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Luo L, Liu Q, Zhang Y, Yu X, Wang L, Sun W, Li T, Xu B, Zhang K, Yu Y, Cui C, Li C, Mei L. Precisely edited gut microbiota by tungsten-doped Prussian blue nanoparticles for the treatment of inflammatory bowel disease. J Control Release 2025; 382:113755. [PMID: 40258476 DOI: 10.1016/j.jconrel.2025.113755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 04/23/2025]
Abstract
Inflammatory bowel disease (IBD) is characterized by recurring gastrointestinal inflammation, accompanied by a significant rise in global prevalence and disease severity. The overaccumulation of reactive oxygen and nitrogen species (RONS) in the intestinal environment disrupts redox homeostasis and drives pathological overgrowth of Escherichia coli, which are central to IBD pathogenesis. Herein, we designed a multifunctional nanozyme (W-PB) to enable sustained and targeted regulation of intestinal homeostasis through dual mechanisms: specific inhibition of E. coli overgrowth during colitis and efficient RONS clearance. To ensure colon-specific delivery, W-PB was encapsulated in an electrostatically crosslinked hydrogel composed of alginate and chitosan. This formulation protects W-PB from degradation in harsh gastrointestinal conditions and releases the nanoparticles selectively under weakly alkaline intestinal pH. The released tungsten ions suppress E. coli growth via competitive displacement of molybdenum in the molybdopterin cofactor, while W-PB simultaneously neutralizes excess RONS to shield intestinal cells from oxidative damage. In DSS-induced colitis models, the W-PB gel demonstrated significant therapeutic efficacy, achieved through intestinal microbiota remodeling and oxidative stress mitigation.
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Affiliation(s)
- Lingpeng Luo
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Qingyun Liu
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Yushi Zhang
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Xuya Yu
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Ling Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China
| | - Weiting Sun
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Tingxuan Li
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Bin Xu
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China
| | - Kai Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Yongkang Yu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
| | - Chunhui Cui
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China.
| | - Chen Li
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China.
| | - Lin Mei
- State Key Laboratory of Advanced Medical Materials and Devices, Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Tianjin Institute of Health Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 301600, PR China; Furong Laboratory, Central South University, Changsha 410008, PR China.
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Zhang R, Li Z, Huang L, Kong W, Zheng Y, Wang Y, Shen X, Huang L, Wang X, Zheng Q, Wu L, Ke Y, Mao R, Peng Z, Sun C, Feng ST, Lin S, Wang Y, Li X. Altered gut microbiome-metabolite interactions link intestinal inflammation severity and MR enterography abnormalities in Crohn's disease. iScience 2025; 28:112310. [PMID: 40292324 PMCID: PMC12033948 DOI: 10.1016/j.isci.2025.112310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 02/06/2025] [Accepted: 03/25/2025] [Indexed: 04/30/2025] Open
Abstract
Altered gut microbiota‒metabolite interactions may result in intestinal inflammation severity variation in Crohn's disease (CD). Magnetic resonance enterography (MRE) advances anti-inflammatory strategy development. We aimed to identify inflammation-related multiomics factors and MRE interactions for CD management, analyzing 425 CD patients and 42 healthy controls undergoing MRE, ileocolonoscopy, and fecal/blood sampling (microbiota/metabolite analyses), with intestinal inflammation categorized by MRE and ileocolonoscopy. Ruminococcus species were enriched in CD patients versus healthy controls, while Pseudomonas and Staphylococcus dominated moderate-severe versus no-mild inflammation groups, suggesting inflammation-level associations. Ruminococcus gauvreauii suppressed intestinal inflammation by regulating serum PC(O-34:3), ePE(38:6), and ceramides (all p < 0.05). Serum N-acetylneuraminic acid and guanidinoacetic acid correlated with intestinal morphological changes (e.g., MRE-detectable effusion and wall thickness) and inflammation severity (P ACME < 0.05). A link was established between microscopic microbiota-metabolite markers and macroscopic imaging of inflammatory features, which could offer valuable insights into inflammation management.
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Affiliation(s)
- Ruonan Zhang
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Zhoulei Li
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Li Huang
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Weimiao Kong
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yidong Zheng
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yangdi Wang
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Xiaodi Shen
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Lili Huang
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Xinyue Wang
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Qingzhu Zheng
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Luyao Wu
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Yaoqi Ke
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, P.R. China
| | - Zhenpeng Peng
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Canhui Sun
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Shi-Ting Feng
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Shaochun Lin
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
| | - Yejun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, P.R. China
| | - Xuehua Li
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, People's Republic of China
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3
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Singh S, Saini V, Jha HC. The role of secondary genomes in neurodevelopment and co-evolutionary dynamics. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2025; 180:245-297. [PMID: 40414634 DOI: 10.1016/bs.irn.2025.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
Abstract
This chapter examines how human biology and microbial "secondary genomes" have co-evolved to shape neurodevelopment through the gut-brain axis. Microbial communities generate metabolites that cross blood-brain and placental barriers, influencing synaptogenesis, immune responses, and neural circuit formation. Simultaneously, Human Accelerated Regions (HARs) and Endogenous Retroviruses (ERVs) modulate gene expression and immune pathways, determining which microbes thrive in the gut and impacting brain maturation. These factors converge to form a dynamic host-microbe dialogue with significant consequences for neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Building on evolutionary perspectives, the chapter elucidates how genetic and immune mechanisms orchestrate beneficial and pathological host-microbe interactions in early brain development. It then explores therapeutic strategies, such as probiotics, prebiotics, fecal microbiota transplantation, and CRISPR-driven microbial engineering, targeting gut dysbiosis to mitigate or prevent neurodevelopmental dysfunctions. Furthermore, innovative organ-on-chip models reveal mechanistic insights under physiologically relevant conditions, offering a translational bridge between in vitro experiments and clinical applications. As the field continues to evolve, this work underscores the translational potential of manipulating the microbiome to optimize neurological outcomes. It enriches our understanding of the intricate evolutionary interplay between host genomes and the microbial world.
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Affiliation(s)
- Siddharth Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India.
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India.
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Murgiano M, Bartocci B, Puca P, di Vincenzo F, Del Gaudio A, Papa A, Cammarota G, Gasbarrini A, Scaldaferri F, Lopetuso LR. Gut Microbiota Modulation in IBD: From the Old Paradigm to Revolutionary Tools. Int J Mol Sci 2025; 26:3059. [PMID: 40243712 PMCID: PMC11988433 DOI: 10.3390/ijms26073059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/18/2025] [Accepted: 03/26/2025] [Indexed: 04/18/2025] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders primarily comprising two main conditions: ulcerative colitis and Crohn's disease. The gut microbiota's role in driving inflammation in IBD has garnered significant attention, yet the precise mechanisms through which the microbiota influences IBD pathogenesis remain largely unclear. Given the limited therapeutic options for IBD, alternative microbiota-targeted therapies-including prebiotics, probiotics, postbiotics, and symbiotics-have been proposed. While these approaches have shown promising results, microbiota modulation is still mainly considered an adjunct therapy to conventional treatments, with a demonstrated impact on patients' quality of life. Fecal microbiota transplantation (FMT), already approved for treating Clostridioides difficile infection, represents the first in a series of innovative microbiota-based therapies under investigation. Microbial biotherapeutics are emerging as personalized and cutting-edge tools for IBD management, encompassing next-generation probiotics, bacterial consortia, bacteriophages, engineered probiotics, direct metabolic pathway modulation, and nanotherapeutics. This review explores microbial modulation as a therapeutic strategy for IBDs, highlighting current approaches and examining promising tools under development to better understand their potential clinical applications in managing intestinal inflammatory disorders.
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Affiliation(s)
- Marco Murgiano
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
| | - Bianca Bartocci
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
| | - Pierluigi Puca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Medicina Interna e Gastroenterologia, CEMAD Centro Malattie dell’Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Gemelli IRCCS, 00168 Rome, Italy
| | - Federica di Vincenzo
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
| | - Angelo Del Gaudio
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
| | - Alfredo Papa
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Medicina Interna e Gastroenterologia, CEMAD Centro Malattie dell’Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Cammarota
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Medicina Interna e Gastroenterologia, CEMAD Centro Malattie dell’Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Gemelli IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Medicina Interna e Gastroenterologia, CEMAD Centro Malattie dell’Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Gemelli IRCCS, 00168 Rome, Italy
| | - Franco Scaldaferri
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Medicina Interna e Gastroenterologia, CEMAD Centro Malattie dell’Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario Gemelli IRCCS, 00168 Rome, Italy
| | - Loris Riccardo Lopetuso
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (B.B.); (P.P.); (F.d.V.); (A.D.G.); (A.P.); (G.C.); (A.G.); (F.S.)
- Dipartimento di Scienze della Vita, della Salute e delle Professioni Sanitarie, Università degli Studi Link, 00165 Rome, Italy
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Zhao X, Xu J, Wu D, Chen N, Liu Y. Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course. Biomedicines 2025; 13:708. [PMID: 40149684 PMCID: PMC11940770 DOI: 10.3390/biomedicines13030708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/06/2025] [Accepted: 03/11/2025] [Indexed: 03/29/2025] Open
Abstract
Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.
