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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Members of the microbiome may drastically affect the growth of co-habitants.
“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
Carbohydrate consumption is associated with the proportion of the archaeon Methanobrevibacter in the intestinal microbiota.
“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]
Diet has been associated with other gut microbes, including archaea, fungi, and bacteriophage.
“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]
Infections with C. albicans range from superficial mucosal and dermatological infections to life-threatening infections of the bloodstream and vital organs.
“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<i>Candida albicans</i> (2020) · cites this paper as [1]
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Strains, functions and dynamics in the expanded Human Microbiome Project
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works
Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation
Fujimura, K. E., Sitarik, A. R., Havstad, S. L., Lin, D. L., Levan, S., Fadrosh, D. W., Panzer, A. R., LaMere, B. J., Rackaityte, E., Lukacs, N. W., et al. (2016) · Nature Medicine · doi:10.1038/nm.4176 · Cited by 1,168 · see citing works
Gut Microbiome: Profound Implications for Diet and Disease
Hills, R. D., Pontefract, B., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2019) · Nutrients · doi:10.3390/nu11071613 · Cited by 1,107 · see citing works
The gut mycobiome of the Human Microbiome Project healthy cohort
Nash, A. K., Auchtung, T. A., Wong, M. C., Smith, D. P., Gesell, J. R., Ross, M. C., Stewart, C. J., Metcalf, G., Muzny, D. M., Gibbs, R. A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0373-4 · Cited by 987 · see citing works
“In a study investigating correlations of archaea and fungi with diet, volunteers had an abundance of Candida and Saccharomyces species in their stool, with high Candida abundance associated with recent consumption of carbohydrates [9].”
BackgroundLewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works
“Graphical abstract INTRODUCTION The human gut microbiota is densely populated by microbes from all three domains of life together with their viruses (Hoffmann et al., 2013; Human Microbiome Project, 2012; Samuel et al., 2007).”
BackgroundInfluentialLagier, J., Hugon, P., Khelaifia, S., Fournier, P., Scola, B. L., & Raoult, D. (2015) · Clinical Microbiology Reviews · doi:10.1128/cmr.00014-14 · Cited by 839 · see citing works
The amazing potential of fungi: 50 ways we can exploit fungi industrially
Hyde, K. D., Xu, J., Rapior, S., Jeewon, R., Lumyong, S., Niego, A. G. T., Abeywickrama, P. D., Aluthmuhandiram, J. V. S., Brahamanage, R. S., Brooks, S., et al. (2019) · Fungal Diversity · doi:10.1007/s13225-019-00430-9 · Cited by 826 · see citing works
Sartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808 · see citing works
Bacterial–fungal interactions: ecology, mechanisms and challenges
Deveau, A., Bonito, G. M., Uehling, J., Paoletti, M., Becker, M., Bindschedler, S., Hacquard, S., Hervé, V., Labbé, J., Lastovetsky, O. A., et al. (2018) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuy008 · Cited by 790 · see citing works
Khan, I., Ullah, N., Zha, L., Bai, Y., Khan, A., Zhao, T., Che, T., & Zhang, C. (2019) · Pathogens · doi:10.3390/pathogens8030126 · Cited by 771 · see citing works
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Shkoporov, A. N., & Hill, C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.017 · Cited by 760 · see citing works
“Instead, it seems that the metabolic cost of resistance leads to slower growth of bacteria, while the generally lower efficiency of generalist phages toward a particular host prevents them from taking over the specialists (Howard-Varona et al., 2018).”
BackgroundHuman gut microbiota in health and disease: Unveiling the relationship
Afzaal, M., Saeed, F., Shah, Y. A., Hussain, M., Rabail, R., Socol, C. T., Hassoun, A., Pateiro, M., Lorenzo, J. M., Rusu, A. V., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.999001 · Cited by 762 · see citing works
“It is a prominent and essential Archean in the gut microbiota (Hoffmann et al., 2013; Berry, 2016).”
