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Ocius KL, Kolli SH, Ahmad SS, Dressler JM, Chordia MD, Jutras BL, Rutkowski MR, Pires MM. Noninvasive Analysis of Peptidoglycan from Living Animals. Bioconjug Chem 2024; 35:489-498. [PMID: 38591251 PMCID: PMC11036361 DOI: 10.1021/acs.bioconjchem.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activates peptidoglycan sensors in human cells, including the nucleotide-binding oligomerization domain-containing protein 2. When present in the gastrointestinal tract, both the polymeric form (sacculi) and depolymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To utilize this growing area of biology toward therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and noninvasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a noninvasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for noninvasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.
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Affiliation(s)
- Karl L. Ocius
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Sree H. Kolli
- Department
of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Saadman S. Ahmad
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jules M. Dressler
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Mahendra D. Chordia
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brandon L. Jutras
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Melanie R. Rutkowski
- Department
of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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Xie Z, Huang J, Sun G, He S, Luo Z, Zhang L, Li L, Yao M, Du C, Yu W, Feng Y, Yang D, Zhang J, Ge C, Li H, Geng M. Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder. Psychiatry Res 2024; 334:115804. [PMID: 38417224 DOI: 10.1016/j.psychres.2024.115804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/18/2023] [Accepted: 02/17/2024] [Indexed: 03/01/2024]
Abstract
Major depressive disorder (MDD) involves systemic changes in peripheral blood and gut microbiota, but the current understanding is incomplete. Herein, we conducted a multi-omics analysis of fecal and blood samples obtained from an observational cohort including MDD patients (n = 99) and healthy control (HC, n = 50). 16S rRNA sequencing of gut microbiota showed structural alterations in MDD, as characterized by increased Enterococcus. Metagenomics sequencing of gut microbiota showed substantial functional alterations including upregulation in the superpathway of the glyoxylate cycle and fatty acid degradation and downregulation in various metabolic pathways in MDD. Plasma metabolomics revealed decreased amino acids and bile acids, together with increased sphingolipids and cholesterol esters in MDD. Notably, metabolites involved in arginine and proline metabolism were decreased while sphingolipid metabolic pathway were increased. Mass cytometry analysis of blood immune cell subtypes showed rises in proinflammatory immune subsets and declines in anti-inflammatory immune subsets in MDD. Furthermore, our findings revealed disease severity-related factors of MDD. Interestingly, we classified MDD into two immune subtypes that were highly correlated with disease relapse. Moreover, we established discriminative signatures that differentiate MDD from HC. These findings contribute to a comprehensive understanding of the MDD pathogenesis and provide valuable resources for the discovery of biomarkers.
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Affiliation(s)
- Zuoquan Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingjing Huang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Guangqiang Sun
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Shen He
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Zhiyu Luo
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Linna Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Liang Li
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Min Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Du
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Wenjuan Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Yuan Feng
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Dabing Yang
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Jing Zhang
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Changrong Ge
- Green Valley (shanghai) pharmaceutical technology Co., Ltd., Shanghai 201203, China
| | - Huafang Li
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
| | - Meiyu Geng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China.
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Zhang Y, Pan Y, Lin H, Chen X, He P, Wang Y, Chen P, Chu Q. Crude Tieguanyin oolong tea polysaccharides regulate intestinal immune and gut microflora in dextran sulfate sodium-induced mice colitis. J Sci Food Agric 2024; 104:3156-3166. [PMID: 38073022 DOI: 10.1002/jsfa.13206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024]
Abstract