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Affiliation(s)
- Xiaolei Zhao
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China;
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
| | - Jun Xu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China;
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
| | - Dong Wu
- Department of Gastroenterology, Peking Union Medical College Hospital, Beijing 100730, China;
| | - Ning Chen
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China;
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China;
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
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Amari Y, Hosonuma M, Mizukami T, Isobe J, Azetsu Y, Funayama E, Maruyama Y, Tsurui T, Tajima K, Sasaki A, Yamazaki Y, Nakano R, Sano Y, Ishida A, Nakanishi T, Mochizuki S, Yoshizawa Y, Kumagai S, Yasuhara S, Ryu K, Oguchi T, Kuramasu A, Yoshimura K, Sambe T, Kobayashi S, Uchida N. Association between the ABCC11 gene polymorphism-determined earwax properties and external auditory canal microbiota in healthy adults. Microbiol Spectr 2025; 13:e0169824. [PMID: 39817749 PMCID: PMC11792512 DOI: 10.1128/spectrum.01698-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 11/12/2024] [Indexed: 01/18/2025] Open
Abstract
The concept of genome-microbiome interactions, in which the microenvironment determined by host genetic polymorphisms regulates the local microbiota, is important in the pathogenesis of human disease. In otolaryngology, the resident bacterial microbiota is reportedly altered in non-infectious ear diseases, such as otitis media pearls and exudative otitis media. We hypothesized that a single-nucleotide polymorphism in the ATP-binding cassette sub-family C member 11 (ABCC11) gene, which determines earwax properties, regulates the ear canal microbiota. We analyzed ABCC11 gene polymorphisms and ear canal microbiota in healthy individuals to understand the relationship between genome-microbiome interactions in the ear canal. The study included 21 subjects who were divided into two groups: 538GA (9) and 538AA (12). Staphylococcus auricularis and Corynebacterium spp. were observed in the 538GA group, whereas Methylocella spp. was observed in the 538AA group. PICRUSt analysis revealed significant enrichment of certain pathways, such as superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation, chlorosalicylate degradation, mycothiol biosynthesis, and enterobactin biosynthesis in the GA group, whereas allantoin degradation IV (anaerobic), nitrifier denitrification, starch degradation III, L-valine degradation I, and nicotinate degradation I were significantly enriched in the AA group. The ABCC11 gene polymorphism regulates the composition of the ear canal microbiota and its metabolic pathways. This study revealed a genome-microbiome interaction within the resident microbiota of the external auditory canal that may help to elucidate the pathogenesis of ear diseases and develop novel therapies. IMPORTANCE The ABCC11 gene polymorphism, which determines earwax characteristics, regulates the composition of the ear canal microbiota and its metabolic pathways. We determined the presence of genome-microbiome interactions in the resident microbiota of the ear canal. Future studies should focus on ABCC11 gene polymorphisms to elucidate the pathogenesis of ear diseases and develop therapeutic methods.
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Affiliation(s)
- Yasunobu Amari
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Department of Otolaryngology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Masahiro Hosonuma
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Department of Medicine, Division of Medical Oncology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
| | - Takuya Mizukami
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Junya Isobe
- Department of Hospital Pharmaceutics, School of Pharmacy, Showa University Graduate School of Pharmacy, Shinagawa, Tokyo, Japan
| | - Yuki Azetsu
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
- Department of Pharmacology, Showa University Graduate School of Dentistry, Shinagawa, Tokyo, Japan
| | - Eiji Funayama
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
- Department of Pharmacology, Showa University Graduate School of Pharmacy, Shinagawa, Tokyo, Japan
| | - Yuki Maruyama
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
| | - Toshiaki Tsurui
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Department of Medicine, Division of Medical Oncology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
| | - Kohei Tajima
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Department of Gastroenterological Surgery, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Aya Sasaki
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
| | - Yoshitaka Yamazaki
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
- Department of Pharmacology, Showa University Graduate School of Pharmacy, Shinagawa, Tokyo, Japan
- Department of Toxicology, Showa University Graduate School of Pharmacy, Shinagawa, Tokyo, Japan
| | - Ryota Nakano
- Department of Physiology, Showa University Graduate School of Pharmacy, Shinagawa, Tokyo, Japan
| | - Yutaka Sano
- Department of Orthopaedic Surgery, Nihon University School of Medicine, Itabashi, Tokyo, Japan
| | - Atsushi Ishida
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
- Department of Medicine, Division of Neurology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Tatsuya Nakanishi
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
- Department of Medicine, Division of Neurology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Seiji Mochizuki
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Yuri Yoshizawa
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Sumito Kumagai
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Sakiko Yasuhara
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Kakei Ryu
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Tatsunori Oguchi
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Pharmacological Research Center, Showa University, Shinagawa, Tokyo, Japan
| | - Atsuo Kuramasu
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
| | - Kiyoshi Yoshimura
- Department of Clinical Immuno Oncology, Clinical Research Institute for Clinical Pharmacology & Therapeutics, Showa University, Setagaya, Tokyo, Japan
- Department of Medicine, Division of Medical Oncology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
| | - Takehiko Sambe
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
- Showa University Research Administration Center, Shinagawa, Tokyo, Japan
| | - Sei Kobayashi
- Department of Otolaryngology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Naoki Uchida
- Department of Pharmacology, Showa University Graduate School of Medicine, Shinagawa, Tokyo, Japan
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Escalante J, Artaiz O, Diwakarla S, McQuade RM. Leaky gut in systemic inflammation: exploring the link between gastrointestinal disorders and age-related diseases. GeroScience 2025; 47:1-22. [PMID: 39638978 PMCID: PMC11872833 DOI: 10.1007/s11357-024-01451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2024] [Indexed: 12/07/2024] Open
Abstract
Global average life expectancy has steadily increased over the last several decades and is projected to reach ~ 77 years by 2050. As it stands, the number of people > 60 years currently outnumbers children younger than 5 years, and by 2050, it is anticipated that the global population of people aged > 60 years will double, surpassing 2.1 billion. This demographic shift in our population is expected to have substantial consequences on health services globally due to the disease burden associated with aging. Osteoarthritis, chronic obstructive pulmonary disease, diabetes, cardiovascular disease, and cognitive decline associated with dementia are among the most common age-related diseases and contribute significantly to morbidity and mortality in the aged population. Many of these age-related diseases have been linked to chronic low-grade systemic inflammation which often accompanies aging. Gastrointestinal barrier dysfunction, also known as "leaky gut," has been shown to contribute to systemic inflammation in several diseases including inflammatory bowel disease and irritable bowel syndrome, but its role in the development and/or progression of chronic low-grade systemic inflammation during aging is unclear. This review outlines current literature on the leaky gut in aging, how leaky gut might contribute to systemic inflammation, and the links between gastrointestinal inflammatory diseases and common age-related diseases to provide insight into a potential relationship between the intestinal barrier and inflammation.
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Affiliation(s)
- Jonathan Escalante
- Gut-Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, 3021, Australia
| | - Olivia Artaiz
- Gut-Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, 3021, Australia
| | - Shanti Diwakarla
- Gut-Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, 3021, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3010, Australia
| | - Rachel M McQuade
- Gut-Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, 3021, Australia.
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3010, Australia.
- Australian Institute for Musculoskeletal Science (AIMSS), The Melbourne University and Western Health, Melbourne, VIC, 3021, Australia.
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8
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Duan D, Wang M, Han J, Li M, Wang Z, Zhou S, Xin W, Li X. Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications. Front Microbiol 2025; 15:1509117. [PMID: 39831120 PMCID: PMC11739165 DOI: 10.3389/fmicb.2024.1509117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 12/13/2024] [Indexed: 01/22/2025] Open
Abstract
The gut microbiota actually shares the host's physical space and affects the host's physiological functions and health indicators through a complex network of interactions with the host. However, its role as a determinant of host health and disease is often underestimated. With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. With the enrichment of multi-omics integrated analysis methods based on the microbiome, an increasing number of complex statistical analysis methods have also been proposed. In this review, we summarized the multi-omics research analysis methods currently used to study the interaction between the microbiome and the host. We analyzed the advantages and limitations of various methods and briefly introduced their application progress.
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Affiliation(s)
- Dongdong Duan
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Mingyu Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Jinyi Han
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Mengyu Li
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Zhenyu Wang
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Shenping Zhou
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Wenshui Xin
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Xinjian Li
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
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9
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Week B, Ralph PL, Tavalire HF, Cresko WA, Bohannan BJM. Quantitative Genetics of Microbiome Mediated Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.16.628599. [PMID: 39763787 PMCID: PMC11702574 DOI: 10.1101/2024.12.16.628599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2025]
Abstract
Multicellular organisms host a rich assemblage of associated microorganisms, collectively known as their "microbiomes". Microbiomes have the capacity to influence their hosts' fitnesses, but the conditions under which such influences contribute to evolution are not clear. This is due in part to a lack of a comprehensive theoretical framework for describing the combined effects of host and associated microbes on phenotypic variation. Here we begin to address this gap by extending the foundations of quantitative genetic theory to include host-associated microbes, as well as alleles of hosts, as factors that explain quantitative host trait variation. We introduce a way to partition host-associated microbiomes into componenents relevant for predicting a microbiome-mediated response to selection. We then apply our general framework to a simulation model of microbiome inheritance to illustrate principles for predicting host trait dynamics, and to generalize classical narrow and broad sense heritabilities to account for microbial effects. We demonstrate that microbiome-mediated responses to host selection can arise from various transmission modes, not solely vertical, with the contribution of non-vertical modes depending on host life history. Our work lays a foundation for integrating microbiome-mediated host variation and adaptation into our understanding of natural variation.
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10
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Caruso R, Lo BC, Chen GY, Núñez G. Host-pathobiont interactions in Crohn's disease. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00997-y. [PMID: 39448837 DOI: 10.1038/s41575-024-00997-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/23/2024] [Indexed: 10/26/2024]
Abstract
The mammalian intestine is colonized by trillions of microorganisms that are collectively referred to as the gut microbiota. The majority of symbionts have co-evolved with their host in a mutualistic relationship that benefits both. Under certain conditions, such as in Crohn's disease, a subtype of inflammatory bowel disease, some symbionts bloom to cause disease in genetically susceptible hosts. Although the identity and function of disease-causing microorganisms or pathobionts in Crohn's disease remain largely unknown, mounting evidence from animal models suggests that pathobionts triggering Crohn's disease-like colitis inhabit certain niches and penetrate the intestinal tissue to trigger inflammation. In this Review, we discuss the distinct niches occupied by intestinal symbionts and the evidence that pathobionts triggering Crohn's disease live in the mucus layer or near the intestinal epithelium. We also discuss how Crohn's disease-associated mutations in the host disrupt intestinal homeostasis by promoting the penetration and accumulation of pathobionts in the intestinal tissue. Finally, we discuss the potential role of microbiome-based interventions in precision therapeutic strategies for the treatment of Crohn's disease.
