The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
1 retracted
RETRACTED: Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal
Hamad, I., Sokhna, C., Raoult, D., & Bittar, F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040888 · Cited by 99 · cited 1×
“We detected no fewer than 62 fungal genera and 184 species level OTUs, paralleling and extending a study of one subject, which also yielded a high number of fungal lineages [35].”
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×
“Sequences obtained were decoded and quality controlled using the QIIME pipeline [54].”
MethodSelf-citationMeasures of the Amount of Ecologic Association Between Species
Dice, L. R. (1945) · Ecology · doi:10.2307/1932409 · Cited by 12,187 · cited 1×
“Co-occurrence The Dice index [58] was used to determine the co-occurrence of genera across the entire dataset.”
MethodGardes, M., & Bruns, T. (1993) · Molecular Ecology · doi:10.1111/j.1365-294x.1993.tb00005.x · Cited by 10,249 · cited 1×
“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
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · cited 1×
“Inspection of published work showed detection of Nitrosophaera in metagenomic sequences from one of two individuals studied by [25], and in both 16S and metagenomic sequences in another cohort [41].”
BackgroundHuman gut microbiome viewed across age and geography
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×
“Inspection of published work showed detection of Nitrosophaera in metagenomic sequences from one of two individuals studied by [25], and in both 16S and metagenomic sequences in another cohort [41].”
BackgroundInfluentialEnterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548
The ade4 Package: Implementing the Duality Diagram for Ecologists
Dray, S., & Dufour, A. (2007) · Journal of Statistical Software · doi:10.18637/jss.v022.i04 · Cited by 6,740
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · cited 10×
“Bacterial 16S sequences data and diet data from [10] was used here.”
BackgroundMethodInfluentialThe Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873 · cited 1×
“Taxonomy was assigned to OTU representative sequences using the RDPclassifier [55] for archaeal sequences and BROCC [36] for fungal sequences.”
Method
Flagged first, then by citations
Cited by
Sorted by citations
Items 301–400 of 815
Li, J., Chen, D., Yu, B., He, J., Huang, Z., Mao, X., Zheng, P., Yu, J. Z., Luo, J., Tian, G., et al. (2019) · Microbial Biotechnology · doi:10.1111/1751-7915.13507 · Cited by 44
“Our results showed that Basidiomycota and Ascomycota were the two most predominant fungal phyla in the faeces of pigs, which is consistent with previous findings in the gut of humans and mice (Scupham et al., 2006; Hoffmann et al., 2013; Hallen-Adams et al., 2015).”
BackgroundResultInfluentialThe triple interactions between gut microbiota, mycobiota and host immunity
Yang, J., Yang, H., & Li, Y. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2022.2094888 · Cited by 44
“A carbohydrate-rich diet promoted the colonization of Candida in the gut, while SCFAs produced through microbial metabolism significantly reduced the number of Aspergillus spp. (Hoffmann et al. 2013).”
BackgroundFrom Birth and Throughout Life: Fungal Microbiota in Nutrition and Metabolic Health
Fiers, W. D., Leonardi, I., & Iliev, I. D. (2020) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-013120-043659 · Cited by 42
“Changes within the mycobiota correlate with the much larger bacterial community dynamics, resulting in increases in obligate anaerobic genera such as Bacteroides(52, 133).”
BackgroundResultInfluentialAssembly and dynamics of the apple carposphere microbiome during fruit development and storage
Zhimo, V. Y., Kumar, A., Biasi, A., Abdelfattah, A., Sharma, V. K., Salim, S., Feygenberg, O., Bartuv, R., Freilich, S., Whitehead, S. R., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.928888 · Cited by 47
Jiang, H., Wu, C., Li, S., Huang, M., Lin, L., Su, Q., Li, G., Ahmad, H. I., Li, L., Zhang, X., et al. (2020) · MicrobiologyOpen · doi:10.1002/mbo3.1050 · Cited by 38
“This difference may be associated with the high protein content in the tiger diet, because Candida was negatively correlated with diets high in amino acids, proteins, and fatty acids, but was positively correlated with diets high in carbohydrates (Hoffmann et al., 2013).”
