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Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis
Open accessAbstract
BACKGROUND: Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle. OBJECTIVE: Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear. METHODS: The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses. RESULTS: We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease. CONCLUSIONS: The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin.
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“Gut dysbiosis has been observed in conditions such as atopic dermatitis [82].”
From Boosting the Photoaged Skin: The Potential Role of Dietary Components (2021) · cites this paper as [82]
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Could Fecal Phenylacetic and Phenylpropionic Acids Be Used as Indicators of Health Status?
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Potential Clinical Applications of the Postbiotic Butyrate in Human Skin Diseases
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“found different Faecalibacterium prausnitzii subspecies in faeces from atopic dermatitis patients compared to controls [41].”
BackgroundEffects ofLactobacillus pentosusin Children with Allergen-Sensitized Atopic Dermatitis
Ahn, S. H., Yoon, W., Lee, S., Shin, H. S., Lim, M. Y., Nam, Y., & Yoo, Y. (2020) · Journal of Korean Medical Science · doi:10.3346/jkms.2020.35.e128 · Cited by 34
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“In addition, the SCFA-producing gut microbiota was confirmed to be present in a larger proportion of AD patients than healthy individuals (Song et al., 2016).”
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BackgroundMicrobial Therapeutics Designed for Infant Health
Watkins, C., Stanton, C., Ryan, C. A., & Ross, R. P. (2017) · Frontiers in Nutrition · doi:10.3389/fnut.2017.00048 · Cited by 30
“…of a Bacteroides xylanisolvens isolate has recently been reported (73), in addition to the beneficial effects of Faecalibacterium prausnitzii (74, 75), and bacterial strains belonging to the Eggerthellaceae family, which produce metabolites with anti-inflammatory and cardioprotective properties…”
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ResultAtopic Dermatitis and Psoriasis: Similarities and Differences in Metabolism and Microbiome
Chen, Y., Peng, C., Zhu, L., Wang, J., Cao, Q., Chen, X., & Li, J. (2024) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-024-08995-3 · Cited by 27
“This is ascribed to the reduction of SCFA-producing bacteria, such as Akkermansia muciniphila , which impairs the intestinal epithelial barrier and ultimately exacerbates type 2 responses [193].”
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“prausnitzii has been associated with other inflammatory dermatoses, including atopic dermatitis [110].”
BackgroundFrom anaerobes to aerointolerant prokaryotes
Ndongo, S., Khelaifia, S., Lagier, J., & Raoult, D. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2019.100068 · Cited by 28
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“28 Furthermore, strain-specific anti-inflammatory functions have been reported for the core Faecalibacterium amplicon sequence variant within a healthy Korean cohort.”
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“In addition, the faecal calprotectin level can be used to assess the effectiveness of probiotic administration as an adjuvant treatment of AD.”
BackgroundInfluentialQi, X., Xiao, Y., Zhang, X., Zhu, Z., Zhang, H., Wei, J., Zhao, Z., Li, J., & Chen, T. (2024) · Food & Function · doi:10.1039/d4fo03083d · Cited by 25
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“Butyrate is the final product of the anaerobic fermentation of dietary fiber by intestinal microorganisms (17), and butyrate levels in stool samples from patients with atopic dermatitis have been demonstrated to be decreased (18).”
BackgroundIntestinal inflammation alters the antigen-specific immune response to a skin commensal
Merana, G. R., Dwyer, L. R., Dhariwala, M. O., Weckel, A., Gonzalez, J. R., Okoro, J. N., Cohen, J. N., Tamaki, C. M., Han, J., Tasoff, P., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110891 · Cited by 24
“While shared genetic features may increase the risk of simultaneous skin and gut disease (Marzano et al., 2014), there is evidence that gut microbiome perturbation can be closely tied to skin inflammation (Myers et al., 2019; Song et al., 2016).”
Microbial interactions in the atopic march
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Gut Dysbiosis and Adult Atopic Dermatitis: A Systematic Review
Díez-Madueño, K., de la Cueva, P., Torres‐Rojas, I., Fernández-Gosende, M., Hidalgo-Cantabrana, C., & Coto‐Segura, P. (2024) · Journal of Clinical Medicine · doi:10.3390/jcm14010019 · Cited by 26
“Gut dysbiosis and the microbiota–intestinal epithelium interaction (leaky gut theory) [48].”
Du, B., Shama, A., Zhang, Y., Chen, B., Bu, Y., Chen, P.-A., Lin, C., Liu, J., Zheng, J., Li, Z., et al. (2025) · World Allergy Organization Journal · doi:10.1016/j.waojou.2024.101017 · Cited by 23
Gut microbiome-based medical methodologies for early-stage disease prevention
Wang, J.-Z., Du, W.-T., Xu, Y., Cheng, S.-Z., & Liu, Z. (2017) · Microbial Pathogenesis · doi:10.1016/j.micpath.2017.02.024 · Cited by 25
Advances in atopic dermatitis and urticarial in 2016
Honda, T., Nomura, T., & Kabashima, K. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.06.005 · Cited by 22
Wang, Y., Choy, C. T., Lin, Y., Wang, L., Hou, J., Tsui, J. C. C., Zhou, J., Wong, C. H., Yim, T. K., Tsui, W.-K., et al. (2022) · Biomedicines · doi:10.3390/biomedicines10112904 · Cited by 21
“of short-chain fatty acids (SCFAs) [20,82], including but not limited to acetate, butyrate, and propionate [83–86].”
