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Kuo J, Uzunovic J, Jacobson A, Dourado M, Gierke S, Rajendram M, Keilberg D, Mar J, Stekol E, Curry J, Verstraete S, Lund J, Liang Y, Tamburini FB, Omattage NS, Masureel M, Rutherford ST, Hackos DH, Tan MW, Byrd AL, Keir ME, Skippington E, Storek KM. Toxigenic Clostridium perfringens Isolated from At-Risk Paediatric Inflammatory Bowel Disease Patients. J Crohns Colitis 2024; 18:985-1001. [PMID: 38267224 PMCID: PMC11302968 DOI: 10.1093/ecco-jcc/jjae016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND AND AIMS This study aimed to identify microbial drivers of inflammatory bowel disease [IBD], by investigating mucosal-associated bacteria and their detrimental products in IBD patients. METHODS We directly cultured bacterial communities from mucosal biopsies from paediatric gastrointestinal patients and examined for pathogenicity-associated traits. Upon identifying Clostridium perfringens as toxigenic bacteria present in mucosal biopsies, we isolated strains and further characterized toxicity and prevalence. RESULTS Mucosal biopsy microbial composition differed from corresponding stool samples. C. perfringens was present in eight of nine patients' mucosal biopsies, correlating with haemolytic activity, but was not present in all corresponding stool samples. Large IBD datasets showed higher C. perfringens prevalence in stool samples of IBD adults [18.7-27.1%] versus healthy controls [5.1%]. In vitro, C. perfringens supernatants were toxic to cell types beneath the intestinal epithelial barrier, including endothelial cells, neuroblasts, and neutrophils, while the impact on epithelial cells was less pronounced, suggesting C. perfringens may be particularly damaging when barrier integrity is compromised. Further characterization using purified toxins and genetic insertion mutants confirmed perfringolysin O [PFO] toxin was sufficient for toxicity. Toxin RNA signatures were found in the original patient biopsies by PCR, suggesting intestinal production. C. perfringens supernatants also induced activation of neuroblast and dorsal root ganglion neurons in vitro, suggesting C. perfringens in inflamed mucosal tissue may directly contribute to abdominal pain, a frequent IBD symptom. CONCLUSIONS Gastrointestinal carriage of certain toxigenic C. perfringens may have an important pathogenic impact on IBD patients. These findings support routine monitoring of C. perfringens and PFO toxins and potential treatment in patients.
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Affiliation(s)
- James Kuo
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Jasmina Uzunovic
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Amanda Jacobson
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Michelle Dourado
- Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Sarah Gierke
- Department of Pathology, Genentech Inc., South San Francisco, CA, USA
| | - Manohary Rajendram
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Daniela Keilberg
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Jordan Mar
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Emily Stekol
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Joanna Curry
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Sofia Verstraete
- Department of Pediatrics, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA, 94158, USA
| | - Jessica Lund
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Fiona B Tamburini
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Natalie S Omattage
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - David H Hackos
- Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
| | - Allyson L Byrd
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Mary E Keir
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech Inc., South San Francisco, CA, USA
| | - Elizabeth Skippington
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases and Host-Microbe Interactions, Genentech Inc., South San Francisco, CA, USA
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Yamaguchi H, Hsu JM, Sun L, Wang SC, Hung MC. Advances and prospects of biomarkers for immune checkpoint inhibitors. Cell Rep Med 2024; 5:101621. [PMID: 38906149 PMCID: PMC11293349 DOI: 10.1016/j.xcrm.2024.101621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/22/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Immune checkpoint inhibitors (ICIs) activate anti-cancer immunity by blocking T cell checkpoint molecules such as programmed death 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Although ICIs induce some durable responses in various cancer patients, they also have disadvantages, including low response rates, the potential for severe side effects, and high treatment costs. Therefore, selection of patients who can benefit from ICI treatment is critical, and identification of biomarkers is essential to improve the efficiency of ICIs. In this review, we provide updated information on established predictive biomarkers (tumor programmed death-ligand 1 [PD-L1] expression, DNA mismatch repair deficiency, microsatellite instability high, and tumor mutational burden) and potential biomarkers currently under investigation such as tumor-infiltrated and peripheral lymphocytes, gut microbiome, and signaling pathways related to DNA damage and antigen presentation. In particular, this review aims to summarize the current knowledge of biomarkers, discuss issues, and further explore future biomarkers.
