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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]
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
RETRACTED: Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal
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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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“Co-occurrence The Dice index [58] was used to determine the co-occurrence of genera across the entire dataset.”
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“Archaeal specific 16S rDNA primers and ITS1 fungal primers were adapted from the literature and used to amplify a rDNA 16S fragment; the final PCR cycling conditions were optimized to maximize specificity [51], [52], [38], [40],(Tables S5 and S6).”
MethodDiversity of the Human Intestinal Microbial Flora
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BackgroundInfluentialEnterotypes of the human gut microbiome
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“Taxonomy was assigned to OTU representative sequences using the RDPclassifier [55] for archaeal sequences and BROCC [36] for fungal sequences.”
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Items 201–300 of 815
Dysbiosis of Gut Fungal Microbiota in Children with Autism Spectrum Disorders
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“The microbiome of the gut has been extensively studied, particularly in humans, during the past few years, including major metagenomic projects in the USA [16–19] and Europe [20–22].”
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“Overall and in contrast to many of the other early-life environmental factors examined, breastfeeding was more significantly associated with gut mycobiota communities at 1 year of age, when more dietary heterogeneity existed among subjects, in line with studies showing diet to be a major driver of gut fungal communiti…”
BackgroundResultAkiyama, S., Nishijima, S., Kojima, Y., Kimura, M., Ohsugi, M., Ueki, K., Mizokami, M., Hattori, M., Tsuchiya, K., Uemura, N., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54797-8 · Cited by 82
“While the study provides valuable insights, addressing these concerns would strengthen the reliability and relevance of the findings.”
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“8S region (forward 5=-GTG AAT CAT CGA RTC TTT GAA C-3=) and the 28S region (reverse 5=-TAT GCT TAA GTT CAG CGG GTA-3=) (1, 16).”
BackgroundXu, T., Ge, Y., Du, H., Li, Q., Xu, X., Yi, H., Wu, X., Kuang, T., Fan, G., & Zhang, Y. (2021) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2021.113995 · Cited by 69
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Gut mycobiota under scrutiny: fungal symbionts or environmental transients?
Fiers, W. D., Gao, I. H., & Iliev, I. D. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.010 · Cited by 68
“They identified many fungal taxa in common, with the top three being Saccharomyces, Candida, and Cladosporium [23].”
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Klimesova, K., Jiraskova Zakostelska, Z., & Tlaskalova-Hogenova, H. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00774 · Cited by 67
“The most common genera residing in a healthy gut are Candida, Saccharomyces, and Cladosporium (Hoffmann et al., 2013).”
BackgroundInfluentialBiodiversity of protists and nematodes in the wild nonhuman primate gut
Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M. M., Fiore, A. D., Link, A., Goldberg, T. L., Tecot, S. R., et al. (2019) · The ISME Journal · doi:10.1038/s41396-019-0551-4 · Cited by 65
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“with which an individual lives in symbiosis throughout lifetime.(25) Host genetics is believed to contribute to the profile of the gut microbiome, living conditions including dietary hab-”
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“4; Hoffmann et al. 2013).”
Factors Influencing the Intestinal Microbiome During the First Year of Life
Zimmermann, P., & Curtis, N. C. (2018) · The Pediatric Infectious Disease Journal · doi:10.1097/inf.0000000000002103 · Cited by 69
Alzheimer's disease and symbiotic microbiota: an evolutionary medicine perspective
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Ballway, J. W., & Song, B.-J. (2021) · Antioxidants · doi:10.3390/antiox10030384 · Cited by 72
Gut mycobiome: A promising target for colorectal cancer
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“Previous studies have also shown their abundance is lower than their bacterial counterparts (Hoffmann et al., 2013); however, it is likely that this community was not sequenced deeply enough to detail their role.”
BackgroundBacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions
Djemai, K., Drancourt, M., & Alou, M. T. (2021) · Microbial Ecology · doi:10.1007/s00248-021-01796-7 · Cited by 64
Colon Cancer: From Epidemiology to Prevention
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Gut Microbiome Dysbiosis in Alcoholism: Consequences for Health and Recovery
Day, A. W., & Kumamoto, C. A. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.840164 · Cited by 63
“Fungi have also been shown to increase in abundance in the GI tract following diets rich in meats and cheeses (David et al., 2014), recent carbohydrate consumption (Hoffmann et al., 2013), and most notably for this review: chronic alcohol consumption (Yang et al., 2017).”
BackgroundMicrobiota and COVID-19: Long-term and complex influencing factors
Gang, J., Wang, H., Xue, X., & Zhang, S. J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.963488 · Cited by 62
“The reason for several conflicting conclusions of these studies is not apparent, but may be associated with age, sex, and eating habits (Hoffmann et al., 2013; Strati et al., 2016; Fiers et al., 2020).”
BackgroundGut mycobiome and metabolic diseases: The known, the unknown, and the future
Wang, L., Zhang, K., Zeng, Y., Luo, Y., Peng, J., Zhang, J., Kuang, T., & Fan, G. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106807 · Cited by 67
An overview of the bacterial contribution to Crohn disease pathogenesis
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“Bacteria account for largest contribution to the intestinal microbiome, although Archaea, viruses, fungi and protozoa are also present (Tlaskalov a-Hogenov a et al., 2011; Hoffmann et al., 2013).”
Role of Yeasts in Healthy and Impaired Gut Microbiota: The Gut Mycome
Ianiro, G., Bruno, G., Lopetuso, L. R., Beghella, F., Laterza, L., D’Aversa, F., Gigante, G. E., Cammarota, G., & Gasbarrini, A. (2014) · Current Pharmaceutical Design · doi:10.2174/13816128113196660723 · Cited by 62
“Since Candida is able to degrade starches, a role for Candida to assist in breaking down starch in carbohydrate rich foods has been proposed [12].”
BackgroundMcDonough, L., Mishra, A. A., Tosini, N., Kakade, P., Penumutchu, S., Liang, S.-H., Maufrais, C., Zhai, B., Taur, Y., Belenky, P. A., et al. (2021) · mBio · doi:10.1128/mbio.02878-21 · Cited by 59
“Candida albicans, a pathobiont that 58 is found in over 70% of individuals, is a prominent member of the gastrointestinal (GI) mycobiota 59 (8, 9).”
BackgroundThe virota and its transkingdom interactions in the healthy infant gut
Beller, L., Deboutte, W., Vieira‐Silva, S., Falony, G., Tito, R. Y., Rymenans, L., Yinda, C. K., Vanmechelen, B., Espen, L. V., Jansen, D., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114619119 · Cited by 58
Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China
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Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas
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“1C–1D and 2B) (Hoffmann et al., 2013).”
BackgroundInfluentialTissue-resident memory Th17 cells maintain stable fungal commensalism in the oral mucosa
Kirchner, F. R., & LeibundGut-Landmann, S. (2021) · Mucosal Immunology · doi:10.1038/s41385-020-0327-1 · Cited by 59
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“While it has previously been reported that dietinduced shifts can modulate the populations of these microbes(66), the review found no significant changes to the diversity or the relative abundance of archaea, with only one study(34) to report a decrease in various fungal OTUs following nut intake.”
BackgroundPostbiotic-Enabled Targeting of the Host-Microbiota-Pathogen Interface: Hints of Antibiotic Decline?
