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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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“Besides bacteria, fungal population such as the most common fungal genus Candida , genera of Saccharomyces , Mucor , Fusarium , Malassezia , Penicillium , Aspergillus , Cryptococcus , Malassezia and Cladosporium are also prevalent in the resident gut microbiome [ 26, 28– 30].”
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“…Candida albicans infections, there is a long-standing association between carbohydrate diets and strong intestinal colonization by Candida albicans [99, 100]; in contrast, coconut oil [101], sodium houttuyfonate derived from Houttuynia cordata Thunb [102], capric acid and caprylic acid [103], and…”
Fungal microbiota signatures anticipate neoadjuvant immunochemotherapy outcomes in esophageal cancer
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Fungi: Friend or Foe? A Mycobiome Evaluation in Children With Autism and Gastrointestinal Symptoms
Alookaran, J. J., Liu, Y., Auchtung, T. A., Tahanan, A., Hessabi, M., Asgarisabet, P., Rahbar, M. H., Fatheree, N. Y., Pearson, D. A., Mansour, R., et al. (2022) · Digital Commons-TMC (Texas Medical Center) · Cited by 6
Human Archaea and Associated Metabolites in Health and Disease
Cai, M., & Tang, X. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00232 · Cited by 5
Romo, J. A., & Kumamoto, C. A. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2549-1_20 · Cited by 6
Myeong, S., Lee, Y. J., Do Hyun, K. I. M., & Kim, T. (2023) · Journal of the Korean Wood Science and Technology · doi:10.5658/wood.2023.51.5.358 · Cited by 6
“The human microbiota is composed of various microorganisms, including bacteria, viruses, fungi, and archaea (Hoffmann et al., 2013; Kong, 2011; Wade, 2013).”
BackgroundČížková, D., Schmiedová, L., Kváč, M., Sak, B., Macholán, M., Piálek, J., & Kreisinger, J. (2023) · Molecular Ecology · doi:10.1111/mec.17192 · Cited by 5
“Interestingly, Kazachastania is present at very low levels or not at all in captive mice, while Saccharomyces is a common genus (Iliev et al., 2012; Mims et al., 2021) that has been strongly associated with metabolic disorders and weight gain (Mims et al.”
BackgroundLi, Y., & Tong, W. (2024) · Neurogastroenterology & Motility · doi:10.1111/nmo.14795 · Cited by 7
“First, a previous study suggested that heavy-carbohydrate diets are positively related to the abundance of Methanobrevibacter in the feces, 26 which is significantly associated with stool consistency.”
BackgroundHaute, M. J. S. V. (2015) · Lincoln (University of Nebraska) · Cited by 6
Future Perspectives: Microbiome, Cancer and Therapeutic Promise
Banerjee, S., & Robertson, E. S. (2019) · Current cancer research · doi:10.1007/978-3-030-04155-7_17 · Cited by 6
Clinical Parasitology and Parasitome Maps as Old and New Tools to Improve Clinical Microbiomics
Pane, S., Ristori, M. V., Gardini, S., Russo, A., CHIERICO, F. D., & Putignani, L. (2021) · Pathogens · doi:10.3390/pathogens10121550 · Cited by 6
“Nutritional modification may have an effect on the fungal microbiota; in particular, plant-based diets increase the levels of Candida, whereas animal-based diets improve the presence of Penicillium species [41,42].”
BackgroundReynoso-García, J., Narganes-Storde, Y. M., Santiago-Rodríguez, T. M., & Toranzos, G. A. (2022) · Microorganisms · doi:10.3390/microorganisms10020459 · Cited by 6
“was not detected [76] or was detected less consistently [77] in other studies.”