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Affiliation(s)
- Hirohito Yamaguchi
- Graduate Institute of Cell Biology, China Medical University, Taichung City 406040, Taiwan; Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Jung-Mao Hsu
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Linlin Sun
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan.
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3
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Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB. Framework for exploring the sensory repertoire of the human gut microbiota. mBio 2024; 15:e0103924. [PMID: 38757952 PMCID: PMC11237719 DOI: 10.1128/mbio.01039-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.
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Affiliation(s)
- Patricia A. Ross
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ekaterina Jalomo-Khayrova
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Patrick H. Bradley
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
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4
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Svačina MKR, Gao T, Sprenger-Svačina A, Lin J, Ganesh BP, Lee J, McCullough LD, Sheikh KA, Zhang G. Rejuvenating fecal microbiota transplant enhances peripheral nerve repair in aged mice by modulating endoneurial inflammation. Exp Neurol 2024; 376:114774. [PMID: 38599367 DOI: 10.1016/j.expneurol.2024.114774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
Peripheral nerve injury (PNI) resulting from trauma or neuropathies can cause significant disability, and its prognosis deteriorates with age. Emerging evidence suggests that gut dysbiosis and reduced fecal short-chain fatty acids (SCFAs) contribute to an age-related systemic hyperinflammation (inflammaging), which hinders nerve recovery after injury. This study thus aimed to evaluate the pro-regenerative effects of a rejuvenating fecal microbiota transplant (FMT) in a preclinical PNI model using aged mice. Aged C57BL/6 mice underwent bilateral crush injuries to their sciatic nerves. Subsequently, they either received FMT from young donors at three and four days after the injury or retained their aged gut microbiota. We analyzed gut microbiome composition and SCFA concentrations in fecal samples. The integrity of the ileac mucosal barrier was assessed by immunofluorescence staining of Claudin-1. Flow cytometry was utilized to examine immune cells and cytokine production in the ileum, spleen, and sciatic nerve. Various assessments, including behavioural tests, electrophysiological studies, and morphometrical analyses, were conducted to evaluate peripheral nerve function and repair following injury. Rejuvenating FMT reversed age-related gut dysbiosis by increasing Actinobacteria, especially Bifidobacteriales genera. This intervention also led to an elevation of gut SCFA levels and mitigated age-related ileac mucosal leakiness in aged recipients. Additionally, it augmented the number of T-helper 2 (Th2) and regulatory T (Treg) cells in the ileum and spleen, with the majority being positive for anti-inflammatory interleukin-10 (IL-10). In sciatic nerves, rejuvenating FMT resulted in increased M2 macrophage counts and a higher IL-10 production by IL-10+TNF-α- M2 macrophage subsets. Ultimately, restoring a youthful gut microbiome in aged mice led to improved nerve repair and enhanced functional recovery after PNI. Considering that FMT is already a clinically available technique, exploring novel translational strategies targeting the gut microbiome to enhance nerve repair in the elderly seems promising and warrants further evaluation.
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Affiliation(s)
- Martin K R Svačina
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA; Department of Neurology, Faculty of Medicine and University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Tong Gao
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Alina Sprenger-Svačina
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA; Department of Neurology, Faculty of Medicine and University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Jianxin Lin
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Bhanu P Ganesh
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Juneyoung Lee
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Louise D McCullough
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Kazim A Sheikh
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Gang Zhang
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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5
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Byrne SR, DeMott MS, Yuan Y, Ghanegolmohammadi F, Kaiser S, Fox JG, Alm EJ, Dedon PC. Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596306. [PMID: 38854053 PMCID: PMC11160787 DOI: 10.1101/2024.05.29.596306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically-reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications. Results Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m6dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Firmicutes, Actinobacteria, and Proteobacteria, which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Conclusions The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically-reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.