Puccetti, M., Xiroudaki, S., Ricci, M., & Giovagnoli, S. (2020) · Pharmaceutics · doi:10.3390/pharmaceutics12070624 · Cited by 59
“Since the microbiota-mucosal immune system interaction is critical for the host’s immune balance, alterations in the GM composition and function can result into several ailments, including diabetes, obesity, asthma, cancer, cystic fibrosis [73], inflammatory bowel disease (IBD) [74,75], chronic liver disease [76], ato…”
BackgroundAnderson, F. M., Visser, N. D., Amses, K. R., Hodgins-Davis, A., Weber, A. M., Metzner, K., McFadden, M. J., Mills, R. E., O’Meara, M. J., James, T. Y., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3001822 · Cited by 56
Yeasts of Burden: Exploring the Mycobiome–Bacteriome of the Piglet GI Tract
Arfken, A. M., Frey, J. F., Ramsay, T. G., & Summers, K. L. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02286 · Cited by 57
“It has been hypothesized from observed positive associations between Candida yeasts and Prevotella, that Candida and Prevotella are involved in a mutualistic relationship regarding the degradation and fermentation of complex carbohydrates in the human gut (Hoffmann et al., 2013).”
BackgroundShanahan, E. R., McMaster, J. J., & Staudacher, H. M. (2021) · Journal of Human Nutrition and Dietetics · doi:10.1111/jhn.12868 · Cited by 61
Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens
Jaswal, K., Todd, O. A., & Behnsen, J. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2226916 · Cited by 65
Microbial biotransformations in the human distal gut
Bik, E. M., Ugalde, J. A., Cousins, J., Goddard, A. D., Richman, J., & Apte, Z. S. (2017) · British Journal of Pharmacology · doi:10.1111/bph.14085 · Cited by 60
“In a study of 96 healthy volunteers, fungi were found in all stool samples, with Saccharomyces, Candida and Cladosporium as the most prevalent (Hoffmann et al., 2013).”
BackgroundJayasudha, R., Chakravarthy, S. K., Prashanthi, G. S., Sharma, S., Garg, P., Murthy, S. I., & Shivaji, S. (2018) · Journal of Biosciences · doi:10.1007/s12038-018-9798-6 · Cited by 57
Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome
Sundarraman, D., Hay, E. A., Martins, D. M., Shields, D. S., Pettinari, N. L., & Parthasarathy, R. (2020) · mBio · doi:10.1128/mbio.01667-20 · Cited by 61
“Correlations among relative abundances are often used as measures of interaction strengths (58, 59).”
Within-Host Genomic Diversity of Candida albicans in Healthy Carriers
Sitterlé, E., Maufrais, C., Sertour, N., Palayret, M., d’Enfert, C., & Bougnoux, M.-E. (2019) · Scientific Reports · doi:10.1038/s41598-019-38768-4 · Cited by 51
The intestinal mycobiota and its relationship with overweight, obesity and nutritional aspects
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Structure, functions, and diversity of the healthy human microbiome
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“Diets abundant in carbohydrates, such as glucose and mannose [99], correlated positively with the abundance of gut Candida [100], whereas negative correlations were observed between high-protein diets and the abundance of fungi in healthy volunteers [101].”
BackgroundSchieffer, K. M., Sabey, K. A., Wright, J., Toole, D. R., Drucker, R., Tokarev, V., Harris, L., Deiling, S. M., Eshelman, M. A., Hegarty, J. P., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-06787-8 · Cited by 54
Gut microbiota in children and altered profiles in juvenile idiopathic arthritis
Filippo, C. D., Paola, M. D., Giani, T., Tirelli, F., & Cimaz, R. (2019) · Journal of Autoimmunity · doi:10.1016/j.jaut.2019.01.001 · Cited by 58
40 Years of archaeal virology: Expanding viral diversity
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The fecal mycobiome in patients with Irritable Bowel Syndrome
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Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria
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The gut commensal fungus, Candida parapsilosis, promotes high fat-diet induced obesity in mice
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Molecular point-of-care testing technologies: Current status and challenges
Zu, Y., Chang, H., & Cui, Z. (2025) · Nexus · doi:10.1016/j.ynexs.2025.100059 · Cited by 53
Caenorhabditis elegans as a Model Host to Monitor the Candida Infection Processes
Elkabti, A. B., Issi, L., & Rao, R. P. (2018) · Journal of Fungi · doi:10.3390/jof4040123 · Cited by 51
Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye
Jayasudha, R., Chakravarthy, S. K., Prashanthi, G. S., Sharma, S., Tyagi, M., & Shivaji, S. (2019) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.18-26426 · Cited by 52
van der Merwe, M., Sharma, S., Caldwell, J. L., Smith, N. J., Gomes, C., Bloomer, R. J., Buddington, R. K., & Pierre, J. F. (2019) · Current Developments in Nutrition · doi:10.1093/cdn/nzz145 · Cited by 51
“However, emerging research demonstrates that fungi can also play a contributory role in modulating host signaling, but these organisms remain almost entirely undescribed under many dietary intervention settings (10, 11, 38).”