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Affiliation(s)
- Roberta Caruso
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Bernard C Lo
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
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11
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Dicks LMT. Cardiovascular Disease May Be Triggered by Gut Microbiota, Microbial Metabolites, Gut Wall Reactions, and Inflammation. Int J Mol Sci 2024; 25:10634. [PMID: 39408963 PMCID: PMC11476619 DOI: 10.3390/ijms251910634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 09/26/2024] [Accepted: 10/01/2024] [Indexed: 10/20/2024] Open
Abstract
Cardiovascular disease (CVD) may be inherited, as recently shown with the identification of single nucleotide polymorphisms (SNPs or "snips") on a 250 kb DNA fragment that encodes 92 proteins associated with CVD. CVD is also triggered by microbial dysbiosis, microbial metabolites, metabolic disorders, and inflammatory intestinal epithelial cells (IECs). The epithelial cellular adhesion molecule (Ep-CAM) and trefoil factor 3 (TFF3) peptide keeps the gut wall intact and healthy. Variations in Ep-CAM levels are directly linked to changes in the gut microbiome. Leptin, plasminogen activator inhibitor 1 (PAI1), and alpha-1 acid glycoprotein 1 (AGP1) are associated with obesity and may be used as biomarkers. Although contactin 1 (CNTN1) is also associated with obesity and adiposity, it regulates the bacterial metabolism of tryptophan (Trp) and thus appetite. A decrease in CNTN1 may serve as an early warning of CVD. Short-chain fatty acids (SCFAs) produced by gut microbiota inhibit pro-inflammatory cytokines and damage vascular integrity. Trimethylamine N-oxide (TMAO), produced by gut microbiota, activates inflammatory Nod-like receptors (NLRs) such as Nod-like receptor protein 3 (NLRP3), which increase platelet formation. Mutations in the elastin gene (ELN) cause supra valvular aortic stenosis (SVAS), defined as the thickening of the arterial wall. Many of the genes expressed by human cells are regulated by gut microbiota. The identification of new molecular markers is crucial for the prevention of CVD and the development of new therapeutic strategies. This review summarizes the causes of CVD and identifies possible CVD markers.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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12
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Zhao Y, Chen Z, Dong R, Liu Y, Zhang Y, Guo Y, Yu M, Li X, Wang J. Multiomics analysis reveals the potential mechanism of high-fat diet in dextran sulfate sodium-induced colitis mice model. Food Sci Nutr 2024; 12:8309-8323. [PMID: 39479684 PMCID: PMC11521715 DOI: 10.1002/fsn3.4426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 11/02/2024] Open
Abstract
A high-fat diet (HFD) is recognized as an important contributor to inflammatory bowel disease (IBD). However, the precise underlying mechanism of HFD on IBD remains elusive. This study aimed to investigate the potential mechanism by which HFD affects IBD using 16S rRNA-sequencing and RNA-seq technology. Results indicated that HFD-treated mice exhibited notable alternations in the structure and composition of the gut microbiota, with some of these alternations being associated with the pathogenesis of IBD. Analysis of the colon transcriptome revealed 11 hub genes and 7 hub pathways among control, DSS-induced colitis, and HFD + DSS-treated groups. Further analysis explores the relationship between the hub pathways and genes, as well as the hub genes and gut microbiota. Overall, the findings indicate that the impact of HFD on DSS-induced colitis may be linked to intestinal dysbiosis and specific genes such as Abca8b, Ace2, Apoa1, Apoa4, Apoc3, Aspa, Dpp4, Maob, Slc34a2, Slc7a9, and Trpm6. These results provide valuable insights for determining potential therapeutic targets for addressing HFD-induced IBD.
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Affiliation(s)
- Yuyang Zhao
- Department of GastroenterologyChina‐Japan Union Hospital of Jilin UniversityChangchunJilinChina
| | - Zhimin Chen
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Ruiyi Dong
- College of Physical Education, Hunan Normal UniversityChangshaChina
| | - Yufan Liu
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Yixin Zhang
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Yan Guo
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Meiyi Yu
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Xiang Li
- Department of PharmacologyCollege of Basic Medical Sciences, Jilin UniversityChangchunJilinChina
| | - Jiangbin Wang
- Department of GastroenterologyChina‐Japan Union Hospital of Jilin UniversityChangchunJilinChina
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13
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Shukla V, Singh S, Verma S, Verma S, Rizvi AA, Abbas M. Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates. Clin Nutr ESPEN 2024; 63:813-820. [PMID: 39178987 DOI: 10.1016/j.clnesp.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 07/15/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024]
Abstract
The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.
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Affiliation(s)
- Vani Shukla
- Department of Food and Nutrition, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Shikha Singh
- Department of Food and Nutrition, Era University, Lucknow 226003, Uttar Pradesh, India.
| | - Shrikant Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Sushma Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Aliya Abbas Rizvi
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
| | - Mohammad Abbas
- Department of Personalized and Molecular Medicine, Era University, Lucknow 226003, Uttar Pradesh, India
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14
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Chatterjee P, Canale V, King SJ, Shawki A, Lei H, Haddad M, Gries CM, McGovern DP, Borneman J, McCole DF. The JAK inhibitor, Tofacitinib, Corrects the Overexpression of CEACAM6 and Limits Susceptibility to AIEC Caused by Reduced Activity of the IBD Associated Gene, PTPN2. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.26.24314341. [PMID: 39399045 PMCID: PMC11469354 DOI: 10.1101/2024.09.26.24314341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Background and Aims A cohort of patients with inflammatory bowel disease (IBD) exhibit expansion of the gut pathobiont, adherent-invasive E. coli (AIEC). Loss of activity of the IBD susceptibility gene, protein tyrosine phosphatase type 2 (PTPN2), results in dysbiosis of the gut microbiota both in human subjects and mice. Further, constitutive Ptpn2 knock-out (Ptpn2-KO) mice display expansion of AIEC compared to wildtype littermates. CEACAM6, a host cell surface glycoprotein, is exploited by AIEC to attach to and enter intestinal epithelial cells (IECs). Here, we investigate the role of IEC-specific PTPN2 in restricting AIEC invasion. Methods Biopsies from IBD patients heterozygous (CT) or homozygous (CC) for the PTPN2 SNP (single nucleotide polymorphism) rs1893217 were processed for immunohistochemistry. HT-29 intestinal epithelial cells (IEC) were transfected with control shRNA (PTPN2-CTL), or a shRNA targeted towards PTPN2 (PTPN2-KD). The rs1893217 SNP was inserted (PTPN2-KI), or a complete knock-out of PTPN2 (PTPN2-KO) was generated, with CRISPR-Cas9 gene editing of Caco-2BBe IEC lines. Adherence and invasion assays were performed with either the human IBD AIEC isolate, LF82, or a novel fluorescent-tagged mouse adherent-invasive E. coli (mAIECred) at multiplicity of infection (MOI) of 10. IL-6 and the pan-JAK inhibitor tofacitinib were administered to interrogate JAK-STAT signaling. Protein expression was determined by western blotting and densitometry. Results CEACAM6 expression was elevated (colon and ileum) in IBD patients carrying the PTPN2 rs1893217 SNP (CT, CC) compared to wildtype (TT) IBD patients. HT-29 and Caco-2BBe cell lines deficient in PTPN2 expressed significantly higher levels of CEACAM6. Further, PTPN2-KI and PTPN2-KO cell lines also displayed greater adherence and invasion by AIEC LF82 and higher mAIECred invasion. CEACAM6 expression was further elevated after administration of IL-6 in PTPN2-deficient cell lines compared to untreated controls. Silencing of STAT1 and 3 partially reduced CEACAM6 protein expression. Tofacitinib significantly reduced the elevated CEACAM6 protein expression and the higher AIEC adherence and invasion in PTPN2-KI and PTPN2-KO cell lines compared to DMSO controls. Conclusion Our findings highlight a crucial role for PTPN2 in restricting pathobiont entry into host cells. Our study also describes a role for the FDA-approved drug, tofacitinib (Xeljanz) in correcting the JAK-STAT-mediated over-expression of CEACAM6, used by pathobionts as an entry portal into host cells. These findings suggest a role for JAK-inhibitors in mitigating AIEC colonization in IBD-susceptible hosts.
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Affiliation(s)
- Pritha Chatterjee
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Vinicius Canale
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Stephanie J. King
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Ali Shawki
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Hillmin Lei
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Michael Haddad
- Department of Biology, University of California, Riverside, Riverside, California
| | - Casey M. Gries
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
| | - Dermot P.B. McGovern
- Department of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, California
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
| | - Declan F. McCole
- Division of Biomedical Sciences, University of California, Riverside, Riverside, California
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15
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Xu F, Hu J, Li Y, Cheng C, Au R, Tong Y, Wu Y, Cui Y, Fang Y, Chen H, Zhu L, Shen H. Qin-Yu-Qing-Chang decoction reshapes colonic metabolism by activating PPAR-γ signaling to inhibit facultative anaerobes against DSS-induced colitis. Chin Med 2024; 19:130. [PMID: 39327592 PMCID: PMC11425999 DOI: 10.1186/s13020-024-01006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
BACKGROUND Qin-Yu-Qing-Chang decoction (QYQC), an herbal formula from China, is extensively employed to manage ulcerative colitis (UC) and exhibits potential benefits for colonic function. Nevertheless, the fundamental molecular mechanisms of QYQC remain largely uncharted. METHODS The primary constituents of QYQC were determined utilizing UHPLC-MS/MS analysis and the effectiveness of QYQC was assessed in a mouse model of colitis induced by dextran sulfate sodium. Evaluations of colon inflammatory responses and mucosal barrier function were thoroughly assessed. RNA sequencing, molecular docking, colonic energy metabolism, and 16S rRNA sequencing analysis were applied to uncover the complex mechanisms of QYQC in treating UC. Detect the signal transduction of the peroxisome proliferator-activated receptor-γ (PPAR-γ) both in the nucleus and cytoplasm. Furthermore, a PPAR-γ antagonist was strategically utilized to confirm the functional targets that QYQC exerts. RESULTS Utilizing UHPLC-MS/MS, the principal constituents of the nine traditional Chinese medicinal herbs comprising QYQC were systematically identified. QYQC treatment substantially ameliorated colitis in mice, as evidenced by the improvement in symptoms and the reduction in colonic pathological injuries. Besides, QYQC treatment mitigated the inflammatory response and improved mucosal barrier function. Furthermore, QYQC enhanced the mitochondria citrate cycle (TCA cycle) by triggering PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus. This prevented the unconstrained expansion of facultative anaerobes, particularly pathogenic Escherichia coli (E. coli, family Enterobacteriaceae) and thus improved colitis. Results of molecular docking indicated that the representative chemical components of QYQC including Baicalin, Paeoniflorin, Mollugin, and Imperatorin bound well with PPAR-γ. The impact of QYQC on colitis was diminished in the presence of a PPAR-γ antagonist. CONCLUSIONS In summary, QYQC ameliorates UC by activating PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus, which enhances the energy metabolism of intestinal epithelial cells and thereby preventing the uncontrolled proliferation of facultative anaerobes.
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Affiliation(s)
- Feng Xu
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310005, China
- The Third Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jingyi Hu
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
| | - Yanan Li
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Cheng Cheng
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ryan Au
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Academy of Chinese Culture and Health Sciences, Oakland, CA, 94612, USA
| | - Yiheng Tong
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuguang Wu
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuan Cui
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yulai Fang
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
| | - Hongxin Chen
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Lei Zhu
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China.
| | - Hong Shen
- Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of Chinese Medicine), Nanjing, 210029, China.
