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 101–200 of 815
The intestinal microbiota and metabolites in patients with anorexia nervosa
Procházková, P., Roubalová, R., Dvořák, J., Kreisinger, J., Hill, M., Tlaskalová‐Hogenová, H., Tomášová, P., Pelantová, H., Cermakova, M., Kuzma, M., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1902771 · Cited by 145
“related to mycobiome changes associated with diet.(31) One explanation could be the use of primers amplifying the ITS1 region, when primer sequence mismatches may not allow optimal amplification of Malassezia DNA.”
BackgroundFungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions
Li, J., Chen, D., Yu, B., He, J., Zheng, P., Mao, X., Yu, J., Luo, J., Tian, G., Huang, Z., et al. (2017) · Microbial Ecology · doi:10.1007/s00248-017-1105-9 · Cited by 142
“Sequencing analysis based on the 18S rRNA of colonic biopsy mucosa tissues and stool samples of ulcerative colitis patients and healthy individuals showed that the fungal communities between the two groups were remarkably different, and the ulcerative colitis patients were heavily colonized with C. albicans [16], caus…”
InfluentialDigestive tract mycobiota: a source of infection
Gouba, N., & Drancourt, M. (2015) · Médecine et Maladies Infectieuses · doi:10.1016/j.medmal.2015.01.007 · Cited by 138
Candida albicans commensalism in the gastrointestinal tract
Neville, B. A., d’Enfert, C., & Bougnoux, M. (2015) · FEMS Yeast Research · doi:10.1093/femsyr/fov081 · Cited by 141
“These analyses (Hoffmann et al. 2013; David et al. 2014), however, are limited to a discussion of the effect of diet on the genus Candida, rather than on C. albicans or any other Candida species specifically.”
BackgroundMethodInfluentialLongitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization
Raimondi, S., Amaretti, A., Gozzoli, C., Simone, M., Righini, L., Candeliere, F., Brun, P., Ardizzoni, A., Colombari, B., Paulone, S., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01575 · Cited by 143
“Previous studies and the data herein presented consistently indicated Aspergillus, Candida, Debaryomyces, Malassezia, Penicillium, Pichia, and Saccharomyces as the most recurrent and/or dominant fungal genera.”
BackgroundInfluentialHigh-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut
Heisel, T. J., Montassier, E., Johnson, A. J., Al‐Ghalith, G. A., Lin, Y.-W., Wei, L.-N., Knights, D., & Gale, C. A. (2017) · mSphere · doi:10.1128/msphere.00351-17 · Cited by 138
“Candida and bacterial genera Prevotella, Ruminococcus, and Methanobrevibacter (30).”
BackgroundInfluentialMucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease
Basson, A. R., Trotter, A., Rodriguez‐Palacios, A., & Cominelli, F. (2016) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00290 · Cited by 140
Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome
Borrel, G., McCann, A., Deane, J., Neto, M. C., Lynch, D. B., Brugère, J., & O’Toole, P. W. (2017) · The ISME Journal · doi:10.1038/ismej.2017.72 · Cited by 137
“In order to determine the prevalence and abundance of Methanomassiliicoccales representatives in the human microbiome, we made a census of Methanomassiliicoccales sequences present in 10 studies on the human gut microbiota (Mihajlovski et al., 2008; Scanlan et al., 2008; Mihajlovski et al., 2010; Hoffmann et al., 2013…”
BackgroundMethodThe gut microbiome of Mexican children affected by obesity
Maya, O., Murugesan, S., Nirmalkar, K., Alcaraz, L. D., Hoyo‐Vadillo, C., Pizano-Zárate, M. L., & Garcı́a-Mena, J. (2018) · Anaerobe · doi:10.1016/j.anaerobe.2018.10.009 · Cited by 131
Santus, W., Devlin, J. R., & Behnsen, J. (2021) · Infection and Immunity · doi:10.1128/iai.00648-20 · Cited by 142
Sequence-based methods for detecting and evaluating the human gut mycobiome
Haute, M. J. S. V., Banjara, N., & Hallen‐Adams, H. E. (2015) · Letters in Applied Microbiology · doi:10.1111/lam.12539 · Cited by 131
“Common environmental fungi that are also commonly detected in faecal samples (Cladosporium [Hoffmann et al. 2013], Aspergillus, Penicillium and Fusarium) need further investigation to determine which species may actually persist to play any role in gut ecology and which can be discounted based on…”
Methanogenic archaea in the human gastrointestinal tract
Högenauer, C., Hammer, H. F., Mahnert, A., & Moissl‐Eichinger, C. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00673-z · Cited by 129
Myasthenia Gravis: Paradox versus paradigm in autoimmunity
Berrih‐Aknin, S. (2014) · Journal of Autoimmunity · doi:10.1016/j.jaut.2014.05.001 · Cited by 129
“While the general composition of the intestinal microbiota is similar in most healthy people, the species composition is highly personalized and determined by environment and diet [160, 161].”
