The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions

Galloway-Peña, Jessica; Kontoyiannis, Dimitrios P.

doi:10.1371/journal.ppat.1008353

Cited by 25 publications

(19 citation statements)

References 65 publications

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“…In the case of eukaryotes, the predominance of fungi in the eukaryotic microbiome composition (Fig. 1 ) agrees with previous descriptions, as these organisms are the main component of the eukaryotic intestinal microbiota 27 – 29 . However, the absence of differences between the studied groups contrasts with previous reports in which an increased ratio between Basidiomycota/Ascomycota was associated with the pathogenesis of colorectal cancer and inflammatory bowel disease 30 .…”

Section: Discussionsupporting

confidence: 91%

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

Herrera

Vega

Patarroyo

et al. 2021

Sci Rep

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The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Studies showed the impact of CDI on bacterial communities and the importance of some genera and species in recovering from and preventing infection. However, most studies have overlooked important components of the intestinal ecosystem, such as eukaryotes and archaea. We investigated the bacterial, archaea, and eukaryotic intestinal microbiota of patients with health-care-facility- or community-onset (HCFO and CO, respectively) diarrhea who were positive or negative for CDI. The CDI-positive groups (CO/+, HCFO/+) showed an increase in microorganisms belonging to Bacteroidetes, Firmicutes, Proteobacteria, Ascomycota, and Opalinata compared with the CDI-negative groups (CO/−, HCFO/−). Patients with intrahospital-acquired diarrhea (HCFO/+, HCFO/−) showed a marked decrease in bacteria beneficial to the intestine, and there was evidence of increased Archaea and Candida and Malassezia species compared with the CO groups (CO/+, CO/−). Characteristic microbiota biomarkers were established for each group. Finally, correlations between bacteria and eukaryotes indicated interactions among the different kingdoms making up the intestinal ecosystem. We showed the impact of CDI on microbiota and how it varies with where the infection is acquired, being intrahospital-acquired diarrhea one of the most influential factors in the modulation of bacterial, archaea, and eukaryotic populations. We also highlight interactions between the different kingdoms of the intestinal ecosystem, which need to be evaluated to improve our understanding of CDI pathophysiology.

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Section: Discussionsupporting

confidence: 91%

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

Herrera

Vega

Patarroyo

et al. 2021

Sci Rep

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“…Usually, studies focus on analyzing mycobiome in a specific subject or when studying a bacteria-fungi consortium. Therefore, identification techniques must be improved so that fungal taxonomic classification can become more reliable [41].…”

Section: Introductionmentioning

confidence: 99%

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Sodré

Rodrigues

Vieira

et al. 2020

Journal of Oral Microbiology

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Introduction: Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis. Methods: A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients. Results: 21 studies were included and the most identified species was Candida. The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21). Conclusions: Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.

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“…Functional analysis indicates that both the AGAu and non-AGAu groups show a great degree of metabolic plasticity (Fig. 3a) 56,59,60,129 . The only functional difference seen between groups was with CAZymes.…”

Section: Discussionmentioning

confidence: 99%

“…To perform a global functional analysis of Candida species, we collected 49 publicly available genomes of different Candida strains covering 13 different species (Supplementary Table 1). We selected species based on their clinical importance and abundance within the human mycobiome [56][57][58][59][60] . All 49 Candida strains were isolated from different body sites from people in different geographical locations (Fig.…”

Section: Development Of Biofung Database and Functional Annotation Of Candida Proteinencoding Genesmentioning

confidence: 99%

Integrative functional analysis uncovers metabolic differences between Candida species

Begum

Lee

Pellón

et al. 2021

Preprint

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Candida species are a dominant constituent of the human mycobiome and a better understanding of their metabolism from a fungal perspective can provide key insights into their ability to cause pathogenesis. Here, we have developed the BioFung database a fungal specific tool for functional annotation using the KEGG database that provides an efficient method for annotation of protein-encoding gene. Analysis of carbohydrate-active enzyme (CAZymes) and BioFung, uncovered core and accessory features across Candida species demonstrating plasticity, adaptation to the environment and acquired features. Integerative functional analysis revealed that all Candida species can employ amino acid metabolism. However, metabolomics revealed that only a specific cluster of species (AGAu species; C. albicans, C. glabrata and C. auris) utilised amino acid metabolism. We identified critical metabolic pathways in the AGAu clusters with biomarkers and antifungal target potential in the CAZyme profile, polyamine, choline and fatty acid biosynthesis pathways. This study, combining genomic analysis, metabolomics and gene expression validation, highlights the metabolic diversity within AGAu species that underlies their remarkable ability to dominate the mycobiome and cause disease.

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The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions

Cited by 25 publications

References 65 publications

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Integrative functional analysis uncovers metabolic differences between Candida species

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