Gut microbiota in alopecia areata
Brzychcy, K., Dróźdż, I., Skoczylas, S., Płoszaj, T., Sobolewska-Sztychny, D., Skibińska, M., Narbutt, J., & Lesiak, A. (2022) · Advances in Dermatology and Allergology · doi:10.5114/ada.2022.120453 · Cited by 25
Elevated fecal calprotectin levels are associated with severity of atopic dermatitis in children
Seo, S., Ahn, S. H., Ri, S., Yoon, Y., Byeon, J. H., Kim, S., Yoon, W., & Yoo, Y. (2017) · Asian Pacific Journal of Allergy and Immunology · doi:10.12932/ap-100317-0044 · Cited by 22
“8 The gut microbiota appears to play an important role in controlling not only gut specific but also distant immune responses.”
BackgroundInfluentialBacterial Metabolites and Inflammatory Skin Diseases
Jiminez, V. S., & Yusuf, N. (2023) · Metabolites · doi:10.3390/metabo13080952 · Cited by 23
Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema
Oh, S., Yap, G. C., Hong, P., Huang, C., Aw, M., Shek, L. P., Liu, W., & Lee, B. W. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184955 · Cited by 21
Li, D., Luo, Z., Zhu, J., Wang, J., Jin, Z.-Y., Qi, S., Jin, M., & Quan, L. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c06015 · Cited by 20
Etlin, S. M., Rose, J. K., Bielski, L., Walter, C. E., Kleinman, A. S., & Mason, C. E. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00163-22 · Cited by 26
Minot, S. S., Li, N., Srinivasan, H., Ayers, J., Yu, M., Koester, S. T., Stangis, M. M., Dominitz, J. A., Halberg, R. B., Grady, W. M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-70702-1 · Cited by 20
Wang, L., & Xu, L. (2025) · Frontiers in Pediatrics · doi:10.3389/fped.2025.1498965 · Cited by 21
Sturm, E. M., Knuplez, E., & Marsche, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094377 · Cited by 21
“Moreover, by investigating fecal samples, the authors found decreased levels of butyrate and propionate in their cohort of atopic dermatitis patients [218].”
BackgroundSpecific vaginal and gut microbiome and the anti-tumor effect of butyrate in cervical cancer women
Han, M., Wang, N., Han, W., Liu, X., Sun, T., & Xu, J. (2024) · Translational Oncology · doi:10.1016/j.tranon.2024.101902 · Cited by 23
“Some metabolites are derived solely from the microbiota, not the host, and are dominated by the GM [15].”
BackgroundNutritional and Microbial Strategies for Treating Acne, Alopecia, and Atopic Dermatitis
Borrego-Ruiz, A., & Borrego, J. J. (2024) · Nutrients · doi:10.3390/nu16203559 · Cited by 29
“…immune system, and the balance between the microbiome and the host may determine the onset of AD [59] Several studies have reported the reduced abundance of Akkermansia , Bifidobacterium , Faecalibacterium prausnitzii , and Lactobacillus in individuals with AD compared to healthy controls [38,60].”
BackgroundMariman, R., Reefman, E., Tielen, F. J., Persoon-Deen, C., van der Mark, K., Worms, N. B. A., Koning, F., & Nagelkerken, L. M. (2015) · Beneficial Microbes · doi:10.3920/bm2015.0074 · Cited by 20
The Gut Microbiome: Human Health and Inflammatory Skin Diseases
Mann, E. A., Bae, E., Kostyuchek, D., Chung, H. J., & McGee, J. S. (2020) · Annals of Dermatology · doi:10.5021/ad.2020.32.4.265 · Cited by 22
Mikrobiom, atopisches Ekzem und Blockade der Typ-2-Immunität
Köberle, M., & Biedermann, T. (2018) · Der Hautarzt · doi:10.1007/s00105-018-4129-2 · Cited by 19
“Typischerweise wird die Gattung auf der Artebene aufgelöst, aber eine aktuelle Studie deutet darauf hin, dass eineUnterart des Faecalibacterium prausnitzii spezifisch mit dem atopischen Ekzem korrelieren kann [11].”