BACKGROUND The global incidence and prevalence of inflammatory bowel diseases (IBDs) have been increasing. Epidemiological studies, clinical trials, and animal experiments have indicated a negative association between the consumption of tea and IBD. This study aims to investigate the protective effects of crude Tieguanyin oolong tea polysaccharides (CTPS) on experimental colitis, while also exploring the underlying mechanisms. RESULTS The administration of CTPS significantly alleviated IBD in the mouse model, and was found to regulate T-cell mediated immune responses in the colon by modulating cytokine production associated with T cells. Furthermore, CTPS demonstrated a positive impact on the gut microbiota, reversing the increase in pathogenic Helicobacter and enhancing the relative abundances of beneficial bacteria such as Akkermansia, Lachnospiraceae, and Odoribacter. Oral administration of CTPS also led to an improvement in intestinal metabolism, specifically by increasing the levels of short-chain fatty acids. CONCLUSION This study provides the first in vivo evidence of the protective effects of CTPS on colitis in mice. The effects are likely facilitated through the regulation of T cell-mediated responses and modulation of the gut microbiota, suggesting that CTPS may be a potential preventive and therapeutic approach for IBD. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yuxi Zhang
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Yani Pan
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Haiyu Lin
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Xue Chen
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Puming He
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Yuefei Wang
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Ping Chen
- Tea Research Institute, Zhejiang University, Hangzhou, China
| | - Qiang Chu
- Tea Research Institute, Zhejiang University, Hangzhou, China
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Yang Y, Fei Y, Xu X, Yao J, Wang J, Liu C, Ding H. Shikonin attenuates cerebral ischemia/reperfusion injury via inhibiting NOD2/RIP2/NF-κB-mediated microglia polarization and neuroinflammation. J Stroke Cerebrovasc Dis 2024:107689. [PMID: 38527567 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVES Microglia-mediated neuroinflammation plays a crucial role in the pathophysiological process of multiple neurological disorders such as ischemic stroke, which still lacks effective therapeutic agents. Shikonin possesses anti-inflammatory and neuroprotective properties. However, its underlying mechanism remains elusive. This study aimed to investigate whether Shikonin confers protection against cerebral ischemia/reperfusion (I/R) injury by modulating microglial polarization and elucidate the associated mechanisms. METHODS This study employed an oxygen-glucose deprivation and reoxygenation (OGD/R) BV2 microglial cellular model and a middle cerebral artery occlusion/reperfusion (MCAO/R) animal model to investigate the protection and underlying mechanism of Shikonin against ischemic stroke. RESULTS The results demonstrated that Shikonin treatment significantly reduced brain infarction volume and improved neurological function in MCAO/R rats. Simultaneously, Shikonin treatment significantly reduced microglial proinflammatory phenotype and levels of proinflammatory markers (inducible-NO synthase (iNOS), tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and IL-6), increased microglial anti-inflammatory phenotype and levels of anti-inflammatory markers (Arginase-1 (Arg1), transforming growth factor-beta (TGF-β), and IL-10), reversed the expression of Nucleotide-binding oligomerization domain 2 (NOD2) and phosphorylation receptor interacting protein 2 (p-RIP2), and suppressed nuclear factor kappa-B (NF-κB) signaling activation in the ischemic penumbra regions. These effects of Shikonin were further corroborated in OGD/R-treated BV2 cells. Furthermore, overexpression of NOD2 markedly attenuated the neuroprotective effects of Shikonin treatment in MCAO/R rats. NOD2 overexpression also attenuated the regulatory effects of Shikonin on neuroinflammation, microglial polarization, and NF-κB signaling activation. CONCLUSION This study illustrates that Shikonin mitigates inflammation mediated by microglial proinflammatory polarization by inhibiting the NOD2/RIP2/NF-κB signaling pathway, thereby exerting a protective role. The findings uncover a potential molecular mechanism for Shikonin in treating ischemic stroke.
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Affiliation(s)
- Ya Yang
- College of Pharmacy, Xinjiang Medical University, No. 567 North Shangde Road, Urumqi, Xinjiang 830017, PR China
| | - Yuxiang Fei
- Department of Pharmacy, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, P.R.China; School of Basic Medicine & Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P.R.China
| | - Xuejiao Xu
- School of Basic Medicine & Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P.R.China
| | - Jun Yao
- College of Pharmacy, Xinjiang Medical University, No. 567 North Shangde Road, Urumqi, Xinjiang 830017, PR China; Xinjiang Key Laboratory of Natural Medicines Active Components and Drug Release Technology, Urumqi, Xinjiang 830017, PR China
| | - Jianing Wang
- Department of Pharmacy, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211100, China.
| | - Chao Liu
- Department of Pharmacy, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, P.R.China; School of Basic Medicine & Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P.R.China.
| | - Haiyan Ding
- College of Pharmacy, Xinjiang Medical University, No. 567 North Shangde Road, Urumqi, Xinjiang 830017, PR China; Xinjiang Key Laboratory of Natural Medicines Active Components and Drug Release Technology, Urumqi, Xinjiang 830017, PR China.
