Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics

被引：0

作者：

Orejudo, Macarena ^{[1
,2
]}

Gomez, Manuel J. ^{[3
]}

Riestra, Sabino ^{[4
,5
]}

Rivero, Montserrat ^{[6
]}

Gutierrez, Ana ^{[7
,8
]}

Rodriguez-Lago, Iago ^{[9
]}

Fernandez-Salazar, Luis ^{[10
]}

Ceballos, Daniel ^{[11
]}

Benitez, Jose Manuel ^{[12
]}

Aguas, Mariam ^{[13
,14
]}

Baston-Rey, Iria ^{[15
]}

Bermejo, Fernando ^{[16
]}

Casanova, Maria Jose ^{[1
,2
]}

Lorente-Poyatos, Rufo H. ^{[17
]}

Ber, Yolanda ^{[18
]}

Ginard, Daniel ^{[19
]}

Esteve, Maria ^{[20
]}

de Francisco, Ruth ^{[4
,5
]}

Garcia, Maria Jose ^{[6
]}

Frances, Ruben ^{[8
,21
,22
,23
]}

Rodriguez, Ainhoa ^{[9
]}

Suarez, Noelia Alcaide ^{[10
]}

del Rio, Elena Guerra ^{[11
]}

Soto, Pilar ^{[12
]}

Nos, Pilar ^{[13
,14
]}

Barreiro-de Acosta, Manuel ^{[15
]}

Guerra, Ivan ^{[16
]}

Cruz, Daniel Hervias ^{[17
]}

Cajal, Manuel Dominguez ^{[18
]}

Royo, Vanesa ^{[19
]}

Aceituno, Montserrat ^{[20
]}

Aldars-Garcia, Laila ^{[1
,2
]}

Garre, Ana ^{[1
,2
]}

Ramirez, Cristina ^{[1
,2
]}

Soleto, Irene ^{[1
,2
]}

Schuppe-Koistinen, Ina ^{[24
]}

Engstrand, Lars ^{[24
]}

Baldan-Martin, Montse ^{[1
,2
]}

Sanchez-Cabo, Fatima ^{[3
]}

Gisbert, Javier P. ^{[1
,2
]}

Chaparro, Maria ^{[1
,2
]}

机构：

[1] Univ Autonoma Madrid UAM, Hosp Univ Princesa, Inst Invest Sanitaria Princesa IIS Princesa, Madrid, Spain

[2] Ctr Invest Biomed Red Enfermedades Hepat & Digest, Madrid, Spain

[3] Ctr Nacl Invest Cardiovasc Carlos III CNIC, Madrid, Spain

[4] Hosp Univ Cent Asturias, Gastroenterol Dept, Asturias, Spain

[5] Inst Invest Sanitaria Principado Asturias ISPA, Asturias, Spain

[6] Hosp Univ Marques Valdecilla, Gastroenterol Dept, Grp Invest Clin & Traslac Enfermedades Digest, Inst Invest Valdecilla IDIVAL, Santander, Spain

[7] Hosp Gen Univ Dr Balmis Alicante, Inst Invest Sanitaria & Biomed Alicante ISABIAL, Alicante, Spain

[8] Ctr Invest Biomed Red Enfermedades Hepat & Digest, Alicante, Spain

[9] Hosp Univ Galdakao, Gastroenterol Dept, Galdakao, Vizcaya, Spain

[10] Biobizkaia Hlth Res Inst, Galdakao, Vizcaya, Spain

[11] Univ Valladolid, Hosp Clin Univ Valladolid, Gastroenterol Dept, Valladolid, Spain

[12] Hosp Univ Gran Canaria Dr Negrin, Gastroenterol Dept, Las Palmas Gran Canaria, Spain

[13] Hosp Univ Reina Sofia, Gastroenterol Dept, Cordoba, Spain

[14] Inst Maimonides Invest Biomed Cordoba IMIBIC, Cordoba, Spain

[15] Hosp Univ La Fe, Hlth Res Inst La Fe, Valencia, Spain

[16] Complexo Hosp Univ Santiago, Santiago De Compostela, Spain

[17] Hosp Univ Fuenlabrada, Madrid, Spain

[18] Hosp Gen Univ Ciudad Real, Ciudad Real, Spain

[19] Hosp San Jorge, Huesca, Spain

[20] Hosp Univ Son Espases, Palma De Mallorca, Spain

[21] Hosp Univ Mutua Terrassa, Terrassa, Spain

[22] Univ Miguel Hernandez, Dept Med Clin, Grp Inmunobiol Hepat Intestinal, San Juan, Alicante, Spain

[23] Univ Miguel Hernandez, Inst Inst Invest, Desarrollo Innovac Biotecnol Sanitaria Elche IDIBE, San Juan, Alicante, Spain

[24] Karolinska Inst, Ctr Translat Microbiome Res, Dept Microbiol Tumor & Cell Biol, Solna, Sweden

来源：

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY | 2025年 / 15卷

关键词：

inflammatory bowel disease; Crohn's disease; ulcerative colitis; microbiota; metagenomics; shotgun; ULCERATIVE-COLITIS; ECCO GUIDELINES; THERAPEUTICS; DYSBIOSIS; OMICS;