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16
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Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridoshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda K. Commensal consortia decolonize Enterobacteriaceae via ecological control. Nature 2024; 633:878-886. [PMID: 39294375 PMCID: PMC11424487 DOI: 10.1038/s41586-024-07960-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 08/19/2024] [Indexed: 09/20/2024]
Abstract
Persistent colonization and outgrowth of potentially pathogenic organisms in the intestine can result from long-term antibiotic use or inflammatory conditions, and may perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, although an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5-7. Here we isolated and down-selected commensal bacterial consortia from stool samples from healthy humans that could strongly and specifically suppress intestinal Enterobacteriaceae. One of the elaborated consortia, comprising 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby re-establishing colonization resistance and alleviating Klebsiella- and Escherichia-driven intestinal inflammation in mice. Harnessing these activities in the form of live bacterial therapies may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant Enterobacteriaceae infection.
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Affiliation(s)
- Munehiro Furuichi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takaaki Kawaguchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Marie-Madlen Pust
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Keiko Yasuma-Mitobe
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Naomi Hasegawa
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Ohya
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shakti K Bhattarai
- Department of Microbiology and Physiological Systems, Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Satoshi Sasajima
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshimasa Aoto
- JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo, Japan
| | - Timur Tuganbaev
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- Human Biology Microbiome Quantum Research Center (Bio2Q), Keio University, Tokyo, Japan
| | - Mizuki Yaginuma
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Ueda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo, Japan
| | - Nobuyuki Okahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Kimiko Amafuji
- JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo, Japan
| | - Yuko Kiridoshi
- JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo, Japan
| | - Kayoko Sugita
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Martin Stražar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julian Avila-Pacheco
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kerry Pierce
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary B Clish
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashwin N Skelly
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | | | | | - Takeshi Tanoue
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Makoto Arita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Biology Microbiome Quantum Research Center (Bio2Q), Keio University, Tokyo, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Biology Microbiome Quantum Research Center (Bio2Q), Keio University, Tokyo, Japan
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan.
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Biology Microbiome Quantum Research Center (Bio2Q), Keio University, Tokyo, Japan.
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17
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Hua X, McGoldrick J, Nakrour N, Staller K, Chung DC, Xavier RJ, Khalili H. Gut microbiome structure and function in asymptomatic diverticulosis. Genome Med 2024; 16:105. [PMID: 39180058 PMCID: PMC11342677 DOI: 10.1186/s13073-024-01374-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/07/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown. METHODS In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern. RESULTS Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value = 0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values = 0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction = 0.09). CONCLUSIONS Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.
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Affiliation(s)
- Xinwei Hua
- Department of Cardiology, State Key Laboratory of Vascular Homeostasis and Remodeling, and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translation Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica McGoldrick
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translation Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nour Nakrour
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kyle Staller
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translation Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel Chulyong Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ramnik Joseph Xavier
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Clinical and Translation Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Institute of Environmental Medicine, Karolinska Institutet, C6 Institutet För Miljömedicin, C6, CVD-NUT-EPI Wolk, Stockholm, 171 77, Sweden.
- Crohn's and Colitis Center, Massachusetts General Hospital, 165 Cambridge Street, 9Th Floor, Boston, MA, 02114, USA.
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18
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Qadri H, Shah AH, Almilaibary A, Mir MA. Microbiota, natural products, and human health: exploring interactions for therapeutic insights. Front Cell Infect Microbiol 2024; 14:1371312. [PMID: 39035357 PMCID: PMC11257994 DOI: 10.3389/fcimb.2024.1371312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/03/2024] [Indexed: 07/23/2024] Open
Abstract
The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.
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Affiliation(s)
- Hafsa Qadri
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdul Haseeb Shah
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdullah Almilaibary
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
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Wang C, Chu Q, Dong W, Wang X, Zhao W, Dai X, Liu W, Wang B, Liu T, Zhong W, Jiang C, Cao H. Microbial metabolite deoxycholic acid-mediated ferroptosis exacerbates high-fat diet-induced colonic inflammation. Mol Metab 2024; 84:101944. [PMID: 38642891 PMCID: PMC11070703 DOI: 10.1016/j.molmet.2024.101944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024] Open
Abstract
High-fat diet (HFD) has long been recognized as risk factors for the development and progression of ulcerative colitis (UC), but the exact mechanism remained elusive. Here, HFD increased intestinal deoxycholic acid (DCA) levels, and DCA further exacerbated colonic inflammation. Transcriptome analysis revealed that DCA triggered ferroptosis pathway in colitis mice. Mechanistically, DCA upregulated hypoxia-inducible factor-2α (HIF-2α) and divalent metal transporter-1 (DMT1) expression, causing the ferrous ions accumulation and ferroptosis in intestinal epithelial cells, which was reversed by ferroptosis inhibitor ferrostatin-1. DCA failed to promote colitis and ferroptosis in intestine-specific HIF-2α-null mice. Notably, byak-angelicin inhibited DCA-induced pro-inflammatory and pro-ferroptotic effects through blocking the up-regulation of HIF-2α by DCA. Moreover, fat intake was positively correlated with disease activity in UC patients consuming HFD, with ferroptosis being more pronounced. Collectively, our findings demonstrated that HFD exacerbated colonic inflammation by promoting DCA-mediated ferroptosis, providing new insights into diet-related bile acid dysregulation in UC.
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Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Wenxiao Dong
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Wenjing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Dai
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Wentian Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Weilong Zhong
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Changtao Jiang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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20
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Chi J, Ye J, Zhou Y. A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data. Front Microbiol 2024; 15:1394204. [PMID: 38873138 PMCID: PMC11173601 DOI: 10.3389/fmicb.2024.1394204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Motivation High-throughput sequencing technology facilitates the quantitative analysis of microbial communities, improving the capacity to investigate the associations between the human microbiome and diseases. Our primary motivating application is to explore the association between gut microbes and obesity. The complex characteristics of microbiome data, including high dimensionality, zero inflation, and over-dispersion, pose new statistical challenges for downstream analysis. Results We propose a GLM-based zero-inflated generalized Poisson factor analysis (GZIGPFA) model to analyze microbiome data with complex characteristics. The GZIGPFA model is based on a zero-inflated generalized Poisson (ZIGP) distribution for modeling microbiome count data. A link function between the generalized Poisson rate and the probability of excess zeros is established within the generalized linear model (GLM) framework. The latent parameters of the GZIGPFA model constitute a low-rank matrix comprising a low-dimensional score matrix and a loading matrix. An alternating maximum likelihood algorithm is employed to estimate the unknown parameters, and cross-validation is utilized to determine the rank of the model in this study. The proposed GZIGPFA model demonstrates superior performance and advantages through comprehensive simulation studies and real data applications.
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Affiliation(s)
- Jinling Chi
- School of Mathematics and Statistics, Xidian University, Xi'an, China
| | - Jimin Ye
- School of Mathematics and Statistics, Xidian University, Xi'an, China
| | - Ying Zhou
- School of Mathematical Sciences, Heilongjiang University, Harbin, China
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21
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Scanu M, Toto F, Petito V, Masi L, Fidaleo M, Puca P, Baldelli V, Reddel S, Vernocchi P, Pani G, Putignani L, Scaldaferri F, Del Chierico F. An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients. Front Cell Infect Microbiol 2024; 14:1366192. [PMID: 38779566 PMCID: PMC11109417 DOI: 10.3389/fcimb.2024.1366192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Background Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches. Methods The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis. Results In the UC cohort, we reported the increase of Streptococcus, Bifidobacterium, Enterobacteriaceae, TM7-3, Granulicatella, Peptostreptococcus, Lactobacillus, Veillonella, Enterococcus, Peptoniphilus, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of Akkermansia; Ruminococcaceae; Ruminococcus; Gemmiger; Methanobrevibacter; Oscillospira; Coprococus; Christensenellaceae; Clavispora; Vishniacozyma; Quambalaria; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions. Conclusion In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.
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Affiliation(s)
- Matteo Scanu
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Francesca Toto
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Valentina Petito
- Dipartimento di Scienze Mediche e Chirurgiche, Unità Operativa Semplice di Malattie Infiammatorie Croniche Intestinali, CEMAD, Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Letizia Masi
- Dipartimento di Scienze Mediche e Chirurgiche, Unità Operativa Semplice di Malattie Infiammatorie Croniche Intestinali, CEMAD, Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Marco Fidaleo
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
- CNIS Research Center for Nanotechnology Applied to Engineering, Sapienza University of Rome, Rome, Italy
| | - Pierluigi Puca
- Dipartimento di Scienze Mediche e Chirurgiche, Unità Operativa Semplice di Malattie Infiammatorie Croniche Intestinali, CEMAD, Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Valerio Baldelli
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Sofia Reddel
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Giovambattista Pani
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Research Area of Immunology, Rheumatology and Infectious Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Franco Scaldaferri
- Dipartimento di Scienze Mediche e Chirurgiche, Unità Operativa Semplice di Malattie Infiammatorie Croniche Intestinali, CEMAD, Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Federica Del Chierico
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Wang C, Gu Y, Chu Q, Wang X, Ding Y, Qin X, Liu T, Wang S, Liu X, Wang B, Cao H. Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review. Microbiol Res 2024; 282:127660. [PMID: 38442454 DOI: 10.1016/j.micres.2024.127660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.
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Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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23
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Danne C, Skerniskyte J, Marteyn B, Sokol H. Neutrophils: from IBD to the gut microbiota. Nat Rev Gastroenterol Hepatol 2024; 21:184-197. [PMID: 38110547 DOI: 10.1038/s41575-023-00871-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract that results from dysfunction in innate and/or adaptive immune responses. Impaired innate immunity, which leads to lack of control of an altered intestinal microbiota and to activation of the adaptive immune system, promotes a secondary inflammatory response that is responsible for tissue damage. Neutrophils are key players in innate immunity in IBD, but their roles have been neglected compared with those of other immune cells. The latest studies on neutrophils in IBD have revealed unexpected complexities, with heterogeneous populations and dual functions, both deleterious and protective, for the host. In parallel, interconnections between disease development, intestinal microbiota and neutrophils have been highlighted. Numerous IBD susceptibility genes (such as NOD2, NCF4, LRRK2, CARD9) are involved in neutrophil functions related to defence against microorganisms. Moreover, severe monogenic diseases involving dysfunctional neutrophils, including chronic granulomatous disease, are characterized by intestinal inflammation that mimics IBD and by alterations in the intestinal microbiota. This observation demonstrates the dialogue between neutrophils, gut inflammation and the microbiota. Neutrophils affect microbiota composition and function in several ways. In return, microbial factors, including metabolites, regulate neutrophil production and function directly and indirectly. It is crucial to further investigate the diverse roles played by neutrophils in host-microbiota interactions, both at steady state and in inflammatory conditions, to develop new IBD therapies. In this Review, we discuss the roles of neutrophils in IBD, in light of emerging evidence proving strong interconnections between neutrophils and the gut microbiota, especially in an inflammatory context.