BackgroundEnaud, R., Prével, R., Ciarlo, E., Beaufils, F., Wieërs, G., Guery, B. P., & Delhaès, L. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00009 · Cited by 762 · see citing works
The mycobiota: interactions between commensal fungi and the host immune system
Underhill, D. M., & Iliev, I. D. (2014) · Nature reviews. Immunology · doi:10.1038/nri3684 · Cited by 696 · see citing works
Current and Past Strategies for Bacterial Culture in Clinical Microbiology
Lagier, J., Edouard, S., Pagnier, I., Mediannikov, O., Drancourt, M., & Raoult, D. (2015) · Clinical Microbiology Reviews · doi:10.1128/cmr.00110-14 · Cited by 657 · see citing works
“An increased prevalence of Methanobrevibacter spp. correlated, albeit nonsignificantly, with short-term and long-term carbohydrate ingestion (160), as was the case in anorexic patients (175), whereas the prevalence of Nitrososphaera spp. correlated, albeit…”
BackgroundEngineering Microbiomes to Improve Plant and Animal Health
Mueller, U. G., & Sachs, J. L. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.07.009 · Cited by 628 · see citing works
“Microbiomes of animals and plants are often dominated by eubacteria, but fungi, protozoa, archaea, and viruses also can play important roles in these communities [1–5].”
BackgroundDiet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606 · see citing works
The Role of Lung and Gut Microbiota in the Pathology of Asthma
Barcik, W., Boutin, R. C. T., Sokołowska, M., & Finlay, B. B. (2020) · Immunity · doi:10.1016/j.immuni.2020.01.007 · Cited by 618 · see citing works
The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease
Zuo, T., & Ng, S. C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02247 · Cited by 590 · see citing works
Microbial Ecology along the Gastrointestinal Tract
Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017) · Microbes and Environments · doi:10.1264/jsme2.me17017 · Cited by 586 · see citing works
“Transkingdom commensal relationships among microbiota (including Viruses) are considered to form from infancy (29, 30, 106, 200) and several co-occurring relationships have been identified (35, 75, 76, 85, 214).”
BackgroundInfluentialThe hologenome concept of evolution after 10 years
ROSENBERG, E. B., & Zilber‐Rosenberg, I. (2018) · Microbiome · doi:10.1186/s40168-018-0457-9 · Cited by 532 · see citing works
“The gut microbiome also contains abundant and diverse viruses [12] and fungi [13], but they have not been studied extensively.”
BackgroundFungi in the healthy human gastrointestinal tract
Hallen‐Adams, H. E., & Haute, M. J. S. V. (2016) · Virulence · doi:10.1080/21505594.2016.1247140 · Cited by 528 · see citing works
Candida albicans cell-type switching and functional plasticity in the mammalian host
Noble, S. M., Gianetti, B. A., & Witchley, J. N. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.157 · Cited by 518 · see citing works
Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer
Coker, O. O., Nakatsu, G., Dai, R. Z., Wu, W. K. K., Wong, S. H., Ng, S. C., Chan, F. K. L., Sung, J. J. Y., & Yu, J. (2019) · Gut · doi:10.1136/gutjnl-2018-317178 · Cited by 511 · see citing works
Mycotoxin: Its Impact on Gut Health and Microbiota
Liew, W.-P.-P., & Sabran, M. R. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00060 · Cited by 472 · see citing works
“Nevertheless, the gut microbiota has recently become a blooming research area (Hoffmann et al., 2013).”
