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Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
Open accessAbstract
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
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“In addition, members of the microbiome may drastically affect the growth of co-habitants (Hoffmann et al., 2013).”
From Iron at the Centre of Candida albicans Interactions (2018) · cites this paper as Hoffmann et al., 2013
In the citing paper
“carbohydrate consumption is associated with the proportion of the archaeon, Methanobrevibacter,46 in the intestinal microbiota.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [46]
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“Diet has also been associated with other types of microbes in the gut, such as archaea, fungi, and bacteriophage (Figure 2)45-47.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [46]
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“Infections with C. albicans can range from superficial mucosal and dermatological infections to life-threatening infections of the bloodstream and vital organs.”
From Molecular and genetic basis of azole antifungal resistance in the opportunistic pathogenic fungus Candida albicans (2020) · cites this paper as [1]
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1 retracted
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BackgroundRetractedQIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · cited 1×
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MethodSelf-citationMeasures of the Amount of Ecologic Association Between Species
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MethodDiversity of the Human Intestinal Microbial Flora
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Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · cited 4×
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BackgroundInfluentialEnterotypes of the human gut microbiome
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Human Microbiome: Implications on Health and Disease
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“However, fungal cell walls are more difficult to digest during DNA isolation and the internal transcribed spacer gene varies in length between species 6 .”
Chue, K. M., Wong, S. H., Zuo, T., & Ali, Y. (2025) · Molecular Metabolism · doi:10.1016/j.molmet.2025.102289 · Cited by 4
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InfluentialGut–Brain Inflammation and Disrupted Homeostasis Due to Activation of Mast Cells and Microglia
Katiraei, P., Frye, R. E., & Theoharides, T. C. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27041768 · Cited by 3
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Multi‐Omic Insights Into Mediterranean Diet‐Associated Microbiota
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“Hoffmann et al. [ 40 ] also found a negative correlation between SCFA levels and Aspergillus , which we identified as a biomarker of the LAMD group.”
Documenting the diversity of the Namibian Ju|’hoansi intestinal microbiome
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The Hidden Influence of Methanogens in the Gut Microbiota
Zengin, Ö. D., & Aydın, S. (2025) · IntechOpen eBooks · doi:10.5772/intechopen.1008814 · Cited by 3
Eukaryotic Microorganisms are Part of Holobionts
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Micobioma: diversidad fúngica en el cuerpo humano
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BackgroundAlexandru Vasile, R. U. S. U., Penedo, B. Á., Schwarze, A.-K., & Trif, M. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.92791 · Cited by 3
Osmoregulation and the human mycobiome
Saxena, A., & Sitaraman, R. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00167 · Cited by 3
“The most commonly encountered genera constituting the fungal microbiota or “mycobiome” (Huffnagle and Noverr, 2013) are Candida, Saccharomyces and Cladosporium (Hoffmann et al., 2013).”
InfluentialCommensal microbiota-derived signals regulate host immune system through epigenetic modifications
Takahashi, D., & Hase, K. (2015) · Inflammation and Regeneration · doi:10.2492/inflammregen.35.129 · Cited by 3
Ma, X., Zeng, X., Huang, Z. Z., Li, G., Liu, R., Luo, R., Li, X., Ling, S., Wang, C., & Gu, Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1522289 · Cited by 2
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“Fungi, collectively known as the “mycobi-ome,” contribute to digestion, immune regulation, and gut barrier function, with common species like Candida and Saccharomyces cerevisiae playing beneficial and potentially harmful roles [23].”
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Epithelial and microbial determinants of colonic drug distribution
Hammar, R., Sellin, M. E., & Artursson, P. (2023) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2023.106389 · Cited by 2
“The most abundant fungi in the human gut are facultative anaerobic Candida and Saccharomyces yeasts (Hoffmann et al., 2013).”
BackgroundFungal Rhizomes: Mycorrhizae and Posthumanism
Finzi, J. (2024) · Green Letters · doi:10.1080/14688417.2024.2361359 · Cited by 2
The Effects of Brodalumab on the Fungal Microbiome in Patients with Psoriasis
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“When considering the healthy gut microbiome, Hoffmann et al. (2013) reported that Candida and Saccharomyces are among the most frequently detected fungal genera [25].”
BackgroundRole of gut virome and mycobiome in neurological disorders
Chaudhary, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-21680-0.00017-1 · Cited by 2
Composition-on-composition regression analysis for multi-omics integration of metagenomic data
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“The Prevotella/Bacteriodes ratio was found to be important for the gut microbiome and was also shown to be significantly associated with the overall fungi compositions (Hoffmann et al. 2013).”
Gut Microbiology – A Relatively Unexplored Domain
O’Donovan, C. M., O’Sullivan, Ó., & Cotter, P. D. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.09233-5 · Cited by 2
Gut Microbiota Dysbiosis and Chronic Intestinal Inflammation
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Introduction and Background to Microbiome Research
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Microbial Processes to Produce Food Ingredients and Products
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“In addition, a negative correlation between short chain fatty acids (SCFAs) and Aspergillus has been reported in human and piglet studies (Arfken et al., 2020; Hoffmann et al., 2013).”