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Affiliation(s)
- Camille Danne
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Gastroentérologie, Paris, France.
- Paris Center For Microbiome Medicine (PaCeMM) FHU, Paris, France.
| | - Jurate Skerniskyte
- CNRS, UPR 9002, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, Strasbourg, France
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Benoit Marteyn
- CNRS, UPR 9002, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
- Institut Pasteur, Université de Paris, Inserm 1225 Unité de Pathogenèse des Infections Vasculaires, Paris, France
| | - Harry Sokol
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Gastroentérologie, Paris, France
- Paris Center For Microbiome Medicine (PaCeMM) FHU, Paris, France
- Université Paris-Saclay, INRAe, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Cheng N, Wang X, Zhou Y, Zhao X, Chen M, Zhao H, Cao W. Schisandra chinensis Bee Pollen Ameliorates Colitis in Mice by Modulating Gut Microbiota and Regulating Treg/Th17 Balance. Foods 2024; 13:585. [PMID: 38397562 PMCID: PMC10887782 DOI: 10.3390/foods13040585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Colitis is a chronic disease associated with alterations in the composition of gut microbiota. Schisandra chinensis bee pollen extract (SCPE) has been proved to be rich in phenolic compounds and effective in modulating gut microbiota, but its effect on colitis and the underlying mechanism remains unclear. This study investigates the relationship between colitis amelioration and the gut microbiota regulation of SCPE via fecal microbial transplantation (FMT). The results showed that administration of 20.4 g/kg BW of SCPE could primely ameliorate colitis induced by dextran sulfate sodium (DSS) in mice, showing as more integration of colon tissue structure and the colonic epithelial barrier, as well as lower oxidative stress and inflammation levels compared with colitis mice. Moreover, SCPE supplement restored the balance of T regulatory (Treg) cells and T helper 17 (Th17) cells. Gut microbiota analysis showed SCPE treatment could reshape the gut microbiota balance and improve the abundance of gut microbiota, especially the beneficial bacteria (Akkermansia and Lactobacillus) related to the production of short-chain fatty acids and the regulation of immunity. Most importantly, the protection of 20.4 g/kg BW of SCPE on colitis can be perfectly transmitted by fecal microbiota. Therefore, the gut microbiota-SCFAS-Treg/Th17 axis can be the main mechanism for SCPE to ameliorate colitis. This study suggests that SCPE can be a new promising functional food for prevention and treatment of colitis by reshaping gut microbiota and regulating gut immunity.
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Affiliation(s)
- Ni Cheng
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
- Bee Product Research Center of Shaanxi Province, Xi’an 710065, China
| | - Xiaochao Wang
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
| | - Yaoyao Zhou
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
| | - Xuanxuan Zhao
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
| | - Minghao Chen
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
| | - Haoan Zhao
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
- Bee Product Research Center of Shaanxi Province, Xi’an 710065, China
| | - Wei Cao
- College of Food Science and Technology, Northwest University, Xi’an 710069, China; (N.C.); (X.W.); (H.Z.)
- Bee Product Research Center of Shaanxi Province, Xi’an 710065, China
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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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26
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Honda K, Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta D, Hasegawa N, Ohya T, Bhattarai S, Sasajima S, Yoshimasa A, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Skelly A, Suda W, Hattori M, Nakamoto N, Caballero S, Norman J, Olle B, Tanoue T, Arita M, Bucci V, Atarashi K, Xavier R. Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control. RESEARCH SQUARE 2023:rs.3.rs-3462622. [PMID: 37961431 PMCID: PMC10635318 DOI: 10.21203/rs.3.rs-3462622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Persistent colonization and outgrowth of pathogenic organisms in the intestine may occur due to long-term antibiotic usage or inflammatory conditions, which perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, though an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5-7. In this study, we rationally isolated and down-selected commensal bacterial consortia from healthy human stool samples capable of strongly and specifically suppressing intestinal Enterobacteriaceae. One of the elaborated consortia, consisting of 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby reestablishing colonization resistance and alleviating antibiotic-resistant Klebsiella-driven intestinal inflammation in mice. Harnessing these microbial activities in the form of live bacterial therapeutics may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant bacterial infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Aoto Yoshimasa
- JSR-Keio University Medical and Chemical Innovation Center
| | | | | | | | | | | | | | | | | | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences
| | | | | | - Silvia Caballero
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
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27
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Dzierozynski L, Queen J, Sears CL. Subtle, persistent shaping of the gut microbiome by host genes: A critical determinant of host biology. Cell Host Microbe 2023; 31:1569-1573. [PMID: 37827115 PMCID: PMC11272393 DOI: 10.1016/j.chom.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Although environmental impacts on the host microbiome have been well studied, it is less certain whether and how host genetics impact the microbiome. This commentary discusses current literature supporting host genetic influences on resident species and pathogenic microbes. Mechanistic experimental studies are warranted to understand host gene-microbiome interplay.
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Affiliation(s)
- Lindsey Dzierozynski
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica Queen
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Baltimore, MD, USA.
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28
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Leibovitzh H, Lee SH, Raygoza Garay JA, Espin-Garcia O, Xue M, Neustaeter A, Goethel A, Huynh HQ, Griffiths AM, Turner D, Madsen KL, Moayyedi P, Steinhart AH, Silverberg MS, Deslandres C, Bitton A, Mack DR, Jacobson K, Cino M, Aumais G, Bernstein CN, Panaccione R, Weiss B, Halfvarson J, Xu W, Turpin W, Croitoru K. Immune response and barrier dysfunction-related proteomic signatures in preclinical phase of Crohn's disease highlight earliest events of pathogenesis. Gut 2023; 72:1462-1471. [PMID: 36788016 DOI: 10.1136/gutjnl-2022-328421] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
OBJECTIVE The measure of serum proteome in the preclinical state of Crohn's disease (CD) may provide insight into biological pathways involved in CD pathogenesis. We aimed to assess associations of serum proteins with future CD onset and with other biomarkers predicting CD risk in a healthy at-risk cohort. DESIGN In a nested case-control study within the Crohn's and Colitis Canada Genetics Environment Microbial Project (CCC-GEM) cohort, which prospectively follows healthy first-degree relatives (FDRs), subjects who developed CD (n=71) were matched with four FDRs remaining healthy (n=284). Using samples at recruitment, serum protein profiles using the Olink Proximity Extension Assay platform was assessed for association with future development of CD and with other baseline biomarkers as follows: serum antimicrobial antibodies (AS: positive antibody sum) (Prometheus); faecal calprotectin (FCP); gut barrier function using the fractional excretion of lactulose-to-mannitol ratio (LMR) assay. RESULTS We identified 25 of 446 serum proteins significantly associated with future development of CD. C-X-C motif chemokine 9 (CXCL9) had the highest OR with future risk of CD (OR=2.07 per SD, 95% CI 1.58 to 2.73, q=7.9e-5), whereas matrix extracellular phosphoglycoprotein had the lowest OR (OR 0.44, 95% CI 0.29 to 0.66, q=0.02). Notably, CXCL9 was the only analyte significantly associated with all other CD-risk biomarkers with consistent direction of effect (FCP: OR=2.21; LMR: OR=1.67; AS: OR=1.59) (q<0.05 for all). CONCLUSION We identified serum proteomic signatures associated with future CD development, reflecting potential early biological processes of immune and barrier dysfunction.
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Affiliation(s)
- Haim Leibovitzh
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Juan Antonio Raygoza Garay
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Mingyue Xue
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Neustaeter
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ashleigh Goethel
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hien Q Huynh
- Division of Gastroenterology and Nutrition, Department of Pediatrics, University of Alberta Faculty of Medicine & Dentistry, Edmonton, Alberta, Canada
| | - Anne M Griffiths
- IBD Center, Department of Paediatrics, Faculty of Medicine, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, The Hebrew University of Jerusalem, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Moayyedi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - A Hillary Steinhart
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Colette Deslandres
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Montreal, Saint Justine Hospital, Montreal, Quebec, Canada
| | - Alain Bitton
- Division of Gastroenterology and Hepatology, McGill University Health Centre, Montreal, Quebec, Canada
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, University of Ottawa, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Kevan Jacobson
- Canadian Gastro-Intestinal Epidemiology Consortium, British Columbia Children's Hospital Research Institute, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Maria Cino
- Department of Medicine, Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada
| | - Guy Aumais
- Department of Medicine, Montreal University, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Charles N Bernstein
- University of Manitoba Inflammatory Bowel Disease Clinical and Research Centre and Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Remo Panaccione
- Inflammatory Bowel Disease Clinic, Division of Gastroenterology and Hepatology of Gastroenterology, University of Calgary, Calgary, Alberta, Canada
| | - Batia Weiss
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Sheba Medical Center, Tel-Hashomer, Sackler Faculty of Medicine, Tel-Aviv University, The Edmond and Lily Safra Children's Hospital, Tel Aviv, Israel
| | - Jonas Halfvarson
- School of Medical Sciences. Department of Gastroenterology, Örebro University, Orebro, Sweden
| | - Wei Xu
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
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29
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Terrin M, Migliorisi G, Dal Buono A, Gabbiadini R, Mastrorocco E, Quadarella A, Repici A, Santoro A, Armuzzi A. Checkpoint Inhibitor-Induced Colitis: From Pathogenesis to Management. Int J Mol Sci 2023; 24:11504. [PMID: 37511260 PMCID: PMC10380448 DOI: 10.3390/ijms241411504] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The advent of immunotherapy, specifically of immune checkpoint inhibitors (ICIs), for the treatment of solid tumors has deeply transformed therapeutic algorithms in medical oncology. Approximately one-third of patients treated with ICIs may de velop immune-related adverse events, and the gastrointestinal tract is often affected by different grades of mucosal inflammation. Checkpoint inhibitors colitis (CIC) presents with watery or bloody diarrhea and, in the case of severe symptoms, requires ICIs discontinuation. The pathogenesis of CIC is multifactorial and still partially unknown: anti-tumor activity that collaterally effects the colonic tissue and the upregulation of specific systemic inflammatory pathways (i.e., CD8+ cytotoxic and CD4+ T lymphocytes) are mainly involved. Many questions remain regarding treatment timing and options, and biological treatment, especially with anti-TNF alpha, can be offered to these patients with the aim of rapidly resuming oncological therapies. CIC shares similar pathogenesis and aspects with inflammatory bowel disease (IBD) and the use of ICI in IBD patients is under evaluation. This review aims to summarize the pathogenetic mechanism underlying CIC and to discuss the current evidenced-based management options, including the role of biological therapy, emphasizing the relevant clinical impact on CIC and the need for prompt recognition and treatment.
