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Yang J, Li G, Chen S, Su X, Xu D, Zhai Y, Liu Y, Hu G, Guo C, Yang HB, Occhipinti LG, Hu FX. Machine Learning-Assistant Colorimetric Sensor Arrays for Intelligent and Rapid Diagnosis of Urinary Tract Infection. ACS Sens 2024; 9:1945-1956. [PMID: 38530950 DOI: 10.1021/acssensors.3c02687] [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] [Indexed: 03/28/2024]
Abstract
Urinary tract infections (UTIs), which can lead to pyelonephritis, urosepsis, and even death, are among the most prevalent infectious diseases worldwide, with a notable increase in treatment costs due to the emergence of drug-resistant pathogens. Current diagnostic strategies for UTIs, such as urine culture and flow cytometry, require time-consuming protocols and expensive equipment. We present here a machine learning-assisted colorimetric sensor array based on recognition of ligand-functionalized Fe single-atom nanozymes (SANs) for the identification of microorganisms at the order, genus, and species levels. Colorimetric sensor arrays are built from the SAN Fe1-NC functionalized with four types of recognition ligands, generating unique microbial identification fingerprints. By integrating the colorimetric sensor arrays with a trained computational classification model, the platform can identify more than 10 microorganisms in UTI urine samples within 1 h. Diagnostic accuracy of up to 97% was achieved in 60 UTI clinical samples, holding great potential for translation into clinical practice applications.
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Affiliation(s)
- Jianyu Yang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Ge Li
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Shihong Chen
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Xiaozhi Su
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Dong Xu
- Department of Diagnostic Ultrasound Imaging & Interventional Therapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Wenling Big Data and Artificial Intelligence Institute in Medicine, Taizhou, Zhejiang 317502, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang 310022, China
- Taizhou Key Laboratory of Minimally Invasive Interventional Therapy & Artificial Intelligence, Taizhou Campus of Zhejiang Cancer Hospital, Taizhou, Zhejiang 317502, China
| | - Yueming Zhai
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Yuhang Liu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Guangxuan Hu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Chunxian Guo
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Hong Bin Yang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Luigi G Occhipinti
- Department of Engineering, University of Cambridge, 9 J J Thomson Avenue, Cambridge CB3 0FA, U.K
| | - Fang Xin Hu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
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2
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Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [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: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
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3
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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] [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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Fan D, Liu X, Ren Y, Luo Z, Li Y, Dong J, Wegner SV, Chen F, Zeng W. Harnessing antimicrobial peptide-coupled photosensitizer to combat drug-resistant biofilm infections through enhanced photodynamic therapy. Acta Pharm Sin B 2024; 14:1759-1771. [PMID: 38572100 PMCID: PMC10985124 DOI: 10.1016/j.apsb.2023.12.016] [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: 09/02/2023] [Revised: 11/18/2023] [Accepted: 12/25/2023] [Indexed: 04/05/2024] Open
Abstract
Bacterial biofilm-associated infection was one of the most serious threats to human health. However, effective drugs for drug-resistance bacteria or biofilms remain rarely reported. Here, we propose an innovative strategy to develop a multifunctional antimicrobial agent with broad-spectrum antibacterial activity by coupling photosensitizers (PSs) with antimicrobial peptides (AMPs). This strategy capitalizes on the ability of PSs to generate reactive oxygen species (ROS) and the membrane-targeting property of AMPs (KRWWKWIRW, a peptide screened by an artificial neural network), synergistically enhancing the antimicrobial activity. In addition, unlike conventional aggregation-caused quenching (ACQ) photosensitizers, aggregation-induced emission (AIE) PSs show stronger fluorescence emission in the aggregated state to help visualize the antibacterial mechanism. In vitro antibacterial experiments demonstrated the excellent killing effects of the developed agent against both Gram-positive (G+) and Gram-negative (G-) bacteria. The bacterial-aggregations induced ability enhanced the photoactivatable antibacterial activity against G- bacteria. Notably, it exhibited a significant effect on destroying MRSA biofilms. Moreover, it also showed remarkable efficacy in treating wound infections in mice in vivo. This multifunctional antimicrobial agent holds significant potential in addressing the challenges posed by bacterial biofilm-associated infections and drug-resistant bacteria.
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Affiliation(s)
- Duoyang Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Xiaohui Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Yueming Ren
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ziheng Luo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Yanbing Li
- Xiangya Hospital of Central South University, Changsha 410013, China
| | - Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Seraphine V. Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Münster 48149, Germany
| | - Fei Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Wenbin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
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5
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Pan T, Su L, Zhang Y, Xu L, Chen Y. Advances in Bio-Optical Imaging Systems for Spatiotemporal Monitoring of Intestinal Bacteria. Mol Nutr Food Res 2024; 68:e2300760. [PMID: 38491399 DOI: 10.1002/mnfr.202300760] [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: 10/28/2023] [Revised: 01/26/2024] [Indexed: 03/18/2024]
Abstract
Vast and complex intestinal communities are regulated and balanced through interactions with their host organisms, and disruption of gut microbial balance can cause a variety of diseases. Studying the mechanisms of pathogenic intestinal flora in the host and early detection of bacterial translocation and colonization can guide clinical diagnosis, provide targeted treatments, and improve patient prognosis. The use of in vivo imaging techniques to track microorganisms in the intestine, and study structural and functional changes of both cells and proteins, may clarify the governing equilibrium between the flora and host. Despite the recent rapid development of in vivo imaging of intestinal microecology, determining the ideal methodology for clinical use remains a challenge. Advances in optics, computer technology, and molecular biology promise to expand the horizons of research and development, thereby providing exciting opportunities to study the spatio-temporal dynamics of gut microbiota and the origins of disease. Here, this study reviews the characteristics and problems associated with optical imaging techniques, including bioluminescence, conventional fluorescence, novel metabolic labeling methods, nanomaterials, intelligently activated imaging agents, and photoacoustic (PA) imaging. It hopes to provide a valuable theoretical basis for future bio-intelligent imaging of intestinal bacteria.
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Affiliation(s)
- Tongtong Pan
- Hepatology Diagnosis and Treatment Center, The First Affiliated Hospital of Wenzhou Medical University & Zhejiang Provincial Key Laboratory for Accurate Diagnosis and Treatment of Chronic Liver Diseases, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Lihuang Su
- The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Yiying Zhang
- Alberta Institute, Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Liang Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yongping Chen
- Hepatology Diagnosis and Treatment Center, The First Affiliated Hospital of Wenzhou Medical University & Zhejiang Provincial Key Laboratory for Accurate Diagnosis and Treatment of Chronic Liver Diseases, Ouhai District, Wenzhou, Zhejiang, 325035, China
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6
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Niu C, Lv W, Zhu X, Dong Z, Yuan K, Jin Q, Zhang P, Li P, Mao M, Dong T, Chen Z, Luo J, Hou L, Zhang C, Hao K, Chen S, Huang Z. Intestinal Translocation of Live Porphyromonas gingivalis Drives Insulin Resistance. J Dent Res 2024; 103:197-207. [PMID: 38185909 DOI: 10.1177/00220345231214195] [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] [Indexed: 01/09/2024] Open
Abstract
Periodontitis has been emphasized as a risk factor of insulin resistance-related systemic diseases. Accumulating evidence has suggested a possible "oral-gut axis" linking oral infection and extraoral diseases, but it remains unclear whether periodontal pathogens can survive the barriers of the digestive tract and how they play their pathogenic roles. The present study established a periodontitis mouse model through oral ligature plus Porphyromonas gingivalis inoculation and demonstrated that periodontitis aggravated diet-induced obesity and insulin resistance, while also causing P. gingivalis enrichment in the intestine. Metabolic labeling strategy validated that P. gingivalis could translocate to the gastrointestinal tract in a viable state. Oral administration of living P. gingivalis elicited insulin resistance, while administration of pasteurized P. gingivalis had no such effect. Combination analysis of metagenome sequencing and nontargeted metabolomics suggested that the tryptophan metabolism pathway, specifically indole and its derivatives, was involved in the pathogenesis of insulin resistance caused by oral administration of living P. gingivalis. Moreover, liquid chromatography-high-resolution mass spectrometry analysis confirmed that the aryl hydrocarbon receptor (AhR) ligands, mainly indole acetic acid, tryptamine, and indole-3-aldehyde, were reduced in diet-induced obese mice with periodontitis, leading to inactivation of AhR signaling. Supplementation with Ficz (6-formylindolo (3,2-b) carbazole), an AhR agonist, alleviated periodontitis-associated insulin resistance, in which the restoration of gut barrier function might play an important role. Collectively, these findings reveal that the oral-gut translocation of viable P. gingivalis works as a fuel linking periodontitis and insulin resistance, in which reduction of AhR ligands and inactivation of AhR signaling are involved. This study provides novel insight into the role of the oral-gut axis in the pathogenesis of periodontitis-associated comorbidities.
