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Gut Mycobiome
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Gut Mycobiome

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 7086

Special Issue Editor

Dr. Mysore V Tejesvi

E-Mail Website
Guest Editor
Department of Ecology and Genetics, University of Oulu, Oulu, Finland
Interests: microbiome; mycobiome; antimicrobials; bacteriome; bacteria–fungal interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will be dedicated to gut mycobiome and there are many distinct types of fungus in the human gut, which all play an important role in the host's health. The term "mycobiome" refers to the community of fungi present in the digestive system and recent advances in sequencing technology and computational biology have enabled us to catalogue its enormous diversity. Despite the fact that research into the gut mycobiome is still in its early stages, some findings have shown that it may play a significant role in host homeostasis and disease development. However, its particular mechanism of action remains mostly unknown and studied. This Special Issue attempts to examine recent breakthroughs in research on the gut mycobiome from many aspects. This includes studying the variety of gut fungus as well as how the gut mycobiome influences host defense and the gut–brain axis. Furthermore, we discussed how diet may impact the gut mycobiome by regulating interactions between fungus and bacteria. The research of the gut mycobiome is fascinating and any new findings are welcome.

Dr. Mysore V. Tejesvi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mycobiome
  • Candida
  • host–fungal interactions
  • fungal–bacterial interations
  • mycobiome and gut brain axis
  • mycobiome and fungal metabolites

Related Special Issue

Published Papers (5 papers)