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Affiliation(s)
- Maria Terrin
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Giulia Migliorisi
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Arianna Dal Buono
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
| | - Roberto Gabbiadini
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
| | - Elisabetta Mastrorocco
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Alessandro Quadarella
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
- Division of Gastroenterology and Digestive Endoscopy, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Armando Santoro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
- Medical Oncology and Haematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Alessandro Armuzzi
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
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30
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Chen K, McCulloch J, Das Neves R, Rodrigues G, Hsieh WT, Gong W, Yoshimura T, Huang J, O'hUigin C, Difilippantonio S, McCollum M, Jones G, Durum SK, Trinchieri G, Wang JM. The beneficial effects of commensal E. coli for colon epithelial cell recovery are related with Formyl peptide receptor 2 (Fpr2) in epithelial cells. Gut Pathog 2023; 15:28. [PMID: 37322488 PMCID: PMC10268441 DOI: 10.1186/s13099-023-00557-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Formyl peptide receptor 2 (Fpr2) plays a crucial role in colon homeostasis and microbiota balance. Commensal E. coli is known to promote the regeneration of damaged colon epithelial cells. The aim of the study was to investigate the connection between E. coli and Fpr2 in the recovery of colon epithelial cells. RESULTS The deficiency of Fpr2 was associated with impaired integrity of the colon mucosa and an imbalance of microbiota, characterized by the enrichment of Proteobacteria in the colon. Two serotypes of E. coli, O22:H8 and O91:H21, were identified in the mouse colon through complete genome sequencing. E. coli O22:H8 was found to be prevalent in the gut of mice and exhibited lower virulence compared to O91:H21. Germ-free (GF) mice that were pre-orally inoculated with E. coli O22:H8 showed reduced susceptibility to chemically induced colitis, increased proliferation of epithelial cells, and improved mouse survival. Following infection with E. coli O22:H8, the expression of Fpr2 in colon epithelial cells was upregulated, and the products derived from E. coli O22:H8 induced migration and proliferation of colon epithelial cells through Fpr2. Fpr2 deficiency increased susceptibility to chemically induced colitis, delayed the repair of damaged colon epithelial cells, and heightened inflammatory responses. Additionally, the population of E. coli was observed to increase in the colons of Fpr2-/- mice with colitis. CONCLUSION Commensal E. coli O22:H8 stimulated the upregulation of Fpr2 expression in colon epithelial cells, and the products from E. coli induced migration and proliferation of colon epithelial cells through Fpr2. Fpr2 deficiency led to an increased E. coli population in the colon and delayed recovery of damaged colon epithelial cells in mice with colitis. Therefore, Fpr2 is essential for the effects of commensal E. coli on colon epithelial cell recovery.
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Affiliation(s)
- Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
| | - John McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Rodrigo Das Neves
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Gisele Rodrigues
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Wang-Ting Hsieh
- Animal Health Diagnostic Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Wanghua Gong
- Basic Research Program, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Department of Pathology and Experimental Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Jiaqiang Huang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- College of Life Sciences, Beijing Jiaotong University, Beijing, 100044, People's Republic of China
| | - Colm O'hUigin
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Simone Difilippantonio
- Gnotobiotics Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew McCollum
- Gnotobiotics Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Georgette Jones
- Gnotobiotics Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Scott K Durum
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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31
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Halsey TM, Thomas AS, Hayase T, Ma W, Abu-Sbeih H, Sun B, Parra ER, Jiang ZD, DuPont HL, Sanchez C, El-Himri R, Brown A, Flores I, McDaniel L, Turrubiates MO, Hensel M, Pham D, Watowich SS, Hayase E, Chang CC, Jenq RR, Wang Y. Microbiome alteration via fecal microbiota transplantation is effective for refractory immune checkpoint inhibitor-induced colitis. Sci Transl Med 2023; 15:eabq4006. [PMID: 37315113 PMCID: PMC10759507 DOI: 10.1126/scitranslmed.abq4006] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Immune checkpoint inhibitors (ICIs) target advanced malignancies with high efficacy but also predispose patients to immune-related adverse events like immune-mediated colitis (IMC). Given the association between gut bacteria with response to ICI therapy and subsequent IMC, fecal microbiota transplantation (FMT) represents a feasible way to manipulate microbial composition in patients, with a potential benefit for IMC. Here, we present a large case series of 12 patients with refractory IMC who underwent FMT from healthy donors as salvage therapy. All 12 patients had grade 3 or 4 ICI-related diarrhea or colitis that failed to respond to standard first-line (corticosteroids) and second-line immunosuppression (infliximab or vedolizumab). Ten patients (83%) achieved symptom improvement after FMT, and three patients (25%) required repeat FMT, two of whom had no subsequent response. At the end of the study, 92% achieved IMC clinical remission. 16S rRNA sequencing of patient stool samples revealed that compositional differences between FMT donors and patients with IMC before FMT were associated with a complete response after FMT. Comparison of pre- and post-FMT stool samples in patients with complete responses showed significant increases in alpha diversity and increases in the abundances of Collinsella and Bifidobacterium, which were depleted in FMT responders before FMT. Histologically evaluable complete response patients also had decreases in select immune cells , including CD8+ T cells, in the colon after FMT when compared with non-complete response patients (n = 4). This study validates FMT as an effective treatment strategy for IMC and gives insights into the microbial signatures that may play a critical role in FMT response.
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Affiliation(s)
- Taylor M. Halsey
- Graduate School of Biomedical Sciences, Microbiology and Infectious Diseases, The University of Texas MD Anderson Cancer Center UTHealth Houston; Houston, Texas, USA
| | - Anusha S. Thomas
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Weijie Ma
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University; Wuhan, Hubei Province, People’s Republic of China
| | - Hamzah Abu-Sbeih
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
- Department of Internal Medicine, University of Missouri; Kansas City, Missouri, USA
| | - Baohua Sun
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Zhi-Dong Jiang
- Center for Infectious Diseases, School of Public Health, The University of Texas; Houston, Texas, USA
| | - Herbert L. DuPont
- Center for Infectious Diseases, School of Public Health, The University of Texas; Houston, Texas, USA
- Kelsey Research Foundation; Houston, Texas, USA
| | - Christopher Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Rawan El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Alexandria Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Ivonne Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Lauren McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Miriam Ortega Turrubiates
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | | | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Stephanie S. Watowich
- Department of Immunology, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
- Department of Stem Cell Transplantation, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center; Houston, Texas, USA
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Levine BH, Hoffman JM. Gut Microbiome Transplants and Their Health Impacts across Species. Microorganisms 2023; 11:1488. [PMID: 37374992 DOI: 10.3390/microorganisms11061488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The human gut, required for ingesting and processing food, extracting nutrients, and excreting waste, is made up of not just human tissue but also trillions of microbes that are responsible for many health-promoting functions. However, this gut microbiome is also associated with multiple diseases and negative health outcomes, many of which do not have a cure or treatment. One potential mechanism to alleviate these negative health effects caused by the microbiome is the use of microbiome transplants. Here, we briefly review the gut's functional relationships in laboratory model systems and humans, with a focus on the different diseases they directly affect. We then provide an overview of the history of microbiome transplants and their use in multiple diseases including Alzheimer's disease, Parkinson's disease, as well as Clostridioides difficile infections, and irritable bowel syndrome. We finally provide insights into areas of research in which microbiome transplant research is lacking, but that simultaneously may provide significant health improvements, including age-related neurodegenerative diseases.
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Affiliation(s)
- Benjamin H Levine
- Department of Biological Sciences, Augusta University, Augusta, GA 30912, USA
| | - Jessica M Hoffman
- Department of Biological Sciences, Augusta University, Augusta, GA 30912, USA
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Kedia S, Ahuja V. Human gut microbiome: A primer for the clinician. JGH Open 2023; 7:337-350. [PMID: 37265934 PMCID: PMC10230107 DOI: 10.1002/jgh3.12902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/14/2022] [Accepted: 04/01/2023] [Indexed: 06/03/2023]
Abstract
The human host gets tremendously influenced by a genetically and phenotypically distinct and heterogeneous constellation of microbial species-the human microbiome-the gut being one of the most densely populated and characterized site for these organisms. Microbiome science has advanced rapidly, technically with respect to the analytical methods and biologically with respect to its mechanistic influence in health and disease states. A clinician conducting a microbiome study should be aware of the nuances related to microbiome research, especially with respect to the technical and biological factors that can influence the interpretation of research outcomes. Hence, this review is an attempt to detail these aspects of the human gut microbiome, with emphasis on its determinants in a healthy state.
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Affiliation(s)
- Saurabh Kedia
- Department of GastroenterologyAll India Institute of Medical SciencesNew DelhiIndia
| | - Vineet Ahuja
- Department of GastroenterologyAll India Institute of Medical SciencesNew DelhiIndia
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Markelova M, Senina A, Khusnutdinova D, Siniagina M, Kupriyanova E, Shakirova G, Odintsova A, Abdulkhakov R, Kolesnikova I, Shagaleeva O, Lyamina S, Abdulkhakov S, Zakharzhevskaya N, Grigoryeva T. Association between Taxonomic Composition of Gut Microbiota and Host Single Nucleotide Polymorphisms in Crohn's Disease Patients from Russia. Int J Mol Sci 2023; 24:ijms24097998. [PMID: 37175705 PMCID: PMC10178390 DOI: 10.3390/ijms24097998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Crohn's disease (CD) is a chronic relapsing inflammatory bowel disease of unknown etiology. Genetic predisposition and dysbiotic gut microbiota are important factors in the pathogenesis of CD. In this study, we analyzed the taxonomic composition of the gut microbiota and genotypes of 24 single nucleotide polymorphisms (SNP) associated with the risk of CD. The studied cohorts included 96 CD patients and 24 healthy volunteers from Russia. Statistically significant differences were found in the allele frequencies for 8 SNPs and taxonomic composition of the gut microbiota in CD patients compared with controls. In addition, two types of gut microbiota communities were identified in CD patients. The main distinguishing driver of bacterial families for the first community type are Bacteroidaceae and unclassified members of the Clostridiales order, and the second type is characterized by increased abundance of Streptococcaceae and Enterobacteriaceae. Differences in the allele frequencies of the rs9858542 (BSN), rs3816769 (STAT3), and rs1793004 (NELL1) were also found between groups of CD patients with different types of microbiota communities. These findings confirm the complex multifactorial nature of CD.