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Affiliation(s)
- Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yifeng Yuan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Farzan Ghanegolmohammadi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kaiser
- Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore
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6
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Zhang J, Qi H, Li M, Wang Z, Jia X, Sun T, Du S, Su C, Zhi M, Du W, Ouyang Y, Wang P, Huang F, Jiang H, Li L, Bai J, Wei Y, Zhang X, Wang H, Zhang B, Feng Q. Diet Mediate the Impact of Host Habitat on Gut Microbiome and Influence Clinical Indexes by Modulating Gut Microbes and Serum Metabolites. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310068. [PMID: 38477427 PMCID: PMC11109649 DOI: 10.1002/advs.202310068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/04/2024] [Indexed: 03/14/2024]
Abstract
The impact of external factors on the human gut microbiota and how gut microbes contribute to human health is an intriguing question. Here, the gut microbiome of 3,224 individuals (496 with serum metabolome) with 109 variables is studied. Multiple analyses reveal that geographic factors explain the greatest variance of the gut microbiome and the similarity of individuals' gut microbiome is negatively correlated with their geographic distance. Main food components are the most important factors that mediate the impact of host habitats on the gut microbiome. Diet and gut microbes collaboratively contribute to the variation of serum metabolites, and correlate to the increase or decrease of certain clinical indexes. Specifically, systolic blood pressure is lowered by vegetable oil through increasing the abundance of Blautia and reducing the serum level of 1-palmitoyl-2-palmitoleoyl-GPC (16:0/16:1), but it is reduced by fruit intake through increasing the serum level of Blautia improved threonate. Besides, aging-related clinical indexes are also closely correlated with the variation of gut microbes and serum metabolites. In this study, the linkages of geographic locations, diet, the gut microbiome, serum metabolites, and physiological indexes in a Chinese population are characterized. It is proved again that gut microbes and their metabolites are important media for external factors to affect human health.
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Affiliation(s)
- Jiguo Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Houbao Qi
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Meihui Li
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Zhihong Wang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Xiaofang Jia
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Tianyong Sun
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Shufa Du
- Department of NutritionGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Chang Su
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Mengfan Zhi
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Wenwen Du
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Yifei Ouyang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Pingping Wang
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Feifei Huang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Hongru Jiang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Li Li
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Jing Bai
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Yanli Wei
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Xiaofan Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Huijun Wang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Bing Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Qiang Feng
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
- State key laboratory of microbial technologySD UniversityQingdao266237China
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7
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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8
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Rodziewicz A, Szewczyk A, Bryl E. Gluten-Free Diet Alters the Gut Microbiome in Women with Autoimmune Thyroiditis. Nutrients 2024; 16:685. [PMID: 38474814 DOI: 10.3390/nu16050685] [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: 01/11/2024] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The gut microbiome may contribute to the development of autoimmune diseases, such as autoimmune thyroiditis (AIT). Diet has a critical impact on the gut microbiome, and it has been shown that a gluten-free diet can negatively affect its composition. A gluten-free diet is popular among patients, and therefore the aim of this study was to check whether it affects thyroid function and gut microbiome composition in AIT. Thirty-one women with AIT complied with a gluten-free diet for 8 weeks. After the first 4 weeks, participants were divided into two groups: the first group received gluten in capsules and the other one-rice starch (placebo). Blood and stool samples were examined before diet (T0), after 4 weeks (T1) and after 8 weeks of diet (T2). The only significant difference in blood parameters was observed between T1 and T2 in the placebo group for the thyroid peroxidase antibody level. After the first 4 weeks, a significant increase in Desulfobacterota, Proteobacteria, Prevotella and Parasutterella and a significant decrease in Actinobacteriota, Coriobacteriaceae and Bifidobacterium were observed. The detected microbiome alterations may indicate increasing inflammation; however, further research is required, and for now, a gluten-free diet should be used cautiously in AIT.
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Affiliation(s)
- Aleksandra Rodziewicz
- Department of Pathology and Experimental Rheumatology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
- Department of Pathophysiology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Adrian Szewczyk
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
- Department of Pathophysiology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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9
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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10
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Delavy M, Sertour N, Patin E, Le Chatelier E, Cole N, Dubois F, Xie Z, Saint-André V, Manichanh C, Walker AW, Quintana-Murci L, Duffy D, d’Enfert C, Bougnoux ME, Consortium MI. Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response. Gut Microbes 2023; 15:2287618. [PMID: 38017705 PMCID: PMC10732203 DOI: 10.1080/19490976.2023.2287618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.