BackgroundMahmud, M. R., Akter, S., Tamanna, S. K., Mazumder, L., Esti, I. Z., Banerjee, S., Akter, S., Hasan, M. R., Acharjee, M., Hossain, M. S., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2096995 · Cited by 498 · see citing works
“Retrieved from https://app.biorender.com/biorender-templates, associated information based on .25–27,28 and Thermoplasma.33,35 Viruses and phages, on the other hand, can act as reservoirs of genetic material in the gut and destroy microbial cells.36”
BackgroundInfluentialZhang, J., Guo, Z., Xue, Z., Sun, Z., Zhang, M., Wang, L., Wang, G., Wang, F., Xu, J., Cao, H., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.11 · Cited by 458 · see citing works
“%) was relatively higher than that reported previously (Dridi et al., 2009, Hoffmann et al., 2013, Lecours et al., 2014).”
BackgroundResultThe Human Microbiome and Its Impacts on Health
Ogunrinola, G. A., Oyewale, J. O., Oshamika, O. O., & Olasehinde, G. I. (2020) · International Journal of Microbiology · doi:10.1155/2020/8045646 · Cited by 459 · see citing works
“Also, the intestinal microbiota helps to improve and maintain the gastrointestinal functions [31].”
BackgroundArchaea and the Human Gut: New Beginning of an Old Story
Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W., & Brugère, J.-F. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i43.16062 · Cited by 422 · see citing works
The Gut Microbiota in Immune-Mediated Inflammatory Diseases
Forbes, J. D., Domselaar, G. V., & Bernstein, C. N. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01081 · Cited by 430 · see citing works
“Figure 1 shows a schematic illustration of the interaction between the immune system and gut microbiota in IMID.”
BackgroundCommunity characteristics of the gut microbiomes of competitive cyclists
Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., Sodergren, E., & Weinstock, G. M. (2017) · Microbiome · doi:10.1186/s40168-017-0320-4 · Cited by 377 · see citing works
“smithii is positively associated with diets high in carbohydrates [22].”
BackgroundRichard, M. L., & Sokol, H. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0121-2 · Cited by 414 · see citing works
Ménage à trois in the human gut: interactions between host, bacteria and phages
Mirzaei, M. K., & Maurice, C. F. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.30 · Cited by 404 · see citing works
Zhang, F., Aschenbrenner, D., Yoo, J. Y., & Zuo, T. (2022) · The Lancet Microbe · doi:10.1016/s2666-5247(22)00203-8 · Cited by 406 · see citing works
Fungal dysbiosis: immunity and interactions at mucosal barriers
Iliev, I. D., & Leonardi, I. (2017) · Nature reviews. Immunology · doi:10.1038/nri.2017.55 · Cited by 392 · see citing works
Host–microorganism interactions in lung diseases
Marsland, B. J., & Gollwitzer, E. S. (2014) · Nature reviews. Immunology · doi:10.1038/nri3769 · Cited by 351 · see citing works
d’Enfert, C., Kaune, A.-K., Alaban, L. R., Chakraborty, S., Cole, N. L., Delavy, M., Kosmala, D., Marsaux, B., Fróis-Martins, R., Morelli, M., et al. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa060 · Cited by 351 · see citing works
Commensal Fungi in Health and Disease
Limon, J. J., Skalski, J. H., & Underhill, D. M. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.07.002 · Cited by 336 · see citing works
“In a study looking at human fecal material from 96 healthy individuals, a total of 66 fungal genera were reported (Hoffmann et al., 2013).”
BackgroundFungal Dysbiosis in Mucosa-associated Microbiota of Crohn’s Disease Patients
Liguori, G., Lamas, B., Richard, M. L., Brandi, G., Costa, G. D., Hoffmann, T. W., Simone, M. P. D., Calabrese, C., Poggioli, G., Langella, P., et al. (2015) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjv209 · Cited by 332 · see citing works
Chong, P.-P., Chin, V., Looi, C., Wong, W., Madhavan, P., & Yong, V. C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01136 · Cited by 293 · see citing works
Mitsou, E. K., Kakali, A., Antonopoulou, S., Mountzouris, K. C., Yannakoulia, M., Panagiotakos, D. B., & Kyriacou, A. (2017) · British Journal of Nutrition · doi:10.1017/s0007114517001593 · Cited by 325 · see citing works
“Candida and other yeasts are associated with features of diet((43,44)), and the connection of high adherence with increased levels of yeasts could be attributed to ingestion of foodstuff that are carriers of yeasts, such as fruits, juices and fermented food products((44,45)).”
Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria
Jiang, T. T., Shao, T., Ang, W. X. G., Kinder, J. M., Turner, L. H., Pham, G. H., Whitt, J., Alenghat, T., & Way, S. S. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.10.013 · Cited by 296 · see citing works
“…Overturns Disease Susceptibility Induced by Commensal Bacteria Depletion Saccharomyces cerevisiae, another yeast naturally found in the mammalian gut (Hoffmann et al., 2013; Sokol et al., 2017), was used to evaluate whether these protective benefits are shared by other species of commensal fungi.”
BackgroundGut microbiota as a source of novel antimicrobials
García-Gutiérrez, E., Mayer, M. J., Cotter, P. D., & Narbad, A. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1455790 · Cited by 295 · see citing works
“Despite the fact that bacteria have been most extensively studied, there are other groups of microbes in the human GI tract that have not been as well researched but have an important role in the ecological dynamics, like archaea, viruses and eukaryotes.(10,20) Archaea is represented by Euryarcheota and Crenarchaeota.”
BackgroundInvestigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi
Auchtung, T. A., Fofanova, T. Y., Stewart, C. J., Nash, A. K., Wong, M. C., Gesell, J. R., Auchtung, J. M., Ajami, N. J., & Petrosino, J. F. (2018) · mSphere · doi:10.1128/msphere.00092-18 · Cited by 290 · see citing works
“(37) observed a positive correlation between fecal Candida levels and the consumption of carbohydrates.”
BackgroundGut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD
Matijašić, M., Meštrović, T., Paljetak, H. Č., Perić, M., Barešić, A., & Verbanac, D. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082668 · Cited by 293 · see citing works
“Reports suggest that the human gut is populated by three fungal phyla, Ascomycota, Basidiomycota, and Zygomycota [25,26], with the “core” 10 genera identified in the majority of gastrointestinal tract samples consisting of Candida (particularly C.”
BackgroundInfluentialForgotten fungi—the gut mycobiome in human health and disease
Huseyin, C. E., O’Toole, P. W., Cotter, P. D., & Scanlan, P. D. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw047 · Cited by 275 · see citing works
“For example, Candida and Saccharomyces specieswere positively correlated with the Archaea Methanobrevibacter and both fungal species were also negatively correlated with Nitrososphaera prevalence in one study of the gut mycobiome (Hoffmann et al. 2013).”
BackgroundMethodResultInfluentialGut microbiomes of wild great apes fluctuate seasonally in response to diet
Hicks, A. L., Lee, K. J., Couto-Rodriguez, M., Patel, J., Sinha, R., Guo, C., Olson, S. H., Seimon, A., Seimon, T. A., Ondzie, A. U., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04204-w · Cited by 271 · see citing works
Fungal identification biases in microbiome projects
Tedersoo, L., & Lindahl, B. D. (2016) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12438 · Cited by 271 · see citing works
“(LaTuga et al., 2011; Huffnagle and Noverr, 2013; Hallen-Adams et al., 2015).”
Obesity changes the human gut mycobiome
Rodríguez, M. M., Pérez, D., Chaves, F. J., Esteve, E., Marín-García, P., Xifra, G., Vendrell, J. J., Jové, M., Pamplona, R., Ricart, W., et al. (2015) · Scientific Reports · doi:10.1038/srep14600 · Cited by 270 · see citing works
Accounting for reciprocal host–microbiome interactions in experimental science
Stappenbeck, T. S., & Virgin, H. W. (2016) · Nature · doi:10.1038/nature18285 · Cited by 270 · see citing works
Kalan, L., Loesche, M. A., Hodkinson, B. P., Heilmann, K. P., Ruthel, G. T., Gardner, S. E., & Grice, E. A. (2016) · mBio · doi:10.1128/mbio.01058-16 · Cited by 273 · see citing works
“Although this saprophytic dematiaceous fungus is widespread in the environment, it has been reported as one of the most common fungal species associated with the human body in different body sites, including the oral, nasal, vaginal, and gut mycobiomes (31, 34, 48–50).”