BackgroundTakada, K., Nakagawa, S., Kryukov, K. A., Ozawa, M., & Watanabe, T. (2024) · FEBS Open Bio · doi:10.1002/2211-5463.13881 · Cited by 2
DETECTION OF A NEGATIVE BIOMARKER FOR AMEBIASIS (ENTAMOEBA HISTOLYTICA) IN THE HUMAN GUT MYCOBIOME
Abuljadayel, D., ATEF, A., Al-Matary, M. A., Edris, S., AL-QUWAIE, D. A. H., Alsubhi, N. H., Al-Hindi, R. R., Sabir, J. S. M., Hall, N., & Bahieldin, A. (2020) · Applied Ecology and Environmental Research · doi:10.15666/aeer/1802_23632394 · Cited by 1
“…in healthy subjects mainly comprises Ascomycota and Basidiomycota as the most abundant phyla, and the Candida, Saccharomyces and Malassezia and as the most abundant genera (Ott et al., 2008; Moran et al., 2012; Hoffmann et al., 2013; Rajilic-Stojanovic and de Vos, 2014; Nash et al., 2017).”
BackgroundCell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human PrimatesPreprint
Kowarsky, M., Vlaminck, I. D., Okamoto, J., Neff, N., Lebreton, M., Nwobegabay, J., Tamoufe, U., LeDoux, J. E., Tafon, B., Kiyang, J. A., et al. (2018) · bioRxiv · doi:10.1101/481093 · Cited by 2
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Live Malassezia strains isolated from the mucosa of patients with ulcerative colitisPreprint
Cho, Y., Yang, J., Shin, S. Y., Kim, H. K., Rintarhat, P., Park, M., Sung, M., Lagree, K., Underhill, D. M., Lee, D.-W., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.28.569113 · Cited by 2
Role of the Gut Flora in Human Nutrition and Gut Health
Alvarado‐Martinez, Z., Filho, S., Mihalik, M., Rha, R., & Snyder, M. (2020) · Springer eBooks · doi:10.1007/978-3-030-47384-6_5 · Cited by 2
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Mouzan, M. I. E., Al‐Hussaini, A. A., Sarkhy, A. A. A., & Assiri, A. A. (2023) · Arab Journal of Gastroenterology · doi:10.1016/j.ajg.2023.11.001 · Cited by 1
The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts
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Global hotspots and trends in gut mycological research: a visual analytics and bibliometric approach
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Inflammatory Bowel Diseases and Gut Microbiota
Jana, B. K., Singh, M., Sarkar, T., Sadhu, P., Chetia, D., & Mazumder, B. (2025) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9789815324549125010005 · Cited by 1
Gut fungi are associated with human genetic variation and disease risk
Syoc, E. P. V., Davenport, E., & Bordenstein, S. R. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003339 · Cited by 2
“Widespread perception of gut fungi as diet-derived transient passengers through the gastrointestinal tract [8,9] has hindered the investigation of how fungi assemble into a complex, multidimensional community, even with mounting evidence that gut fungi underpin human diseases [10,11] and gut…”
Nutritional and Physiological Demands Shape the Gut Microbiome of Female World Tour Cyclists
Ampe, T., Decroix, L., Pauw, K. D., MEEUSEN, R. R., Demuyser, T., & Roelands, B. (2025) · Microorganisms · doi:10.3390/microorganisms13102345 · Cited by 1
“…tract is home to trillions of microorganisms, including bacteria, viruses, fungi, and archaea [1], which make up a complex ecological community with versatile functions, like energy production, regulating the immune system, producing hormones, and communicating with the brain [2–5].”
Associations and interactions between prokaryotes and other gut biota in non-human primates
Bambi, M., Hauffe, H. C., & Barelli, C. (2025) · Primates · doi:10.1007/s10329-025-01224-1 · Cited by 1
Optimized Selective Media Enhance the Isolation and Characterization of Gut-Derived Probiotic Yeasts
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“(Hoffmann et al. 2013) Among these, Candida species are frequently found in the human microflora, as they are capable of colonizing the oral, intestinal and vaginal mucosa, as well as the skin of healthy individuals (Sparber and Leibundgut-landmann 2015).”
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Metadata
- Authors
- Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D.
- Affiliations
- Universidade Federal de Goiás (BR)
- University of Pennsylvania (US)
- Harvard University (US)
- Corresponding author
- Wu, Gary D.
- Lewis, James D.
- Bushman, Frederic D.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-06-17
- Volume
- 8
- Issue
- 6
- Pages
- e66019
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3684604
- OpenAlex
- W2110345840
- Cited by
- 808
- References
- 62
- Citations by year
- 2026: 38 · 2025: 56 · 2024: 73 · 2023: 59 · 2022: 86 · 2021: 85 · 2020: 87 · 2019: 76 · 2018: 60 · 2017: 62 · 2016: 36 · 2015: 45 · 2014: 40 · 2013: 4
- FWCI
- 18.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Pennsylvania Department of Health
- University of Pennsylvania (UL1 RR024134)
- National Institutes of Health (and K24, DK050306)
- National Institute of Diabetes and Digestive and Kidney Diseases (K24DK078228, DK 089472, R01DK089472, UH2/3 DK083981, UH3DK083981, UH2DK083981, P30DK050306)
- National Center for Research Resources (UL1RR024134, S10RR024525)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, archaea, fungi, diet, Methanobrevibacter, Candida, Ascomycota, carbohydrate intake, long-term diet, microbial co-occurrence, human health
- MeSH terms
- Archaea, Bacteria, Diet, Fungi, Humans, Intestines, Microbiota
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