BackgroundImmunity to Commensal Fungi: Detente and Disease
Wheeler, M. L., Limon, J. J., & Underhill, D. M. (2017) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-052016-100342 · Cited by 124
“cerevisiae are common residents of human skin and gastrointestinal tract (49, 50).”
Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases
Iliev, I. D., & Cadwell, K. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.06.100 · Cited by 128
Iron at the Centre of Candida albicans Interactions
Fourie, R., Kuloyo, O. O., Mochochoko, B. M., Albertyn, J., & Pohl, C. H. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00185 · Cited by 118
“In addition, members of the microbiome may drastically affect the growth of co-habitants (Hoffmann et al., 2013).”
BackgroundNovel ITS1 Fungal Primers for Characterization of the Mycobiome
Usyk, M., Zolnik, C. P., Patel, H., Levi, M. H., & Burk, R. D. (2017) · mSphere · doi:10.1128/msphere.00488-17 · Cited by 125
Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body
Pausan, M.-R., Csorba, C., Singer, G., Till, H., Schöpf, V., Santigli, E., Klug, B., Högenauer, C., Blohs, M., & Moissl‐Eichinger, C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02796 · Cited by 121
“Such archaea are regularly detected in the oral cavity and the gastrointestinal tract (Horz and Conrads, 2011; Gaci et al., 2014; Chaudhary et al., 2015; Nkamga et al., 2017).”
BackgroundYan, Q., Li, S., Yan, Q., Huo, X., Wang, C., Wang, X., Sun, Y., Zhao, W., Yu, Z., Zhang, Y., et al. (2024) · Cell · doi:10.1016/j.cell.2024.04.043 · Cited by 127
Bacterial microbiome of lungs in COPD
Sin, D. D., Sze, M. A., & Hogg, J. C. (2014) · International Journal of COPD · doi:10.2147/copd.s38932 · Cited by 125
Zhang, Z., Li, J. J., Zheng, W., Zhao, G., Zhang, H., Wang, X., Guo, Y., Qin, C., & Shi, Y. (2016) · Immunity · doi:10.1016/j.immuni.2016.01.004 · Cited by 121
“In human, this strain is uncommon in the gut microbiota (Hoffmann et al., 2013).”
Boix-Amorós, A., Puente‐Sánchez, F., du Toit, E., Linderborg, K. M., Zhang, Y., Yang, B., Salminen, S., Isolauri, E., Tamames, J., Mira, Á., et al. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02994-18 · Cited by 124
Giuffrè, M., Campigotto, M., Campisciano, G., Comar, M., & Crocè, L. S. (2020) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00161.2019 · Cited by 122
Ng, S. C., Kamm, M. A., Yeoh, Y. K., Chan, P. K. S., Zuo, T., Tang, W., Sood, A., Andoh, A., Ohmiya, N., Zhou, Y., et al. (2019) · Gut · doi:10.1136/gutjnl-2019-319407 · Cited by 121
Mims, T. S., Abdallah, Q. A., Stewart, J. D., Watts, S., White, C. T., Rousselle, T. V., Gosain, A., Bajwa, A., Han, J. C., Willis, K. A., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01820-z · Cited by 119
A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease?