Legrand, T. P. R. A., Wynne, J. W., Weyrich, L. S., & Oxley, A. P. A. (2019) · Reviews in Aquaculture · doi:10.1111/raq.12375 · Cited by 269 · see citing works
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease
Chehoud, C., Albenberg, L. G., Judge-Golden, C. P., Hoffmann, C., Grunberg, S., Bittinger, K. L., Baldassano, R. N., Lewis, J. D., Bushman, F. D., & Wu, G. D. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000454 · Cited by 265 · see citing works
“Fungi and archaea are known to be normal components of the gut microbiota.(1,4,5,48) In this study, we recovered abundant”
InfluentialBorrel, G., Brugère, J., Gribaldo, S., Schmitz, R. A., & Moissl‐Eichinger, C. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0407-y · Cited by 255 · see citing works
Microbial impact on cholesterol and bile acid metabolism: current status and future prospects
Kriaa, A., Bourgin, M., Potiron, A., Mkaouar, H., Jablaoui, A., Gérard, P., Maguin, E., & Rhimi, M. (2019) · Journal of Lipid Research · doi:10.1194/jlr.r088989 · Cited by 264 · see citing works
“microbial communities, including bacteria, viruses, archaea, parasites, and fungi (10, 11).”
Gut microorganisms as promising targets for the management of type 2 diabetes
Delzenne, N. M., Cani, P. D., Everard, A., Neyrinck, A. M., & Bindels, L. B. (2015) · Diabetologia · doi:10.1007/s00125-015-3712-7 · Cited by 264 · see citing works
“15 he al th y in di vi du al s; cr os so ve r in te rv en tio n B re ak fa st co nt ai ni ng 6 g of A X = po st pr an di al gl yc ae m ia ,↓ po st pr an di al in su lin ae m ia [1 08 ]”
BackgroundInfluentialXu, J. (2016) · Genome · doi:10.1139/gen-2016-0046 · Cited by 257 · see citing works
The microbiota in inflammatory bowel disease
Sheehan, D., Moran, C. P., & Shanahan, F. (2015) · Journal of Gastroenterology · doi:10.1007/s00535-015-1064-1 · Cited by 249 · see citing works
Fungi as mediators linking organisms and ecosystems
Bahram, M., & Netherway, T. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab058 · Cited by 250 · see citing works
“Carbohydrate substrates of fungi play an important role in their fitness in the gut, as evidenced by increased abundance of Candida following the consumption of carbohydrate rich foods, whereas they respond negatively to saturated fatty acids (Hoffmann et al. 2013).”
Gut Mycobiota in Immunity and Inflammatory Disease
Li, X. V., Leonardi, I., & Iliev, I. D. (2019) · Immunity · doi:10.1016/j.immuni.2019.05.023 · Cited by 246 · see citing works
Fungal-Bacterial Interactions in Health and Disease
Krüger, W., Vielreicher, S., Kapitan, M., Jacobsen, I. D., & Niemiec, M. J. (2019) · Pathogens · doi:10.3390/pathogens8020070 · Cited by 228 · see citing works
“Defining the gut mycobiota from healthy stool identified Ascomycota and Basidiomycota as the most abundant taxa, and the dominant genera are Saccharomyces , Candida , Malassezia , and Cladosporium [53,54,205].”
Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract
Strati, F., Paola, M. D., Stefanini, I., Albanese, D., Rizzetto, L., Lionetti, P., Calabrò, A., Jousson, O., Donati, C., Cavalieri, D., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01227 · Cited by 224 · see citing works
“As occurs for the bacterial microbiota, the intestinal mycobiota is shaped by host’s age, gender, diet, and geographical environment (Yatsunenko et al., 2012; Hoffmann et al., 2013; David et al., 2014).”
BackgroundFungi stabilize connectivity in the lung and skin microbial ecosystems
Tipton, L., Müller, C. L., Kurtz, Z. D., Huang, L., Kleerup, E. C., Morris, A. M., Bonneau, R., & Ghedin, E. (2018) · Microbiome · doi:10.1186/s40168-017-0393-0 · Cited by 224 · see citing works
Homeostasis and dysbiosis of the gut microbiome in health and disease
Das, B., & Nair, G. B. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9926-y · Cited by 217 · see citing works
Impact of Diet on Human Intestinal Microbiota and Health
Salonen, A., & de Vos, W. M. (2014) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030212-182554 · Cited by 215 · see citing works
Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1
Hiergeist, A., Gläsner, J., Reischl, U., & Gessner, A. (2015) · ILAR Journal · doi:10.1093/ilar/ilv017 · Cited by 214 · see citing works
“…least half of the gut-residing bacteria are gram-positive (Gossling and Slack 1974; Lagier, Million et al. 2012), and the commonly hardto-lyse domain of the Archaea is represented predominantly by methanogenicMethanobrevibacter spp.with a variable and overall low prevalence (Hoffmann et al. 2013).”
BackgroundThe Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host
Sam, Q. H., Chang, M. W., & Chai, L. Y. A. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18020330 · Cited by 214 · see citing works
“[17] reported a strong link between consumed foods and fungal abundance in the gut.”
Mycobiota in gastrointestinal diseases
Mukherjee, P. K., Sendid, B., Hoarau, G., Colombel, J., Poulain, D., & Ghannoum, M. A. (2014) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2014.188 · Cited by 212 · see citing works
Microbial ‘old friends’, immunoregulation and socioeconomic status
Rook, G. A. W., Raison, C. L., & Lowry, C. A. (2014) · Clinical & Experimental Immunology · doi:10.1111/cei.12269 · Cited by 207 · see citing works
Diet and Inflammatory Bowel Disease: Review of Patient-Targeted Recommendations
Hou, J. K., Lee, D. Y., & Lewis, J. D. (2013) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2013.09.063 · Cited by 204 · see citing works
“For example, Candida may utilize starch, liberating simple carbohydrates that are used by bacteria such as Prevotella and Ruminococcus , which in turn produce substrates for fermentation that can be used by Methanobrevibacter to produce CH 4 and or CO 2 .”
The human gut mycobiome: pitfalls and potentials—a mycologist’s perspective
Haute, M. J. S. V., & Hallen‐Adams, H. E. (2015) · Mycologia · doi:10.3852/15-147 · Cited by 197 · see citing works
“An estimated 75% of women will suffer a yeast infection during their lifetime and roughly 20–25% of the world’s population has skin mycoses (Sobel 2007, Havlickova et al. 2008).”
BackgroundModelling approaches for studying the microbiome
Kumar, M., Ji, B., Zengler, K., & Nielsen, J. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0491-9 · Cited by 194 · see citing works
Norman, J. M., Handley, S. A., & Virgin, H. W. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.02.001 · Cited by 186 · see citing works
Tan, D.-X., Zheng, X., Kong, J., Manchester, L., Hardeland, R., Kim, S., Xu, X., & Reiter, R. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms150915858 · Cited by 188 · see citing works
“Many archaea also inhabit the gastrointestinal tract of animals including that of the human [146,147].”