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Affiliation(s)
- Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Natacha Sertour
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | | | - Nathaniel Cole
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Florian Dubois
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Zixuan Xie
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Violaine Saint-André
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Chaysavanh Manichanh
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Alan W. Walker
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
| | - Milieu Intérieur Consortium
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
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11
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Shibasaki S, Mitri S. A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability. iScience 2023; 26:107499. [PMID: 37670791 PMCID: PMC10475486 DOI: 10.1016/j.isci.2023.107499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/11/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
Given the importance of gut microbial communities for human health, we may want to ensure their stability in terms of species composition and function. Here, we built a mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species' growth. First, we found that communities in our model are more stable if they assemble through species invasion over time compared to combining a set of species from the start. Second, downstream communities are more stable when species invade the downstream patch less frequently than the upstream patch. Finally, upstream species that have positive effects on downstream species can further increase downstream community stability. Despite it being quite abstract, our model may inform future research on designing more stable microbial communities or increasing the stability of existing ones.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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12
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Revel-Muroz A, Akulinin M, Shilova P, Tyakht A, Klimenko N. Stability of human gut microbiome: Comparison of ecological modelling and observational approaches. Comput Struct Biotechnol J 2023; 21:4456-4468. [PMID: 37745638 PMCID: PMC10511340 DOI: 10.1016/j.csbj.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/27/2023] [Accepted: 08/27/2023] [Indexed: 09/26/2023] Open
Abstract
The gut microbiome plays a pivotal role in the human body, and perturbations in its composition have been linked to various disorders. Stability is an essential property of a healthy human gut microbiome, which allows it to maintain its functional richness under the external influences. This property has been explored through two distinct methodologies - mathematical modelling based on ecological principles and statistical analysis drawn from observations in interventional studies. Here we conducted a meta-analysis aimed to compare the two approaches utilising the data from 9 interventional and time series studies encompassing 3512 gut microbiome profiles obtained via 16S rRNA gene sequencing. By employing the previously published compositional Lotka-Volterra method, we modelled the dynamics of the microbial community and evaluated ecological stability measures. These measures were compared to those based on observed microbiome changes. There was a substantial correlation between the outcomes of the two approaches. Particularly, local stability assessed within the ecological paradigm was positively correlated with observational stability measures accounting for the compositional nature of microbiome data. Additionally, we were able to reproduce the previously reported inverse relationship between the community's robustness to microorganism loss and local stability, attributed to the distinct impacts of coefficient characterising the network decomposition on these two stability assessments. Our findings demonstrate harmonisation between the ecological and observational approaches to microbiome analysis, advancing the understanding of healthy gut microbiome concept. This paves the way to develop efficient microbiome-targeting interventions for disease prevention and treatment.
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Affiliation(s)
- Anastasia Revel-Muroz
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Akulinin
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, Russia
| | - Polina Shilova
- Department of Biology, Moscow State University, 1–12 Leninskie Gory, Moscow, Russia
| | - Alexander Tyakht
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Atlas Biomed Group - Knomx LLC, Interchange House, Office 1.58, 81–85 Station Road, Croydon CR0 2AJ, United Kingdom
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Atlas Biomed Group - Knomx LLC, Interchange House, Office 1.58, 81–85 Station Road, Croydon CR0 2AJ, United Kingdom
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13
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Liu Z, Hong L, Ling Z. Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers. Cancer Med 2023; 12:16756-16773. [PMID: 37377377 PMCID: PMC10501248 DOI: 10.1002/cam4.6298] [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: 02/15/2023] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
INTRODUCTION Tumor-associated bacteria and gut microbiota have gained significant attention in recent years due to their potential role in cancer development and therapeutic response. This review aims to discuss the contributions of intratumor bacteria outside the gastrointestinal tract, in addition to exploring the mechanisms, functions, and implications of these bacteria in cancer therapy. METHODS We reviewed current literature on intratumor bacteria and their impact on tumorigenesis, progression, metastasis, drug resistance, and anti-tumor immune modulation. Additionally, we examined techniques used to detect intratumor bacteria, precautions necessary when handling low microbial biomass tumor samples, and the recent progress in bacterial manipulation for tumor treatment. RESULTS Research indicates that each type of cancer uniquely interacts with its microbiome, and bacteria can be detected even in non-gastrointestinal tumors with low bacterial abundance. Intracellular bacteria have the potential to regulate tumor cells' biological behavior and contribute to critical aspects of tumor development. Furthermore, bacterial-based anti-tumor therapies have shown promising results in cancer treatment. CONCLUSIONS Understanding the complex interactions between intratumor bacteria and tumor cells could lead to the development of more precise cancer treatment strategies. Further research into non-gastrointestinal tumor-associated bacteria is needed to identify new therapeutic approaches and expand our knowledge of the microbiota's role in cancer biology.
