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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]
In the citing paper
“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]
In the citing paper
“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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MethodSelf-citationMeasures of the Amount of Ecologic Association Between Species
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Unraveling the Interplay: Intestinal Parasites and Gut Microbiome in Immune-Mediated Bowel DiseasePreprint
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Dietary changes and lifestyle shifts affect the gut microbiomes of giant pandasPreprint
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Additional file 6 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720358
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Additional file 1 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720343
Additional file 5 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720355
Additional file 8 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720364
Bai, X., Sun, Y., Li, Y., Li, M., Cao, Z., Huang, Z., Zhang, F., Yan, P., Wang, L., Luo, J., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21102283
Liu, Q., Zhang, W., Pei, Y., Tao, H., Ma, J., Li, R., Zhang, F., Wang, L., Shen, L., Liu, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26634168
Additional file 3 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720349
Liu, Q., Zhang, W., Pei, Y., Tao, H., Ma, J., Li, R., Zhang, F., Wang, L., Shen, L., Liu, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24465177
Additional file 2 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720346
Additional file 7 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720361
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Additional file 4 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720352
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Detection of Fungal Translocation in Patients With Alcohol Use Disorder Using a Real‐Time PCR Assay
Pansu, N., Drakulovski, P., Krasteva, D., Bellet, V., Lavigne, J., Dunyach‐Remy, C., Salipante, F., Yahiaoui-Martinez, A., Donnadieu‐Rigole, H., & Bertout, S. (2026) · Apmis · doi:10.1111/apm.70181
“Indeed, aside from gut bacteria, the microbiota contains at least archaeal and fungal cells [8, 9].”
Solano-Aguilar, G. I., Lakshman, S., Chen, C., Beshah, E., Molokin, A., Vinyard, B. T., Dawson, H. D., Santı́n, M., Bruna, G., Smith, A., et al. (2026) · Nutrients · doi:10.3390/nu18060937
“Similar to bacterial communities, the gut myco-biome can be significantly influenced by diet—one of the most important factors shaping its composition [113–117].”
Interkingdom Interactions in the Gut: Ecological Mechanisms, Homeostasis, and Therapeutic Modulation
Wei, R., Sun, X., Huang, H., Zhao, Y., Liu, S., & Liu, C. (2026) · Gut Medicine · doi:10.1002/gtm2.70009 · Cited by 1
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“This compositional pattern indicated limited microbial specialization for cellulose degradation due to the panda’s short, carnivore-like gastrointestinal tract and rapid digesta transit time, which is consistent with studies reported by Hoffmann et al. [18], Mariat et al. [31].”
Demography-dependent variability in the human tumor mycobiome
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“For example, the abundance of Candida spp. in the gut correlates with a Western-type carbohydrate-rich diet and is negatively associated with a protein-or fatty acid-rich diet (37).”
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Role of macrophages in colon homeostasis
Chikina, A. S. (2020) · theses.fr (ABES) · doi:10.70675/914bf102zc92ez4351zb4dbz1945d4116eea
Impact des antibiotiques sur le phageome intestinal humain : de la méthode à l’application
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Caractérisation in vivo des propriétés antimicrobiennes de la souche probiotique Lcr35®
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“Ce mycobiote est ainsi prédominé par certains genres dont Candida, Saccharomyces, Fusarium, Debaryomyces, Penicillium, Galactomyces, Pichia, Cladosporium, Malassezia, Cyberlindnera et Aspergillus (Hoffmann et al. 2013 ; Strati et al. 2016 ; Nash et al. 2017).”
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Impact du microbiome intestinal sur la cholestérolémie : concepts et applications
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Effet des thérapies protéiques sur l’axe intestin-poumon dans la mucoviscidose
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The Microbiome and Cancer: Exploring the Gut Connection
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Fungi and colorectal cancer: from dysregulation to clinical translation
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“…consumption of Mediterranean diets [91], high-fiber foods [92], and polyphenol-rich nutrients [93, 94], combined with reduced intake of high-fat, high-sugar, and high-protein foods [95], promotes beneficial fungal growth while suppressing pathogenic fungi ( Candida and Aspergillus species) [96].”
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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