BackgroundStress and the gut microbiota-brain axis
Molina‐Torres, G., Rodríguez-Arrastia, M. J., Román, P., Sánchez‐Labraca, N., & Cardona, D. (2019) · Behavioural Pharmacology · doi:10.1097/fbp.0000000000000478 · Cited by 181 · see citing works
“Despite previous probiotic health claims having been exaggerated (Shanahan, 2002; Hoffmann et al., 2013; Sanders, 2016), it is particularly interesting to consider the possibility that probiotics can affect emotion in health and disease by modulating the GMB and confer a health benefit on the host (Dinan et al.”
Early gut mycobiota and mother-offspring transfer
Schei, K., Avershina, E., Øien, T., Rudi, K., Follestad, T., Salamati, S., & Ødegård, R. A. (2017) · Microbiome · doi:10.1186/s40168-017-0319-x · Cited by 179 · see citing works
“These fungi consume nutrients and may facilitate nutrient extraction and assist in digestion through enzyme and vitamin production [7, 8].”
BackgroundReview article: the gut microbiome in inflammatory bowel disease—avenues for microbial management
Mcilroy, J. R., Ianiro, G., Mukhopadhya, I., Hansen, R., & Hold, G. L. (2017) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14384 · Cited by 175 · see citing works
Viral communities of the human gut: metagenomic analysis of composition and dynamics
Aggarwala, V., Liang, G., & Bushman, F. D. (2017) · Mobile DNA · doi:10.1186/s13100-017-0095-y · Cited by 175 · see citing works
Fungi of the human gut microbiota: Roles and significance
Pérez, J. C. (2021) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2021.151490 · Cited by 175 · see citing works
Meta'omic Analytic Techniques for Studying the Intestinal Microbiome
Morgan, X. C., & Huttenhower, C. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.049 · Cited by 173 · see citing works
Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities
Wu, X., Xia, Y., He, F., Zhu, C., & Ren, W. (2021) · Microbiome · doi:10.1186/s40168-021-01024-x · Cited by 167 · see citing works
Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community
Hallen‐Adams, H. E., Kachman, S. D., Kim, J., Legge, R. M., & Martínez, I. (2015) · Fungal ecology · doi:10.1016/j.funeco.2015.01.006 · Cited by 165 · see citing works
“…it is expected that the role of human-associated eukaryotes will come under increasing scrutiny in the next several years, and papers are just beginning to address the role of organisms other than bacteria in the healthy human ( Andersen et al., 2013, Gouba et al., 2013 and Hoffmann et al., 2013).”
InfluentialShuai, M., Fu, Y., Zhong, H., Gou, W., Jiang, Z., Liang, Y., Miao, Z., Xu, J., Huynh, T., Wahlqvist, M. L., et al. (2022) · Gut · doi:10.1136/gutjnl-2021-326298 · Cited by 165 · see citing works
Cross-Domain and Viral Interactions in the Microbiome
Rowan-Nash, A. D., Korry, B. J., Mylonakis, E. E., & Belenky, P. A. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-18 · Cited by 164 · see citing works
“A few groups have used ITS sequencing in humans to identify potential members of a core oral mycobiome, including Candida, Cladosporium, Alternaria, Aspergillus, Fusarium, Cryptococcus, and Aureobasidium (211–213).”
BackgroundInfluentialVemuri, R., Shankar, E. M., Chieppa, M., Eri, R., & Kavanagh, K. (2020) · Microorganisms · doi:10.3390/microorganisms8040483 · Cited by 162 · see citing works
“For example, Candida abundance is found to be strongly associated with the recent ingestion of carbohydrates [100].”
BackgroundYeasts as probiotics: Mechanisms, outcomes, and future potential
Sen, S., & Mansell, T. J. (2020) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2020.103333 · Cited by 162 · see citing works
Mycobiome in the Gut: A Multiperspective Review
Chin, V. K., Yong, P. V. C., Chong, P. P., Nordin, S. A., Basir, R., & Abdullah, M. (2020) · Mediators of Inflammation · doi:10.1155/2020/9560684 · Cited by 156 · see citing works
“Although this study has identified various fungal communities in the gut, one of the concerns raised in this study is whether these fungal mycobiota identified are permanent residents in the gut or just transient species [19].”