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Affiliation(s)
- Zhu Liu
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of SciencesHangzhouZhejiangChina
| | - Lian‐Lian Hong
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of SciencesHangzhouZhejiangChina
| | - Zhi‐Qiang Ling
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of SciencesHangzhouZhejiangChina
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14
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Mendes I, Vale N. How Can the Microbiome Induce Carcinogenesis and Modulate Drug Resistance in Cancer Therapy? Int J Mol Sci 2023; 24:11855. [PMID: 37511612 PMCID: PMC10380870 DOI: 10.3390/ijms241411855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Over the years, cancer has been affecting the lives of many people globally and it has become one of the most studied diseases. Despite the efforts to understand the cell mechanisms behind this complex disease, not every patient seems to respond to targeted therapies or immunotherapies. Drug resistance in cancer is one of the limiting factors contributing to unsuccessful therapies; therefore, understanding how cancer cells acquire this resistance is essential to help cure individuals affected by cancer. Recently, the altered microbiome was observed to be an important hallmark of cancer and therefore it represents a promising topic of cancer research. Our review aims to provide a global perspective of some cancer hallmarks, for instance how genetic and epigenetic modifications may be caused by an altered human microbiome. We also provide information on how an altered human microbiome can lead to cancer development as well as how the microbiome can influence drug resistance and ultimately targeted therapies. This may be useful to develop alternatives for cancer treatment, i.e., future personalized medicine that can help in cases where traditional cancer treatment is unsuccessful.
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Affiliation(s)
- Inês Mendes
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- School of Life and Environmental Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Edifício de Geociências, 5000-801 Vila Real, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
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15
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Desilets A, Elkrief A. Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events. Curr Opin Oncol 2023; 35:248-253. [PMID: 37222188 DOI: 10.1097/cco.0000000000000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
PURPOSE OF REVIEW Although immune checkpoint inhibition has reshaped the therapeutic landscape leading to improved outcomes across an array of both solid and hematologic malignancies, a significant source of morbidity is caused by immune-related adverse events (irAEs) caused by these agents. RECENT FINDINGS The gut microbiota has emerged as a biomarker of response to these agents, and more recently, also as a key determinant of development of irAEs. Emerging data have revealed that enrichment of certain bacterial genera is associated with an increased risk of irAEs, with the most robust evidence pointing to an intimate connection with the development of immune-related diarrhea and colitis. These bacteria include Bacteroides , Enterobacteriaceae, and Proteobacteria (such as Klebsiella and Proteus ) . Lachnospiraceae spp. and Streptococcus spp. have been implicated irAE-wide in the context of ipilimumab. SUMMARY We review recent lines of evidence pointing to the role of baseline gut microbiota on the development of irAE, and the potentials for therapeutic manipulation of the gut microbiota in order to reduce irAE severity. The connections between gut microbiome signatures of response and toxicity will need to be untangled in further studies.
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Affiliation(s)
| | - Arielle Elkrief
- University of Montreal, Department of Hematology-Oncology
- University of Montreal Hospital Research Centre (CR-CHUM), Montreal, Quebec, Canada
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16
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Zhang H, Jin K, Xiong K, Jing W, Pang Z, Feng M, Cheng X. Disease-associated gut microbiome and critical metabolomic alterations in patients with colorectal cancer. Cancer Med 2023; 12:15720-15735. [PMID: 37260140 PMCID: PMC10417192 DOI: 10.1002/cam4.6194] [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: 02/06/2023] [Revised: 04/26/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear. METHODS We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50 + 52 samples) and shotgun metagenomic sequencing (8 + 6 samples), respectively, with particular attention paid to gut-colonized oral bacteria. RESULTS AND CONCLUSIONS The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.