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Affiliation(s)
- Maria Markelova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Anastasia Senina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Dilyara Khusnutdinova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Maria Siniagina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Elena Kupriyanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | | | | | - Rustam Abdulkhakov
- Hospital Therapy Department, Kazan State Medical University, 420012 Kazan, Russia
| | - Irina Kolesnikova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Olga Shagaleeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Svetlana Lyamina
- Molecular Pathology of Digestion Laboratory, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473 Moscow, Russia
| | - Sayar Abdulkhakov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Natalia Zakharzhevskaya
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Tatiana Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
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Zimmerman S, Tierney BT, Patel CJ, Kostic AD. Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems. mSystems 2023; 8:e0011823. [PMID: 37022232 PMCID: PMC10134805 DOI: 10.1128/msystems.00118-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.
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Affiliation(s)
- Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Braden T. Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Aleksandar D. Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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36
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Palasantzas VEJM, Tamargo-Rubio I, Le K, Slager J, Wijmenga C, Jonkers IH, Kumar V, Fu J, Withoff S. iPSC-derived organ-on-a-chip models for personalized human genetics and pharmacogenomics studies. Trends Genet 2023; 39:268-284. [PMID: 36746737 DOI: 10.1016/j.tig.2023.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/24/2022] [Accepted: 01/12/2023] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have now correlated hundreds of genetic variants with complex genetic diseases and drug efficacy. Functional characterization of these factors remains challenging, particularly because of the lack of human model systems. Molecular and nanotechnological advances, in particular the ability to generate patient-specific PSC lines, differentiate them into diverse cell types, and seed and combine them on microfluidic chips, have led to the establishment of organ-on-a-chip (OoC) platforms that recapitulate organ biology. OoC technology thus provides unique personalized platforms for studying the effects of host genetics and environmental factors on organ physiology. In this review we describe the technology and provide examples of how OoCs may be used for disease modeling and pharmacogenetic research.
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Affiliation(s)
- Victoria E J M Palasantzas
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Isabel Tamargo-Rubio
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kieu Le
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jelle Slager
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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37
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Shirwaikar Thomas A, Hanauer S, Wang Y. Immune Checkpoint Inhibitor Enterocolitis vs Idiopathic Inflammatory Bowel Disease. Clin Gastroenterol Hepatol 2023; 21:878-890. [PMID: 36270617 DOI: 10.1016/j.cgh.2022.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 02/07/2023]
Abstract
Immune checkpoint inhibitors have revolutionized management of advanced malignancies. However, their use is frequently complicated by immune related adverse events (irAEs), immune checkpoint inhibitor enterocolitis (IMEC) being the most common toxicity. IMEC is a distinct form of bowel inflammation that is highly reminiscent of idiopathic inflammatory bowel disorders (Crohn's disease, ulcerative colitis, and microscopic colitis). In this review, we highlight the similarities and differences in the pathophysiology, clinical presentation, evaluation, and management of these overlapping immune inflammatory bowel disorders. IMEC is an inflammatory bowel disease-like irAE that occurs as an outcome of disruption of intestinal immune surveillance and gut dysbiosis. Clinical and endoscopic presentation of both entities is strikingly similar, which often guides management. Though well established in inflammatory bowel disease, little is known about the long term outcomes of IMEC.
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Affiliation(s)
- Anusha Shirwaikar Thomas
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Hanauer
- Division of Gastroenterology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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38
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Fadeeva N, Khatkov I, Bodunova N, Knyazev O, Bordin D, Parfenov A, Nikolskaya K, Nikolaev S, Rumyantsev K, Polyakova V, Yanova T. Personalized Medicine for IBD Patients. BIONANOSCIENCE 2023; 13:330-337. [DOI: 10.1007/s12668-023-01067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
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Abstract
Studies of the human microbiome share both technical and conceptual similarities with genome-wide association studies and genetic epidemiology. However, the microbiome has many features that differ from genomes, such as its temporal and spatial variability, highly distinct genetic architecture and person-to-person variation. Moreover, there are various potential mechanisms by which distinct aspects of the human microbiome can relate to health outcomes. Recent advances, including next-generation sequencing and the proliferation of multi-omic data types, have enabled the exploration of the mechanisms that connect microbial communities to human health. Here, we review the ways in which features of the microbiome at various body sites can influence health outcomes, and we describe emerging opportunities and future directions for advanced microbiome epidemiology.
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40
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Sharma A, Junge O, Szymczak S, Rühlemann MC, Enderle J, Schreiber S, Laudes M, Franke A, Lieb W, Krawczak M, Dempfle A. Network-based quantitative trait linkage analysis of microbiome composition in inflammatory bowel disease families. Front Genet 2023; 14:1048312. [PMID: 36755569 PMCID: PMC9901208 DOI: 10.3389/fgene.2023.1048312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction: Inflammatory bowel disease (IBD) is characterized by a dysbiosis of the gut microbiome that results from the interaction of the constituting taxa with one another, and with the host. At the same time, host genetic variation is associated with both IBD risk and microbiome composition. Methods: In the present study, we defined quantitative traits (QTs) from modules identified in microbial co-occurrence networks to measure the inter-individual consistency of microbial abundance and subjected these QTs to a genome-wide quantitative trait locus (QTL) linkage analysis. Results: Four microbial network modules were consistently identified in two cohorts of healthy individuals, but three of the corresponding QTs differed significantly between IBD patients and unaffected individuals. The QTL linkage analysis was performed in a sub-sample of the Kiel IBD family cohort (IBD-KC), an ongoing study of 256 German families comprising 455 IBD patients and 575 first- and second-degree, non-affected relatives. The analysis revealed five chromosomal regions linked to one of three microbial module QTs, namely on chromosomes 3 (spanning 10.79 cM) and 11 (6.69 cM) for the first module, chr9 (0.13 cM) and chr16 (1.20 cM) for the second module, and chr13 (19.98 cM) for the third module. None of these loci have been implicated in a microbial phenotype before. Discussion: Our study illustrates the benefit of combining network and family-based linkage analysis to identify novel genetic drivers of microbiome composition in a specific disease context.
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Affiliation(s)
- Arunabh Sharma
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Silke Szymczak
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Malte Christoph Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Janna Enderle
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany,Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Laudes
- Institute of Diabetology and Clinical Metabolic Research, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Wolfgang Lieb
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany,*Correspondence: Astrid Dempfle,
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41
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Thriene K, Michels KB. Human Gut Microbiota Plasticity throughout the Life Course. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1463. [PMID: 36674218 PMCID: PMC9860808 DOI: 10.3390/ijerph20021463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/02/2023]
Abstract
The role of the gut microbiota in human health and disease has garnered heightened attention over the past decade. A thorough understanding of microbial variation over the life course and possible ways to influence and optimize the microbial pattern is essential to capitalize on the microbiota's potential to influence human health. Here, we review our current understanding of the concept of plasticity of the human gut microbiota throughout the life course. Characterization of the plasticity of the microbiota has emerged through recent research and suggests that the plasticity in the microbiota signature is largest at birth when the microbial colonization of the gut is initiated and mode of birth imprints its mark, then decreases postnatally continuously and becomes less malleable and largely stabilized with advancing age. This continuing loss of plasticity has important implication for the impact of the exposome on the microbiota and health throughout the life course and the identification of susceptible 'windows of opportunity' and methods for interventions.
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Affiliation(s)
- Kerstin Thriene
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79110 Freiburg, Germany
| | - Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79110 Freiburg, Germany
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
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Wang D, Zhang X, Du H. Inflammatory bowel disease: A potential pathogenic factor of Alzheimer's disease. Prog Neuropsychopharmacol Biol Psychiatry 2022; 119:110610. [PMID: 35908596 DOI: 10.1016/j.pnpbp.2022.110610] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD) is a central nervous system disease characterised by degenerative cognitive dysfunction and memory loss. In a society where the global population is gradually ageing, the health threats and financial burdens caused by AD are becoming increasingly severe since AD often occurs in old age. With the in-depth study of AD, many new pathogenic mechanisms have been proposed, among which bidirectional communication between intestinal microbes and the brain has attracted widespread attention. The aetiology of inflammatory bowel disease (IBD) is related to the imbalance of the gut microbiota. Epidemiological investigations have shown that patients with IBD are more likely to suffer from AD. Targeting IBD as a potential AD treatment target has attracted considerable interest. Here, we reviewed the link between chronic intestinal inflammation and central nervous system inflammation and found that IBD patients had a higher risk of AD than non-IBD patients. Preclinical models based on AD also showed that IBD aggravated the condition of AD. We discussed possible biological links between AD and IBD, including the gut-brain axis, autoimmunity, and the gut microbiota. In addition, IBD-induced changes in intestinal microbial metabolites, such as short-chain fatty acids, bile acids, and tryptophan, which aggravate the development of AD, were also discussed.
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Affiliation(s)
- Donghui Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoshuang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Hongwu Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
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43
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Ramos Meyers G, Samouda H, Bohn T. Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability. Nutrients 2022; 14:5361. [PMID: 36558520 PMCID: PMC9788597 DOI: 10.3390/nu14245361] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.
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Affiliation(s)
- Guilherme Ramos Meyers
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, 1 A-B, Rue Thomas Edison, 1445 Strassen, Luxembourg
- Doctoral School in Science and Engineering, University of Luxembourg, 2, Avenue de l'Université, 4365 Esch-sur-Alzette, Luxembourg
| | - Hanen Samouda
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, 1 A-B, Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, 1 A-B, Rue Thomas Edison, 1445 Strassen, Luxembourg
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44
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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45
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Bae UJ, Jang HN, Lee SH, Kim JY, Kim GC. Oenanthe javanica Ethanolic Extract Alleviates Inflammation and Modifies Gut Microbiota in Mice with DSS-Induced Colitis. Antioxidants (Basel) 2022; 11:antiox11122429. [PMID: 36552637 PMCID: PMC9774932 DOI: 10.3390/antiox11122429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Oenanthe javanica, commonly known as water dropwort, has long been used to treat acute and chronic hepatitis, abdominal pain, alcohol hangovers, and inflammation in various traditional medicine systems in Asia. However, whether O. javanica has beneficial effects on colitis-induced intestinal damage remains elusive. This study tested the hypothesis that O. javanica has anti-inflammatory and antioxidant activities in mice with dextran sulfate sodium (DSS)-induced colitis. First, treatment of O. javanica ethanol extract (OJE) inhibited the production of inflammatory cytokines in lipopolysaccharide-affected macrophages. Second, in mice with DSS-induced colitis, OJE administration reduced pathological damage to the colon while alleviating weight gain and decreasing colon length, including inflammation and mucosal necrosis. In addition, OJE significantly (p < 0.01) restricted the activation of nuclear factor-κB (NF-κB) and the secretion of pro-inflammatory mediators and increased the expression of Nrf2-phase 2 antioxidant enzymes. The results of 16S rRNA gene sequencing workflows for taxonomic assignment analysis confirmed that the diversity (richness and evenness) of fecal microbiota was markedly elevated in the OJE group. OJE administration reduced the abundance of Proteobacteria including Escherichia and increased the abundance of the genus Muribaculum. These results suggested that OJE exerts beneficial effects on inflammation and gut microbial composition in a mouse model of colitis.