D O I：

10.3389/fcimb.2025.1595884

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

Introduction Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-na & iuml;ve IBD patients.Methods Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis.Results A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial diversity to HC, which was unaffected by disease activity. Taxonomic abundance analysis revealed a tendency towards a higher relative abundance of Escherichia coli and a lower relative abundance of Faecalibacterium prausnitzii in IBD patients compared to HC. However, the most significant differences in these patients compared to HC were observed in less abundant species, such as Toxoplasma gondii, Gemella morbillorum, and several species of the Adlercreutzia genera. Functional analysis in these patients highlighted changes in carbohydrate and nucleotide pathways.Discussion Our data suggest that newly diagnosed CD patients show significant microbiota composition disparities compared to UC patients and HC. Microbiota differences in these patients are linked to dysbiosis, characterized by a reduction in beneficial genera such as Gemella and Adlercreutzia, and a rise in pathogenic species.

引用

页数：21

共 82 条

[11] IMPAIRMENT OF BACTERIAL-FLORA IN HUMAN ULCERATIVE-COLITIS AND EXPERIMENTAL COLITIS IN THE RAT [J].

FABIA, R ;

ARRAJAB, A ;

JOHANSSON, ML ;

ANDERSSON, R ;

WILLEN, R ;

JEPPSSON, B ;

MOLIN, G ;

BENGMARK, S .

DIGESTION, 1993, 54 (04) :248-255

[12] Gut Microbiota and Dietary Factors as Modulators of the Mucus Layer in Inflammatory Bowel Disease [J].

Fernandez-Tome, Samuel ;

Ortega Moreno, Lorena ;

Chaparro, Maria ;

Gisbert, Javier P. .

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (19)

[13] Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases [J].

Frank, Daniel N. ;

Amand, Allison L. St. ;

Feldman, Robert A. ;

Boedeker, Edgar C. ;

Harpaz, Noam ;

Pace, Norman R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (34) :13780-13785

[14] Species-level functional profiling of metagenomes and metatranscriptomes [J].

Franzosa, Eric A. ;

McIver, Lauren J. ;

Rahnavard, Gholamali ;

Thompson, Luke R. ;

Schirmer, Melanie ;

Weingart, George ;

Lipson, Karen Schwarzberg ;

Knight, Rob ;

Caporaso, J. Gregory ;

Segata, Nicola ;

Huttenhower, Curtis .

NATURE METHODS, 2018, 15 (11) :962-+

[15] Sequencing and beyond: integrating molecular 'omics' for microbial community profiling [J].

Franzosa, Eric A. ;

Hsu, Tiffany ;

Sirota-Madi, Alexandra ;

Shafquat, Afrah ;

Abu-Ali, Galeb ;

Morgan, Xochitl C. ;

Huttenhower, Curtis .

NATURE REVIEWS MICROBIOLOGY, 2015, 13 (06) :360-372

[16] Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis [J].

Galipeau, Heather J. ;

Caminero, Alberto ;

Turpin, Williams ;

Bermudez-Brito, Miriam ;

Santiago, Alba ;

Libertucci, Josie ;

Constante, Marco ;

Garay, Juan Antonio Raygoza ;

Rueda, Gaston ;

Armstrong, Sarah ;

Clarizio, Alex ;

Smith, Michelle, I ;

Surette, Michael G. ;

Bercik, Premysl ;

Croitoru, Kenneth ;

Verdu, Elena F. .

GASTROENTEROLOGY, 2021, 160 (05) :1532-1545

[17] Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases [J].

Ghavami, Shaghayegh Baradaran ;

Rostami, Elham ;

Sephay, Abbas Akhavan ;

Shahrokh, Shabnam ;

Balaii, Hedieh ;

Aghdaei, Hamid Asadzadeh ;

Zali, Mohammad Reza .

MICROBIAL PATHOGENESIS, 2018, 117 :285-289

[18] Irritable Bowel Syndrome, Particularly the Constipation-Predominant Form, Involves an Increase in Methanobrevibacter smithii, Which Is Associated with Higher Methane Production [J].

Ghoshal, Ujjala ;

Shukla, Ratnakar ;

Srivastava, Deepakshi ;

Ghoshal, Uday C. .

GUT AND LIVER, 2016, 10 (06) :932-938

[19] Location-specific signatures of Crohn's disease at a multi-omics scale [J].

Gonzalez, Carlos G. ;

Mills, Robert H. ;

Zhu, Qiyun ;

Sauceda, Consuelo ;

Knight, Rob ;

Dulai, Parambir S. ;

Gonzalez, David J. .

MICROBIOME, 2022, 10 (01)

[20] Gut Microbiota Is a Potential Biomarker in Inflammatory Bowel Disease [J].

Guo, Xue ;

Huang, Chen ;

Xu, Jing ;

Xu, Haoming ;

Liu, Le ;

Zhao, Hailan ;

Wang, Jiaqi ;

Huang, Wenqi ;

Peng, Wu ;

Chen, Ye ;

Nie, Yuqiang ;

Zhou, Yongjian ;

Zhou, Youlian .

FRONTIERS IN NUTRITION, 2022, 8

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