Forbes, J. D., Bernstein, C. N., Tremlett, H. L., Domselaar, G. V., & Knox, N. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03249 · Cited by 122
“, 2010) and an early study which included 96 stool samples from healthy volunteers found 66 genera (Hoffmann et al., 2013).”
BackgroundInfluentialThe Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis
Enaud, R., Vandenborght, L., Coron, N., Bazin, T., Prével, R., Schaeverbeke, T., Berger, P., Fayon, M. J., Lamireau, T., & Delhaès, L. (2018) · Microorganisms · doi:10.3390/microorganisms6010022 · Cited by 122
“Briefly, the fungal composition of gut flora is influenced by several factors such as age, host genetics, host immunity, diet, and medication [32,33], as well as the bacterial microbiome that also impacts the mycobiome through inter-kingdom interactions [33].”
BackgroundResultInfluentialRichard, M. L., Lamas, B., Liguori, G., Hoffmann, T. W., & Sokol, H. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000261 · Cited by 118
Exploring the impact of Helicobacter pylori on gut microbiome composition
Dash, N. R., Khoder, G., Nada, A. M., & Bataineh, M. T. A. (2019) · PLoS ONE · doi:10.1371/journal.pone.0218274 · Cited by 118
Hygiene and other early childhood influences on the subsequent function of the immune system
Rook, G. A. W., Lowry, C. A., & Raison, C. L. (2015) · Brain Research · doi:10.1016/j.brainres.2014.04.004 · Cited by 109
“Diet, apart from the issue of duration (if any) of breastfeeding, has received little attention in infants, but it has profound effects on all components of the gut microbiota (Hoffmann et al., 2013; Wu et al., 2011).”
Teoh, F., & Pavelka, N. (2016) · Pathogens · doi:10.3390/pathogens5010006 · Cited by 121
“albicans colonizes the GI tract of most healthy individuals [19,132], it might thus have ample opportunity to get exposed to chemotherapeutic drugs in cancer patients undergoing treatment, and to be likewise affected by them.”
BackgroundThe role of gut mycobiome in health and diseases
Zhang, L., Zhan, H., Xu, W., Yan, S., & Ng, S. C. (2021) · Therapeutic Advances in Gastroenterology · doi:10.1177/17562848211047130 · Cited by 118
The Human Mycobiome: Colonization, Composition and the Role in Health and Disease
Belvončíková, P., Šplíchalová, P., Videnska, P., & Gardlík, R. (2022) · Journal of Fungi · doi:10.3390/jof8101046 · Cited by 115
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Hansen, M. E. B., Rubel, M. A., Bailey, A. G., Ranciaro, A., Thompson, S. R., Campbell, M. C., Beggs, W., Dave, J. R., Mokone, G. G., Mpoloka, S. W., et al. (2019) · Genome Biology · doi:10.1186/s13059-018-1616-9 · Cited by 110
Self-citationMetagenomic assessment of the global diversity and distribution of bacteria and fungi
Bahram, M., Netherway, T., Frioux, C., Ferretti, P., Coelho, L. P., Geisen, S., Bork, P., & Hildebrand, F. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15314 · Cited by 108
“Aside from other abiotic factors, the composition of microbial communities appears to depend on the prevailing and dominant available source of organic carbon (C) in a given habitat (Hoffmann et al., 2013).”
BackgroundAssociation between Gut Dysbiosis and the Occurrence of SIBO, LIBO, SIFO and IMO
Banaszak, M., Górna, I., Woźniak, D., Przysławski, J., & Drzymała-Czyż, S. (2023) · Microorganisms · doi:10.3390/microorganisms11030573 · Cited by 113
“[10] determined that Candida and Saccharomyces fungi positively correlate with Methanobrevibacter archaea and Prevotella bacteria.”