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5
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Xu J, Peng WR, Zhang D, Sun HX, Li L, Sun F, Gu ZC, Lin HW. Marine sponge-derived alkaloid ameliorates DSS-induced IBD via inhibiting IL-6 expression through modulating JAK2-STAT3-SOCS3 pathway. Int Immunopharmacol 2024; 129:111576. [PMID: 38350353 DOI: 10.1016/j.intimp.2024.111576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/18/2024] [Indexed: 02/15/2024]
Abstract
Cyanogramide (AC14), a novel alkaloid, isolated from the fermentation broth of the marine-derived Actinoalloteichus cyanogriseus. However, the exact role of AC14 in inflammatory bowel disease (IBD) is poorly understood. Our results demonstrated that AC14 exhibited significant inhibition of IL-6 release in THP-1 cells and a "Caco-2/THP-1" coculture system after stimulation with LPS for 24 h. However, no significant effect on TNF-α production was observed. Furthermore, in 2.5 % DSS-induced colitis mice, AC14 treatment led to improvement in body weight, colon length, and intestine mucosal barrier integrity. AC14 also suppressed serum IL-6 production and modulated dysregulated microbiota in the mice. Mechanistically, AC14 was found to inhibit the phosphorylation of Janus kinase (JAK) 2 and signal transducers and activators of transcription (STAT) 3, while simultaneously elevating the expression of suppressor of cytokine signaling (SOCS) 3, both in vivo and in vitro. These findings suggest that AC14 exerts its suppressive effects on IL-6 production in DSS-induced IBD mice through the JAK2-STAT3-SOCS3 signaling pathway. Our study highlights the potential of AC14 as a therapeutic agent for the treatment of IBD.
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Affiliation(s)
- Jing Xu
- School of Medicine, Tongji University, Shanghai 200092, People's Republic of China; Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Wen-Rui Peng
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China; School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Die Zhang
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Hong-Xin Sun
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Lei Li
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Fan Sun
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
| | - Zhi-Chun Gu
- Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
| | - Hou-Wen Lin
- School of Medicine, Tongji University, Shanghai 200092, People's Republic of China; Research Center for Marine Drugs, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
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6
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Liu M, Ma J, Xu J, Huangfu W, Zhang Y, Ali Q, Liu B, Li D, Cui Y, Wang Z, Sun H, Zhu X, Ma S, Shi Y. Fecal microbiota transplantation alleviates intestinal inflammatory diarrhea caused by oxidative stress and pyroptosis via reducing gut microbiota-derived lipopolysaccharides. Int J Biol Macromol 2024; 261:129696. [PMID: 38280701 DOI: 10.1016/j.ijbiomac.2024.129696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/07/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Infancy is a critical period in the maturation of the gut microbiota and a phase of susceptibility to gut microbiota dysbiosis. Early disturbances in the gut microbiota can have long-lasting effects on host physiology, including intestinal injury and diarrhea. Fecal microbiota transplantation (FMT) can remodel gut microbiota and may be an effective way to treat infant diarrhea. However, limited research has been conducted on the mechanisms of infant diarrhea and the regulation of gut microbiota balance through FMT, primarily due to ethical challenges in testing on human infants. Our study demonstrated that elevated Lipopolysaccharides (LPS) levels in piglets with diarrhea were associated with colon microbiota dysbiosis induced by early weaning. Additionally, LPS upregulated NLRP3 levels by activating TLR4 and inducing ROS production, resulting in pyroptosis, disruption of the intestinal barrier, bacterial translocation, and subsequent inflammation, ultimately leading to diarrhea in piglets. Through microbiota regulation, FMT modulated β-PBD-2 secretion in the colon by increasing butyric acid levels. This modulation alleviated gut microbiota dysbiosis, reduced LPS levels, attenuated oxidative stress and pyroptosis, inhibited the inflammatory response, maintained the integrity of the intestinal barrier, and ultimately reduced diarrhea in piglets caused by colitis. These findings present a novel perspective on the pathogenesis, pathophysiology, prevention, and treatment of diarrhea diseases, underscoring the significance of the interaction between FMT and the gut microbiota as a critical strategy for treating diarrhea and intestinal diseases in infants and farm animals.
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Affiliation(s)
- Mengqi Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Jixiang Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Junying Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Weikang Huangfu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Qasim Ali
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Boshuai Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Defeng Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Yalei Cui
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Zhichang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Hao Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Xiaoyan Zhu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Sen Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China
| | - Yinghua Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China; Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China; Henan Forage Engineering Technology Research Center, Zhengzhou, Henan 450002, China.