BackgroundMetabolic Interactions between Bacteria and Fungi in Commensal Oral Biofilms
Lof, M., Janus, M., & Krom, B. (2017) · Journal of Fungi · doi:10.3390/jof3030040 · Cited by 51
“Seemingly, this also feeds nitrogen to the gut microbial community [32].”
BackgroundDynamics of the Gut Mycobiome in Patients With Ulcerative Colitis
Jangi, S., Hsia, K., Zhao, N., Kumamoto, C. A., Friedman, S., Singh, S., & Michaud, D. S. (2023) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2023.09.023 · Cited by 52
Fungal Dysbiosis and Intestinal Inflammation in Children With Beta-Cell Autoimmunity
Honkanen, J. K., Vuorela, A., Muthas, D., Orivuori, L., Luopajärvi, K., Tejesvi, M. V., Lavrinienko, A., Pirttilä, A. M., Fogarty, C. L., Härkönen, T., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00468 · Cited by 51
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization
Santus, W., Rana, A. P., Devlin, J. R., Kiernan, K. A., Jacob, C. C., Tjokrosurjo, J., Underhill, D. M., & Behnsen, J. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01267-w · Cited by 53
Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Horz, H. (2015) · Life · doi:10.3390/life5021333 · Cited by 53
“has also been confirmed in the human gut, though with low abundance [56].”
BackgroundDietary Yeasts Reduce Inflammation in Central Nerve System via Microflora
Takata, K., Tomita, T., Okuno, T., Kinoshita, M., Koda, T., Honorat, J. A., Takei, M., Hagihara, K., Sugimoto, T., Mochizuki, H., et al. (2014) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.153 · Cited by 50
Diagnosis of Invasive Candidiasis: From Gold Standard Methods to Promising Leading-edge Technologies
Pitarch, A., Nombela, C., & Gil, C. (2018) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026618666181025093146 · Cited by 51
“These are common members of the normal microbiota on the oropharyngeal cavity, gastrointestinal tract and vagina of many healthy individuals [10-12].”
BackgroundThe gut mycobiota of rural and urban individuals is shaped by geography
Kabwe, M. H., Vikram, S., Mulaudzi, K., Jansson, J. K., & Makhalanyane, T. P. (2020) · BMC Microbiology · doi:10.1186/s12866-020-01907-3 · Cited by 56
Angebault, C., Ghozlane, A., Volant, S., Botterel, F., d’Enfert, C., & Bougnoux, M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0201174 · Cited by 51
“This huge variability of the fungal intestinal microbiota assessed through metagenomics has already been highlighted by previous authors [16,21,37].”
BackgroundHost-mycobiome metabolic interactions in health and disease
Begum, N., Harzandi, A., Lee, S., Uhlén, M., Moyes, D. L., & Shoaie, S. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2121576 · Cited by 47
“including age, gender, diet, host genetics, therapeutic intervention and host lifestyle affect individual mycobiome composition.(5,8,14,26) Diets with high carbohydrates can drive the increased gut presence of Candida species.”