Forster, C. S., Hsieh, M. H., & Cabana, M. D. (2020) · Pediatric Research · doi:10.1038/s41390-020-01298-1 · Cited by 19
Han, C.-Y., Kwon, S.-K., Yeom, M., Hahm, D., Park, J.-W., Park, H., & Kim, K. (2022) · Journal of Clinical Medicine · doi:10.3390/jcm11133690 · Cited by 19
“Another study reported an increase in the proportions of Faecalibacterium prausnitzii subspecies, which might be associated with reductions in the proportions of SCFAs, such as propionate, acetate, and butyrate, which damage GI epithelial barrier integrity and induce abnormal Th2 immune response [7,11].”
BackgroundEffects of prebiotics on the gut microbiota in vitro associated with functional diarrhea in children
Zhi, D., Li, J., Li, W., Fu, H., Ding, J., Ren, G., Zhou, L., Pi, X., & Ye, X. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1233840 · Cited by 19
“org Accumulating evidence has demonstrated that the gut microbiota maintains normal gut function, and an improvement in the gut’s microbial structure facilitates the amelioration of diarrhea (Palm et al., 2015; Song et al., 2016; Liu et al., 2018; Li et al., 2021b).”
BackgroundDessì, A., Pintus, R., Fanos, V., & Bosco, A. (2024) · Metabolites · doi:10.3390/metabo14030157 · Cited by 19
“…increased intestinal permeability may lead to the passage of undigested foods, toxins, and pathogenic microbes into the systemic circulation and be responsible for aberrant TH2-type immune responses to such foreign substances, leading to increased inflammation in the deep layers of the skin [39].”
Zhang, Z., Wang, R., Mao, L., & Lu, M. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1613315 · Cited by 20
Obesity and the microbiome in atopic dermatitis: Therapeutic implications for PPAR-γ agonists
McAleer, J. P. (2023) · Frontiers in Allergy · doi:10.3389/falgy.2023.1167800 · Cited by 19
“In support, metabolic pathways responsive to oxidative stress are upregulated in the microbiome of AD patients (46).”
BackgroundRoach, L. A., Meyer, B. J., Fitton, J. H., & Winberg, P. C. (2023) · Marine Drugs · doi:10.3390/md21070379 · Cited by 18
“In atopic dermatitis, the majority of trials investigated infants and have reported reductions in Bifidobacterium [21,22] Staphylococcus aureus [21] and mucin-degrading bacteria [23] when compared to healthy controls, while increases in lactic acid bacteria [22], Escherichia coli [24], Clostridia and a subspecies of F…”
BackgroundProbiotics in Infancy and Childhood for Food Allergy Prevention and Treatment
Costanzo, M. D., Vella, A., Infantino, C., Morini, R., Bruni, S., Esposito, S., & Biasucci, G. (2024) · Nutrients · doi:10.3390/nu16020297 · Cited by 18
“Interestingly, Song et al. found an increase in F. prausnitzii strain L2-6 (belonging to clade A) in atopic dermatitis, suggesting a role of this F. prausnitzii clade in allergy development [23].”
BackgroundHuang, Y., Chen, L., Liu, F., Xiong, X., Ouyang, Y., & Deng, Y. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1300378 · Cited by 21
Kim, M., Kim, J., Kang, M., Won, M., Hong, S., & Her, Y. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21113968 · Cited by 17
“For example, a metagenomic analysis of fecal samples from patients with AD has demonstrated a significant reduction in Faecalibaterium prausnitzii compared to in control patients [10].”
BackgroundUm, H.-N., Baek, J.-O., Park, S.-H., Lee, E. H., Jang, J., Park, W., Roh, J. Y., & Jung, Y. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-03534-w · Cited by 17
Metadata
- Authors
- Song, H., Yoo, Y., Hwang, J., Na, Y.-C., & Kim, H. S.
- Affiliations
- Korea University (KR)
- Korea Basic Science Institute (KR)
- Corresponding author
- Kim, Heenam Stanley
- Venue
- Journal of Allergy and Clinical Immunology
- Publisher
- Elsevier BV
- Published
- 2016-03
- Volume
- 137
- Issue
- 3
- Pages
- 852-860
- ISSN
- 0091-6749 (ISSN-L)
- OpenAlex
- W1822404940
- Cited by
- 416
- References
- 61
- Citations by year
- 2026: 27 · 2025: 40 · 2024: 64 · 2023: 57 · 2022: 43 · 2021: 55 · 2020: 28 · 2019: 28 · 2018: 39 · 2017: 18 · 2016: 16
- FWCI
- 10.71
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Allergy and Clinical Immunology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Research Foundation of Korea
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Dermatology › Dermatology and Skin Diseases
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- atopic dermatitis, Faecalibacterium prausnitzii, gut dysbiosis, short-chain fatty acids, butyrate, propionate, intestinal epithelial barrier, Th2 immune response, Crohn's disease, intestinal immune regulation
- MeSH terms
- Eubacteriales, Gastrointestinal Microbiome, Dermatitis, Atopic, Feces, Female, Humans, Male, Models, Biological, Phylogeny, RNA, Ribosomal, 16S, Cluster Analysis, Sequence Analysis, DNA, Computational Biology, Metagenome, Metagenomics, Dysbiosis
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