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Affiliation(s)
- Hongze Zhang
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Kai Jin
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Surgical Intensive Care UnitHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Kunlong Xiong
- Department of Respiratory and Critical MedicineNingbo First HospitalNingboChina
| | - Wenwen Jing
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Zhen Pang
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Hand Surgery, Huashan HospitalFudan UniversityShanghaiChina
| | - Meng Feng
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical SciencesFudan UniversityShanghaiChina
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17
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Han B, Zhai Y, Li X, Zhao H, Sun C, Zeng Y, Zhang W, Lu J, Kai G. Total flavonoids of Tetrastigma hemsleyanum Diels et Gilg inhibits colorectal tumor growth by modulating gut microbiota and metabolites. Food Chem 2023; 410:135361. [PMID: 36610085 DOI: 10.1016/j.foodchem.2022.135361] [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: 06/13/2022] [Revised: 11/29/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Tetrastigma hemsleyanum Diels et Gilg is a dietary supplement in southern China. The total flavonoids of T. hemsleyanum (THTF) can be used for gastrointestinal disease treatment. Colorectal cancer (CRC) is associated with gut microbiota dysbiosis. This study was designed to investigate the effect of THTF on CRC from gut microbiota and fecal metabolomics. THTF (120 mg/kg) oral gavage reduced tumor growth and protected intestinal function (p-p65/p65, ZO-1) in HCT116 xenografts. THTF increased probiotics Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium, Bifidobacterium pseudolongum, and decreased "harmful" bacteria Bacteroidota, Firmicutes, Bacteroidia, Rikenellaceae, Odoribacter, Alistipes richness. Furthermore, THTF restored abnormal fecal metabolite levels. It showed a strong correlation among gut microbiota, metabolites, and tumor weight. Finally, THTF promoted Bifidobacterium pseudolongum growth in vitro, whose cell-free supernatant further inhibited HCT116 cell proliferation and clonogenicity. Together, THTF delays CRC tumor growth by maintaining microbiota homeostasis, restoring fecal metabolites, and protecting intestinal function.
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Affiliation(s)
- Bing Han
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yufei Zhai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xuan Li
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Huan Zhao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Chengtao Sun
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yuqing Zeng
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Weiping Zhang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jinjian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, College of Pharmaceutical Science, The Third Affiliated Hospital, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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18
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Younginger BS, Mayba O, Reeder J, Nagarkar DR, Modrusan Z, Albert ML, Byrd AL. Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype. Cell Rep Med 2023; 4:100920. [PMID: 36706753 PMCID: PMC9975273 DOI: 10.1016/j.xcrm.2023.100920] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 11/22/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023]
Abstract
While the association between colorectal cancer (CRC) features and Fusobacterium has been extensively studied, less is known of other intratumoral bacteria. Here, we leverage whole transcriptomes from 807 CRC samples to dually characterize tumor gene expression and 74 intratumoral bacteria. Seventeen of these species, including 4 Fusobacterium spp., are classified as orally derived and are enriched among right-sided, microsatellite instability-high (MSI-H), and BRAF-mutant tumors. Across consensus molecular subtypes (CMSs), integration of Fusobacterium animalis (Fa) presence and tumor expression reveals that Fa has the most significant associations in mesenchymal CMS4 tumors despite a lower prevalence than in immune CMS1. Within CMS4, the prevalence of Fa is uniquely associated with collagen- and immune-related pathways. Additional Fa pangenome analysis reveals that stress response genes and the adhesion FadA are commonly expressed intratumorally. Overall, this study identifies oral-derived bacteria as enriched in inflamed tumors, and the associations of bacteria and tumor expression are context and species specific.
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Affiliation(s)
- Brett S Younginger
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Oleg Mayba
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, USA
| | - Jens Reeder
- Department of Oncology Bioinformatics, Genentech, Inc., South San Francisco, CA, USA
| | - Deepti R Nagarkar
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, Inc., South San Francisco, CA, USA
| | | | - Allyson L Byrd
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA.
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19
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Long Y, Tang L, Zhou Y, Zhao S, Zhu H. Causal relationship between gut microbiota and cancers: a two-sample Mendelian randomisation study. BMC Med 2023; 21:66. [PMID: 36810112 PMCID: PMC9945666 DOI: 10.1186/s12916-023-02761-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Evidence from observational studies and clinical trials suggests that the gut microbiota is associated with cancer. However, the causal association between gut microbiota and cancer remains to be determined. METHODS We first identified two sets of gut microbiota based on phylum, class, order, family, and genus level information, and cancer data were obtained from the IEU Open GWAS project. We then performed two-sample Mendelian randomisation (MR) to determine whether the gut microbiota is causally associated with eight cancer types. Furthermore, we performed a bi-directional MR analysis to examine the direction of the causal relations. RESULTS We identified 11 causal relationships between genetic liability in the gut microbiome and cancer, including those involving the genus Bifidobacterium. We found 17 strong associations between genetic liability in the gut microbiome and cancer. Moreover, we found 24 associations between genetic liability in the gut microbiome and cancer using multiple datasets. CONCLUSIONS Our MR analysis revealed that the gut microbiota was causally associated with cancers and may be useful in providing new insights for further mechanistic and clinical studies of microbiota-mediated cancer.