BackgroundFungal infections and the fungal microbiome in hepatobiliary disorders
Hartmann, P., & Schnabl, B. (2022) · Journal of Hepatology · doi:10.1016/j.jhep.2022.12.006 · Cited by 50
Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon
Sprockett, D. D., Martin, M. A., Costello, E. K., Burns, A. R., Holmes, S., Gurven, M., & Relman, D. A. (2020) · Nature Communications · doi:10.1038/s41467-020-17541-6 · Cited by 46
Microbiome dysbiosis in cancer: Exploring therapeutic strategies to counter the disease
Sharma, V., Singh, M. P., Kumar, V., Yadav, M. K., Sehrawat, N., Sharma, D. K., & Sharma, A. K. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.07.006 · Cited by 49
The cross-talk between opportunistic fungi and the mammalian host via microbiota’s metabolism
Romani, L., Zelante, T., Palmieri, M., Napolioni, V., Picciolini, M., Velardi, A., Aversa, F., & Puccetti, P. (2015) · Seminars in Immunopathology · doi:10.1007/s00281-014-0464-2 · Cited by 47
Do Viruses Exchange Genes across Superkingdoms of Life?
Malik, S. S., Azem-e-Zahra, S., Kim, K. M., Caetano‐Anollés, G., & Nasir, A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02110 · Cited by 46
“Indeed, Archaea constitute an important part of the animalmicrobiota (Hoffmann et al., 2013; Lurie-Weinberger and Gophna, 2015), an ecosystem that is considered a “hot spot” for genetic exchange (Shterzer and Mizrahi, 2015).”
BackgroundGubatan, J. M. B., Boye, T. L., Temby, M., Sojwal, R. S., Holman, D., Sinha, S. R., Rogalla, S., & Nielsen, O. H. (2022) · Microorganisms · doi:10.3390/microorganisms10071371 · Cited by 47
“Additionally, the microbiome is affected by the diet of the host [34,35].”
BackgroundCD4+ T-cell survival in the GI tract requires dectin-1 during fungal infection
Drummond, R. A., Dambuza, I. M., Vautier, S., Taylor, J. A., Reid, D. M., Bain, C. C., Underhill, D. M., Masopust, D., Kaplan, D. H., & Brown, G. D. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.79 · Cited by 49
Martinez, K., Pierre, J. F., & Chang, E. B. (2016) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2016.07.001 · Cited by 51
An expanding stage for commensal microbes in host immune regulation
Shi, Y., & Mu, L. (2017) · Cellular and Molecular Immunology · doi:10.1038/cmi.2016.64 · Cited by 46
The gut mycobiome composition is linked to carotid atherosclerosis
Chacón, M. R., Lozano-Bartolomé, J., Portero‐Otín, M., Rodríguez, M. M., Xifra, G., Puig, J., Blasco, G., Ricart, W., Chaves, F. J., & Fernández‐Real, J. M. (2017) · Beneficial Microbes · doi:10.3920/bm2017.0029 · Cited by 47
Bratburd, J. R., Keller, C., Vivas, E. I., Gemperline, E., Li, L., Rey, F. E., & Currie, C. R. (2018) · mBio · doi:10.1128/mbio.02032-18 · Cited by 50
Coufal, Š., Galanová, N., Bajer, L., Gajdárová, Z., Schierová, D., Zakostelska, Z. J., Kostovcikova, K., Jackova, Z., Stehlíková, Z., Drastich, P., et al. (2019) · Cells · doi:10.3390/cells8070719 · Cited by 47
Manipulation of Gut Microbiota as a Key Target for Crohn's Disease
Rashed, R. T., Valcheva, R. S., & Dieleman, L. A. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.887044 · Cited by 52
Fiedorová, K., Radvanský, M., Bosák, J., Grombiříková, H., Němcová, E., Králíčková, P., Černochová, M., Kotásková, I., Lexa, M., Litzman, J., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01914 · Cited by 46
“The mentioned fungal genera were also found in various abundance in the stool samples by others (62, 64, 66), however, some genera such as Malassezia or Cryptococcus, commonly detected elsewhere (62, 67), were not present in our samples.”