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Affiliation(s)
- C Niu
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - W Lv
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, P. R. China
| | - X Zhu
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Z Dong
- Department of Oral Implantology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, P. R. China
| | - K Yuan
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Q Jin
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - P Zhang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - P Li
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - M Mao
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - T Dong
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Z Chen
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - J Luo
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - L Hou
- Department of Nursing, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - C Zhang
- Department of Oral Implantology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, P. R. China
| | - K Hao
- Department of Oral Implantology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, P. R. China
| | - S Chen
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, P. R. China
- Department of Oral Implantology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, P. R. China
| | - Z Huang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P. R. China
- National Clinical Research Center for Oral Diseases, National Center for Stomatology, Shanghai, P. R. China
- Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
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7
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Lin Y, Liang X, Li Z, Gong T, Ren B, Li Y, Peng X. Omics for deciphering oral microecology. Int J Oral Sci 2024; 16:2. [PMID: 38195684 PMCID: PMC10776764 DOI: 10.1038/s41368-023-00264-x] [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: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.
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Affiliation(s)
- Yongwang Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyue Liang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhengyi Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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8
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Yang R, Chen Z, Cai J. Fecal microbiota transplantation: Emerging applications in autoimmune diseases. J Autoimmun 2023; 141:103038. [PMID: 37117118 DOI: 10.1016/j.jaut.2023.103038] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/12/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
Both genetic susceptibility and environmental factors are important contributors to autoimmune disease pathogenesis. As an environmental factor, the gut microbiome plays a crucial role in the development and progression of autoimmune diseases. Thus, strategies targeting gut microbiome alterations can potentially be used to treat autoimmune disease. Microbiota-based interventions, such as prebiotics, probiotics, dietary interventions, and fecal microbiota transplantation (FMT), have attracted growing interest as novel treatment approaches. FMT is an effective method for treating recurrent Clostridioides difficile infections; moreover, it is emerging as a promising treatment for patients with inflammatory bowel disease and other autoimmune diseases. Although the mechanisms underpinning the interaction between the gut microbiome and host are not fully understood in patients with autoimmune disease, FMT has been shown to restore altered gut microbiota composition, rebuild the intestinal microecosystem, and mediate innate and adaptive immune responses to achieve a therapeutic effect. In this review, we provide an overview of FMT and discuss how FMT can be used as a novel treatment approach for autoimmune diseases. Furthermore, we discuss recent challenges and offer future research directions.
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Affiliation(s)
- Ruixue Yang
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beilishi Road 167, Xicheng District, Beijing, 100037, China
| | - Zhenzhen Chen
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beilishi Road 167, Xicheng District, Beijing, 100037, China
| | - Jun Cai
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beilishi Road 167, Xicheng District, Beijing, 100037, China.
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9
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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10
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Marcos-Fernández R, Sánchez B, Ruiz L, Margolles A. Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology. Crit Rev Microbiol 2023; 49:556-577. [PMID: 35749433 DOI: 10.1080/1040841x.2022.2086035] [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: 07/19/2021] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.
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Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
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11
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Wang Y, Chen Z, Zhao F, Yang H. Metabolome shifts triggered by chlorine sanitisation induce Escherichia coli on fresh produce into the viable but nonculturable state. Food Res Int 2023; 171:113084. [PMID: 37330837 DOI: 10.1016/j.foodres.2023.113084] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Facing the increasing occurrence of "big six" Escherichia coli outbreaks linked to fresh produce, chlorine-based sanitisers are widely used for fresh produce decontamination in recent years. However, latest finding that chlorine may induce E. coli cells into a viable not nonculturable (VBNC) state is bringing a new challenge to the fresh produce industry. VBNC cells are undetectable by the plate count test, and yet they retain pathogenicity and are more antibiotic-resistant than culturable cells. As a result, their eradication is critical to ensure the safety of fresh produce. Understanding VBNC cells at the metabolic level may provide a breakthrough for their eradication. Therefore, this study was carried out to collect the VBNC pathogenic E. coli (O26:H11, O121:H19, and O157:H7) cells from chlorine-treated pea sprouts and characterise them using NMR-based metabolomics. From the globally increased metabolite contents detected in the VBNC E. coli cells as compared to the culturable cells, mechanisms underlying E. coli's VBNC induction were elucidated. These include rendering the energy generation scheme to become more compatible with the lowered energy needs, disaggregating protein aggregates to release amino acids for osmoprotection and later resuscitation, as well as increasing cAMP content to downregulate RpoS. These identified metabolic characteristics can inspire future development of targeted measures for VBNC E. coli cell inhibition. Our methods can also be applied to other pathogens to help lower the risk of overall foodborne diseases.
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Affiliation(s)
- Yue Wang
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore.
| | - Zihui Chen
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Fengnian Zhao
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Hongshun Yang
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, 312000, China.
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12
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Shen Y, Jiang B, Zhang C, Wu Q, Li L, Jiang P. Combined Inhibition of the TGF-β1/Smad Pathway by Prevotella copri and Lactobacillus murinus to Reduce Inflammation and Fibrosis in Primary Sclerosing Cholangitis. Int J Mol Sci 2023; 24:11010. [PMID: 37446187 DOI: 10.3390/ijms241311010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Primary sclerosing cholangitis (PSC) is a chronic cholestatic disease characterized by inflammation and fibrosis of the bile ducts. Cholestasis may lead to hepatic inflammation and fibrosis, and amelioration of cholestasis may allow recovery from inflammatory and fibrotic pathological damage. Prevotella copri (P. copri) interventions have been reported to significantly improve cholestasis and liver fibrosis in 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced PSC mouse models. Even though P. copri treatment alone cannot bring about recovery from DDC-induced inflammation, it increases the abundance of Lactobacillus murinus (L. murinus) compared with DDC treatment, which has been reported to have anti-inflammatory effects. The abundance of L. murinus still not recovering to a normal level may underlie hepatic inflammation in P. copri + DDC mice. Separate or combined interventions of P. copri and L. murinus were used to investigate the molecular mechanism underlying the improvement in PSC inflammation and fibrosis. P. copri and L. murinus significantly reduced the hepatic inflammatory cell aggregation and inflammatory factor expression as well as the hepatic collagen content and fibrin factor expression in the PSC mice. Further analysis of phosphorylation and dephosphorylation levels revealed that treating the PSC mice with the P. copri and L. murinus combined intervention inhibited the activity of the DDC-activated TGF-β1/Smad pathway, thereby reducing liver inflammation and fibrosis. The combination of P. copri and L. murinus inhibits the TGF-β1/Smad pathway and reduces inflammation and fibrosis in PSC.
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Affiliation(s)
- Yu Shen
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Baorong Jiang
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Chenchen Zhang
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Qian Wu
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Lei Li
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Ping Jiang
- Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
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13
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Wang T, Shen P, He Y, Zhang Y, Liu J. Spatial transcriptome uncovers rich coordination of metabolism in E. coli K12 biofilm. Nat Chem Biol 2023:10.1038/s41589-023-01282-w. [PMID: 37055614 DOI: 10.1038/s41589-023-01282-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 02/02/2023] [Indexed: 04/15/2023]
Abstract
Microbial communities often display region-specific properties, which give rise to complex interactions and emergent behaviors that are critical to the homeostasis and stress response of the communities. However, systems-level understanding of these properties still remains elusive. In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. We uncovered three modes of community-level coordination, including cross-regional resource allocation, local cycling and feedback signaling, which were mediated by strengthened transmembrane transport and spatially specific activation of metabolism. As a consequence of such coordination, the nutrient-limited region of the community maintained an unexpectedly high level of metabolism, enabling it to express many signaling genes and functionally unknown genes with potential sociality functions. Our work provides an extended understanding of the metabolic interplay in biofilms and presents a new approach of investigating complex interactions in bacterial communities on the systems level.