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7
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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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Zhao J, Yao C, Qin Y, Zhu H, Guo H, Ji B, Li X, Sun N, Li R, Wu Y, Zheng K, Pan Y, Zhao T, Yang J. Blockade of C5aR1 resets M1 via gut microbiota-mediated PFKM stabilization in a TLR5-dependent manner. Cell Death Dis 2024; 15:120. [PMID: 38331868 PMCID: PMC10853248 DOI: 10.1038/s41419-024-06500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Targeting C5aR1 modulates the function of infiltrated immune cells including tumor-associated macrophages (TAMs). The gut microbiome plays a pivotal role in colorectal cancer (CRC) tumorigenesis and development through TAM education. However, whether and how the gut flora is involved in C5aR1 inhibition-mediated TAMs remains unclear. Therefore, in this study, genetic deletion of C5ar1 or pharmacological inhibition of C5aR1 with anti-C5aR1 Ab or PMX-53 in the presence or absence of deletion Abs were utilized to verify if and how C5aR1 inhibition regulated TAMs polarization via affecting gut microbiota composition. We found that the therapeutic effects of C5aR1 inhibition on CRC benefited from programming of TAMs toward M1 polarization via driving AKT2-mediated 6-phosphofructokinase muscle type (PFKM) stabilization in a TLR5-dependent manner. Of note, in the further study, we found that C5aR1 inhibition elevated the concentration of serum IL-22 and the mRNA levels of its downstream target genes encoded antimicrobial peptides (AMPs), leading to gut microbiota modulation and flagellin releasement, which contributed to M1 polarization. Our data revealed that high levels of C5aR1 in TAMs predicted poor prognosis. In summary, our study suggested that C5aR1 inhibition reduced CRC growth via resetting M1 by AKT2 activation-mediated PFKM stabilization in a TLR5-dependent manner, which relied on IL-22-regulated gut flora.
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Affiliation(s)
- Jie Zhao
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Immunology, Medical College, Yangzhou University, Yangzhou, China
| | - Chen Yao
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yongqin Qin
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hanyong Zhu
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hui Guo
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Binbin Ji
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xueqin Li
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Na Sun
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Rongqing Li
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuzhang Wu
- Chongqing International Institute for Immunology, Chongqing, China
| | - Kuiyang Zheng
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Yuchen Pan
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Tingting Zhao
- Chongqing International Institute for Immunology, Chongqing, China.
| | - Jing Yang
- Jiangsu International Laboratory of Immunity and Metabolism, Jiangsu Province Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu, China.
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9
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Kwan JMC, Liang Y, Ng EWL, Sviriaeva E, Li C, Zhao Y, Zhang XL, Liu XW, Wong SH, Qiao Y. In silico MS/MS prediction for peptidoglycan profiling uncovers novel anti-inflammatory peptidoglycan fragments of the gut microbiota. Chem Sci 2024; 15:1846-1859. [PMID: 38303944 PMCID: PMC10829024 DOI: 10.1039/d3sc05819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Peptidoglycan is an essential exoskeletal polymer across all bacteria. Gut microbiota-derived peptidoglycan fragments (PGNs) are increasingly recognized as key effector molecules that impact host biology. However, the current peptidoglycan analysis workflow relies on laborious manual identification from tandem mass spectrometry (MS/MS) data, impeding the discovery of novel bioactive PGNs in the gut microbiota. In this work, we built a computational tool PGN_MS2 that reliably simulates MS/MS spectra of PGNs and integrated it into the user-defined MS library of in silico PGN search space, facilitating automated PGN identification. Empowered by PGN_MS2, we comprehensively profiled gut bacterial peptidoglycan composition. Strikingly, the probiotic Bifidobacterium spp. manifests an abundant amount of the 1,6-anhydro-MurNAc moiety that is distinct from Gram-positive bacteria. In addition to biochemical characterization of three putative lytic transglycosylases (LTs) that are responsible for anhydro-PGN production in Bifidobacterium, we established that these 1,6-anhydro-PGNs exhibit potent anti-inflammatory activity in vitro, offering novel insights into Bifidobacterium-derived PGNs as molecular signals in gut microbiota-host crosstalk.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Yaquan Liang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Evan Wei Long Ng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Ekaterina Sviriaeva
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Chenyu Li
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Yilin Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Xiao-Lin Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Xue-Wei Liu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
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10
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Wan T, Wang Y, He K, Zhu S. Microbial sensing in the intestine. Protein Cell 2023; 14:824-860. [PMID: 37191444 PMCID: PMC10636641 DOI: 10.1093/procel/pwad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gut microbiota plays a key role in host health and disease, particularly through their interactions with the immune system. Intestinal homeostasis is dependent on the symbiotic relationships between the host and the diverse gut microbiota, which is influenced by the highly co-evolved immune-microbiota interactions. The first step of the interaction between the host and the gut microbiota is the sensing of the gut microbes by the host immune system. In this review, we describe the cells of the host immune system and the proteins that sense the components and metabolites of the gut microbes. We further highlight the essential roles of pattern recognition receptors (PRRs), the G protein-coupled receptors (GPCRs), aryl hydrocarbon receptor (AHR) and the nuclear receptors expressed in the intestinal epithelial cells (IECs) and the intestine-resident immune cells. We also discuss the mechanisms by which the disruption of microbial sensing because of genetic or environmental factors causes human diseases such as the inflammatory bowel disease (IBD).