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Affiliation(s)
- Yiwen Long
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Lanhua Tang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Shushan Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Hong Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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20
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Wang T, Xing Y, Peng B, Yang K, Zhang C, Chen Y, Geng G, Li Q, Fu J, Li M, Luo Z, Fu Z, Wang J. Respiratory Microbiome Profile of Pediatric Pulmonary Hypertension Patients Associated With Congenital Heart Disease. Hypertension 2023; 80:214-226. [PMID: 36353996 PMCID: PMC9722361 DOI: 10.1161/hypertensionaha.122.19182] [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] [Indexed: 11/11/2022]
Abstract
BACKGROUND Pulmonary hypertension (PH) associated with congenital heart disease (CHD) is the most common type of PH in pediatric patients. The airway microbiome profile in CHD-PH patients remains rarely studied. METHODS A total of 158 children were recruited for collection of oropharyngeal swabs to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome, to establish a correlation between these bacterial groups and echocardiography indicators in CHD-PH patients. RESULTS Bacterial α- and β-diversity of the airway microbiome indicated a significantly lower richness in the CHD-PH group and compositional differences associated with the specific taxa and their relative abundances in the upper respiratory tract. Principal coordinate analysis showed that the pharynx microbiota composition in the CHD-PH group varied from that in the CHD or control group. The linear discriminant analysis effect size also highlighted an increased presence of Streptococcus and Rothia in pediatric CHD-PH patients. Comparison of microbial composition between pediatric and adult PH patients showed significant differences and separation of microbiota. The correlation between bacterial abundance and transthoracic echocardiography indexes in CHD-associated PH indicated that different groups of microbiomes may be related to different PH grades. CONCLUSIONS In summary, our study reported the systematic definition and divergent profile of the upper respiratory tract microbiota in pediatric PH patients, CHD and reference subjects, as well as between pediatric and adult PH patients.
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Affiliation(s)
- Ting Wang
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Yue Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (Y.X., K.Y., C.Z., Y.C., J.W.)
| | - Bingming Peng
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Kai Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (Y.X., K.Y., C.Z., Y.C., J.W.)
| | - Chenting Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (Y.X., K.Y., C.Z., Y.C., J.W.)
| | - Yuqin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (Y.X., K.Y., C.Z., Y.C., J.W.)
| | - Gang Geng
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Qubei Li
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Jian Fu
- Department of thoracic and Cardiac Surgery Children’s Hospital of Chongqing Medical University (J.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Mi Li
- Department of Cardiovascular Medicine Children’s Hospital of Chongqing Medical University (M.L.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Zhengxiu Luo
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Zhou Fu
- Department of Respiratory Children’s Hospital of Chongqing Medical University (T.W., B.P., G.G., Q.L., Z.L., Z.F.), National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (Y.X., K.Y., C.Z., Y.C., J.W.)
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21
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Tan R, Jin M, Chen Z, Shao Y, Song Y, Yin J, Wang L, Chen T, Li J, Yang D. Exogenous antibiotic resistance gene contributes to intestinal inflammation by modulating the gut microbiome and inflammatory cytokine responses in mouse. Gut Microbes 2023; 15:2156764. [PMID: 36573825 PMCID: PMC9809935 DOI: 10.1080/19490976.2022.2156764] [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: 12/28/2022] Open
Abstract
Dysregulation of the gut microbiota by environmental factors is associated with a variety of autoimmune and immune-mediated diseases. In addition, naturally-occurring extracellular antibiotic resistance genes (eARGs) might directly enter the gut via the food chain. However, following gut microbiota exposure to eARGs, the ecological processes shaping the microbiota community assembly, as well as the interplay between the microbiota composition, metabolic function, and the immune responses, are not well understood. Increasing focus on the One Health approach has led to an urgent need to investigate the direct health damage caused by eARGs. Herein, we reveal the significant influence of eARGs on microbiota communities, strongly driven by stochastic processes. How eARGs-stimulate variations in the composition and metabolomic function of the gut microbiota led to cytokine responses in mice of different age and sex were investigated. The results revealed that cytokines were significantly associated with immunomodulatory microbes, metabolites, and ARGs biomarkers. Cytokine production was associated with specific metabolic pathways (arachidonic acid and tryptophan metabolic pathways), as confirmed by ex vivo cytokine responses and recovery experiments in vivo. Furthermore, the gut microbial profile could be applied to accurately predict the degree of intestinal inflammation ascribed to the eARGs (area under the curve = 0.9616). The present study provided a comprehensive understanding of the influence of an eARGs on immune responses and intestinal barrier damage, shedding light on the interplay between eARGs, microbial, metabolites, and the gut antibiotic resistome in modulating the human immune system.