ResultSmith, C. J., Dethlefsen, L., Gardner, C. D., Nguyen, L. A. B., Feldman, M. W., Costello, E. K., Kolodny, O., & Relman, D. A. (2022) · mBio · doi:10.1128/mbio.01051-22 · Cited by 7
Wiesmann, C., Lehr, K., Kupčinskas, J., Vilchez‐Vargas, R., & Link, A. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2110638 · Cited by 6
Modelling the Gut Fungal-Community in TIM-2 with a Microbiota from Healthy Individuals
Maas, E., Penders, J., & Venema, K. (2023) · Journal of Fungi · doi:10.3390/jof9010104 · Cited by 6
“There are several examples that show that diet can have an influence on the gut mycobiome; for example, it was shown that mice on a high-fat diet had a different mycobiota compared to mice on a standard diet [10], and that Methanobrevibacter and Candida abundance was correlated with a high-carbohydrate diet [11].”
BackgroundMethodInfluentialMycobiome and Gut Inflammation
Witherden, E. A., & Moyes, D. L. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805417-8.00022-6 · Cited by 11
Tan, Z., Yang, C., Zhao, Y., Yang, X., & Li, T. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c04034 · Cited by 6
Lange, T., Sprague, J. L., Vij, R., Alonso‐Román, R., Jablonowski, N., Radosa, S., Krüger, T., Kniemeyer, O., Hillmann, F., Brakhage, A. A., et al. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013542 · Cited by 6
“Diets enriched in carbohydrates, which are hallmarks of western-style diets, have been shown to facilitate growth and gut colonization of C. albicans in vivo [29–31].”
Harnessing Probiotics to Combat Candidiasis: Mechanisms, Evidence, and Future Directions
Wright, E., Valand, N., & Girija, U. V. (2025) · Journal of Fungi · doi:10.3390/jof11110779 · Cited by 5
“Diets high in carbohydrates have been identified as a risk factor for gut candidiasis, as these are metabolised by Candida spp., fermenting them into starches and sugars that fuel fungal growth and can trigger a shift from a commensal to pathogenic form [80].”
Vu, D., de Vries, M., van den Ende, B. G., Houbraken, J. A. M. P., Nilsson, R. H., Brankovics, B., Hernández‐Restrepo, M., Groenewald, J. Z., Crous, P. W., Hagen, F., et al. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.70082 · Cited by 5
“Among them, Saccharomyces cerevi siae, Malassezia restricta, Candida albicans, Candida sake, Cyberlindnera jadinii, Galactomyces candidus (= Geotrichum candidum ), Malassezia globosa and Agaricus bisporus were the eight species also included in the list of the 10 most abundant fungal/yeast species identified in the p…”
InfluentialMycobiome and Mycobiome-Associated Diseases
Hagihara, M., Kato, H., Shibata, Y., Umemura, T., Ariyoshi, T., Hirai, J., Asai, N., Mori, N., & Mikamo, H. (2023) · Medical Mycology Journal · doi:10.3314/mmj.23-002 · Cited by 5
Microbiome-Host Interactions: The Role of Gut Bacteria in Neurological Disorders
Nasir, O., Bibi, R., Qamar, M. U., Fatima, A., Ahsan, Z., Khan, F., & Amjad, S. (2023) · International Journal of Research Publication and Reviews · doi:10.55248/gengpi.4.1023.102705 · Cited by 5
Nguélé, A. T., Mozzicafreddo, M., Chen, H., Piersanti, A., Salum, S. S., Ali, S. M., Zhang, J., & Miceli, C. (2024) · Frontiers in Tropical Diseases · doi:10.3389/fitd.2024.1276210 · Cited by 5
Kemp, J. A., Schultz, J., Modolon, F., Alves, M. R., Rosado, A. S., & Mafra, D. (2024) · International Urology and Nephrology · doi:10.1007/s11255-024-04273-5 · Cited by 6
“Conversely, Hoffman et al. [24] found a significant positive correlation between ASV assigned to Methano-brevibacter and carbohydrates, showing that diet influences the gut microbiome, including the Archaea Domain.”
da Silva, V. G., Roy, N. C., Smith, N. W., Wall, C. R., Mullaney, J. A., & McNabb, W. C. (2025) · Frontiers in Nutrition · doi:10.3389/fnut.2025.1591341 · Cited by 7
“…carbohydrates) were associated with increased fecal abundance of the genera Alistipes , Bacteroides , and Penicillium , and less methanogenic archaea, resulting in higher expression of microbial genes related to bile acid metabolism, amino acid fermentation, and production of BCFAs (108–110).”