BackgroundThe gut mycobiome: a novel player in chronic liver diseases
Jiang, L., Stärkel, P., Fan, J., Fouts, D. E., Bächer, P., & Schnabl, B. (2020) · Journal of Gastroenterology · doi:10.1007/s00535-020-01740-5 · Cited by 42
“In healthy subjects, there was low fungal amplification, and the few fungal reads present in healthy lung samples comprised largely environmental agents such as Davidiellaceae, Cladosporium, and low abundances of Aspergillus [20].”
BackgroundPreterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts
James, S. A., Phillips, S., Telatin, A., Baker, D., Ansorge, R., Clarke, P., Hall, L. J., & Carding, S. R. (2020) · Journal of Fungi · doi:10.3390/jof6040273 · Cited by 45
“albicans in particular being frequently identified both in the infant and adult gut [33,34,53,55,56], as well as in other body sites, including the oral cavity and vagina [50,51,57].”
BackgroundKaźmierczak-Siedlecka, K., Daca, A., Roviello, G., Catalano, M., & Połom, K. (2021) · Gastric Cancer · doi:10.1007/s10120-021-01260-y · Cited by 40
“The most common genera which reside human gut are Candida, Saccharomyces as well as Cladosporium [23, 24].”
BackgroundThe Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy
Gamal, A., Elshaer, M. Y. S., Alabdely, M. H., Kadry, A., McCormick, T. S., & Ghannoum, M. A. (2022) · Cancers · doi:10.3390/cancers14122875 · Cited by 42
“, and Saccharomyces cerevisiae, is the most dominant phylum, accounting for >90% relative abundance at various body sites, followed by Basidiomycota and Zygomycota phyla [10,12,16,17].”
BackgroundDing, T., Liu, C., & Li, Z. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02227-8 · Cited by 44
“C . albicans has been identified as the most abundant fungal species in the human gut [58].”
Natural mummification of the human gut preserves bacteriophage DNA
Santiago-Rodríguez, T. M., Fornaciari, G., Luciani, S., Dowd, S. E., Toranzos, G. A., Marota, I., & Cano, R. J. (2015) · FEMS Microbiology Letters · doi:10.1093/femsle/fnv219 · Cited by 39
“The human gut microbiome is home to diverse communities comprised of bacteria, archaea and eukaryotes (Yatsunenko et al. 2012; Hoffmann et al. 2013); yet, an increasing number of studies have demonstrated that the human gut is also inhabited by diverse viral communities, many of which are…”
BackgroundContrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research
Hooks, K. B., & O’Malley, M. A. (2019) · Journal of Eukaryotic Microbiology · doi:10.1111/jeu.12766 · Cited by 41
“For example, Methanobrevibacter (a genus of Archaea) and Candida were found to correlate positively in the gut shortly after the host eats large amounts of carbohydrate, and negatively in a high-fat, protein diet (Hoffmann et al. 2013).”
BackgroundMercer, E. M., Ramay, H. R., Moossavi, S., Laforest‐Lapointe, I., Reyna, M. E., Becker, A. B., Simons, E., Mandhane, P. J., Turvey, S. E., Moraes, T. J., et al. (2024) · Microbiome · doi:10.1186/s40168-023-01735-3 · Cited by 35
Taguer, M., & Maurice, C. F. (2016) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.366 · Cited by 38
Basson, A. R., Lam, M. C., & Cominelli, F. (2017) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2017.08.002 · Cited by 38
Siriyappagouder, P., Kiron, V., Lokesh, J., Rajeish, M., Kopp, M., & Fernandes, J. M. O. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00387 · Cited by 38
“The dynamic fungal population in the intestine is under the influence of the environment and pathophysiology (Iliev et al., 2012; Dollive et al., 2013; Hoffmann et al., 2013).”
BackgroundVo, T. D., Lynch, B. S., & Roberts, A. S. (2018) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12410 · Cited by 39
Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls, and Challenges
Duperron, S., Halary, S., Gallet, A., & Marie, B. (2020) · Frontiers in Public Health · doi:10.3389/fpubh.2020.00407 · Cited by 41
“However, numerous studies have demonstrated the significance of Archaea and microbial Eukaryotes, including fungi, to host physiology (33, 34), and the key role of phages in regulating bacterial populations (35, 36).”