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Affiliation(s)
- Tingting Wan
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yalong Wang
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kaixin He
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shu Zhu
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
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11
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Yin R, Wang T, Dai H, Han J, Sun J, Liu N, Dong W, Zhong J, Liu H. Immunogenic molecules associated with gut bacterial cell walls: chemical structures, immune-modulating functions, and mechanisms. Protein Cell 2023; 14:776-785. [PMID: 37013853 PMCID: PMC10599643 DOI: 10.1093/procel/pwad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/25/2023] [Indexed: 04/05/2023] Open
Abstract
Interactions between gut microbiome and host immune system are fundamental to maintaining the intestinal mucosal barrier and homeostasis. At the host-gut microbiome interface, cell wall-derived molecules from gut commensal bacteria have been reported to play a pivotal role in training and remodeling host immune responses. In this article, we review gut bacterial cell wall-derived molecules with characterized chemical structures, including peptidoglycan and lipid-related molecules that impact host health and disease processes via regulating innate and adaptive immunity. Also, we aim to discuss the structures, immune responses, and underlying mechanisms of these immunogenic molecules. Based on current advances, we propose cell wall-derived components as important sources of medicinal agents for the treatment of infection and immune diseases.
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Affiliation(s)
- Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningning Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wang Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Luan M, Niu M, Yang P, Han D, Zhang Y, Li W, He Q, Zhao Y, Mao B, Chen J, Mou K, Li P. Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo. BMC Microbiol 2023; 23:265. [PMID: 37737154 PMCID: PMC10515041 DOI: 10.1186/s12866-023-03020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo. METHODS Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases. RESULTS Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs. CONCLUSIONS The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.
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Affiliation(s)
- Mei Luan
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Mengtian Niu
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Pengju Yang
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Dan Han
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Yudan Zhang
- Center for Translational Medicine, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Weizhe Li
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Qiannan He
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Yixin Zhao
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Binyue Mao
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Jianan Chen
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China
| | - Kuanhou Mou
- Department of Dermatology, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China.
| | - Pan Li
- Center for Translational Medicine, the Frist Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, Shaanxi, People's Republic of China.
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13
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Jang KK, Heaney T, London M, Ding Y, Putzel G, Yeung F, Ercelen D, Chen YH, Axelrad J, Gurunathan S, Zhou C, Podkowik M, Arguelles N, Srivastava A, Shopsin B, Torres VJ, Keestra-Gounder AM, Pironti A, Griffin ME, Hang HC, Cadwell K. Antimicrobial overproduction sustains intestinal inflammation by inhibiting Enterococcus colonization. Cell Host Microbe 2023; 31:1450-1468.e8. [PMID: 37652008 PMCID: PMC10502928 DOI: 10.1016/j.chom.2023.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/02/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
Loss of antimicrobial proteins such as REG3 family members compromises the integrity of the intestinal barrier. Here, we demonstrate that overproduction of REG3 proteins can also be detrimental by reducing a protective species in the microbiota. Patients with inflammatory bowel disease (IBD) experiencing flares displayed heightened levels of secreted REG3 proteins that mediated depletion of Enterococcus faecium (Efm) from the gut microbiota. Efm inoculation of mice ameliorated intestinal inflammation through activation of the innate immune receptor NOD2, which was associated with the bacterial DL-endopeptidase SagA that generates NOD2-stimulating muropeptides. NOD2 activation in myeloid cells induced interleukin-1β (IL-1β) secretion to increase the proportion of IL-22-producing CD4+ T helper cells and innate lymphoid cells that promote tissue repair. Finally, Efm was unable to protect mice carrying a NOD2 gene variant commonly found in IBD patients. Our findings demonstrate that inflammation self-perpetuates by causing aberrant antimicrobial activity that disrupts symbiotic relationships with gut microbes.