BackgroundThe Fungal Frontier: A Comparative Analysis of Methods Used in the Study of the Human Gut Mycobiome
Huseyin, C. E., Cabrera‐Rubio, R., O’Sullivan, Ó., Cotter, P. D., & Scanlan, P. D. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01432 · Cited by 108
“Fungi are present in the gastrointestinal tracts of humans as commensal organisms (Scanlan and Marchesi, 2008; Hallen-Adams et al., 2015) and transient colonizers (Gouba et al., 2013, 2014; Hoffmann et al., 2013), but also as opportunistic pathogens (Gouba and Drancourt, 2015).”
InfluentialA straightforward and efficient analytical pipeline for metaproteome characterization
Tanca, A., Palomba, A., Pisanu, S., Deligios, M., Fraumene, C., Manghina, V., Pagnozzi, D., Addis, M. F., & Uzzau, S. (2014) · Microbiome · doi:10.1186/s40168-014-0049-2 · Cited by 106
“Furthermore, in view of the apparently low amount of fungal and archaeal sequences within the metagenome (which may be due to biases in DNA extraction, or a consequence of an actual under-representation of such microbial members within the MFM), we decided to append additional UniProtKB entries belonging to fungal gen…”
InfluentialReynoso-García, J., Miranda-Santiago, A. E., Meléndez-Vázquez, N. M., Acosta-Pagán, K. T., Rosado, M. R. S., Díaz-Rivera, J., Rosado-Quiñones, A. M., Acevedo-Márquez, L., Cruz-Roldán, L., Tosado-Rodríguez, E. L., et al. (2022) · Frontiers in Systems Biology · doi:10.3389/fsysb.2022.951403 · Cited by 117
“Other non-bacterial components of the colonmicrobiome, which are also important residents, include bacteriophages, fungi such as Ascomycota and Basidiomycota, and archaea such asMethanobrevibacter smithii (Hoffmann et al., 2013).”
BackgroundThe bacteriome–mycobiome interaction and antifungal host defense
ten Oever, J., & Netea, M. G. (2014) · European Journal of Immunology · doi:10.1002/eji.201344405 · Cited by 106
Hamad, I., Ranque, S., Azhar, E. I., Yasir, M., Jiman-Fatani, A. A., Tissot‐Dupont, H., Raoult, D., & Bittar, F. (2017) · Scientific Reports · doi:10.1038/s41598-017-17132-4 · Cited by 105
RetractedFactors shaping the abundance and diversity of the gut archaeome across the animal kingdom
Thomas, C. M., Quéméner, E. D., Gribaldo, S., & Borrel, G. (2022) · Nature Communications · doi:10.1038/s41467-022-31038-4 · Cited by 113
Fungal interactions with the human host: exploring the spectrum of symbiosis
Hall, R. A., & Noverr, M. C. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.020 · Cited by 110
“Mycobiome studies have been performed for most mucosal surfaces including the oral cavity [6], GI tract [7,8],”
Sethi, V., Vitiello, G. A., Saxena, D. B., Miller, G., & Dudeja, V. (2019) · Gastroenterology · doi:10.1053/j.gastro.2018.12.045 · Cited by 104
Nishimoto, A. T., Sharma, C., & Rogers, P. D. (2020) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkz400 · Cited by 102
Zeise, K. D., Woods, R. J., & Huffnagle, G. B. (2021) · Clinical Microbiology Reviews · doi:10.1128/cmr.00323-20 · Cited by 107
Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat
Pitta, D. W., Pinchak, W. E., Indugu, N., Vecchiarelli, B., Sinha, R., & Fulford, J. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00689 · Cited by 100
“Microbial communities in diverse settings have been shown to form syntrophic communities, in which end products from one microbe form the substrate for another (Hoffmann et al., 2013).”
BackgroundMethodInfluentialThe Gut-Liver Axis in Cholestatic Liver Diseases
Blesl, A., & Stadlbauer, V. (2021) · Nutrients · doi:10.3390/nu13031018 · Cited by 102
Pareek, S., Kurakawa, T., Das, B., Motooka, D., Nakaya, S., Rongsen‐Chandola, T., Goyal, N. P., Kayama, H., Dodd, D., Okumura, R., et al. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-019-0110-9 · Cited by 91
Overview of the Potential Role of Malassezia in Gut Health and Disease
Spatz, M., & Richard, M. L. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00201 · Cited by 99
Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers
Hajjo, R., Sabbah, D. A., & Bawab, A. Q. A. (2022) · Diagnostics · doi:10.3390/diagnostics12071742 · Cited by 105
“The gut flora supports and optimizes the functionality of the GIT [98,99].”