BackgroundNiu, W., Yang, F., Fu, Z., Dong, Y., Zhang, Z., & Ju, J. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105381 · Cited by 39
Effect of diet on the gut mycobiome and potential implications in inflammatory bowel disease
Buttar, J., Kon, E., Lee, A. H., Kaur, G., & Lunken, G. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2399360 · Cited by 41
“139 Additionally, Pizzo et al. found that high intakes of fructose, glucose, maltose, and sucrose increased the adhesion of Candida species ( C.albicans, C.tropicalis , and C.krusei ) to epithelial cells.”
BackgroundFungal symbiont transmitted by free-living mice promotes type 2 immunity
Liao, Y., Gao, I. H., Kusakabe, T., Lin, W.-Y., Grier, A. R., Pan, X., Morzhanaeva, O., Shea, T., Yano, H., Karo‐Atar, D., et al. (2024) · Nature · doi:10.1038/s41586-024-08213-2 · Cited by 41
“In humans, gut fungi and bacteria coexist, influencing immunity and colonization resistance 11,16,24 .”
Intestinal Microbiota: Facts and Fiction
Kverka, M., & Tlaskalová-Hogenová, H. (2017) · Digestive Diseases · doi:10.1159/000449095 · Cited by 37
Mooser, C., de Agüero, M. G., & Ganal-Vonarburg, S. C. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.07.007 · Cited by 37
Witchley, J. N., Basso, P., Brimacombe, C. A., Abon, N. V., & Noble, S. M. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.019 · Cited by 38
The Modification of the Gut Microbiota via Selected Specific Diets in Patients with Crohn’s Disease
Knez, E., Wzorek, K., Folwarski, M., Kaźmierczak-Siedlecka, K., Stachowska, L., Przewłócka, K., Stachowska, E., & Skonieczna‐Żydecka, K. (2021) · Nutrients · doi:10.3390/nu13072125 · Cited by 41
“Those carbohydrates are substrates for Prevotella and Ruminococcus, producing resources consumed by Methanobrevibacter for methane (CH4) and carbon dioxide (CO2) production [111].”
BackgroundThe human gut mycobiome and the specific role of Candida albicans: where do we stand, as clinicians?
Musumeci, S., Coen, M., Leidi, A., & Schrenzel, J. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.07.034 · Cited by 37
Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health
Duncan, S. H., Conti, E., Ricci, L., & Walker, A. W. (2023) · Biomedicines · doi:10.3390/biomedicines11051338 · Cited by 40
“The abundance of Candida species has been shown to significantly correlate with the consumption of carbohydrate-rich foods [36,37].”
BackgroundMale Tract Microbiota and Male Infertility
Grande, G., Graziani, A., Toni, L. D., Garolla, A., & Ferlin, A. (2024) · Cells · doi:10.3390/cells13151275 · Cited by 38
“On the other hand, in healthy subjects, a diet high in protein is linked to a lower quantity of Methanobrevibacter and Candida species [65].”
BackgroundVujanovic, V., Islam, N., & Daida, P. (2019) · Scientific Reports · doi:10.1038/s41598-019-54328-2 · Cited by 36
Runge, S., & Rosshart, S. P. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.702378 · Cited by 36
The Human Gut Microbiome in Liver Diseases
Davis, B., & Bajaj, J. (2017) · Seminars in Liver Disease · doi:10.1055/s-0037-1602763 · Cited by 34
Engineering chemical interactions in microbial communities
Kenny, D. J., & Balskus, E. P. (2017) · Chemical Society Reviews · doi:10.1039/c7cs00664k · Cited by 40
Metabolic networks of the human gut microbiota
Selber‐Hnatiw, S., Sultana, T., Tse, W., Abdollahi, N., Abdullah, S., Rahbani, J. A., Alazar, D., Alrumhein, N. J., Aprikian, S., Arshad, R., et al. (2019) · Microbiology · doi:10.1099/mic.0.000853 · Cited by 38
Schierová, D., Roubalová, R., Kolář, M., Stehlíková, Z., Rob, F., Jackova, Z., Coufal, Š., Thon, T., Mihula, M., Modrák, M., et al. (2021) · Cells · doi:10.3390/cells10113188 · Cited by 36
“Importantly, fungi detected in stool can be just transient visitors of the gut [67] and heavily depend on diet composition [68,69] hence masking the effect of the treatment.”