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Research

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23 pages, 10143 KiB  
Article
Kazachstania pintolopesii in Blood and Intestinal Wall of Macrophage-Depleted Mice with Cecal Ligation and Puncture, the Control of Fungi by Macrophages during Sepsis
by Pratsanee Hiengrach, Ariya Chindamporn and Asada Leelahavanichkul
J. Fungi 2023, 9(12), 1164; https://doi.org/10.3390/jof9121164 - 04 Dec 2023
Viewed by 1338
Abstract
Although macrophage depletion is a possible emerging therapeutic strategy for osteoporosis and melanoma, the lack of macrophage functions can lead to inappropriate microbial control, especially the regulation of intestinal microbiota. Cecal ligation and puncture (CLP) sepsis was performed in regular mice and in [...] Read more.
Although macrophage depletion is a possible emerging therapeutic strategy for osteoporosis and melanoma, the lack of macrophage functions can lead to inappropriate microbial control, especially the regulation of intestinal microbiota. Cecal ligation and puncture (CLP) sepsis was performed in regular mice and in mice with clodronate-induced macrophage depletion. Macrophage depletion significantly increased the mortality and severity of sepsis-CLP mice, partly through the increased fecal Ascomycota, especially Kazachstania pintolopesii, with polymicrobialbacteremia (Klebsiella pneumoniae, Enterococcus faecalis, and Acinetobacter radioresistens). Indeed, macrophage depletion with sepsis facilitated gut dysbiosis that directly affected gut permeability as yeast cells were located and hidden in the colon crypts. To determine the interactions of fungal molecules on bacterial abundance, the heat-kill lysate of fungi (K. pintolopesii and C. albicans) and purified (1→3)-β-d-glucan (BG; a major component of the fungal cell wall) were incubated with bacteria that were isolated from the blood of macrophage-depleted mice. There was enhanced cytokine production of enterocytes (Caco-2) after the incubation of the lysate of K. pintolopesii (isolated from sepsis mice), the lysate of C. albicans (extracted from sepsis patients), and BG, together with bacterial lysate. These data support a possible influence of fungi in worsening sepsis severity. In conclusion, macrophage depletion enhanced K. pintolopesii in feces, causing the overgrowth of fecal pathogenic bacteria and inducing a gut permeability defect that additively worsened sepsis severity. Hence, the fecal fungus could be spontaneously elevated and altered in response to macrophage-depleted therapy, which might be associated with sepsis severity. Full article
(This article belongs to the Special Issue Gut Mycobiome)
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11 pages, 2860 KiB  
Communication
Delivery Mode and Perinatal Antibiotics Influence the Infant Gut Bacteriome and Mycobiome: A Network Analysis
by Mysore V. Tejesvi, Jenni Turunen, Sonja Salmi, Justus Reunanen, Niko Paalanne and Terhi Tapiainen
J. Fungi 2023, 9(7), 718; https://doi.org/10.3390/jof9070718 - 30 Jun 2023
Cited by 1 | Viewed by 777
Abstract
Both exposure to antibiotics at birth and delivery via Caesarean section influence the gut bacteriome’s development in infants. Using 16S rRNA and internal transcribed spacer sequencing on the Ion Torrent platform, we employed network analysis to investigate the bacterial and fungal interkingdom relationships [...] Read more.
Both exposure to antibiotics at birth and delivery via Caesarean section influence the gut bacteriome’s development in infants. Using 16S rRNA and internal transcribed spacer sequencing on the Ion Torrent platform, we employed network analysis to investigate the bacterial and fungal interkingdom relationships in the gut microbiome from birth to age 18 months in a prospective cohort study of 140 infants. The gut microbiome at ages six and 18 months revealed distinctive microbial interactions, including both positive and negative associations between bacterial and fungal genera in the gut ecosystem. Perinatal factors, delivery mode and intrapartum antibiotic exposure affected the associations between bacterial and fungal species. In infants exposed and unexposed to perinatal antibiotics, the gut microbiome formed distinct networks for the bacteriome and mycobiome. The fungi Saccharomyces, Trichosporon, Pezoloma, Cystofilobasidium, Rigidoporus and Fomitopsis were strongly associated with exposure to antibiotics at birth. Hyaloscypha, Trichosporon, Fomitopsis and Vishniacozyma were strongly associated with the control group that was not exposed to antibiotics. Five distinct networks were formed according to delivery mode. The present study confirms that bacteria and fungi clearly interact in the infant gut ecosystem. Furthermore, perinatal factors appear to influence the relationships between bacteria and fungi in the developing gut microbiome. Full article
(This article belongs to the Special Issue Gut Mycobiome)
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8 pages, 928 KiB  
Communication
Fungal Gut Microbiome in Myasthenia Gravis: A Sub-Analysis of the MYBIOM Study
by Hedda Luise Verhasselt, Elakiya Ramakrishnan, Melina Schlag, Julian R Marchesi, Jan Buer, Christoph Kleinschnitz, Tim Hagenacker and Andreas Totzeck
J. Fungi 2023, 9(5), 569; https://doi.org/10.3390/jof9050569 - 13 May 2023
Viewed by 1574
Abstract
An altered gut microbiota is a possible contributing pathogenic factor in myasthenia gravis (MG), an autoimmune neuromuscular disease. However, the significance of the fungal microbiome is an understudied and neglected part of the intestinal microbiome in MG. We performed a sub-analysis of the [...] Read more.
An altered gut microbiota is a possible contributing pathogenic factor in myasthenia gravis (MG), an autoimmune neuromuscular disease. However, the significance of the fungal microbiome is an understudied and neglected part of the intestinal microbiome in MG. We performed a sub-analysis of the MYBIOM study including faecal samples from patients with MG (n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers (n = 12) by sequencing the internal transcribed spacer 2 (ITS2). Fungal reads were obtained in 51 out of 77 samples. No differences were found in alpha-diversity indices computed between the MG, NIND, CIDP and HV groups, indicating an unaltered fungal diversity and structure. Overall, four mould species (Penicillium aurantiogriseum, Mycosphaerella tassiana, Cladosporium ramonetellum and Alternaria betae-kenyensis) and five yeast species (Candida. albicans, Candida. sake, Candida. dubliniensis, Pichia deserticola and Kregervanrija delftensis) were identified. Besides one MG patient with abundant Ca. albicans, no prominent dysbiosis in the MG group of the mycobiome was found. Not all fungal sequences within all groups were successfully assigned, so further sub-analysis was withdrawn, limiting robust conclusions. Full article
(This article belongs to the Special Issue Gut Mycobiome)
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17 pages, 3235 KiB  
Article
Modelling the Gut Fungal-Community in TIM-2 with a Microbiota from Healthy Individuals
by Evy Maas, John Penders and Koen Venema
J. Fungi 2023, 9(1), 104; https://doi.org/10.3390/jof9010104 - 12 Jan 2023
Cited by 2 | Viewed by 1679
Abstract
Most research on the human microbiome focuses on the bacterial component, and this has led to a lack of information about the fungal component (mycobiota) and how this can influence human health, e.g., by modulation through the diet. The validated, dynamic computer-controlled model [...] Read more.
Most research on the human microbiome focuses on the bacterial component, and this has led to a lack of information about the fungal component (mycobiota) and how this can influence human health, e.g., by modulation through the diet. The validated, dynamic computer-controlled model of the colon (TIM-2) is an in vitro model to study the microbiome and how this is influenced by interventions such as diet. In this study, it was used to the study the gut fungal-community. This was done in combination with next-generation sequencing of the ITS2 region for fungi and 16S rRNA for bacteria. Different dietary interventions (control diet (SIEM), high-carbohydrate, high-protein, glucose as a carbon source) were performed, to see if diet could shape the mycobiome. The mycobiome was investigated after the adaptation period, and throughout the intervention period which lasted 72 h, and samples were taken every 24 h. The fungal community showed low diversity and a greater variability when compared to bacteria. The mycobiome was affected most in the first hours of the adaptation period. Taxonomic classification showed that at the phylum-level Ascomycota and Basidiomycota dominated, while Agaricus, Aspergillus, Candida, Penicillum, Malassezia, Saccharomyces, Aureobasidium, Mycosphaerella, Mucor and Clavispora were the most abundant genera. During the intervention period, it was shown that the change of diet could influence the diversity. Clustering of samples for different time points was analyzed using Bray–Curtis dissimilarities. Samples of t0 clustered together, and samples of all other time points clustered together. The Bray–Curtis-dissimilarity analysis also showed that for the different dietary interventions, samples treated with glucose clustered together and were different from the other groups (p < 0.05, PERMANOVA). Taxonomic classification showed that the genera Alternaria, Thanatephorus, Candida and Dekkera differentially changed for the various diet groups (p < 0.05, Kruskal–Wallis). These results show that the mycobiota could be modelled in TIM-2; however, the low diversity and high variability make studying fungal, as compared to bacterial, communities, much more challenging. Future research should focus on the optimization of the stability of the fungal community to increase the strength of the results. Full article
(This article belongs to the Special Issue Gut Mycobiome)
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Review