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Affiliation(s)
- Tianmin Wang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ping Shen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yihui He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yuzhen Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jintao Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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14
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Zhao SY, Hughes GL, Coon KL. A cryopreservation method to recover laboratory- and field-derived bacterial communities from mosquito larval habitats. PLoS Negl Trop Dis 2023; 17:e0011234. [PMID: 37018374 PMCID: PMC10109488 DOI: 10.1371/journal.pntd.0011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/17/2023] [Accepted: 03/10/2023] [Indexed: 04/06/2023] Open
Abstract
Mosquitoes develop in a wide range of aquatic habitats containing highly diverse and variable bacterial communities that shape both larval and adult traits, including the capacity of adult females of some mosquito species to transmit disease-causing organisms to humans. However, while most mosquito studies control for host genotype and environmental conditions, the impact of microbiota variation on phenotypic outcomes of mosquitoes is often unaccounted for. The inability to conduct reproducible intra- and inter-laboratory studies of mosquito-microbiota interactions has also greatly limited our ability to identify microbial targets for mosquito-borne disease control. Here, we developed an approach to isolate and cryopreserve bacterial communities derived from lab and field-based larval rearing environments of the yellow fever mosquito Aedes aegypti-a primary vector of dengue, Zika, and chikungunya viruses. We then validated the use of our approach to generate experimental microcosms colonized by standardized lab- and field-derived bacterial communities. Our results overall reveal minimal effects of cryopreservation on the recovery of both lab- and field-derived bacteria when directly compared with isolation from non-cryopreserved fresh material. Our results also reveal improved reproducibility of bacterial communities in replicate microcosms generated using cryopreserved stocks over fresh material. Communities in replicate microcosms further captured the majority of total bacterial diversity present in both lab- and field-based larval environments, although the relative richness of recovered taxa as compared to non-recovered taxa was substantially lower in microcosms containing field-derived bacteria. Altogether, these results provide a critical next step toward the standardization of mosquito studies to include larval rearing environments colonized by defined microbial communities. They also lay the foundation for long-term studies of mosquito-microbe interactions and the identification and manipulation of taxa with potential to reduce mosquito vectorial capacity.
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Affiliation(s)
- Serena Y. Zhao
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Topical Disease, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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15
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Beauchemin ET, Hunter C, Maurice CF. Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. Gut Microbes 2023; 15:2180317. [PMID: 36823031 PMCID: PMC9980609 DOI: 10.1080/19490976.2023.2180317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
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Affiliation(s)
- Eve T. Beauchemin
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Claire Hunter
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada,McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada,CONTACT Corinne F. Maurice Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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16
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Apostolos AJ, Chordia MD, Kolli SH, Dalesandro BE, Rutkowski MR, Pires MM. Real-time non-invasive fluorescence imaging of gut commensal bacteria to detect dynamic changes in the microbiome of live mice. Cell Chem Biol 2022; 29:S2451-9456(22)00416-0. [PMID: 36516833 PMCID: PMC10239791 DOI: 10.1016/j.chembiol.2022.11.010] [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: 05/27/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
In mammals, gut commensal microbiota interact extensively with the host, and the same interactions can be dysregulated in diseased states. Animal imaging is a powerful technique that is widely used to diagnose, measure, and track biological changes in model organisms such as laboratory mice. Several imaging techniques have been discovered and adopted by the research community that provide dynamic, non-invasive assessment of live animals, but these gains have not been universal across all fields of biology. Herein, we describe a method to non-invasively image commensal bacteria based on the specific metabolic labeling of bacterial cell walls to illuminate the gut bacteria of live mice. This tagging strategy may additionally provide unprecedented insight into cell wall turnover of gut commensals, which has implications for bacterial cellular growth and division, in a live animal.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sree H Kolli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Melanie R Rutkowski
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
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17
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Li N, Wu G, Tang L, Zhou W, Yang S, Pan Q, Wang M, Wu P, Xiao H, He Y, Tan X, Yang Q. Metabolic Labeling Strategy Boosted Antibacterial Efficiency for Photothermal and Photodynamic Synergistic Bacteria-Infected Wound Therapy. ACS APPLIED MATERIALS & INTERFACES 2022; 14:46362-46373. [PMID: 36198018 DOI: 10.1021/acsami.2c15759] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Pathogenic bacteria infections bring about a substantial risk to human health. Given the development of antibiotic-resistance bacteria, alternative antibacterial strategies with great inactivation efficiency and bacteria-binding ability are extremely attractive. In this work, a metabolic labeling photosensitizer, prepared by the coupling of commercial IR820 and d-propargylglycine (a type of d-amino acid, DAA) via a straightforward one-step incubation (IR820-DAA), could metabolically be incorporated into the bacterial wall via enzymatic reactions, thus enhancing antibacterial efficiency. The laser energy at 808 nm could make IR820-DAA a synergistic photothermal/photodynamic agent for efficient antibacterial therapy and wound healing. Furthermore, IR820-DAA exhibits good water solubility and biological safety for clinical translation and even possesses biofilm degradation activity toward methicillin-resistant Staphylococcus aureus (MRSA). Overall, the proposed IR820-DAA holds great promise as a nonantibiotic tool for the treatment of bacteria-related diseases and offers a blueprint for building the precise synergistic antibacterial therapeutic platform.
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Affiliation(s)
- Na Li
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Guilong Wu
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Li Tang
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Wei Zhou
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Sha Yang
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Qi Pan
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Minghui Wang
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Peixian Wu
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Hao Xiao
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Yuxuan He
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Xiaofeng Tan
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Qinglai Yang
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
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18
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Liang J, Li T, Zhao J, Wang C, Sun H. Current understanding of the human microbiome in glioma. Front Oncol 2022; 12:781741. [PMID: 36003766 PMCID: PMC9393498 DOI: 10.3389/fonc.2022.781741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
There is mounting evidence that the human microbiome is highly associated with a wide variety of central nervous system diseases. However, the link between the human microbiome and glioma is rarely noticed. The exact mechanism of microbiota to affect glioma remains unclear. Recent studies have demonstrated that the microbiome may affect the development, progress, and therapy of gliomas, including the direct impacts of the intratumoral microbiome and its metabolites, and the indirect effects of the gut microbiome and its metabolites. Glioma-related microbiome (gut microbiome and intratumoral microbiome) is associated with both tumor microenvironment and tumor immune microenvironment, which ultimately influence tumorigenesis, progression, and responses to treatment. In this review, we briefly summarize current knowledge regarding the role of the glioma-related microbiome, focusing on its gut microbiome fraction and a brief description of the intratumoral microbiome, and put forward the prospects in which microbiome can be applied in the future and some challenges still need to be solved.
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Affiliation(s)
- Jianhao Liang
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Li
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiajia Zhao
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cheng Wang
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haitao Sun
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine, Clinical Biobank Center, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- *Correspondence: Haitao Sun,
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19
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Cao Z, Wang L, Liu R, Lin S, Wu F, Liu J. Encoding with a fluorescence-activating and absorption-shifting tag generates living bacterial probes for mammalian microbiota imaging. Mater Today Bio 2022; 15:100311. [PMID: 35711290 PMCID: PMC9194656 DOI: 10.1016/j.mtbio.2022.100311] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/12/2022] Open
Abstract
The mammalian microbiota plays essential roles in health. A primary determinant to understand the interaction with the host is the distribution and viability of its key microorganisms. Here, a strategy of encoding with a fluorescence-activating and absorption-shifting tag (FAST) is reported to prepare living bacterial probes for real-time dynamic, dual-modal, and molecular oxygen-independent imaging of the host microbiota. Carrying FAST endows bacteria with rapid on-demand turn on-off fluorescence by adding or removal of corresponding fluorogens. Encoded bacteria are able to reversibly switch emission bands for dual-color fluorescence imaging via fluorogen exchange. Due to molecular oxygen-independent emission of FAST, encoded bacteria can emit fluorescence under anaerobic environments including the gut and tumor. These living probes demonstrate the applicability to quantify the vitality of bacteria transplanted to the gut microbiota. This work proposes a unique fluorescence probe for investigating the dynamics of the host microbiota. Living bacterial probes for real-time dynamic, dual-modal, and molecular oxygen-independent imaging of mammalian microbiota. Engineered bacteria showing on-demand turn on-off fluorescence by adding or removal of corresponding fluorogens. Fluorescence emission under anaerobic in vivo environments including the gut and tumor. A fluorescence probe to determine the vitality of transplanted bacteria and investigate the dynamics of the host microbiota.
