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The Gut Mycobiome of the Human Microbiome Project Healthy Cohort Andrea K

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The Gut Mycobiome of the Human Microbiome Project Healthy Cohort Andrea K Nash et al. Microbiome (2017) 5:153 DOI 10.1186/s40168-017-0373-4 RESEARCH Open Access The gut mycobiome of the Human Microbiome Project healthy cohort Andrea K. Nash1, Thomas A. Auchtung1, Matthew C. Wong1, Daniel P. Smith1, Jonathan R. Gesell1, Matthew C. Ross1, Christopher J. Stewart1, Ginger A. Metcalf2, Donna M. Muzny2, Richard A. Gibbs2, Nadim J. Ajami1 and Joseph F. Petrosino1* Abstract Background: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Results: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia,andCandida,withS. cerevisiae, M. restricta,andC. albicans operational taxonomic units (OTUs) present in 96. 8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta,andC. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Conclusions: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia,andCandida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples. Keywords: Fungi, Microbiota, Microbiome, Fungal microbiome, Fecal microbiome, HMP, ITS2, There was a high degree o Spacer, Metagenomics * Correspondence: [email protected] 1Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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. Nash et al. Microbiome (2017) 5:153 Page 2 of 13 Background donor stool, the relative abundance of these core OTUs Fungi are ubiquitous in our environment and are known were found to vary nearly 5000-fold [18]. This suggests to participate in natural and industrial processes includ- that what constitutes a healthy gut microbiome can be ing production of antibiotics, bread, cheese, and alco- very different among individuals. However, the myco- holic beverages; decomposing natural debris; and biome was not investigated in initial HMP studies. providing nutrients to plants in soil. Of the estimated Using DNA previously extracted from longitudinally 5.1 million different species of fungi in the world, only collected stool samples (two to three samples per volun- around 300 cause disease regularly in humans [1, 2]. teer, collected over an approximately 1-year period) from These relatively few fungi are responsible for millions of HMP volunteers recruited at Baylor College of Medicine infections each year, from superficial infections of the (Houston, TX), we characterized the “healthy” human skin and nails, to invasive infections of the lungs, blood, gut mycobiome. Internal Transcribed Spacer 2 (ITS2) se- and brain [3]. However, with the high prevalence of quencing confirmed that fungal diversity in the gut is low. fungi in the environment, it is not surprising that fungi Saccharomyces was found to be the most abundant fungal are also found on and in our bodies as constituents of genus in healthy human stool, followed by Malassezia and the human microbiome. The fungal microbiome, known Candida. These three genera were present in at least one as the mycobiome, is an understudied component of the sample from nearly every volunteer in this study, although human microbiome. Although the mycobiota make up a the mycobiome was highly variable within and between small proportion of the entire human microbiome [4], individuals. Sequencing of the 18S rRNA gene revealed culture-independent methods utilizing high-throughput similar results to the ITS2 sequencing, but included sequencing techniques have allowed scientists to begin the addition of the non-fungal microbial eukaryote to uncover the identity of our fungal commensals and (microeukaryote) Blastocystis as a prominent eukaryotic determine their role in human health and disease. member of the gut microbiome. Additionally, fungi identi- Fungi have been detected in the guts of several mam- fied in metagenomic sequences from HMP stool samples mals, including humans, mice, rats, pigs, and many rumin- agreed with the ITS2 sequencing results; however, deeper ant and non-ruminant herbivores [5–7]. Characterization metagenomic sequencing is likely required to fully survey of C57BL/6 mice feces revealed greater than 97% of fungal the fungal constituents of the gut. It is important to sequences belonged to only 10 fungal species, identifying understand what constitutes a healthy human gut myco- Candida tropicalis and Saccharomyces cerevisiae as the biome as this allows for further understanding of fungal- most abundant commensal fungi [5]. In humans, fungi bacterial and fungal-host interactions, which may have been found to colonize the gut shortly after birth [8]. contribute to human health and disease. In a study investigating correlations of archaea and fungi with diet, volunteers had an abundance of Candida and Saccharomyces species in their stool, with high Candida Results abundance associated with recent consumption of carbo- Fungal diversity and composition in healthy human stool hydrates [9]. Fungi have been implicated in the exacerba- To investigate gut fungal diversity and composition, a tion of several human diseases, including inflammatory total of 333 HMP stool sample microbial DNA extrac- bowel disease, graft versus host disease, Hirschsprung- tions were retrieved and underwent ITS2 amplification associated enterocolitis, colorectal cancer, and advanced and sequencing. After rarefaction, the number of sam- progression of hepatitis B virus infections [5, 10–15]. The ples analyzed was reduced to 317 (from 147 volunteers), confirmed presence of fungi as a part of the human micro- with each sample normalized to 1954 sequences. Missing biome, as well as their potential role as contributors to taxonomic information in databases resulted in many health and disease, highlight the need to characterize the fungal OTUs being classified as “Fungi sp.” These OTUs healthy human mycobiome more deeply. Knowledge of a constituted 17% of the total OTUs. Altogether, 701 healthy mycobiome will aid in research identifying disease- fungal OTUs were detected in the sample set, capturing contributing fungal species and better define fungal- 247 named genera. bacterial relationships that are important for health. Observed OTUs within samples ranged from 2 to 92 One of the initial goals of the Human Microbiome (Table 1). The Shannon diversity index, which measures Project (HMP) was to characterize the “healthy” human evenness and richness of communities within a sample, var- microbiome as a baseline for reference and comparison ied between 0.004 and 2.94, indicating low alpha diversity studies [16]. Microbial communities in HMP healthy for most samples (Table 1). There was a significant differ- donor stool samples were largely comprised of bacteria ence between bacterial and fungal communities in both the from the Bacteroidetes and Firmicutes phyla, but varied number of observed OTUs and the Shannon diversity greatly between volunteers [17]. Although core oper- index values (Fig. 1a), supporting previous studies suggest- ational taxonomic units (OTUs) were identified in HMP ing fungal diversity is lower than that of bacteria in a Nash et al. Microbiome (2017) 5:153 Page 3 of 13 Table 1 Alpha Diversity of fungal communities in HMP stool including the three listed above as well as Cyberlindnera,
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