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Plaza-Diaz J, Radar AM, Baig AT, Leyba MF, Costabel MM, Zavala-Crichton JP, Sanchez-Martinez J, MacKenzie AE, Solis-Urra P. Physical Activity, Gut Microbiota, and Genetic Background for Children and Adolescents with Autism Spectrum Disorder. CHILDREN (BASEL, SWITZERLAND) 2022; 9:1834. [PMID: 36553278 PMCID: PMC9777368 DOI: 10.3390/children9121834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
It is estimated that one in 100 children worldwide has been diagnosed with autism spectrum disorder (ASD). Children with ASD frequently suffer from gut dysbiosis and gastrointestinal issues, findings which possibly play a role in the pathogenesis and/or severity of their condition. Physical activity may have a positive effect on the composition of the intestinal microbiota of healthy adults. However, the effect of exercise both on the gastrointestinal problems and intestinal microbiota (and thus possibly on ASD) itself in affected children is unknown. In terms of understanding the physiopathology and manifestations of ASD, analysis of the gut-brain axis holds some promise. Here, we discuss the physiopathology of ASD in terms of genetics and microbiota composition, and how physical activity may be a promising non-pharmaceutical approach to improve ASD-related symptoms.
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Affiliation(s)
- Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
| | - Ana Mei Radar
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Aiman Tariq Baig
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Marcos Federico Leyba
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Maria Macarena Costabel
- Children’s Hospital of Eastern Ontario, Division of Urology, Department of Surgery, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | | | - Javier Sanchez-Martinez
- Escuela de Kinesiología, Facultad de Salud, Universidad Santo Tomás, Viña del Mar 2520298, Chile
| | - Alex E. MacKenzie
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Patricio Solis-Urra
- Faculty of Education and Social Sciences, Universidad Andres Bello, Viña del Mar 2531015, Chile
- PROFITH “PROmoting FITness and Health through Physical Activity” Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Servicio de Medicina Nuclear, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
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Moltzau Anderson J, Lachnit T, Lipinski S, Falk-Paulsen M, Rosenstiel P. Impact of antibiotic perturbation on fecal viral communities in mice. G3 (BETHESDA, MD.) 2022; 13:6839982. [PMID: 36413074 PMCID: PMC9836353 DOI: 10.1093/g3journal/jkac293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Viruses and bacteriophages have a strong impact on intestinal barrier function and the composition and functional properties of commensal bacterial communities. Shifts of the fecal virome might be involved in human diseases, including inflammatory bowel disease (IBD). Loss-of-function variants in the nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene are associated with an increased risk of developing Crohn's disease, a subtype of human chronic IBD, where specific changes in fecal viral communities have also been described. To improve our understanding of the dynamics of the enteric virome, we longitudinally characterized the virome in fecal samples from wild-type C57BL/6J and NOD2 knock-out mice in response to an antibiotic perturbation. Sequencing of virus-like particles demonstrated both a high diversity and high interindividual variation of the murine fecal virome composed of eukaryotic viruses and bacteriophages. Antibiotics had a significant impact on the fecal murine virome. Viral community composition only partially recovered in the observation period (10 weeks after cessation of antibiotics) irrespective of genotype. However, compositional shifts in the virome and bacteriome were highly correlated, suggesting that the loss of specific phages may contribute to prolonged dysregulation of the bacterial community composition. We suggest that therapeutic interference with the fecal virome may represent a novel approach in microbiota-targeted therapies.
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Affiliation(s)
- Jacqueline Moltzau Anderson
- Present address for Jacqueline Moltzau Anderson: Department of Medicine, University of California San Francisco, 94117 San Francisco, CA, USA
| | | | - Simone Lipinski
- Present address for Simone Lipinski: University Cancer Center Schleswig-Holstein, University Medical Center Campus Kiel, 24105 Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, 24098 Kiel, Germany
| | - Philip Rosenstiel
- Corresponding author: Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University (CAU) Kiel, Rosalind-Franklin-Str. 12, Kiel 24105, Germany.
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48
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Di Rosa C, Altomare A, Imperia E, Spiezia C, Khazrai YM, Guarino MPL. The Role of Dietary Fibers in the Management of IBD Symptoms. Nutrients 2022; 14:nu14224775. [PMID: 36432460 PMCID: PMC9696206 DOI: 10.3390/nu14224775] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic, progressive, immune-mediated diseases of the intestinal tract. The main subtypes of IBDs are Chron's disease (CD) and ulcerative colitis (UC). The etiology is still unclear, but there are genetic, environmental and host-related factors that contribute to the development of these diseases. Recent literature has shown that dietary therapy is the cornerstone of IBD treatment in terms of management of symptoms, relapse and care of the pathology. IBD patients show that microbiota dysbiosis and diet, especially dietary fiber, can modulate its composition. These patients are more at risk of energy protein malnutrition than the general population and are deficient in micronutrients. So far, no dietary component is considered responsible for IBD and there is not a specific therapeutic diet for it. The aim of this review is to evaluate the role of dietary fibers in CD and UC and help health professionals in the nutritional management of these pathologies. Further studies are necessary to determine the appropriate amount and type of fiber to suggest in the case of IBD to ameliorate psychosocial conditions and patients' quality of life.
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Affiliation(s)
- Claudia Di Rosa
- Research Unit of Food Science and Human Nutrition, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Annamaria Altomare
- Research Unit of Gastroenterology, Department of Medicine, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Operative Research Unit of Gastroenterology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
- Correspondence:
| | - Elena Imperia
- Research Unit of Gastroenterology, Department of Medicine, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Chiara Spiezia
- Research Unit of Food Science and Human Nutrition, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Yeganeh Manon Khazrai
- Research Unit of Food Science and Human Nutrition, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Operative Research Unit of Nutrition and Prevention, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Michele Pier Luca Guarino
- Research Unit of Gastroenterology, Department of Medicine, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Operative Research Unit of Gastroenterology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
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49
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Elmaghrawy K, Fleming P, Fitzgerald K, Cooper S, Dominik A, Hussey S, Moran GP. The oral microbiome in treatment naïve paediatric IBD patients exhibits dysbiosis related to disease severity that resolves following therapy. J Crohns Colitis 2022; 17:553-564. [PMID: 36239621 PMCID: PMC10115232 DOI: 10.1093/ecco-jcc/jjac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND There is a limited literature describing the oral microbiome and its diagnostic potential in paediatric inflammatory bowel disease (IBD). METHODS We examined the dorsum tongue microbiome by V1-V2 sequencing in a cohort of 156 treatment naïve children diagnosed with IBD compared to 102 healthy control children. Microbiome changes over time following treatment were examined in a subset of patients and associations between IBD diagnosis and dysbiosis were explored. RESULTS Analysis of community structure of the microbiome in tongue samples revealed that IBD samples significantly diverged from healthy control samples (PERMANOVA P=0.0009) and exhibited a reduced abundance of Clostridia in addition to several major oral genera (Veillonella, Prevotella, Fusobacterium species) with an increased abundance of streptococci. This dysbiosis was more marked in patients with severe disease. Higher levels of the potential pathobionts Klebsiella and Pseudomonas spp. were also associated with IBD. In terms of predicted functions, the IBD oral microbiome was potentially more acidogenic and exhibited reduced capacity for B vitamin biosynthesis. We used a machine learning approach to develop a predictive model of IBD which exhibited a mean-prediction AUC: 0.762. Finally, we examined a subset of 53 patients following 12 months of therapy and could show resolution of oral dysbiosis demonstrated by a shift towards a healthy community structure and a significant reduction in oral dysbiosis. CONCLUSION Oral dysbiosis found in children with IBD is disease severity related and resolves over time following successful IBD treatment.
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Affiliation(s)
- Khalid Elmaghrawy
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin 2, Republic of Ireland
| | - Paddy Fleming
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin 2, Republic of Ireland
| | - Kirsten Fitzgerald
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin 2, Republic of Ireland
| | - Sarah Cooper
- National Children's Research Centre, Crumlin, Dublin, Republic of Ireland
| | - Anna Dominik
- National Children's Research Centre, Crumlin, Dublin, Republic of Ireland
| | - Seamus Hussey
- National Children's Research Centre, Crumlin, Dublin, Republic of Ireland.,Department of Paediatrics, University of Medicine and Health Sciences, RCSI, Dublin and University College Dublin, Ireland
| | - Gary P Moran
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin 2, Republic of Ireland
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Fraschilla I, Amatullah H, Rahman RU, Jeffrey KL. Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease. Cell Host Microbe 2022; 30:1370-1381.e5. [PMID: 36130593 PMCID: PMC10266544 DOI: 10.1016/j.chom.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Speckled Protein 140 (SP140) is an immune-restricted chromatin "reader" that is associated with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the disease-causing mechanisms of SP140 remain undefined. Here, we identify an immune-intrinsic role for SP140 in regulating phagocytic defense responses to prevent the expansion of inflammatory bacteria. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis that was transmissible upon cohousing and ameliorated with antibiotics. Loss of SP140 results in blooms of Proteobacteria, including Helicobacter in Sp140-/- mice and Enterobacteriaceae in humans bearing the CD-associated SP140 loss-of-function variant. Phagocytes from patients with the SP140 loss-of-function variant and Sp140-/- mice exhibited altered antimicrobial defense programs required for control of pathobionts. Thus, mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by microbiota.
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Affiliation(s)
- Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Raza-Ur Rahman
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Institute of Technology Center for Microbiome, Informatics and Therapeutics, Cambridge, MA 02139, USA.
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