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20
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Gao X, Li M, Zhao M, Wang X, Wang S, Liu Y. Metabolism-Triggered Colorimetric Sensor Array for Fingerprinting and Antibiotic Susceptibility Testing of Bacteria. Anal Chem 2022; 94:6957-6966. [PMID: 35500293 DOI: 10.1021/acs.analchem.1c05006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rapid identification and antibiotic susceptibility testing (AST) of bacteria would help us to accurately identify the infectious sources as well as guide the use of antibiotics, which are crucial for improving the survival rate and antimicrobial resistance. Herein, a colorimetric sensor array for bacteria fingerprinting was constructed with d-amino acid (d-AA)-modified gold nanoparticles (AuNPs) as probes (Au/d-AA). Bacteria can metabolize the d-AA, triggering the aggregation of AuNPs. Making use of different metabolic capabilities of bacteria toward different d-AA, eight kinds of bacteria including antibiotic-resistant bacteria and strains of the same bacterial species are successfully differentiated via learning the response patterns. Meanwhile, the sensor array also performs well in quantitative analysis of single bacterium and differentiation of bacteria mixtures. More interestingly, a rapid colorimetric AST approach has been developed based on the Au/d-AA nanoprobes by monitoring the d-AA metabolic activity of bacteria toward various antibiotic treatments. In this regard, the outlined work here would promote clinical practicability and facilitate antibiotic stewardship.
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Affiliation(s)
- Xia Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Miaomiao Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Minyang Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xinke Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
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21
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Fu A, Yao B, Dong T, Chen Y, Yao J, Liu Y, Li H, Bai H, Liu X, Zhang Y, Wang C, Guo Y, Li N, Cai S. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell 2022; 185:1356-1372.e26. [PMID: 35395179 DOI: 10.1016/j.cell.2022.02.027] [Citation(s) in RCA: 287] [Impact Index Per Article: 143.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/10/2022] [Accepted: 02/24/2022] [Indexed: 12/12/2022]
Abstract
Tumor-resident intracellular microbiota is an emerging tumor component that has been documented for a variety of cancer types with unclear biological functions. Here, we explored the functional significance of these intratumor bacteria, primarily using a murine spontaneous breast-tumor model MMTV-PyMT. We found that depletion of intratumor bacteria significantly reduced lung metastasis without affecting primary tumor growth. During metastatic colonization, intratumor bacteria carried by circulating tumor cells promoted host-cell survival by enhancing resistance to fluid shear stress by reorganizing actin cytoskeleton. We further showed that intratumor administration of selected bacteria strains isolated from tumor-resident microbiota promoted metastasis in two murine tumor models with significantly different levels of metastasis potential. Our findings suggest that tumor-resident microbiota, albeit at low biomass, play an important role in promoting cancer metastasis, intervention of which might therefore be worth exploring for advancing oncology care.
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Affiliation(s)
- Aikun Fu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Bingqing Yao
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Dong
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yongyi Chen
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, 310000, China
| | - Jia Yao
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yu Liu
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hang Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Huiru Bai
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaoqin Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Zhang
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Chunhui Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yajing Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Shang Cai
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
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22
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Zhao J, He D, Lai HM, Xu Y, Luo Y, Li T, Liang J, Yang X, Guo L, Ke Y, Zhou H, Wu W, Guo H, Sun H. Comprehensive histological imaging of native microbiota in human glioma. JOURNAL OF BIOPHOTONICS 2022; 15:e202100351. [PMID: 34936211 DOI: 10.1002/jbio.202100351] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Mounting evidence suggests that distinct microbial communities reside in tumors and play important roles in tumor physiology. Recently, a previous study profiled the composition and localization of intratumoral bacteria using 16S ribosomal DNA (rDNA) sequencing and histological visualization methods across seven tumor types, including human glioblastoma. However, their results based on traditional histological examinations should be further validated considering potential sources of contamination originating from sample collection and processing. Here, we aim to propose a three-dimensional (3D) in situ intratumoral microbiota visualization and quantification protocol avoiding surface contamination and provide a comprehensive histological investigation on local bacteria within human glioma samples. We develop a 3D quantitative in situ intratumoral microbiota imaging strategy, combining tissue clearing, immunofluorescent labeling, optical sectioning microscopy, and image processing, to visualize bacterial lipopolysaccharide (LPS) within gliomas in a direct, contaminant-free, and unambiguous manner. Through an automated statistical algorithm, reliable signals can be distinguished for further analysis of their sizes, distribution, and fluorescence intensities. In tandem, we also combined 2D images obtained from thin-section histological methods, including immunohistochemistry and fluorescence in situ hybridization, to provide comprehensive histological imaging for local bacterial components within human glioma samples. We have, for the first time, achieved 3D quantitative imaging of bacterial LPS colonized in gliomas in a contamination-free manner within human glioma samples. We also built the multiple histological evidence chain demonstrating the irregular shapes and sparse distribution of bacterial components within human glioma samples, mostly localized near nuclear membranes or in the intercellular space. This study provides favorable evidence for the presence of microbiota in human gliomas and provides information on the feature and distribution of bacterial components. The results, along with the integrated 3D quantitative intratumoral microbiota imaging method, are promising to provide insightful information into the direct interactions between the microbial community and the host in the tumor microenvironment.
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Affiliation(s)
- Jiajia Zhao
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Biobank Centre, Microbiome Medicine Centre, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Dian He
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yingying Xu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, China
| | - Yunhao Luo
- Clinical Biobank Centre, Microbiome Medicine Centre, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Li
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianhao Liang
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaodu Yang
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yiquan Ke
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongwei Zhou
- Clinical Biobank Centre, Microbiome Medicine Centre, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wutian Wu
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration (GHMICR), Jinan University, Guangzhou, China
- Re-Stem Biotechnology Co., Ltd, Suzhou, China
| | - Hongbo Guo
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haitao Sun
- Neurosurgery Centre, The National Key Clinical Specialty, The Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Biobank Centre, Microbiome Medicine Centre, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Centre for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
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23
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Miranda RR, Parthasarathy A, Hudson AO. Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.845469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Approximately 2.8 million people worldwide are infected with bacteria that are deemed resistant to clinically relevant antibiotics. This accounts for 700,000 deaths every year and represents a major public health threat that has been on the rise for the past two decades. In contrast, the pace of antibiotic discovery to treat these resistant pathogens has significantly decreased. Most antibiotics are complex natural products that were isolated from soil microorganisms during the golden era of antibiotic discovery (1940s to 1960s) employing the “Waksman platform”. After the collapse of this discovery platform, other strategies and approaches emerged, including phenotype- or target-based screenings of large synthetic compound libraries. However, these methods have not resulted in the discovery and/or development of new drugs for clinical use in over 30 years. A better understanding of the structure and function of the molecular components that constitute the bacterial system is of paramount importance to design new strategies to tackle drug-resistant pathogens. Herein, we review the traditional approaches as well as novel strategies to facilitate antibiotic discovery that are chemical biology-focused. These include the design and application of chemical probes that can undergo bioorthogonal reactions, such as copper (I)-catalyzed azide-alkyne cycloadditions (CuAAC). By specifically interacting with bacterial proteins or being incorporated in the microorganism’s metabolism, chemical probes are powerful tools in drug discovery that can help uncover new drug targets and investigate the mechanisms of action and resistance of new antibacterial leads.