BackgroundThe evidence for fungus in Crohn’s disease pathogenesis
Miyoshi, J., Sofia, M., & Pierre, J. F. (2018) · Clinical Journal of Gastroenterology · doi:10.1007/s12328-018-0886-9 · Cited by 37
Organ-specific mechanisms linking innate and adaptive antifungal immunity
Drummond, R. A., & Lionakis, M. S. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.01.008 · Cited by 33
Rhodotorula spp. in the gut – foe or friend?
Hof, H. (2019) · Europe PMC (PubMed Central) · doi:10.3205/id000042 · Cited by 34
“It has been discussed that several yeast antigens, for example mannans, mannoproteins as well as several enzymes such as enolase, in the gut may stimulate the intestinal and furthermore the systemic immune system leading to hypersensitivity against inhaled as well as ingested antigens [35], [36], [37], [38].”
BackgroundPoolchanuan, P., Unagul, P., Thongnest, S., Wiyakrutta, S., Ngamrojanavanich, N., Mahidol, C., Ruchirawat, S., & Kittakoop, P. (2020) · Scientific Reports · doi:10.1038/s41598-020-66251-y · Cited by 34
Gut non-bacterial microbiota contributing to alcohol-associated liver disease
Gao, W., Zhu, Y., Ye, J., & Chu, H. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1984122 · Cited by 35
Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis
Cai, M., Kandalai, S., Tang, X., & Zheng, Q. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02367-21 · Cited by 33
Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals
Maas, E., Penders, J., & Venema, K. (2023) · Journal of Fungi · doi:10.3390/jof9020139 · Cited by 34
“When using the ITS regions for the identification of fungi, the whole ITS region can be used, but the separate use of the ITS1 and ITS2 is described [1,9,10].”
MethodYin, G., Chen, F., Chen, G., Yang, X., Huang, Q., Chen, L., Chen, M., Zhang, W., Ou, M., Cao, M., et al. (2022) · Journal of Ovarian Research · doi:10.1186/s13048-022-01051-8 · Cited by 35
Harrison, X. A., McDevitt, A. D., Dunn, J. C., Griffiths, S. M., Benvenuto, C., Birtles, R. J., Boubli, J. P., Bown, K. J., Bridson, C., Brooks, D. R., et al. (2021) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2021.0552 · Cited by 34
Liu, H., Han, X., Zhao, N., Hu, L., Wang, X., Luo, C., Chen, Y., Zhao, X., & Xu, S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.949002 · Cited by 35
“When H2 accumulates during bacterial catabolism, archaeal growth is stimulated by H2 incorporation into greenhouse gases (GHG) such as methane and carbon dioxide (Matarazzo et al., 2012; Hoffmann et al., 2013).”
BackgroundLi, J., Li, J. L., Xie, Y., Wang, Y., Shen, X. N., Qian, Y., Han, J., Chen, Y., & Fang, J. (2020) · Journal of Digestive Diseases · doi:10.1111/1751-2980.12930 · Cited by 32
“being among the most commonly encountered genera.(6) Previous studies have revealed significant fungal microbial dysbiosis in digestive diseases.”
BackgroundInorganic nanoparticles as food additives and their influence on the human gut microbiota
Gangadoo, S., Nguyen, N. H., Rajapaksha, P., Zreiqat, H., Latham, K., Cozzolino, D., Chapman, J., & Truong, V. K. (2021) · Environmental Science Nano · doi:10.1039/d1en00025j · Cited by 33
Symbiosis and Dysbiosis of the Human Mycobiome
Mishra, K., Bukavina, L., & Ghannoum, M. A. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.636131 · Cited by 34
Gutierrez, M. W., Bernardes, E. V. T., Changirwa, D., McDonald, B., & Arrieta, M. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00515-w · Cited by 34
Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology
Liu, H., Li, S., Ogamune, K. J., Ahmed, A. A., Kim, I. H., Zhang, Y., & Cai, D. (2025) · Microorganisms · doi:10.3390/microorganisms13010070 · Cited by 36
“In vivo, the abundance of C. albicans displayed a negative correlation with amino acid content [179].”