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Affiliation(s)
- Kyung Ku Jang
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Thomas Heaney
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Mariya London
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Yi Ding
- Department of Laboratory Medicine, Geisinger Health, Danville, PA 17822, USA
| | - Gregory Putzel
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Frank Yeung
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Defne Ercelen
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ying-Han Chen
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jordan Axelrad
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sakteesh Gurunathan
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chaoting Zhou
- Cell and Molecular Biology Graduate Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Magdalena Podkowik
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Infectious Diseases and Immunology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Natalia Arguelles
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anusha Srivastava
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Infectious Diseases and Immunology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Victor J Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - A Marijke Keestra-Gounder
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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14
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He X, Zhou H. Decoding the IBD paradox: A triadic interplay between REG3, enterococci, and NOD2. Cell Host Microbe 2023; 31:1425-1427. [PMID: 37708849 DOI: 10.1016/j.chom.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
In this issue of Cell Host & Microbe, Jang et al. decode an intriguing paradox: excessive antimicrobial peptide-regenerating family member 3 (REG3) expression in inflammatory bowel disease (IBD) patients depletes protective enterococci. This depletion impairs the NOD2 anti-inflammatory pathway and perpetuates inflammation, thus providing insight into IBD pathogenesis.
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Affiliation(s)
- Xiaolong He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510655, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510655, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong, 510655, China.
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15
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Ocius KL, Kolli SH, Ahmad SS, Dressler JM, Chordia MD, Jutras BL, Rutkowski MR, Pires MM. Non-invasive Analysis of Peptidoglycan from Living Animals. bioRxiv 2023:2023.07.21.549941. [PMID: 37693563 PMCID: PMC10491127 DOI: 10.1101/2023.07.21.549941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activate peptidoglycan sensors in human cells, including the Nucleotide-binding oligomerization domain containing protein 2 (NOD2). When present in the gastrointestinal tract, both the polymeric form (sacculi) and de-polymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To leverage this growing area of biology towards therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and non-invasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a non-invasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for non-invasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.
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16
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Abstract
This is a literature review describes Crohn's disease (CD) concomitant with breast cancer and summarizes possible common pathogenic mechanisms shared by the two diseases involving the IL-17 and NF-κB signaling pathways. Inflammatory cytokines including TNF-α and Th17 cells in CD patients can induce activation of the ERK1/2, NF-κB and Bcl-2 pathways. Hub genes are involved in the generation of cancer stem cells (CSCs) and are related to inflammatory mediators, including CXCL8, IL1-β and PTGS2, which promote inflammation and breast cancer growth, metastasis, and development. CD activity is highly associated with altered intestinal microbiota processes, including secretion of complex glucose polysaccharides by Ruminococcus gnavus colonies; furthermore, γ-proteobacteria and Clostridium are associated with CD recurrence and active CD, while Ruminococcaceae, Faecococcus and Vibrio desulfuris are associated with CD remission. Intestinal microbiota disorder promotes breast cancer occurrence and development. Bacteroides fragilis can produce toxins that induce breast epithelial hyperplasia and breast cancer growth and metastasis. Gut microbiota regulation can also improve chemotherapy and immunotherapy efficacy in breast cancer treatment. Intestinal inflammation can affects the brain through the brain-gut axis, which activates the hypothalamic‒pituitary‒adrenal (HPA) axis to induce anxiety and depression in patients; these effects can inhibit the antitumor immune responses of the immune system and promote breast cancer occurrence in patients with CD. There are few studies on the treatment of patients with CD concomitant with breast cancer, but published studies show three main strategies: new biological agents combined with breast cancer treatment methods, intestinal fecal bacteria transplantation, and dietary treatment.
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Affiliation(s)
- Sisi Zhou
- Department of Gastroenterology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong Province, China
| | - Jing Yu
- Department of Gastroenterology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong Province, China.
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17
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Gao J, Wang L, Jiang J, Xu Q, Zeng N, Lu B, Yuan P, Sun K, Zhou H, He X. A probiotic bi-functional peptidoglycan hydrolase sheds NOD2 ligands to regulate gut homeostasis in female mice. Nat Commun 2023; 14:3338. [PMID: 37286542 DOI: 10.1038/s41467-023-38950-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
Secreted proteins are one of the direct molecular mechanisms by which microbiota influence the host, thus constituting a promising field for drug discovery. Here, through bioinformatics-guided screening of the secretome of clinically established probiotics from Lactobacillus, we identify an uncharacterized secreted protein (named LPH here) that is shared by most of these probiotic strains (8/10) and demonstrate that it protects female mice from colitis in multiple models. Functional studies show that LPH is a bi-functional peptidoglycan hydrolase with both N-Acetyl-β-D-muramidase and DL-endopeptidase activities that can generate muramyl dipeptide (MDP), a NOD2 ligand. Different active site mutants of LPH in combination with Nod2 knockout female mice confirm that LPH exerts anti-colitis effects through MDP-NOD2 signaling. Furthermore, we validate that LPH can also exert protective effects on inflammation-associated colorectal cancer in female mice. Our study reports a probiotic enzyme that enhances NOD2 signaling in vivo in female mice and describes a molecular mechanism that may contribute to the effects of traditional Lactobacillus probiotics.