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24
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Lin L, Song J, Li J, Zuo X, Wei H, Yang C, Wang W. Imaging the in vivo growth patterns of bacteria in human gut Microbiota. Gut Microbes 2022; 13:1960134. [PMID: 34428120 PMCID: PMC8386752 DOI: 10.1080/19490976.2021.1960134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
How to study the unculturable bacteria in the laboratory is one of the major challenges in human gut microbiota research. The resulting lack of microbiology knowledge of this "dark matter" greatly hinders further understanding of our gut microbiota. Here, to characterize the in vivo growth and division of human gut bacteria, we report the integrative use of STAMP (sequential tagging with D-amino acid-based metabolic probes) and fluorescence in situ hybridization (FISH) in a human microbiota-associated mouse model. After stable colonization of the human fecal microbiotas in germ-free mice, two fluorescent D-amino acid probes were sequentially administered by gavage, and the dually labeled peptidoglycan of the bacteria provided a chronological recording of their cell wall syntheses. Following taxonomic identification with FISH staining, the growth patterns of 32 species, including 5 currently unculturables, were identified. Surprisingly, we found that many bacterial species in the human microbiota were significantly shorter than those in the mouse gut microbiota. An imaging database for gut bacteria ̶ Microbiome Atlas was built for summarizing STAMP imaging of bacteria from different microbiotas, which can be contributed by the microbiota research community worldwide. This integrative imaging strategy and the database will promote our understanding of the bacterial cytology in gut microbiotas and facilitate communications among cellular microbiologists.
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Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Li
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Wei
- Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China,State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, P. R. China,Hong Wei Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People’s Hospital, Tongji University, Shanghai200435, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China,Chaoyong Yang Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,CONTACT Wei Wang Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200127, China
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25
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Li N, Tan X, Yang Q. Recent Progress on Strategies and Applications of Imaging for Intestinal Microflora. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Katasonov AB. [Gut microbiome as a therapeutic target in the treatment of depression and anxiety]. Zh Nevrol Psikhiatr Im S S Korsakova 2021; 121:129-135. [PMID: 34932298 DOI: 10.17116/jnevro2021121111129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There is a bi-directional connection between the gut microbiome and the brain. Changes in the composition of the microbiome affect emotions, behavior, and the stress response involved in the pathogenesis of depression. Depression and anxiety are often associated with dysbiosis and inflammatory bowel disease. Dysbiosis enhances stress response and low-grade systemic inflammation, and vice versa. This vicious circle may be responsible for the formation of depression. Antidepressants therapy should be accompanied by the elimination of dysbiosis. For these purposes diet, prebiotics, probiotics and faecal microbiota transplantation can be used. The advantages and disadvantages of each method are considered. The manipulation of microbiome composition has been shown to have great therapeutic potential in the treatment of depression and anxiety.
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27
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Shan C, Li M, Liu Z, Xu R, Qiao F, Du ZY, Zhang ML. Pediococcus pentosaceus Enhances Host Resistance Against Pathogen by Increasing IL-1β Production: Understanding Probiotic Effectiveness and Administration Duration. Front Immunol 2021; 12:766401. [PMID: 34899717 PMCID: PMC8662542 DOI: 10.3389/fimmu.2021.766401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Probiotic administration is a potential strategy against enteric pathogen infection in either clinical treatment or animal nutrition industry, but the administration duration of probiotics varied and the underlying mechanisms remain unclear. A strain (YC) affiliated to Pediococcus pentosaceus, a commonly used probiotic, was isolated from fish gut and the potential role of YC against Aeromonas hydrophila was detected in zebrafish. We found that 3- or 4-week YC administration (YC3W or YC4W) increased the resistance against A. hydrophila while 1- or 2-week treatment (YC1W or YC2W) did not. To determine the possible reason, intestinal microbiota analysis and RNAseq were conducted. The results showed that compared with CON and YC1W, YC4W significantly increased the abundance of short-chain fatty acids (SCFAs) producing bacteria and elevated the gene expression of nlrp3. Higher butyrate content and enhanced expression of IL1β were subsequently found in YC4W. To identify the causal relationship between butyrate and the higher pathogen resistance, different concentrations of sodium butyrate (SB) were supplemented. The results suggested that 10 mmol/kg SB addition mirrored the protective effect of YC4W by increasing the production of IL-1β. Furthermore, the increased IL-1β raised the percentage of intestinal neutrophils, which endued the zebrafish with A. hydrophila resistance. In vivo knockdown of intestinal il1b eliminated the anti-infection effect. Collectively, our data suggested that the molecular mechanism of probiotics determined the administration duration, which is vital for the efficiency of probiotics. Promoting host inflammation by probiotic pretreatment is one potential way for probiotics to provide their protective effects against pathogens.
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Affiliation(s)
- Chengjie Shan
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Miao Li
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhu Liu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China.,School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Xu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Qiao
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
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28
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Jiang Z, Sun B, Wang Y, Gao H, Ren H, Zhang H, Lu T, Ren X, Wei W, Wang X, Zhang L, Li J, Ding D, Lovell JF, Zhang Y. Surfactant-Stripped Micelles with Aggregation-Induced Enhanced Emission for Bimodal Gut Imaging In Vivo and Microbiota Tagging Ex Vivo. Adv Healthc Mater 2021; 10:e2100356. [PMID: 34160147 DOI: 10.1002/adhm.202100356] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Aggregation-induced emission luminogens (AIEgens) hold promise for biomedical imaging and new approaches facilitating their aggregation state are desirable for fluorescence enhancement. Herein, a series of surfactant-stripped AIEgen micelles (SSAMs) with improved fluorescence are developed by a low-temperature surfactant-stripping method to encapsulate AIEgens in temperature-sensitive Pluronic block copolymer. After stripping excessive surfactant, SSAMs exhibit altered optical properties and significantly higher fluorescence quantum yield. Using this method, a library of highly concentrated fluorescent nanoparticles are generated with tunable absorption and emission wavelengths, permitting imaging of deep tissues at different wavelengths. SSAMs remain physiologically stable and can pass safely through gastrointestinal tract (GI) without degradation in the harsh conditions, allowing for fluorescence and photoacoustic imaging of intestine with high resolution. d-amino acids (DAA), a natural metabolite for bacteria, can be chemically conjugated on the surface of SSAMs, enabling non-invasive monitoring of the microbial behavior of ex vivo fluorescently labeled gut microbiota in the GI tract.
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Affiliation(s)
- Zhen Jiang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Boyang Sun
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Yueqi Wang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Heqi Gao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, P. R. China
| | - He Ren
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Hao Zhang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Tong Lu
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Xiangkui Ren
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Wei Wei
- South China Normal University, Guangzhou, Guangdong Province, 510631, P. R. China
| | - Xiaoli Wang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, R. P. China
| | - Lei Zhang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
| | - Jiao Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, P. R. China
| | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, P. R. China
| | - Jonathan F Lovell
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Yumiao Zhang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, P. R. China
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29
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Chen QW, Qiao JY, Liu XH, Zhang C, Zhang XZ. Customized materials-assisted microorganisms in tumor therapeutics. Chem Soc Rev 2021; 50:12576-12615. [PMID: 34605834 DOI: 10.1039/d0cs01571g] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms have been extensively applied as active biotherapeutic agents or drug delivery vehicles for antitumor treatment because of their unparalleled bio-functionalities. Taking advantage of the living attributes of microorganisms, a new avenue has been opened in anticancer research. The integration of customized functional materials with living microorganisms has demonstrated unprecedented potential in solving existing questions and even conferring microorganisms with updated antitumor abilities and has also provided an innovative train of thought for enhancing the efficacy of microorganism-based tumor therapy. In this review, we have summarized the emerging development of customized materials-assisted microorganisms (MAMO) (including bacteria, viruses, fungi, microalgae, as well as their components) in tumor therapeutics with an emphasis on the rational utilization of chosen microorganisms and tailored materials, the ingenious design of biohybrid systems, and the efficacious antitumor mechanisms. The future perspectives and challenges in this field are also discussed.
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Affiliation(s)
- Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Ji-Yan Qiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Cheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
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30
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Lin H, Lin L, Du Y, Gao J, Yang C, Wang W. Biodistributions of l,d-Transpeptidases in Gut Microbiota Revealed by In Vivo Labeling with Peptidoglycan Analogs. ACS Chem Biol 2021; 16:1164-1171. [PMID: 34185512 DOI: 10.1021/acschembio.1c00346] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
By catalyzing a 3-3 cross-link in peptidoglycan, l,d-transpeptidases (Ldts) can cause resistance to β-lactams in some pathogens in vitro. However, the prevalence of Ldt and Ldt-mediated responses to different β-lactams in vivo have never been explored. Here, we apply an in vivo metabolic labeling strategy to study their biodistributions and Ldt-induced bacterial responses to β-lactams in the mouse gut microbiota. A tetrapeptide-based fluorescent probe that functions as a substrate for Ldts in Gram-positive bacteria efficiently labels ∼18% of total gut bacteria after gavage, suggesting Ldts' high prevalence in gut microbiota. The cellular distributions of 3-3 cross-links on three gut bacterial species were then identified with the aid of fluorescence in situ hybridization to identify the bacterial taxa. After oral administration of two β-lactams, ampicillin and meropenem, only the latter efficiently inhibits the tetrapeptide labeling, suggesting that Ldts may be able to cause resistance to some β-lactams in the mammalian gut.
