pancreatic, and brain functions, and we present possible opportunities for the application of gut mycobiota to alleviate/treat human diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40168-021-01024-x.

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Most cited references 189

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A human gut microbial gene catalogue established by metagenomic sequencing.

Junjie Qin, Ruiqiang Li, Jeroen Raes … (2010)

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

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Neutrophil extracellular traps in immunity and disease

Venizelos Papayannopoulos (2017)

Neutrophils are innate immune phagocytes that have a central role in immune defence. Our understanding of the role of neutrophils in pathogen clearance, immune regulation and disease pathology has advanced dramatically in recent years. Web-like chromatin structures known as neutrophil extracellular traps (NETs) have been at the forefront of this renewed interest in neutrophil biology. The identification of molecules that modulate the release of NETs has helped to refine our view of the role of NETs in immune protection, inflammatory and autoimmune diseases and cancer. Here, I discuss the key findings and concepts that have thus far shaped the field of NET biology.

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C. L. Schoch, K. A. Seifert, S. Huhndorf … (2012)

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

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Author and article information

Contributors

Xiaoyan Wu: xiaoyanwu2020@126.com

Yaoyao Xia: yaoyaoxia2018@126.com

Fang He: hefang2017@sina.com

Congrui Zhu: congruiz@ksu.edu

Wenkai Ren:

ORCID: http://orcid.org/0000-0002-8145-8907

renwenkai19@scau.edu.cn

Journal

Journal ID (nlm-ta): Microbiome

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: BioMed Central (London )

ISSN (Electronic): 2049-2618

Publication date (Electronic): 14 March 2021

Publication date PMC-release: 14 March 2021

Publication date Collection: 2021

Volume: 9

Electronic Location Identifier: 60

Affiliations

[1 ]GRID grid.20561.30, ISNI 0000 0000 9546 5767, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, , South China Agricultural University, ; Guangzhou, 510642 China

[2 ]GRID grid.263906.8, College of Animal Science and Technology, , Southwest University, ; Chongqing, 400716 China

[3 ]GRID grid.36567.31, ISNI 0000 0001 0737 1259, College of Veterinary Medicine, , Kansas State University, ; Manhattan, KS USA

Author information

Wenkai Ren http://orcid.org/0000-0002-8145-8907

Article

Publisher ID: 1024

DOI: 10.1186/s40168-021-01024-x

PMC ID: 7958491

PubMed ID: 33715629

SO-VID: a96679d5-ada2-4ab0-9fd0-24f9e205d329

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 13 November 2020

Date accepted : 4 February 2021

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 31922079, 31872365, and 31790411

Award Recipient : Wenkai Ren

Funded by: Guangdong Basic and Applied Basic Research Foundation

Award ID: 2019B1515210002

Award Recipient : Wenkai Ren

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Keywords: intestinal mycobiota,intestinal immunity,gut-liver axis,gut-lung axis,gut-brain axis

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Keywords: intestinal mycobiota, intestinal immunity, gut-liver axis, gut-lung axis, gut-brain axis

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities

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Abstract

Supplementary Information

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Most cited references 189

A human gut microbial gene catalogue established by metagenomic sequencing.

Neutrophil extracellular traps in immunity and disease

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

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