BackgroundBai, X., Sun, Y., Li, Y., Li, M., Cao, Z., Huang, Z., Zhang, F., Yan, P., Wang, L., Luo, J., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01335-7 · Cited by 49
“M. smithii was at the central hub of archaealbacterial interactions in the gut microecology, where it was positively correlated with the abundances of a multitude of short chain fatty acid (SCFA)-producing bacteria (including Roseburia faecis, Collinsella aerofaciens, and Prevotella copri).”
BackgroundInfluentialMetabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients
Hamad, I., Abdallah, R. A., Ravaux, I., Mokhtari, S., Tissot‐Dupont, H., Michelle, C., Stein, A., Lagier, J., Raoult, D., & Bittar, F. (2018) · PLoS ONE · doi:10.1371/journal.pone.0191913 · Cited by 45
Osakunor, D. N. M., Munk, P., Mduluza, T., Petersen, T. N., Brinch, C., Ivens, A. C., Chimponda, T. N., Amanfo, S., Murray, J., Woolhouse, M. E. J., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-0859-7 · Cited by 45
Microbial pathogenesis in inflammatory bowel diseases
Kumar, S., & Kumar, A. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105383 · Cited by 50
Host Factors Associated with Gut Mycobiome Structure
Szóstak, N., Handschuh, L., Samelak-Czajka, A., Tomela, K., SCHMIDT, M. T., Pruss, Ł., Milanowska, K., Kozłowski, P., & Philips, A. (2023) · mSystems · doi:10.1128/msystems.00986-22 · Cited by 49
“reports (6), whereas the Sporisorium genus was not previously described as a member of”
BackgroundMethodResultInfluentialPhylogenetics and the Human Microbiome
Matsen, F. A., IV (2014) · Systematic Biology · doi:10.1093/sysbio/syu053 · Cited by 47
“Changes in archaeal and fungal populations have been shown to covary with bacterial residents (Hoffmann et al. 2013) and have a nonuniform distribution across the human skin (Findley et al.”
BackgroundHu, Y., Ye, Z., Wu, M., She, Y., Li, L., Xu, Y.-J., Qin, K., Hu, Z., Yang, M., Lu, F., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.766126 · Cited by 44
“And meat-based diets promote the abundance of Penicillium fungi (58, 59).”
BackgroundBroecker, F., Klumpp, J., & Moelling, K. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13100 · Cited by 43
Gutiérrez-Sarmiento, W., Sáyago‐Ayerdi, S. G., Goñi, I., Gutiérrez-Miceli, F. A., Abud‐Archila, M., Rejón-Orantes, J. D. C., Rincón-Rosales, R., Peña-Ocaña, B. A., & Ruíz-Valdiviezo, V. M. (2020) · Nutrients · doi:10.3390/nu12030683 · Cited by 46
“Nitrososphaera is an ammonia-oxidizing and degraded urea member associated with the ingestion of proteins and amino acids from the diet [40].”
BackgroundGoing Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease
Houshyar, Y., Massimino, L., Lamparelli, L. A., Danese, S., & Ungaro, F. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.783295 · Cited by 42
“, 2020) and their colonization rate ranges from 25 to 95% of human stools (Stewart et al., 2006; Dridi et al., 2009; Hoffmann et al., 2013).”
BackgroundSobocki, B. K., Kaźmierczak-Siedlecka, K., Folwarski, M., Hawryłkowicz, V., Makarewicz, W., & Stachowska, E. (2021) · Nutrients · doi:10.3390/nu13124425 · Cited by 43
The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei
Li, J., Jiang, H., Li, L., Zhang, X., & Chen, J. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00889 · Cited by 42
“It has been reported that Candida species had a higher level in hosts with carbohydrate diets (Hoffmann et al., 2013).”
Background
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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