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Affiliation(s)
- Huibin Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Liyuan Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yahui Du
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Juan Gao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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Lin L, Du Y, Song J, Wang W, Yang C. Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut. Acc Chem Res 2021; 54:2076-2087. [PMID: 33856204 DOI: 10.1021/acs.accounts.1c00068] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As a newly discovered organ, gut microbiota has been extensively studied in the last two decades, with their highly diverse and fundamental roles in the physiology of many organs and systems of the host being gradually revealed. However, most of the current research heavily relies on DNA sequencing-based methodologies. To truly understand the complex physiological and pathological functions demonstrated by commensal and pathogenic gut bacteria, we need more powerful methods and tools, among which imaging strategies suitable for approaching this ecosystem in different settings are one of the most desirable. Although the phrase gut "dark matter" is often used in referring to the unculturability of many gut bacteria, it is also applicable to describing the formidable difficulties in visualizing these microbes in the intestines. To develop suitable and versatile chemical and biological tools for imaging bacteria in the gut, great efforts have been devoted in the past several years.In this Account, we highlight the recent progress made by our group and other laboratories in the development of visualization strategies for commensal microbiota and pathogenic bacteria in the gut. First, we summarize our efforts toward the development of derivatized antibiotic staining probes that directly bind to specific bacterial surface structures for selective labeling of different groups of gut bacteria. Next, metabolic labeling-based imaging strategies, using unnatural amino acids, unnatural sugars, and stable isotopes, for imaging gut bacteria on various scales and in different settings are discussed in detail. We then introduce nucleic acid staining-based bacterial imaging, using either general nucleic acid-binding reagents or selective-labeling techniques (e.g., fluorescence in situ hybridization) to meet the diverse needs in gut microbiota research. This classical imaging strategy has witnessed a renaissance owing to a series of new technical advancements. Furthermore, despite the notorious difficulties of performing genetic manipulations in many commensal gut bacteria, great effort has been made recently in engineering gut bacteria with reporters like fluorescent proteins and acoustic response proteins.Our perspectives on the current limitations of the chemical tools and strategies and the future directions for improvement are also presented. We hope that this Account can offer valuable references to spark new ideas and invite new efforts to help decipher the complex biological and chemical interactions between commensal microbiota and pathogenic bacteria and the hosts.
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Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yahui Du
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Ye X, Feng T, Li L, Wang T, Li P, Huang W. Theranostic platforms for specific discrimination and selective killing of bacteria. Acta Biomater 2021; 125:29-40. [PMID: 33582362 DOI: 10.1016/j.actbio.2021.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/04/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Bacterial infections are serious threats to public health due to lack of advanced techniques to rapidly and accurately diagnose these infections in clinics. Although bacterial infections can be treated with broad-spectrum antibiotics based on empirical judgment, the emergence of antimicrobial resistance has attracted global attention due to long-term misuse and abuse of antibiotics by humans in recent decades. Therefore, it is imperative to selectively discriminate and precisely eliminate pathogenic bacteria. Herein, in addition to the conventional methods for bacterial identification, we comprehensively reviewed the recently developed theranostic platforms for specific discrimination and selective killing of bacteria according to their different interactions with the target bacteria, such as electrostatic and hydrophobic interactions, molecular recognition, microenvironment response, metabolic labeling, bacteriophage targeting, and others. These theranostic agents not only benefit from improved therapeutic efficiency but also present limited susceptibility to induce bacterial resistance. The strategies summarized in this review will open up new avenues in developing effective antimicrobial materials to accurately diagnose and treat bacterial infections in the post-antibiotic era. STATEMENT OF SIGNIFICANCE: Bacterial infections are difficult to be rapidly and accurately diagnosed, and are generally treated with broad-spectrum antibiotics, which leads to the development of drug resistance. By integrating imaging modalities and therapeutic methods in a single treatment, various theranostic agents have been developed to address the abovementioned issues. Therefore, the emerging theranostic platforms for selective identification and elimination of bacteria based on the distinct interactions of the theranostic agents with the target bacteria are summarized in this review. We believe that the information provided in this review will guide researchers in designing advanced antibacterial theranostics for practical applications in the post-antibiotic era.
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Affiliation(s)
- Xiaoting Ye
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Tao Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China; Ningbo Institute of Northwestern Polytechnical University, Ningbo 315103, China; Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Chongqing 401120, China.
| | - Lin Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China; Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing 211816, China.
| | - Tengjiao Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China; Ningbo Institute of Northwestern Polytechnical University, Ningbo 315103, China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China.
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China; Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing 211816, China; Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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Liu W, Li R, Deng F, Yan C, Zhou X, Miao L, Li X, Xu Z. A Cell Membrane Fluorogenic Probe for Gram-Positive Bacteria Imaging and Real-Time Tracking of Bacterial Viability. ACS APPLIED BIO MATERIALS 2021; 4:2104-2112. [PMID: 35014338 DOI: 10.1021/acsabm.0c01269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial infections are a global healthcare problem, resulting in serious clinical morbidities and mortality. Real-time monitoring of live bacteria by fluorescent imaging technology has potential in diagnosis of bacterial infections, elucidating antimicrobial agents' mode of action, assessing drug toxicity, and examining bacterial antimicrobial resistance. In this work, a naphthalimide-derived fluorescent probe ZTRS-BP was developed for wash-free Gram-positive bacteria imaging. The probe aggregated in aqueous solutions and exhibited aggregation-caused fluorescence quenching (ACQ). The interaction with Gram-positive bacteria cell walls would selectively disaggregate the probe and the liberated probes were dispersed on the outside of the bacteria cell walls to achieve surface fluorescence imaging. There were no such interactions with Gram-negative bacteria, which indicates that selective binding and imaging of Gram-positive bacteria was achieved. The binding of zinc ions by ZTRS-BP can enhance the fluorescent signals on the bacterial surface by inhibiting the process of photoinduced electron transfer. ZTRS-BP-Zn(II) complex was an excellent dye to discriminate mixed Gram-positive and Gram-negative bacteria. Also, live and dead bacteria can be differentially imaged by ZTRS-BP-Zn(II). Furthermore, ZTRS-BP-Zn(II) was used for real-time monitoring bacteria viability such as B. cereus treated with antibiotic vancomycin.
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Affiliation(s)
- Weiwei Liu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ruihua Li
- The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Fei Deng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China
| | - Chunyu Yan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,Zhang Dayu Schoole of Chemistry, Dalian University of Technology, Dalian 116012, China
| | - Xuelian Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,Zhang Dayu Schoole of Chemistry, Dalian University of Technology, Dalian 116012, China
| | - Lu Miao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaolian Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Zhaochao Xu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,Zhang Dayu Schoole of Chemistry, Dalian University of Technology, Dalian 116012, China
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34
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Han Z, Thuy-Boun PS, Pfeiffer W, Vartabedian VF, Torkamani A, Teijaro JR, Wolan DW. Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome. Sci Rep 2021; 11:4763. [PMID: 33637779 PMCID: PMC7910532 DOI: 10.1038/s41598-021-83875-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.