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Affiliation(s)
- Jie Gao
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China
| | - Lei Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China
| | - Jing Jiang
- Department Gerontology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, 610072, Chengdu, Sichuan, China
| | - Qian Xu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China
| | - Nianyi Zeng
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China
| | - Bingyun Lu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, 518101, Shenzhen, Guangdong, China
| | - Peibo Yuan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China
| | - Kai Sun
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, Guangdong, China.
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China.
- State Key Laboratory of Organ Failure Research, Southern Medical University, 510655, Guangzhou, Guangdong, China.
| | - Xiaolong He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 510655, Guangzhou, Guangdong, China.
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18
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Chow EWL, Mei Pang L, Wang Y. Impact of the host microbiota on fungal infections: new possibilities for intervention? Adv Drug Deliv Rev 2023; 198:114896. [PMID: 37211280 DOI: 10.1016/j.addr.2023.114896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Many human fungal pathogens are opportunistic. They are primarily benign residents of the human body and only become infectious when the host's immunity and microbiome are compromised. Bacteria dominate the human microbiome, playing an essential role in keeping fungi harmless and acting as the first line of defense against fungal infection. The Human Microbiome Project, launched by NIH in 2007, has stimulated extensive investigation and significantly advanced our understanding of the molecular mechanisms governing the interaction between bacteria and fungi, providing valuable insights for developing future antifungal strategies by exploiting the interaction. This review summarizes recent progress in this field and discusses new possibilities and challenges. We must seize the opportunities presented by researching bacterial-fungal interplay in the human microbiome to address the global spread of drug-resistant fungal pathogens and the drying pipelines of effective antifungal drugs.
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Affiliation(s)
- Eve W L Chow
- A*STAR Infectious Diseases Laboratories (ID Labs), Agency for Science and Technology Research (A*STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648
| | - Li Mei Pang
- A*STAR Infectious Diseases Laboratories (ID Labs), Agency for Science and Technology Research (A*STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648
| | - Yue Wang
- A*STAR Infectious Diseases Laboratories (ID Labs), Agency for Science and Technology Research (A*STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore.
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19
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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20
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Ma N, Ma D, Liu X, Zhao L, Ma L, Ma D, Dong S. Bisphenol P exposure in C57BL/6 mice caused gut microbiota dysbiosis and induced intestinal barrier disruption via LPS/TLR4/NF-κB signaling pathway. Environ Int 2023; 175:107949. [PMID: 37126915 DOI: 10.1016/j.envint.2023.107949] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/30/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
Despite being one of the most world's widely used and mass-produced compounds, bisphenol A (BPA) has a wide range of toxic effects. Bisphenol P (BPP), an alternative to BPA, has been detected in many foods. The effects of BPP dietary exposure on gut microbiota and the intestinal barrier were unclear. We designed three batches of animal experiments: The first studied mice were exposed to BPP (30 µg/kg BW/day) for nine weeks and found that they gained weight and developed dysbiosis of the gut microbiota. The second, using typical human exposure levels (L, 0.3 µg/kg BW/day BPP) and higher concentrations (M, 30 µg/kg BW/day BPP; H, 3000 µg/kg BW/day BPP), caused gut microbiota dysbiosis in mice, activated the Lipopolysaccharide (LPS) /TLR4/NF-κB signaling pathway, triggered an inflammatory response, increased intestinal permeability, and promoted bacterial translocation leading to intestinal barrier disruption. The third treatment used a combination of antibiotics and alleviated intestinal inflammation and injury. This study demonstrated the mechanism of injury and concentration effects of intestinal damage caused by BPP exposure, providing reference data for BPP use and control and yielding new insights for human disease prevention.
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Affiliation(s)
- Nana Ma
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Diao Ma
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Xia Liu
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Lining Zhao
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Lei Ma
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Dan Ma
- College of Life Science, Hebei University, Baoding, Hebei 071002, China
| | - Sijun Dong
- College of Life Science, Hebei University, Baoding, Hebei 071002, China.
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21
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Yadav J, Philpott DJ. A gut bacterial strain rescues stunted growth. Science 2023; 379:756-757. [PMID: 36821690 DOI: 10.1126/science.adg6247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Lactiplantibacillus plantarum promotes growth in undernourished mice.