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15 pages, 2360 KiB  
Review
Gut Mycobiome and Asthma
by Amjad N. Kanj and Joseph H. Skalski
J. Fungi 2024, 10(3), 192; https://doi.org/10.3390/jof10030192 - 01 Mar 2024
Viewed by 1161
Abstract
This review explores the ‘gut–lung axis’ in asthma with a focus on commensal fungal organisms. We explore how changes to the intestinal commensal fungal community composition alter lung immune function. We comprehensively review available studies that have profiled the composition of the gut [...] Read more.
This review explores the ‘gut–lung axis’ in asthma with a focus on commensal fungal organisms. We explore how changes to the intestinal commensal fungal community composition alter lung immune function. We comprehensively review available studies that have profiled the composition of the gut mycobiome in adults and children with asthma, and discuss mechanisms of gut–lung interactions that have been described in animal models of asthma. Studies indicate that intestinal fungal dysbiosis, such as an increased abundance of certain fungi like Candida, can elevate the risk of asthma in children and exacerbate it in adults. This effect is mediated through various pathways: the host immune system’s sensing of dysbiosis via C-type lectin receptors (e.g., Dectin-2), the impact of pro-inflammatory fungal metabolites (e.g., 12,13-diHOME, prostaglandin E2), and the role of lung immune cells (e.g., group 2 innate lymphoid cells [ILC2], M2 macrophages). We also describe strategies for modulating the gut mycobiome as potential therapies for severe asthma. The review concludes by emphasizing the necessity for further research into the role of the gut mycobiome in asthma to deepen our understanding of these complex interactions. Full article
(This article belongs to the Special Issue Gut Mycobiome)
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