Andrea Nash (4616053)

Christopher Stewart (3608402)

Daniel Smith (6120)

Donna Muzny (54293)

Ginger Metcalf (3548549)

Jonathan Gesell (4616059)

Joseph Petrosino (39790)

Matthew Ross (1408429)

Matthew Wong (1752211)

Nadim Ajami (3526169)

Richard Gibbs (144333)

Thomas Auchtung (4616056)

Microbiome

ITS2 and 18S gene HMP study primers. Description â Table S6: ITS2 sequencing and index primers used in this study. Table S7: 18S sequencing primers used in this study. (XLSX 24Â kb

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Additional file 6: of The gut mycobiome of the Human Microbiome Project healthy cohort

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, and Candida, with S. cerevisiae, M. restricta, and C. 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, and C. 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, and Candida. 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

Nash, Andrea K.

Auchtung, Thomas A.

Wong, Matthew C.

Smith, Daniel P.

Gesell, Jonathan R.

Ross, Matthew C.

Stewart, Christopher J.

Metcalf, Ginger A.

Muzny, Donna M.

Gibbs, Richard A.

Ajami, Nadim J.

Petrosino, Joseph F.

UNL | Libraries

English

The gut mycobiome of the Human Microbiome Project healthy cohort

Extraction methods comparison. Description â Fungal DNA extraction methods comparison methods and results. Figure S2: a Alpha diversity (Observed OTUs and Shannon diversity) of both fungal DNA extraction methods. b Beta diversity (Bray-Curtis dissimilarity) of samples, colored by method, shaped by donor. c Relative abundance of fungal taxa. (PDF 344Â kb

Additional file 5: of The gut mycobiome of the Human Microbiome Project healthy cohort

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, and Candida, with S. cerevisiae, M. restricta, and C. 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, and C. 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, and Candida. 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

Andrea K. Nash

Thomas A. Auchtung

Matthew C. Wong

Daniel P. Smith

Jonathan R. Gesell

Matthew C. Ross

Christopher J. Stewart

Ginger A. Metcalf

Donna M. Muzny

Richard A. Gibbs

Nadim J. Ajami

Joseph F. Petrosino

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