BackgroundSoldi, S., Vasileiadis, S., Uggeri, F., Campanale, M. C., Morelli, L., Calanni, F., Grimaldi, M., Gasbarrini, A., & Fogli, M. V. (2015) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s89999 · Cited by 98
Wu, L. H., Zeng, T., Deligios, M., Milanesi, L., Langille, M. G. I., Zinellu, A., Rubino, S., Carru, C., & Kelvin, D. J. (2020) · mSphere · doi:10.1128/msphere.00558-19 · Cited by 96
“Previous studies have shown that diet can modulate the fungal communities in the murine gut (61).”
BackgroundGut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy
Jayasudha, R., Das, T., Chakravarthy, S. K., Prashanthi, G. S., Bhargava, A., Tyagi, M., Rani, P. K., Pappuru, R. R., & Shivaji, S. (2020) · PLoS ONE · doi:10.1371/journal.pone.0243077 · Cited by 98
“Discrepancy in identification of a genus or genera could also be due to the differences in methodologies or in the cohorts itself as observed in volunteers from Houston and Pennsylvania for the genusMalassezia [70, 71].”
BackgroundThe microbiota and helminths: sharing the same niche in the human host
Glendinning, L., Nausch, N., Free, A., Taylor, D. W., & Mutapi, F. (2014) · Parasitology · doi:10.1017/s0031182014000699 · Cited by 100
“Apart from other bacteria, there are several parasites ranging from viruses, fungi, protozoans and helminths that can share the gastro-intestinal niche with bacteria (McKenna et al. 2008; Parfrey et al. 2011; Hoffmann et al. 2013).”
BackgroundTranscriptional control of hyphal morphogenesis in Candida albicans
Villa, S., Hamideh, M., Weinstock, A., Qasim, M. N., Hazbun, T. R., Sellam, A., Hernday, A. D., & Thangamani, S. (2020) · FEMS Yeast Research · doi:10.1093/femsyr/foaa005 · Cited by 104
“Candida albicans is a commensal and opportunistic fungal pathogen that resides within the gastrointestinal tract (Hoffmann et al. 2013; Noble, Gianetti and Witchley 2017), the female reproductive system (Drell et al.”
BackgroundMontoya-Ciriaco, N. M., Gómez-Acata, S., Muñoz-Arenas, L. C., Dendooven, L., Estrada‐Torres, A., de la Vega-Pérez, A. H. D., & Navarro‐Noya, Y. E. (2020) · Microbiome · doi:10.1186/s40168-020-0783-6 · Cited by 97
Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
Raymann, K., Moeller, A. H., Goodman, A. L., & Ochman, H. (2017) · mSphere · doi:10.1128/msphere.00026-17 · Cited by 100
“members of distinct gut enterotypes (40), so their cooccurrence in all great ape species was not anticipated, although later studies have reported positive associations between these taxa (29, 41).”
Infant fungal communities: current knowledge and research opportunities
Ward, T., Knights, D., & Gale, C. A. (2017) · BMC Medicine · doi:10.1186/s12916-017-0802-z · Cited by 98
“1% of the microbes in the adult intestine are fungi, and these fungi are estimated to represent approximately 60 unique species [2, 3].”
BackgroundInfluentialA Molecular Window into the Biology and Epidemiology of Pneumocystis spp
Ma, L., Cissé, O. H., & Kovacs, J. A. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00009-18 · Cited by 98
Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria
Kapitan, M., Niemiec, M. J., Steimle, A., Frick, J.-S., & Jacobsen, I. D. (2018) · Current topics in microbiology and immunology · doi:10.1007/82_2018_117 · Cited by 101
The mammalian mycobiome: A complex system in a dynamic relationship with the host
Lai, G. C., Tan, T. G., & Pavelka, N. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1438 · Cited by 92
“Similarly, Candida abundance is found to be strongly associated with recent ingestion of carbohydrates (Hoffmann et al., 2013).”
