Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization

Abstract

The fungal component of the intestinal microbiota of eight healthy subjects was studied over 12 months using metagenome survey and culture-based approaches. Aspergillus , Candida , Debaryomyces , Malassezia , Penicillium , Pichia , and Saccharomyces were the most recurrent and/or dominant fungal genera, according to metagenomic analysis. The biodiversity of fungal communities was lower and characterized by greater unevenness, when compared to bacterial microbiome. The dissimilarities both among subjects and over the time within the same subject suggested that most of the fungi passed through the gastro-intestinal tract (GIT) without becoming stable colonizers. Certain genera, such as Aspergillus and Penicillium , were isolated in a minority of cases, although they recurred abundantly and frequently in the metagenomics survey, likely being environmental or food-borne fungi that do not inhabit the GIT. Candida genus was recurrently detected. Candida albicans isolates dominated among the cultivable mycobiota and longitudinally persisted, likely as commensals inhabiting the intestine or regularly reaching it from Candida -colonized districts, such as the oral cavity. Other putative colonizers belonged to Candida zeylanoides , Geotrichum candidum , and Rhodotorula mucilaginosa , with persisting biotypes being identified. Phenotyping of fungal isolates indicated that C. albicans adhered to human epithelial cells more efficiently and produced greater amounts of biofilm in vitro than non- albicans Candida (NAC) and non- Candida fungi (NCF). The C. albicans isolates also induced the highest release of HBD-2 by human epithelial cells, further differing from NAC and NCF. Nine representative isolates were administered to mice to evaluate the ability to colonize the intestine. Only two out of three C. albicans strains persisted in stools of animals 2 weeks after the end of the oral administration, whereas NAC and NCF did not. These results confirm the allochthonous nature of most the intestinal fungi, while C. albicans appears to be commonly involved in stable colonization. A combination of specific genetic features in the microbe and in the host likely allow colonization from fungi normally present solely as passengers. It remains to be established if other species identified as potential colonizers, in addition to Candida , are true inhabitants of the GIT or rather reach the intestine spreading from other body districts.

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

“…Such association between feed and fungal gut might also apply for the plant pathogens Ustilago hordei and Mycosphaerella tassiana, found in about 3% of the animals. Former results are in agreement with previous reports on humans and nonhuman primates (Hallen-Adams et al 2015;Mann et al 2019;Nash et al 2017;Raimondi et al 2019), and suggest that, differently to pig gut prokaryotes (Xiao et al 2016), the pig gut mycobiome may lack a stable core. Consequently, it is expected that a large proportion of the fungi detected in pig fecal samples may be transients from dietary or environmental origin.…”

The gut mycobiota of rural and urban individuals is shaped by geography

“…The second reason for the observed differences has been attributed to differences in cohort characteristics, such as diet and/or geographical location. Strati (2016) and Raimondi's (2019) investigating cohorts in Italy, detected same dominant fungal genera [58,61], and the investigation of cohorts in two different states in the USA observed different results [6,45]. We used ITS1 and ITS4 in this study and found that the genera Pichia, Candida and Cladosporium dominated the urban cohort, whereas genera Pichia, Candida and Aspergillus dominated the rural cohort.…”

“…A review of the literature suggest that C. albicans carriage in healthy individuals ranges from 30-60% [68] and that living mammals are considered a niche for these species as they are not found in signi cant concentrations in soil, food or air [69,70]. reported that C. albicans was frequently detected and dominated the cultivable mycobiota of different faecal samples [61].…”

“…We provide the rst insights regarding the drivers of mycobiome community structure and potential biomarkers speci c to individuals from urban and rural locations. Previous studies of the gut mycobiome have primarily investigated small groups with fewer than 20 individuals [25,30,31] with very few studies investigating larger groups [6,7]. This study represents the rst analysis of the faecal mycobiota in a large group of healthy sub-Saharan individuals (100 volunteers).…”

Colonization with the commensal fungusCandida albicansperturbs the gut-brain axis through dysregulation of endocannabinoid signaling

“…Candida albicans is a commensal fungus that colonizes the GI tract of ~60% of the human population (Raimondi et al, 2019). Although a major colonizer of humans, its role as a commensal microbe is largely uncharacterized.…”