Gut Mycobiota and Fungal Metabolites in Human Homeostasis
Mogilnicka, I., & Ufnal, M. (2018) · Current Drug Targets · doi:10.2174/1389450119666180724125020 · Cited by 31
Panelli, S., Epis, S., Cococcioni, L., Perini, M., Paroni, M., Bandi, C., Drago, L., & Zuccotti, G. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104962 · Cited by 30
Salamon, D., Sroka-Oleksiak, A., Gurgul, A., Arent, Z., Szopa, M., Bulanda, M., Malecki, M. T., & Gosiewski, T. (2021) · Nutrients · doi:10.3390/nu13041066 · Cited by 32
“The gut mycobiota composition seems to be influenced by diet, including consumption of carbohydrates, which correlate positively with fungi of the genus Candida [14].”
BackgroundInfluentialMicrobiota as the unifying factor behind the hallmarks of cancer
Benešová, I., Křížová, Ľ., & Kverka, M. (2023) · Journal of Cancer Research and Clinical Oncology · doi:10.1007/s00432-023-05244-6 · Cited by 34
“Human gut microbiota forms a complex ecosystem that consists of more than 1000 species of bacteria, over 140 thousand viruses, mostly bacteriophages, and a less diverse ecosystem of archaea and fungi (Camarillo-Guerrero et al. 2021; Kim et al. 2020; Hoffmann et al. 2013; Qin et al. 2010).”
BackgroundThapa, R., Magar, A. T., Shrestha, J., Panth, N., Idrees, S., Sadaf, T., Bashyal, S., Elwakil, B. H., Sugandhi, V. V., Rojekar, S. V., et al. (2024) · MedComm · doi:10.1002/mco2.70018 · Cited by 33
Culturing Human Gut Microbiomes in the Laboratory
Renwick, S., Ganobis, C. M., Elder, R., Gianetto-Hill, C., Higgins, G., Robinson, A. V., Vancuren, S. J., Wilde, J., & Allen‐Vercoe, E. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-031021-084116 · Cited by 30
A Synthetic System That Senses Candida albicans and Inhibits Virulence Factors
Tscherner, M., Giessen, T. W., Markey, L., Kumamoto, C. A., & Silver, P. A. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00457 · Cited by 30
Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases
Avershina, E., Qureshi, A., Winther-Larsen, H. C., & Rounge, T. B. (2025) · Microbiome · doi:10.1186/s40168-025-02048-3 · Cited by 31
“Ascomycota is the most prevalent phylum in the gut of healthy individuals, with Basidiomycota following closely behind [2, 3].”
InfluentialBamboo nutrients and microbiome affect gut microbiome of giant panda
Jin, L., Wu, D., Li, C., Zhang, A., Xiong, Y., Wei, R., Zhang, G., Yang, S., Deng, W., Li, T., et al. (2020) · Symbiosis · doi:10.1007/s13199-020-00673-0 · Cited by 28
“The dominant phyla in human (Christian et al. 2013), dog (Stefanie et al.”
BackgroundFunctional food addressing heart health: do we have to target the gut microbiota?
Ryan, P. M., Ross, R. P., Fitzgerald, G. F., Caplice, N. M., & Stanton, C. (2015) · Current Opinion in Clinical Nutrition and Metabolic Care · doi:10.1097/mco.0000000000000224 · Cited by 28
“Archaea have largely been an overlooked component of the human gut microbiome, which were recently reported as being present at detectable levels in approximately half of a healthy cohort [60].”