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Affiliation(s)
- Zhen Han
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Peter S. Thuy-Boun
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Wayne Pfeiffer
- grid.266100.30000 0001 2107 4242San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093 USA
| | - Vincent F. Vartabedian
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Ali Torkamani
- grid.214007.00000000122199231Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - John R. Teijaro
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Dennis W. Wolan
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
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35
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Janket SJ, Conte HA, Diamandis EP. Inappropriate extrapolations abound in fecal microbiota research. Clin Chem Lab Med 2021; 59:e307-e308. [PMID: 33567176 DOI: 10.1515/cclm-2020-1862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/29/2021] [Indexed: 11/15/2022]
Affiliation(s)
- Sok-Ja Janket
- Translational Oral Medicine, Forsyth Institute, Cambridge, MA, USA
| | - Harry A Conte
- Department of Infectious Diseases, Saint Francis Hospital, Hartford, CT, USA.,Department of Emergency Medicine, Johnson Memorial Hospital, Stafford Springs, CT, USA
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36
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Wang W, Zhang N, Du Y, Gao J, Li M, Lin L, Czajkowsky DM, Li X, Yang C, Shao Z. Three‐Dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Wei Wang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Ni Zhang
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yahui Du
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Min Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Liyuan Lin
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Daniel M. Czajkowsky
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Xiaowei Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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37
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Liu W, Miao L, Li X, Xu Z. Development of fluorescent probes targeting the cell wall of pathogenic bacteria. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213646] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Gheorghe CE, Ritz NL, Martin JA, Wardill HR, Cryan JF, Clarke G. Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls. Gut Microbes 2021; 13:1941711. [PMID: 34328058 PMCID: PMC8331043 DOI: 10.1080/19490976.2021.1941711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023] Open
Abstract
In recent years, studies investigating the role of the gut microbiota in health and diseases have increased enormously - making it essential to deepen and question the research methodology employed. Fecal microbiota transplantation (FMT) in rodent studies (either from human or animal donors) allows us to better understand the causal role of the intestinal microbiota across multiple fields. However, this technique lacks standardization and requires careful experimental design in order to obtain optimal results. By comparing several studies in which rodents are the final recipients of FMT, we summarize the common practices employed. In this review, we document the limitations of this method and highlight different parameters to be considered while designing FMT Studies. Standardizing this method is challenging, as it differs according to the research topic, but avoiding common pitfalls is feasible. Several methodological questions remain unanswered to this day and we offer a discussion on issues to be explored in future studies.
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Affiliation(s)
- Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jason A. Martin
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
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Wang W, Zhang N, Du Y, Gao J, Li M, Lin L, Czajkowsky DM, Li X, Yang C, Shao Z. Three‐Dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut. Angew Chem Int Ed Engl 2020; 60:3055-3061. [DOI: 10.1002/anie.202010921] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/13/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Wei Wang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Ni Zhang
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yahui Du
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Min Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Liyuan Lin
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Daniel M. Czajkowsky
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Xiaowei Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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Aguirre de Cárcer D. Experimental and computational approaches to unravel microbial community assembly. Comput Struct Biotechnol J 2020; 18:4071-4081. [PMID: 33363703 PMCID: PMC7736701 DOI: 10.1016/j.csbj.2020.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.
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41
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Kumar P, Sinha R, Shukla P. Artificial intelligence and synthetic biology approaches for human gut microbiome. Crit Rev Food Sci Nutr 2020; 62:2103-2121. [PMID: 33249867 DOI: 10.1080/10408398.2020.1850415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gut microbiome comprises a variety of microorganisms whose genes encode proteins to carry out crucial metabolic functions that are responsible for the majority of health-related issues in human beings. The advent of the technological revolution in artificial intelligence (AI) assisted synthetic biology (SB) approaches will play a vital role in the modulating the therapeutic and nutritive potential of probiotics. This can turn human gut as a reservoir of beneficial bacterial colonies having an immense role in immunity, digestion, brain function, and other health benefits. Hence, in the present review, we have discussed the role of several gene editing tools and approaches in synthetic biology that have equipped us with novel tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) systems to precisely engineer probiotics for diagnostic, therapeutic and nutritive value. A brief discussion over the AI techniques to understand the metagenomic data from the healthy and diseased gut microbiome is also presented. Further, the role of AI in potentially impacting the pace of developments in SB and its current challenges is also discussed. The review also describes the health benefits conferred by engineered microbes through the production of biochemicals, nutraceuticals, drugs or biotherapeutics molecules etc. Finally, the review concludes with the challenges and regulatory concerns in adopting synthetic biology engineered microbes for clinical applications. Thus, the review presents a synergistic approach of AI and SB toward human gut microbiome for better health which will provide interesting clues to researchers working in the area of rapidly evolving food and nutrition science.
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Affiliation(s)
- Prasoon Kumar
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, India.,Department of Medical Devices, National Institute of Pharmaceutical Education and Research, Ahmedabad, India
| | | | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India.,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Lin L, Wu Q, Song J, Du Y, Gao J, Song Y, Wang W, Yang C. Revealing the in vivo growth and division patterns of mouse gut bacteria. SCIENCE ADVANCES 2020; 6:6/36/eabb2531. [PMID: 32917613 PMCID: PMC7473744 DOI: 10.1126/sciadv.abb2531] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Current techniques for studying gut microbiota are unable to answer some important microbiology questions, like how different bacteria grow and divide in the gut. We propose a method that integrates the use of sequential d-amino acid-based in vivo metabolic labeling with fluorescence in situ hybridization (FISH), for characterizing the growth and division patterns of gut bacteria. After sequentially administering two d-amino acid-based probes containing different fluorophores to mice by gavage, the resulting dual-labeled peptidoglycans provide temporal information on cell wall synthesis of gut bacteria. Following taxonomic identification with FISH probes, the growth and division patterns of the corresponding bacterial taxa, including species that cannot be cultured separately in vitro, are revealed. Our method offers a facile yet powerful tool for investigating the in vivo growth dynamics of the bacterial gut microbiota, which will advance our understanding of bacterial cytology and facilitate elucidation of the basic microbiology of this gut "dark matter."
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Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qiuyue Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jia Song
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yahui Du
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Juan Gao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yanling Song
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Lin L, Song J, Du Y, Wu Q, Gao J, Song Y, Yang C, Wang W. Quantification of Bacterial Metabolic Activities in the Gut by
d
‐Amino Acid‐Based In Vivo Labeling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Jia Song
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Yahui Du
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Qiuyue Wu
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Yanling Song
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Wei Wang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
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Yue YY, Fan XY, Zhang Q, Lu YP, Wu S, Wang S, Yu M, Cui CW, Sun ZR. Bibliometric analysis of subject trends and knowledge structures of gut microbiota. World J Clin Cases 2020; 8:2817-2832. [PMID: 32742991 PMCID: PMC7360702 DOI: 10.12998/wjcc.v8.i13.2817] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut microbiota is an emerging field of research, with related research having breakthrough development in the past 15 years. Bibliometric analysis can be applied to analyze the evolutionary trends and emerging hotspots in this field.
AIM To study the subject trends and knowledge structures of gut microbiota related research fields from 2004 to 2018.
METHODS The literature data on gut microbiota were identified and downloaded from the PubMed database. Through biclustering analysis, strategic diagrams, and social network analysis diagrams, the main trend and knowledge structure of research fields concerning gut microbiota were analyzed to obtain and compare the research hotspots in each period.
RESULTS According to the strategic coordinates and social relationship network map, Clostridium Infections/microbiology, Clostridium Infections/therapy, RNA, Ribosomal, 16S/genetics, Microbiota/genetics, Microbiota/immunology, Dysbiosis/immunology, Infla-mmation/immunology, Fecal Microbiota Transplantation/methods, Fecal Microbiota Transplantation can be used as an emerging research hotspot in the past 5 years (2014-2018).
CONCLUSION Some subjects were not yet fully studied according to the strategic coordinates; and the emerging hotspots in the social network map can be considered as directions of future research.
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Affiliation(s)
- Yuan-Yi Yue
- Department of Gastroenterology Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Xin-Yue Fan
- Student Affairs Department, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Qiang Zhang
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province
| | - Yi-Ping Lu
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Si Wu
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Shuang Wang
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Miao Yu
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Chang-Wan Cui
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Zheng-Rong Sun
- BioBank, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
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Qiao Y, Hayashi H, Chong Teo S. Chemical Toolbox to Decode the Microbiota Lexicon. Chem Asian J 2020; 15:2117-2128. [PMID: 32558250 DOI: 10.1002/asia.202000541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/14/2020] [Indexed: 12/15/2022]
Abstract
The human microbiota deploys a diverse range of molecules and metabolites to engage in chemical communications with the host, mediating fundamental aspects of host health. Studies of the structures and activities of bioactive molecules produced by the microbiota are imperative to address their implications in microbiota associated diseases in human. By drawing experiences from different research fields, chemists and chemical biologists, who are experts in dealing with chemical molecules, are uniquely positioned to contribute to the emerging knowledge of human microbiota. In this minireview, we discuss the current chemical tools and methods that are pertinent to the discovery of microbiota molecules and metabolites, characterizations of their protein targets, as well as evaluations of their biodistributions in hosts. These are key aspects in understanding the chemical underpinnings of the microbiota-host interactions that would enable future development of diagnostics and therapeutics targeting the human microbiota.
