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Fungal-Bacterial Interactions: Importance for Health and Disease

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A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Pathogenesis and Disease Control".

Deadline for manuscript submissions: closed (1 September 2023) | Viewed by 8338

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Special Issue Editor

Dr. Laure Nicolas Annick Ries

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Guest Editor

MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
Interests: Candida albicans; Aspergillus fumigatus; Gram-negative bacteria; fungal cell wall; type 6 secretion system; signal transduction; protein kinases

Special Issue Information

Dear Colleagues,

Fungi are ubiquitous microorganisms that are essential for maintaining animal, plant and soil health. Some fungi, such as Candida albicans, are commensal organisms of the human flora with a predicted evolutionary benefit of training the immune system against other fungal and bacterial diseases. Despite this, some fungal species have evolved into important pathogens, which decimate animal numbers and cause serious infections in human patients. Indeed, opportunistic fungal infections affect over a billion people worldwide, and systemic fungal infections now kill more patients annually than malaria or breast cancer.

In their natural environment, fungi exist within polymicrobial communities, where they share their habitat with a range of other microorganisms, including bacteria. Fungal–bacterial interactions can be contact-dependent or independent, resulting in synergistic, antagonistic or additive interactions. Furthermore, infections with one species can predispose a certain environment to colonisation by another species. Fungal–bacterial interactions are influenced by a range of external factors, such as the status of the immune system, pH, temperature, quorum-sensing molecules, toxins and availability of nutrients. The output of these interactions can have severe consequences, such as an increase in resistance to antimicrobial agents in patients who are already critically ill.

Despite our awareness of these polymicrobial communities and the potential interactions within, our understanding of these interactions is still in its infancy. Particularly, how and when fungal–bacterial interactions occur as well as how they maintain health or cause a shift towards disease is very poorly understood. I therefore would like to invite submissions of studies addressing all aspects of mechanisms underlying fungal bacterial interactions and how these sustain animal health or disease. I expect this Special Issue to significantly contribute to our understanding of the exciting and underexplored topic of the role of fungal–bacterial interactions in animal health and disease.

Dr. Laure Nicolas Annick Ries
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

fungal–bacterial interactions
Gram-positive and Gram-negative bacteria
health and disease
quorum sensing
mycotoxins
synergism, antagonism
immune system
sensing and signalling

Published Papers (5 papers)

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Research

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23 pages, 3826 KiB

Open AccessArticle

The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME^® Model

by Benoît Marsaux, Frédéric Moens, Massimo Marzorati and Tom Van de Wiele

J. Fungi 2023, 9(9), 877; https://doi.org/10.3390/jof9090877 - 26 Aug 2023

Viewed by 1076

Abstract

From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health—both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi–bacteria interactions remains limited. Here, we used the SHIME^® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn’s disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME^®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME^® reactors from Crohn’s disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn’s disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal–bacterial dynamics in the human gut. Full article

(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)

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16 pages, 1208 KiB

Open AccessArticle

In Search for Reasons behind Helicobacter pylori Eradication Failure–Assessment of the Antibiotics Resistance Rate and Co-Existence of Helicobacter pylori with Candida Species

by Ana Bačić, Vladimir Milivojević, Isidora Petković, Dušan Kekić, Ina Gajić, Branislava Medić Brkić, Dušan Popadić, Tomica Milosavljević and Mirjana Rajilić-Stojanović

J. Fungi 2023, 9(3), 328; https://doi.org/10.3390/jof9030328 - 07 Mar 2023

Cited by 2 | Viewed by 1353

Abstract

Helicobacter pylori eradication is characterized by decreasing successful eradication rates. Although treatment failure is primarily associated with resistance to antibiotics, other unknown factors may influence the eradication outcome. This study aimed to assess the presence of the antibiotics resistance genes in H. pylori and the presence of Candida spp., which are proposed to be endosymbiotic hosts of H. pylori, in gastric biopsies of H. pylori-positive patients while simultaneously assessing their relationship. The detection and identification of Candida yeasts and the detection of mutations specific for clarithromycin and fluoroquinolones were performed by using the real-time PCR (RT-PCR) method on DNA extracted from 110 gastric biopsy samples of H. pylori-positive participants. Resistance rate to clarithromycin and fluoroquinolone was 52% and 47%, respectively. Antibiotic resistance was associated with more eradication attempts (p < 0.05). Candida species were detected in nine (8.18%) patients. Candida presence was associated with older age (p < 0.05). A high rate of antibiotic resistance was observed, while Candida presence was scarce, suggesting that endosymbiosis between H. pylori and Candida may not be a major contributing factor to the eradication failure. However, the older age favored Candida gastric mucosa colonization, which could contribute to gastric pathologies and microbiome dysbiosis. Full article

(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)