BackgroundFukuyama, J. (2019) · Genome biology · doi:10.1186/s13059-019-1735-y · Cited by 28
Health Impact and Therapeutic Manipulation of the Gut Microbiome
Daliri, E. B., Ofosu, F. K., Chelliah, R., Lee, B. H., & Oh, D. (2020) · Microarrays · doi:10.3390/ht9030017 · Cited by 28
Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV
Gosalbes, M. J., Jiménez‐Hernández, N., Moreno, E., Artacho, A., Pons, X., Ruíz-Pérez, S., Navia, B., Estrada, V., Manzano, M., Talavera-Rodríguez, A., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2089002 · Cited by 30
“35 However, in healthy controls, Faecalibacterium prausnitzii inversely correlated with different fungal species, such as Malassezia restricta, Rhodotorula mucilaginosa , and Meyerozyma guilliermondii .”
BackgroundInfluentialHuman milk mycobiota composition: relationship with gestational age, delivery mode, and birth weight
Dinleyici, M., Pérez‐Brocal, V., Arslanoğlu, S., Aydemir, Ö., Ozumut, S. S., Tekın, N., Vandenplas, Y., Moyá, A., & Dinleyici, E. Ç. (2020) · Beneficial Microbes · doi:10.3920/bm2019.0158 · Cited by 28
NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation
Anderson, J. M., Lipinski, S., Sommer, F., Pan, W.-H., Boulard, O., Rehman, A., Falk‐Paulsen, M., Stengel, S. T., Aden, K., Häsler, R., et al. (2020) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2020.03.008 · Cited by 27
“Our findings are supported by a study investigating the role of diet and microbial interactions on gut fungi that also identified numerous correlations between Prevotella and fungal taxa as possible means of influencing host health.(57) To formally test whether the alterations of the postantibiotic microbiota, which w…”
ResultInitiation and Pathogenesis of Severe Asthma with Fungal Sensitization
Tiwary, M., & Samarasinghe, A. E. (2021) · Cells · doi:10.3390/cells10040913 · Cited by 30
The microbiome impacts host hybridization and speciation
Miller, A. K., Westlake, C. S., Cross, K. L., Leigh, B. A., & Bordenstein, S. R. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001417 · Cited by 27
Fungal dysbiosis of the gut microbiota is associated with colorectal cancer in Chinese patients.
Wang, Y., Ren, Y., Huang, Y., Yu, X., Yang, Y., Wang, D., Shi, L., Tao, K.-X., Wang, G., & Wu, K. (2021) · PubMed Central · Cited by 27
Praneenararat, S. (2014) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s67776 · Cited by 28
“can also be found as a component of human colonic mycobiota.(62) Zygomycetes can be divided into two orders, Mucorales and Entomophthorales.”
The Mycobiome: Impact on Health and Disease States
El‐Jurdi, N., & Ghannoum, M. A. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.funk-0045-2016 · Cited by 27
The Role of Yeasts in Human Health: A Review
Caetano, C. F., Gaspar, C., Martinez‐de‐Oliveira, J., Palmeira‐de‐Oliveira, A., & Rolo, J. (2023) · Life · doi:10.3390/life13040924 · Cited by 31
Gut Microbiota Modulation in IBD: From the Old Paradigm to Revolutionary Tools
Murgiano, M., Bartocci, B., Puca, P., Vincenzo, F. D., GAUDIO, A. D., Papa, A., Cammarota, G., Gasbarrini, A., Scaldaferri, F., & Lopetuso, L. R. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26073059 · Cited by 30
“More than 90% of the human gut microbiota belongs to four main phyla: Firmicutes , Bacteroidetes , Actinobacteria , and Proteobacteria [41,42].”
Szabó, G. (2018) · Hepatology · doi:10.1002/hep.30055 · Cited by 26
“Studies in healthy individuals revealed 66 different fungal genera in the fecal material where the most common genera were Saccharomyces, Candida, and Cladosporium (2).”
BackgroundThe Hologenome Concept of Evolution: Medical Implications
ROSENBERG, E. B., & Zilber‐Rosenberg, I. (2019) · Rambam Maimonides Medical Journal · doi:10.5041/rmmj.10359 · Cited by 28
Lv, J., Niu, Y., Yuan, R., & Wang, S. (2021) · Microorganisms · doi:10.3390/microorganisms9040782 · Cited by 26
“Consistent with this view, archaea found in many ecosystems, such as seawater [90], hydrothermal vents [91], and subsurface surfaces [92], whereas microbial communities associated with humans [93] are less diverse, which is due to archaea evolving more slowly than bacteria.”