BackgroundGarcia‐Carbonell, R., Yao, S.-J., Das, S., & Gumá, M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01094 · Cited by 92
Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease
Liang, G., Conrad, M. A., Kelsen, J. R., Kessler, L. R., Breton, J., Albenberg, L. G., Marakos, S., Galgano, A. C., Devas, N., Erlichman, J., et al. (2020) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjaa094 · Cited by 94
Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study
Borgo, F., Verduci, E., Riva, A., Lassandro, C., Riva, E., Morace, G., & Borghi, E. (2016) · Childhood Obesity · doi:10.1089/chi.2015.0194 · Cited by 98
RETRACTED: Eukaryote Culturomics of the Gut Reveals New Species
Gouba, N., Raoult, D., & Drancourt, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106994 · Cited by 90
“Indeed, of twelve studies, three issued from individuals in Europe [4,7,8], three from the USA [6,12,14], two from China [3,15], one from India [16], one from Turkey [17], one from Korea [11] and one from Senegal [5].”
BackgroundResultInfluentialRetractedKantarcioglu, A. S., Kiraz, N., & Aydin, A. (2016) · Mycopathologia · doi:10.1007/s11046-015-9949-3 · Cited by 89
The Potential Role of Gut Mycobiome in Irritable Bowel Syndrome
Gu, Y., Zhou, G., Qin, X., Huang, S., Wang, B., & Cao, H. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01894 · Cited by 87
“Emerging evidence proposes that managements targeted at pathophysiologic mechanisms could be more effective and economical (Chang and Talley, 2010; Mayer et al., 2015; Holtmann et al., 2017).”
Fungal Gut Microbiota Dysbiosis and Its Role in Colorectal, Oral, and Pancreatic Carcinogenesis
Kaźmierczak-Siedlecka, K., Dvořák, A., Folwarski, M., Daca, A., Przewłócka, K., & Makarewicz, W. (2020) · Cancers · doi:10.3390/cancers12051326 · Cited by 90
“Its composition varies individually; however, Candida, Saccharomyces, and Cladosporium are the most common genera residing in the healthy human gut [13].”
BackgroundInfluentialA systematic review on the role of microbiota in the pathogenesis and treatment of eating disorders
Carbone, E. A., D'Amato, P., Vicchio, G., Fazio, P. D., & Segura‐Garcìa, C. (2020) · European Psychiatry · doi:10.1192/j.eurpsy.2020.109 · Cited by 99
“smithii (methane producers) seem to increase significantly in the intestinal epithelium of malnourished patients, providing a more efficient and increased supply of energy and calories [25,63,64].”
BackgroundRoles of the gut virome and mycobiome in faecal microbiota transplantation
Lam, S., Bai, X., Shkoporov, A. N., Park, H., Wu, X., Lan, P., & Zuo, T. (2022) · The Lancet. Gastroenterology & hepatology · doi:10.1016/s2468-1253(21)00303-4 · Cited by 89
Helminth–Bacterial Interactions: Cause and Consequence
Rapin, A., & Harris, N. L. (2018) · Trends in Immunology · doi:10.1016/j.it.2018.06.002 · Cited by 89
The Gut Microbiota in Inflammatory Bowel Disease
Sheehan, D., & Shanahan, F. (2017) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2016.09.011 · Cited by 88
Cuffaro, B., Assohoun, A. L. W., Boutillier, D., Súkeníková, L., Desramaut, J., Boudebbouze, S., Salomé‐Desnoulez, S., Hrdý, J., Waligora‐Dupriet, A., Maguin, E., et al. (2020) · Cells · doi:10.3390/cells9092104 · Cited by 91
Hager, C. L., & Ghannoum, M. A. (2017) · Digestive and Liver Disease · doi:10.1016/j.dld.2017.08.025 · Cited by 88
Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis
Qiu, X., Ma, J., Jiao, C., Mao, X., Zhao, X., Lu, M., Wang, K., & Zhang, H. (2017) · Oncotarget · doi:10.18632/oncotarget.22534 · Cited by 87
“Lim [26] showed that Trametes versicolor has antiinflammatory properties in attenuating colitis in murine IBD.”
BackgroundInfluentialAssessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review
Cuadros-Orellana, S. (2013) · Fungal Genomics & Biology · doi:10.4172/2165-8056.1000110 · Cited by 84
“[127] suggested a syntrophic association.”
Stewart, H. L., Southwood, L. L., Indugu, N., Vecchiarelli, B., Engiles, J. B., & Pitta, D. (2018) · Equine Veterinary Journal · doi:10.1111/evj.13010 · Cited by 84
Review article: fungal alterations in inflammatory bowel diseases
Lam, S., Zuo, T., Ho, M., Chan, F. K. L., Chan, P. K. S., & Ng, S. C. (2019) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.15523 · Cited by 87
Singh, A., Kumari, R., Yadav, A. N., Mishra, S. K., Sachan, A., & Sachan, S. G. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820526-6.00001-4 · Cited by 84
Biodiversity of the human oral mycobiome in health and disease
Bandara, N., Panduwawala, C., & Samaranayake, L. P. (2018) · Oral Diseases · doi:10.1111/odi.12899 · Cited by 85
Chong, C. W., Ahmad, A. F., Lim, Y. A. L., Teh, C. S. J., Yap, I. K. S., Lee, S. C., Chin, Y. T., Loke, P., & Chua, K. H. (2015) · Scientific Reports · doi:10.1038/srep13338 · Cited by 83
Saeed, H., Díaz, L. A., Gil‐Gómez, A., Burton, J. P., Bajaj, J. S., Romero‐Gómez, M., Arrese, M. A., Arab, J. P., & Khan, M. Q. (2024) · Clinical and Molecular Hepatology · doi:10.3350/cmh.2024.0811 · Cited by 84
“Furthermore, a complex syntrophic relationship between the mycobiome and microbiome has also been postulated to be influenced by a carbohydrate-rich diet 121 .”
Host–microbe interactions: commensal fungi in the gut
Paterson, M. J., Oh, S., & Underhill, D. M. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.11.012 · Cited by 82
Characterization of the fecal microbiota of healthy horses
Stewart, H. L., Pitta, D., Indugu, N., Vecchiarelli, B., Engiles, J. B., & Southwood, L. L. (2018) · American Journal of Veterinary Research · doi:10.2460/ajvr.79.8.811 · Cited by 84
Jenkins, T. P., Formenti, F., Castro, C., Piubelli, C., Perandin, F., Buonfrate, D., Otranto, D., Griffin, J. L., Krause, L., Bisoffi, Z., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-33937-3 · Cited by 79
Malmuthuge, N., Liang, G., Griebel, P. J., & Guan, L. L. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02534-18 · Cited by 82
“S1B), which were the most abundant fungi identified in the present study, was also reported in a metagenomics-based study conducted using fecal samples of healthy humans (21).”
BackgroundRizzetto, L., Filippo, C. D., & Cavalieri, D. (2014) · European Journal of Immunology · doi:10.1002/eji.201344403 · Cited by 79
The fungal microbiota of de-novo paediatric inflammatory bowel disease
Mukhopadhya, I., Hansen, R., Meharg, C., Thomson, J., Russell, R. K., Berry, S. H., El-Omar, E. M., & Hold, G. L. (2014) · Microbes and Infection · doi:10.1016/j.micinf.2014.12.001 · Cited by 78
“A recent fungal mycobiome analysis of healthy subject faecal samples demonstrated positivity in all subject samples tested (around 100 subjects) finding 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota [22].”
BackgroundAlshehri, D., Saadah, O. I., Mosli, M. H., Edris, S., Al-Hindi, R. R., & Bahieldin, A. (2020) · Biomolecules and Biomedicine · doi:10.17305/bjbms.2020.5016 · Cited by 82
“smithii, Saccharomyces, and Candida are frequently found together in individuals that have carbohydrate-rich diets (34).”