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Affiliation(s)
- Yuan Qiao
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Hirohito Hayashi
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Seng Chong Teo
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
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Citrobacter Species Increase Energy Harvest by Modulating Intestinal Microbiota in Fish: Nondominant Species Play Important Functions. mSystems 2020; 5:5/3/e00303-20. [PMID: 32546671 PMCID: PMC7300360 DOI: 10.1128/msystems.00303-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This study shows that the ability of gut microbiota members to enhance host energy harvest from a high-fat diet is a conserved feature of host-microbe interactions in fish, as in mammals. It also underscores that gut microbiota members are able to significantly impact host biology even when at low abundance. An efficient energy harvesting mechanism is likely critical for animals in their natural environment. Intestinal microbiota enriched by a high-fat diet aid in lipid accumulation, a strategy likely evolved for energy harvest in mammals. However, whether this strategy is conserved among vertebrate organisms remains unclear. A bacterial strain (S1), enriched on soybean oil rich medium, was isolated from the gut of Nile tilapia and demonstrated to be a member of the Citrobacter genus. Although a high-fat diet increased the number of Citrobacter spp., these bacteria were not abundant in the intestine by high-throughput sequencing. Addition of bacterium S1 to a high-fat diet modulated intestinal microbial composition and increased high-fat diet-induced lipid accumulation in mesenteric adipose tissue, accompanied by (i) increased triglyceride absorption efficiency and triglyceride reesterification and (ii) increased intestinal permeability. Collectively, our results provide evidence that specific intestinal bacteria aid the host in harvesting more energy from a high-fat diet in fish. Furthermore, the results from the present study also suggest that nondominant bacteria in the gut may play an important role in regulating host metabolism. IMPORTANCE This study shows that the ability of gut microbiota members to enhance host energy harvest from a high-fat diet is a conserved feature of host-microbe interactions in fish, as in mammals. It also underscores that gut microbiota members are able to significantly impact host biology even when at low abundance.
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Lin L, Song J, Du Y, Wu Q, Gao J, Song Y, Yang C, Wang W. Quantification of Bacterial Metabolic Activities in the Gut by
d
‐Amino Acid‐Based In Vivo Labeling. Angew Chem Int Ed Engl 2020; 59:11923-11926. [DOI: 10.1002/anie.202004703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Indexed: 01/20/2023]
Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Jia Song
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Yahui Du
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Qiuyue Wu
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Yanling Song
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Wei Wang
- Institute of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
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48
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Fluorescent amino acids as versatile building blocks for chemical biology. Nat Rev Chem 2020; 4:275-290. [PMID: 37127957 DOI: 10.1038/s41570-020-0186-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Fluorophores have transformed the way we study biological systems, enabling non-invasive studies in cells and intact organisms, which increase our understanding of complex processes at the molecular level. Fluorescent amino acids have become an essential chemical tool because they can be used to construct fluorescent macromolecules, such as peptides and proteins, without disrupting their native biomolecular properties. Fluorescent and fluorogenic amino acids with unique photophysical properties have been designed for tracking protein-protein interactions in situ or imaging nanoscopic events in real time with high spatial resolution. In this Review, we discuss advances in the design and synthesis of fluorescent amino acids and how they have contributed to the field of chemical biology in the past 10 years. Important areas of research that we review include novel methodologies to synthesize building blocks with tunable spectral properties, their integration into peptide and protein scaffolds using site-specific genetic encoding and bioorthogonal approaches, and their application to design novel artificial proteins, as well as to investigate biological processes in cells by means of optical imaging.
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49
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Hong S, Zheng DW, Zhang QL, Deng WW, Song WF, Cheng SX, Sun ZJ, Zhang XZ. An RGB-emitting molecular cocktail for the detection of bacterial fingerprints. Chem Sci 2020; 11:4403-4409. [PMID: 33209242 PMCID: PMC7643548 DOI: 10.1039/d0sc01704c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 01/27/2023] Open
Abstract
Accumulating evidence indicates that colonized microbes play a crucial role in regulating health and disease in the human body. Detecting microbes should be essential for understanding the relationship between microbes and diseases, as well as increasing our ability to detect diseases. Here, a combined metabolic labeling strategy was developed to identify different bacterial species and microbiota by the use of three different fluorescent metabolite derivatives emitting red, green, and blue (RGB) fluorescence. Upon co-incubation with microbes, these fluorescent metabolite derivatives are incorporated into bacteria, generating unique true-color fingerprints for different bacterial species and different microbiota. A portable spectrometer was also fabricated to automate the colorimetric analysis in combination with a smartphone to conveniently identify different bacterial species and microbiota. Herein, the effectiveness of this system was demonstrated by the identification of certain bacterial species and microbiota in mice with different diseases, such as skin infections and bacteremia. By analyzing the microbiota fingerprints of saliva samples from clinical patients and healthy people, this system was proved to precisely distinguish oral squamous cell carcinoma (OSCC, n = 29) samples from precancerous (n = 10) and healthy (n = 5) samples.
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Affiliation(s)
- Sheng Hong
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Di-Wei Zheng
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Qiu-Ling Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Wei-Wei Deng
- Department of Oral Maxillofacial Head Neck Oncology , School and Hospital of Stomatology , Wuhan University , Wuhan 430072 , P. R. China
| | - Wen-Fang Song
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Zhi-Jun Sun
- Department of Oral Maxillofacial Head Neck Oncology , School and Hospital of Stomatology , Wuhan University , Wuhan 430072 , P. R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
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Ramos-Casals M, Brahmer JR, Callahan MK, Flores-Chávez A, Keegan N, Khamashta MA, Lambotte O, Mariette X, Prat A, Suárez-Almazor ME. Immune-related adverse events of checkpoint inhibitors. Nat Rev Dis Primers 2020; 6:38. [PMID: 32382051 PMCID: PMC9728094 DOI: 10.1038/s41572-020-0160-6] [Citation(s) in RCA: 690] [Impact Index Per Article: 172.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 02/06/2023]
Abstract
Cancer immunotherapies have changed the landscape of cancer treatment during the past few decades. Among them, immune checkpoint inhibitors, which target PD-1, PD-L1 and CTLA-4, are increasingly used for certain cancers; however, this increased use has resulted in increased reports of immune-related adverse events (irAEs). These irAEs are unique and are different to those of traditional cancer therapies, and typically have a delayed onset and prolonged duration. IrAEs can involve any organ or system. These effects are frequently low grade and are treatable and reversible; however, some adverse effects can be severe and lead to permanent disorders. Management is primarily based on corticosteroids and other immunomodulatory agents, which should be prescribed carefully to reduce the potential of short-term and long-term complications. Thoughtful management of irAEs is important in optimizing quality of life and long-term outcomes.
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Affiliation(s)
- Manuel Ramos-Casals
- Department of Autoimmune Diseases, ICMiD, Barcelona, Spain. .,Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, Barcelona, Spain. .,Department of Medicine, University of Barcelona, Hospital Clínic, Barcelona, Spain.
| | - Julie R. Brahmer
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Margaret K. Callahan
- Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Weill Cornell Medical College, New York, NY, USA,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Niamh Keegan
- Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Weill Cornell Medical College, New York, NY, USA
| | - Munther A. Khamashta
- Lupus Clinic, Rheumatology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Olivier Lambotte
- APHP Médecine Interne/Immunologie Clinique, Hôpital Bicêtre, Paris, France,Université Paris-Saclay – INSERM U1184 - CEA, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses and Le Kremlin-Bicêtre, France
| | - Xavier Mariette
- Université Paris-Saclay, INSERM, CEA, Centre de recherche en Immunologie des infections virales et des maladies auto-immunes ; AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Rheumatology Department, Le Kremlin Bicêtre, France
| | - Aleix Prat
- Translational Genomic and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Maria E. Suárez-Almazor
- Section of Rheumatology/Clinical Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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