Fungi, host immune response, and tumorigenesis
Elaskandrany, M., Patel, R., Patel, M. M., Miller, G., Saxena, D., & Saxena, A. D. (2021) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00025.2021 · Cited by 28
Marfil-Sánchez, A., Zhang, L., Alonso-Pernas, P., Mirhakkak, M. H., Mueller, M., Seelbinder, B., Ni, Y., Santhanam, R., Busch, A., Beemelmanns, C., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1993598 · Cited by 31
“, and Cladosporium spp.(25,26) Despite the recent findings showcasing the fungal role on host health, host–microbe and microbe– microbe interactions, only less than 0.”
BackgroundAmoroso, M., Langgartner, D., Lowry, C. A., & Reber, S. O. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222312938 · Cited by 28
Analyzing the human gut mycobiome – A short guide for beginners
Thielemann, N., Herz, M., Kurzai, O., & Martin, R. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.01.008 · Cited by 28
The ileal fungal microbiota is altered in Crohn's disease and is associated with the disease course
Olaisen, M., Richard, M. L., Beisvåg, V., Granlund, A. V. B., Røyset, E. S., Rué, O., Martinsen, T. C., Sandvik, A. K., Sokol, H., & Fossmark, R. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.868812 · Cited by 27
Chen, Q., Fan, Y., Zhang, B., Yan, C., Chen, Z., Wang, L., Hu, Y., Huang, Q., Su, J., Ren, J., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.1086885 · Cited by 25
“Following published reports, Ascomycota and Basidiomycota were the dominant fungal fecal microbiota in both donors and UC patients (Hoffmann et al., 2013; Chehoud et al., 2015; Mukherjee et al., 2015; Richard et al., 2015).”
BackgroundBiopolymers modulate microbial communities in municipal organic waste digestion
Bandini, F., Misci, C., Taskin, E., Cocconcelli, P. S., & Puglisi, E. (2020) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaa183 · Cited by 26
The clinical implications of the microbiome in the development of allergy diseases
Koidl, L., & Untersmayr, E. (2021) · Expert Review of Clinical Immunology · doi:10.1080/1744666x.2021.1874353 · Cited by 25
Worsley, S. F., Davies, C. S., Mannarelli, M., Komdeur, J., Dugdale, H. L., & Richardson, D. S. (2022) · Microbiome · doi:10.1186/s40168-022-01432-7 · Cited by 26
Epigenetic determinants of phenotypic plasticity in Candida albicans
Rai, L. S., Singha, R., Brahma, P., & Sanyal, K. (2017) · Fungal Biology Reviews · doi:10.1016/j.fbr.2017.07.002 · Cited by 24
The Microbiome in Inflammatory Bowel Disease
Jauregui-Amezaga, A., & Smet, A. (2024) · Journal of Clinical Medicine · doi:10.3390/jcm13164622 · Cited by 28
“However, other intestinal microorganisms, such as fungi, protozoa, viruses, and bacteriophages, may be involved in the pathogenesis of IBD [3].”
BackgroundWang, Y., Chen, J., Ni, Y., Liu, Y., Xiang, G., Tse, M. A., Panagiotou, G., & Xu, A. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2416928 · Cited by 24
“12 Likewise, low-calorie diet intervention could effectively restore the Mucor abundance in obese patients.”
BackgroundEukaryotic and Prokaryotic Microbiota Interactions
Kodio, A., Menu, E., & Ranque, S. (2020) · Microorganisms · doi:10.3390/microorganisms8122018 · Cited by 25
García-Durán, C., Martínez‐López, R., Zapico, I., Pérez, E., Romeu, E., Arroyo, J., Hernáez, M. L., Pitarch, A., Monteoliva, L., & Gil, C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.618566 · Cited by 23
“The KOs related to SCFA production that were assigned to Bacteroidetes were not directly involved in the biosynthetic pathway, instead, they were related to acetyl-CoA production from pyruvate and the interconversion of succinate-fumarate (Figure S1).”