Slater, R., Frau, A., Hodgkinson, J. E., Archer, D., & Probert, C. S. (2021) · Animals · doi:10.3390/ani11030755 · Cited by 5
“Furthermore, in healthy human subjects consuming a high-carbohydrate diet, a correlation was observed between the fungal genus Candida and members of Prevotellaceae (genus Prevotella) [80].”
InfluentialGut mycobiome dysbiosis in rats showing retinal changes indicative of diabetic retinopathy
Padakandla, S. R., Das, T., Prashanthi, G. S., Angadi, K. K., Reddy, S. S., Reddy, G. B., & Shivaji, S. (2022) · PLoS ONE · doi:10.1371/journal.pone.0267080 · Cited by 5
Combined effects of host genetics and diet on porcine intestinal fungi and their pathogenic genes
Wang, T., Liu, J., Luo, Y., Yu, B., Kong, X., Zheng, P., Huang, Z., Mao, X., Yu, J., Luo, J., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1192288 · Cited by 6
“These findings differ somewhat from the most prevalent fungal phyla reported in previous studies of pig, mouse, and human intestines, likely influenced by variations in pig age and advancements in technology (Scupham et al., 2006; Hoffmann et al., 2013; Li et al., 2020).”
ResultKlaassens, E. S., Baak, M. L., Mekkes, N., Bongoni, R., & Schaubeck, M. (2024) · Microbiome Research Reports · doi:10.20517/mrr.2024.13 · Cited by 6
Immune-mediated Bowel Disease: Role of Intestinal Parasites and Gut Microbiome
Chowdhury, S. R., Dey, A., Gautam, M. K., Mondal, S., Pawar, S. D., Ranade, A. V., Bora, M., Gangwar, M., Teli, A., & Mondal, N. S. (2024) · Current Pharmaceutical Design · doi:10.2174/0113816128326270240816075025 · Cited by 5
Commensalism: The Case of the Human Zymobiome
Inácio, J., & Daniel, H.-M. (2017) · Springer eBooks · doi:10.1007/978-3-319-61575-2_8 · Cited by 5
Sun, B., Huffman, M. A., & Li, J. (2019) · Fascinating life sciences · doi:10.1007/978-3-030-27920-2_11 · Cited by 5
Characterization of the archaeal community in foods: The neglected part of the food microbiota
Mohammadpour, H., Cardin, M., Carraro, L., Fasolato, L., & Cardazzo, B. (2023) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2023.110275 · Cited by 6
The Mycobiome: Impact on Health and Disease States
El‐Jurdi, N., & Ghannoum, M. A. (2017) · ASM Press eBooks · doi:10.1128/9781555819583.ch40 · Cited by 5
Neuman, H., & Koren, O. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-394447-4.20083-7 · Cited by 5
Intestinal Microbes, Metabolites, and Hormones in Alcohol-Associated Liver Disease
Wang, R., Ma, F., Yin, D., Wang, H., & Wei, X. (2025) · Seminars in Liver Disease · doi:10.1055/a-2601-9480 · Cited by 4
“41 Our recent study suggested that soluble dietary fi ber enhances the abundance of Bacteroides acidifaciens in the mouse intestine, thereby mitigating alcohol-induced liver injury.”
The mycobiota of faeces from the critically endangered kākāpō and associated nest litter
West, A. G., Digby, A., Kākāpō Recovery Team, & Taylor, M. W. (2023) · New Zealand Journal of Zoology · doi:10.1080/03014223.2023.2170428 · Cited by 5
“The decrease in faecal fungal richness, and concurrent increase in Inverse Simpson diversity, may also re fl ect changes in diet which can signi fi cantly in fl uence the gut microbiota (Ho ff mann et al. 2013; David et al. 2014).”
Xu, J., Tian, Y., Hu, D., Xi, Y., & Yang, L. (2024) · MedComm – Oncology · doi:10.1002/mog2.85 · Cited by 4
Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates
Syoc, E. P. V., Gomez, A. M., Davenport, E., & Bordenstein, S. R. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003390 · Cited by 4
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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