BackgroundInfluentialMycobiome and Cancer: What Is the Evidence?
Vallianou, N. G., Kounatidis, D. C., Christodoulatos, G. S., Panagopoulos, F., Karampela, Ι., & Dalamaga, Μ. (2021) · Cancers · doi:10.3390/cancers13133149 · Cited by 75
“CRC morbidity and mortality may be diminished by appropriate screening and surveillance [48,49].”
BackgroundKumar, M., Garand, M., & Khodor, S. A. (2019) · Journal of Translational Medicine · doi:10.1186/s12967-019-02174-1 · Cited by 81
The Inuit gut microbiome is dynamic over time and shaped by traditional foods
Dubois, G., Girard, C., Lapointe, F., & Shapiro, B. J. (2017) · Microbiome · doi:10.1186/s40168-017-0370-7 · Cited by 77
Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
Arfken, A. M., Frey, J. F., & Summers, K. L. (2020) · Microorganisms · doi:10.3390/microorganisms8060868 · Cited by 75
“In particular, a negative correlation between SCFAs and potential fungal pathogen Aspergillus has been demonstrated in human diets [50] and several SCFAs have been shown to negatively correlate with relative abundances of Aspergillus in piglet digesta samples [5].”
BackgroundAlterations of the gut mycobiome in patients with MS
Shah, S., Locca, A., Dorsett, Y., Cantoni, C., Ghezzi, L., Lin, Q., Bokoliya, S. C., Panier, H. A., Suther, C., Gormley, M., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103557 · Cited by 75
“…fi ed Saccharomyces ( » 20% relative abundance), Malassezia (4% relative abundance), and Candida (2% relative abundance) as the dominant genera in healthy samples [5], while Hoffman et al. identi fi ed Saccharomyces, Candida , and Cladosporium as the most abundant in healthy control samples [45].”
BackgroundGut Microbiome: Profound Implications for Diet and Disease
Hills, R. D., Pontefract, B., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2022) · Kompass Nutrition & Dietetics · doi:10.1159/000523712 · Cited by 79
“In a mouse model, M. smithii has been shown to increase host adiposity by directing Bacteroides thetaiotaomicron to ferment plant polysaccharides (fructans) in the diet to the SCFA acetate [257].”
BackgroundInfluentialMotooka, D., Fujimoto, K., Tanaka, R. J., Yaguchi, T., Gotoh, K., Maeda, Y., Furuta, Y., Kurakawa, T., Goto, N., Yasunaga, T., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00238 · Cited by 75
“Various genera of fungi have been detected in mycobiota analyses of the healthy human gut, and the genera Saccharomyces, Candida, and Cladosporium have been detected in particularly high percentages (Schulze and Sonnenborn, 2009; Chen et al., 2011; Dollive et al., 2012; Hoffmann et al., 2013).”
BackgroundResultThe Human Mucosal Mycobiome and Fungal Community Interactions
Witherden, E. A., Shoaie, S., Hall, R. A., & Moyes, D. L. (2017) · Journal of Fungi · doi:10.3390/jof3040056 · Cited by 74
“When the authors evaluated the bacterial-fungal relationships in this dataset, they identified a number of significant correlations, including a significant negative correlation between the abundance of Rothia and Cladosporium in the oral cavity of healthy individuals, although no mechanistic justification for this co…”
BackgroundInfluentialThe interplay between gut bacteria and the yeast Candida albicans
Pérez, J. C. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1979877 · Cited by 82
Unraveling the Role of the Human Gut Microbiome in Health and Diseases
Khalil, M., Ciaula, A. D., Mahdi, L., Jaber, N., Palo, D. M. D., Graziani, A., Baffy, G., & Portincasa, P. (2024) · Microorganisms · doi:10.3390/microorganisms12112333 · Cited by 100
“Hoffmann et al. [173] investigated the associations of diet with fungal and archaeal populations in well-characterized individuals.”
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