ResultInfluentialThe biomolecular gastrointestinal corona in oral drug delivery
Aljabbari, A., Kihara, S., Rades, T., & Boyd, B. J. (2023) · Journal of Controlled Release · doi:10.1016/j.jconrel.2023.09.049 · Cited by 26
A new actinomycete from a Guadalupian vertebrate coprolite from Brazil
Dentzien‐Dias, P., Poinar, G. O., & Francischini, H. (2016) · Historical Biology · doi:10.1080/08912963.2016.1241247 · Cited by 24
“However, while commonly associated with the decomposition of organic matter, evidence of actinomycetes in the fossil record is rare and poorly documented in coprolites (Williams et al. 1984; Hunt et al. 1994; Slater et al. 2012; Hoffmann et al. 2013; Taylor et al. 2015).”
BackgroundEkine-Afolabi, B. A., Njan, A. A., Rotimi, S. O., I, A. R., Elbehi, M. A., Cash, E. D., & Adeyeye, A. A. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.583372 · Cited by 25
“are recognized as integrant of the human colonic mycobiota (91).”
BackgroundGut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly DanesPreprint
Ahmad, H. F., Castro-Mejía, J. L., Krych, Ł., Khakimov, B., Kot, W., Bechshøft, R. L., Reitelseder, S., Højfeldt, G. W., Engelsen, S. B., Holm, L., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.16.044693 · Cited by 24
Candeliere, F., Solà, L., Raimondi, S., Rossi, M., & Amaretti, A. (2024) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2023.12.007 · Cited by 20
“For instance, Methanobrevibacter was positively associated with diets rich in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids [8,34] and was also observed at a large scale, also among multiple animal species [9].”
BackgroundHameed, S., Hans, S., Monasky, R. C., Thangamani, S., & Fatima, Z. (2021) · Pathogens · doi:10.3390/pathogens10020183 · Cited by 24
“More consistently found fungi are also restricted, with the genera Candida and Saccharomyces being the prominent ones [26].”
Assessment of the gut bacterial microbiome and metabolome of girls and women with Rett Syndrome
Thapa, S., Venkatachalam, A., Khan, N., Naqvi, M., Balderas, M. A., Runge, J. K., Haag, A. M., Hoch, K. M., Glaze, D. G., Luna, R. A., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251231 · Cited by 23
“Diet has a significant impact on the composition and function of the gut microbiome [64, 65].”
BackgroundAn Integrated Multi-Disciplinary Perspective for Addressing Challenges of the Human Gut Microbiome
Shah, R., McKenzie, E. J., Rosin, M., Jadhav, S. R., Gondalia, S. V., Rosendale, D., & Beale, D. J. (2020) · Metabolites · doi:10.3390/metabo10030094 · Cited by 25
“The degree of richness, complexity and function of the regional gut microbiome is highly dependent on the microenvironmental conditions, nutrients, oxygen and water availability, as well as host site‐specific characteristics [24].”
BackgroundYu, D., Xie, L., Chen, W., Qin, J., Zhang, J., Lei, M., Wang, Y., Tang, H., Xue, S., Liang, X., et al. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.846378 · Cited by 23
Rizzetto, L., Weil, T., & Cavalieri, D. (2015) · Pathogens · doi:10.3390/pathogens4030639 · Cited by 21
“albicans, a permanent member of the human microbiota, present on the skin [3], oral cavity [4], vagina [5,6] and gut mucosa [7] in 30%–70% of healthy individuals.”
BackgroundVega, L., Herrera, G., Muñoz, M., Patarroyo, M. A., Maloney, J. G., Santı́n, M., & Ramírez, J. D. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248185 · Cited by 22
The emerging role of the gut mycobiome in liver diseases
Szóstak, N., Figlerowicz, M., & Philips, A. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2211922 · Cited by 22
“For example, there is an association between the high prevalence of Saccharomyces and the consumption of yeast-containing foods such as beer and bread.(11) Furthermore, even focusing on alcoholism, the mechanisms leading to gut mycobiota dysbiosis in chronic alcohol uptake are unclear.”
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