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Affiliation(s)
- Jitender Yadav
- Department of Immunology, Medical Sciences Building, University of Toronto, Toronto, ON, Canada
| | - Dana J Philpott
- Department of Immunology, Medical Sciences Building, University of Toronto, Toronto, ON, Canada
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22
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Jang KK, Heaney T, London M, Ding Y, Yeung F, Ercelen D, Chen YH, Axelrad J, Gurunathan S, Marijke Keestra-Gounder A, Griffin ME, Hang HC, Cadwell K. Antimicrobial overproduction sustains intestinal inflammation by inhibiting Enterococcus colonization. bioRxiv 2023:2023.01.29.526128. [PMID: 36778381 PMCID: PMC9915521 DOI: 10.1101/2023.01.29.526128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Loss of antimicrobial proteins such as REG3 family members compromises the integrity of the intestinal barrier. Here, we demonstrate that overproduction of REG3 proteins can also be detrimental by reducing a protective species in the microbiota. Patients with inflammatory bowel disease (IBD) experiencing flares displayed heightened levels of secreted REG3 proteins that mediated depletion of Enterococcus faecium ( Efm ) from the gut microbiota. Efm inoculation of mice ameliorated intestinal inflammation through activation of the innate immune receptor NOD2, which was associated with the bacterial DL-endopeptidase SagA. Microbiota sensing by NOD2 in myeloid cells mediated IL-1β secretion and increased the proportion of IL-22-producing CD4 + T helper cells and innate lymphoid cells. Finally, Efm was unable to protect mice carrying a NOD2 gene variant commonly found in IBD patients. Our findings demonstrate that inflammation self-perpetuates by causing aberrant antimicrobial activity that disrupts symbiotic relationships with gut microbes.
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23
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Kwan JMC, Qiao Y. Mechanistic Insights into the Activities of Major Families of Enzymes in Bacterial Peptidoglycan Assembly and Breakdown. Chembiochem 2023; 24:e202200693. [PMID: 36715567 DOI: 10.1002/cbic.202200693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Serving as an exoskeletal scaffold, peptidoglycan is a polymeric macromolecule that is essential and conserved across all bacteria, yet is absent in mammalian cells; this has made bacterial peptidoglycan a well-established excellent antibiotic target. In addition, soluble peptidoglycan fragments derived from bacteria are increasingly recognised as key signalling molecules in mediating diverse intra- and inter-species communication in nature, including in gut microbiota-host crosstalk. Each bacterial species encodes multiple redundant enzymes for key enzymatic activities involved in peptidoglycan assembly and breakdown. In this review, we discuss recent findings on the biochemical activities of major peptidoglycan enzymes, including peptidoglycan glycosyltransferases (PGT) and transpeptidases (TPs) in the final stage of peptidoglycan assembly, as well as peptidoglycan glycosidases, lytic transglycosylase (LTs), amidases, endopeptidases (EPs) and carboxypeptidases (CPs) in peptidoglycan turnover and metabolism. Biochemical characterisation of these enzymes provides valuable insights into their substrate specificity, regulation mechanisms and potential modes of inhibition.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), 21 Nanyang Link, Singapore, 637371, Singapore.,LKC School of Medicine, Nanyang Technological University (NTU) Singapore, 11 Mandalay Road, Singapore, Singapore, 208232, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), Singapore, 21 Nanyang Link, Singapore, 637371, Singapore
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24
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Yu S, Ge X, Xu H, Tan B, Tian B, Shi Y, Dai Y, Li Y, Hu S, Qian J. Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection. Front Cell Infect Microbiol 2023; 13:1129043. [PMID: 36814443 PMCID: PMC9940757 DOI: 10.3389/fcimb.2023.1129043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. Methods We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples. Results We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients. Conclusion IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
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Affiliation(s)
- Si Yu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaomeng Ge
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujie Shi
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yimin Dai
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Jiaming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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25
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VanHook AM. A bacterial hydrolase gives the NOD2 tolerance. Sci Signal 2022; 15:eadf7180. [DOI: 10.1126/scisignal.adf7180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A bacterial endopeptidase that generates NOD2 ligands suppresses colitis.
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26
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Abstract
Loss-of-function mutations in NOD2, a receptor-sensing microbiota-derived muropeptides, is a genetic predisposition for Crohn's disease (CD). In this issue of Cell Host & Microbe, Gao et al. (2022) identify a microbiota-derived peptidoglycan remodeling enzyme that dampens chronic intestinal inflammation via NOD2, offering a potential path to alleviate CD.
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Affiliation(s)
- Benoit Chassaing
- INSERM U1016, "Mucosal microbiota in chronic inflammatory diseases," CNRS UMR 8104, Université Paris Cité, Paris, France.
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