BackgroundKumar, S., Indugu, N., Vecchiarelli, B., & Pitta, D. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00781 · Cited by 156 · see citing works
“The resulting amplified PCR products were bead purified using a Beckman Coulter Agencourt AMPure XP Beads (Beckman-Coulter, Pasadena, CA, USA) as described by Hoffmann et al. (2013).”
MethodMycobiome: Approaches to analysis of intestinal fungi
Tang, J., Iliev, I. D., Brown, J. S., Underhill, D. M., & Funari, V. A. (2015) · Journal of Immunological Methods · doi:10.1016/j.jim.2015.04.004 · Cited by 154 · see citing works
“While most studies of the gastrointestinal microbiota focus on commensal and pathogenic bacteria, we and others have recently begun to explore the fungi that are also present in these communities (Scupham et al., 2006; Iliev et al., 2012; Dollive et al., 2013; Hoffmann et al., 2013).”
BackgroundThe role of the microbiome in nonhealing diabetic wounds
Kalan, L., & Brennan, M. B. (2018) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13926 · Cited by 153 · see citing works
Archaea: Essential Inhabitants of the Human Digestive Microbiota
Nkamga, V. D., Henrissat, B., & Drancourt, M. (2017) · Human Microbiome Journal · doi:10.1016/j.humic.2016.11.005 · Cited by 141 · see citing works
“A higher intake of carbohydrates correlated with Methanobrevibacterpositive samples [59].”
BackgroundStructural diversity, functional aspects and future therapeutic applications of human gut microbiome
Ghosh, S., & Pramanik, S. (2021) · Archives of Microbiology · doi:10.1007/s00203-021-02516-y · Cited by 149 · see citing works
Temporal dynamics in the ruminal microbiome of dairy cows during the transition period
Pitta, D., Kumar, S., Vecchiarelli, B., Shirley, D. J., Bittinger, K. L., Baker, L. D., Ferguson, J. D., & Thomsen, N. K. (2014) · Journal of Animal Science · doi:10.2527/jas.2014-7621 · Cited by 148 · see citing works
The Human MycobiomePreprint
Seed, P. C. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a019810 · Cited by 143 · see citing works
“The investigators suggest that Candida, Prevotella, Ruminococcus, and Methanobrevibacter may form a syntrophic guild with Candida providing metabolisms of complex carbohydrates, whereas Prevotella and Ruminococcus ferment the more simple sugars liberated by Candida.”
BackgroundMethodInfluentialBittinger, K. L., Charlson, E. S., Loy, E., Shirley, D. J., Haas, A. R., Laughlin, A. L., Yi, Y., Wu, G. D., Lewis, J. D., Frank, I., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0487-y · Cited by 145 · see citing works
“However, fungal-bacterial interactions have not been studied extensively using culture-independent sequencebased methods (for a few examples see [5-9]).”
BackgroundHuman Gut Microbiota: Toward an Ecology of Disease
Selber‐Hnatiw, S., Rukundo, B., Ahmadi, M., Akoubi, H., Al-Bizri, H., Aliu, A. F., Ambeaghen, T. U., Avetisyan, L., Bahar, I., Baird, A., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01265 · Cited by 145 · see citing works
“Human-associated Archaea, among which Methanobrevibacter smithii found in almost 96% of healthy subjects, synthesize methane from H2 produced by bacterial catabolism (Hoffmann et al., 2013; Lurie-Weinberger and Gophna, 2015).”
BackgroundInfluentialGeurden, I., Mennigen, J. A., Plagnes‐Juan, E., Véron, V., Cerezo, T., Mazurais, D., Zambonino‐Infante, J., Gatesoupe, F.-J., Cassy, S., & Panserat, S. (2014) · Journal of Experimental Biology · doi:10.1242/jeb.106062 · Cited by 142 · see citing works
- 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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