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17 pages, 4784 KiB

Open AccessArticle

Studying Fungal-Bacterial Relationships in the Human Gut Using an In Vitro Model (TIM-2)

by Evy Maas, John Penders and Koen Venema

J. Fungi 2023, 9(2), 174; https://doi.org/10.3390/jof9020174 - 28 Jan 2023

Cited by 1 | Viewed by 1356

Abstract

The complex microbial community found in the human gut consist of members of multiple kingdoms, among which are bacteria and fungi. Microbiome research mainly focuses on the bacterial part of the microbiota, thereby neglecting interactions that can take place between bacteria and fungi. With the rise of sequencing techniques, the possibilities to study cross-kingdom relationships has expanded. In this study, fungal-bacterial relationships were investigated using the complex, dynamic computer-controlled in vitro model of the colon (TIM-2). Interactions were investigated by disruption of either the bacterial or fungal community by the addition of antibiotics or antifungals to TIM-2, respectively, compared to a control without antimicrobials. The microbial community was analyzed with the use of next generation sequencing of the ITS2 region and the 16S rRNA. Moreover, the production of SCFAs was followed during the interventions. Correlations between fungi and bacteria were calculated to investigate possible cross-kingdom interactions. The experiments showed that no significant differences in alpha-diversity were observed between the treatments with antibiotics and fungicide. For beta-diversity, it could be observed that samples treated with antibiotics clustered together, whereas the samples from the other treatments were more different. Taxonomic classification was done for both bacteria and fungi, but no big shifts were observed after treatments. At the level of individual genera, bacterial genus Akkermansia was shown to be increased after fungicide treatment. SCFAs levels were lowered in samples treated with antifungals. Spearman correlations suggested that cross-kingdom interactions are present in the human gut, and that fungi and bacteria can influence each other. Further research is required to gain more insights in these interactions and their molecular nature and to determine the clinical relevance. Full article

(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)

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12 pages, 1503 KiB

Open AccessArticle

Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals

by Evy Maas, John Penders and Koen Venema

J. Fungi 2023, 9(2), 139; https://doi.org/10.3390/jof9020139 - 19 Jan 2023

Cited by 6 | Viewed by 2178

Abstract

Most studies of the microbiota in the human gut focus on the bacterial part, but increasing information shows that intestinal fungi are also important for maintaining health. This can be either by directly influencing the host or by indirectly influencing the gut bacteria that link to host health. Studies of fungal communities in large cohorts are scarce; therefore, this study aims at obtaining more insight into the mycobiome of healthy individuals and how this mycobiome interacts with the bacterial component of the microbiome. For this purpose, ITS2 and 16S rRNA gene amplicon sequencing was performed on fecal samples from 163 individuals which were available from two separate studies to analyze the fungal and bacterial microbiome, respectively, as well as the cross-kingdom interactions. The results showed a much lower fungal, as compared to bacterial, diversity. Ascomycota and Basidiomycota were the dominant fungal phyla across all the samples, but levels varied enormously between individuals. The ten most abundant fungal genera were Saccharomyces, Candida, Dipodascus, Aureobasidium, Penicillium, Hanseniaspora, Agaricus, Debaryomyces, Aspergillus, and Pichia, and here also extensive inter-individual variation was observed. Correlations were made between bacteria and fungi, and only positive correlations were observed. One of the correlations was between Malassezia restricta and the genus Bacteroides, which have both been previously described as alleviated in IBD. Most of the other correlations found were with fungi that are not known as gut colonizers but originate from food and the environment. To further investigate the importance of the observed correlations found, more research is needed to discriminate between gut colonizers and transient species. Full article

(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)

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Other

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14 pages, 496 KiB

Open AccessSystematic Review

Fungal–Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review

by Farkad Bantun

J. Fungi 2023, 9(6), 598; https://doi.org/10.3390/jof9060598 - 23 May 2023

Cited by 3 | Viewed by 1924

Abstract

This study systematically reviewed fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All articles that exclusively reported the presence of fungal–bacterial co-infections and super-infections among hospitalized COVID-19 patients were included. Seven databases produced 6937 articles as a result of the literature search. Twenty-four articles met the inclusion criteria and were included in the final analysis. The total number of samples across the studies was 10,834, with a total of 1243 (11.5%) patients admitted to the intensive care unit (ICU). Of these patients, 535 underwent mechanical ventilation (4.9%), 2386 (22.0%) were male, and 597 (5.5%) died. Furthermore, hospitalized COVID-19 patients have a somewhat high rate (23.5%) of fungal–bacterial co-infections and super-infections. Moreover, for SARS-CoV-2 patients who have a chest X-ray that suggests a bacterial infection, who require immediate ICU admission, or who have a seriously immunocompromised condition, empiric antibiotic therapy should be taken into consideration. Additionally, the prevalence of co-infections and super-infections among hospitalized COVID-19 patients may have an impact on diagnosis and treatment. It is crucial to check for fungal and bacterial co-infections and super-infections in COVID-19 patients. Full article

(This article belongs to the Special Issue Fungal-Bacterial Interactions: Importance for Health and Disease)

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