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Affiliation(s)
- Rong Tan
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China,Junwen Li Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, No. 1 Dali Road, Tianjin 300050, China
| | - Min Jin
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Zhengshan Chen
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Yifan Shao
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Yuanyuan Song
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Jing Yin
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Lifang Wang
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Tianjiao Chen
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Junwen Li
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China,Junwen Li Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, No. 1 Dali Road, Tianjin 300050, China
| | - Dong Yang
- Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China,CONTACT Dong Yang Department of Environment and Health, Tianjin Institute of Environmental and Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, No. 1 Dali Road, Tianjin300050, China
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22
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Fernandes MR, Aggarwal P, Costa RGF, Cole AM, Trinchieri G. Targeting the gut microbiota for cancer therapy. Nat Rev Cancer 2022; 22:703-722. [PMID: 36253536 DOI: 10.1038/s41568-022-00513-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence suggests that the gut microbiota modulates the efficacy and toxicity of cancer therapy, most notably immunotherapy and its immune-related adverse effects. The poor response to immunotherapy in patients treated with antibiotics supports this influential role of the microbiota. Until recently, results pertaining to the identification of the microbial species responsible for these effects were incongruent, and relatively few studies analysed the underlying mechanisms. A better understanding of the taxonomy of the species involved and of the mechanisms of action has since been achieved. Defined bacterial species have been shown to promote an improved response to immune-checkpoint inhibitors by producing different products or metabolites. However, a suppressive effect of Gram-negative bacteria may be dominant in some unresponsive patients. Machine learning approaches trained on the microbiota composition of patients can predict the ability of patients to respond to immunotherapy with some accuracy. Thus, interest in modulating the microbiota composition to improve patient responsiveness to therapy has been mounting. Clinical proof-of-concept studies have demonstrated that faecal microbiota transplantation or dietary interventions might be utilized clinically to improve the success rate of immunotherapy in patients with cancer. Here, we review recent advances and discuss emerging strategies for microbiota-based cancer therapies.
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Affiliation(s)
- Miriam R Fernandes
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Poonam Aggarwal
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raquel G F Costa
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Alicia M Cole
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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23
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Zhang T, Cheng JK, Hu YM. Gut microbiota as a promising therapeutic target for age-related sarcopenia. Ageing Res Rev 2022; 81:101739. [PMID: 36182084 DOI: 10.1016/j.arr.2022.101739] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/30/2022] [Accepted: 09/25/2022] [Indexed: 01/31/2023]
Abstract
Sarcopenia is characterized by a progressive loss of skeletal muscle mass and function with aging. Recently, sarcopenia has been shown to be closely related with gut microbiota. Strategies such as probiotics and fecal microbiota transplantation have shown potential to ameliorate the muscle loss. This review will focus on the age-related sarcopenia, in particular on the relationship between gut microbiota and age-related sarcopenia, how gut microbiota is engaged in sarcopenia, and the potential role of gut microbiota in the treatment of age-related sarcopenia.
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Affiliation(s)
- Ting Zhang
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China
| | - Jin-Ke Cheng
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yao-Min Hu
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China.
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24
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Clinical Biochemical Indicators and Intestinal Microbiota Testing Reveal the Influence of Reproductive Age Extending from the Mother to the Offspring. Microbiol Spectr 2022; 10:e0107622. [PMID: 35993782 PMCID: PMC9602618 DOI: 10.1128/spectrum.01076-22] [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] [Indexed: 12/30/2022] Open
Abstract
Age is an important factor that determines the physiological functions of the human body, but the changes in maternal physiology, biochemistry, and intestinal flora related to reproductive age and their impact on offspring are not clear. Here, we tested and analyzed the clinical physiological and biochemical indicators and/or intestinal flora, matching the data of 252 parturients and their newborns. We found that 4 clinical indicators, including the white blood cell count and the absolute value of monocytes, were significantly related to the reproductive age (P < 0.05). The composition of the intestinal flora also varied with age, and the intestinal flora of advanced-age women (≥35 years old) was different from that of middle-aged women (>25 and <35 years old). We also found that changes in maternal clinical physiological and biochemical indicators related to reproductive age could reflect changes in the abundance of bacteria, such as Peptococcus and Vibrio, and changes in the intestinal flora spread to offspring. These results provide new evidence to explain the increased adverse pregnancy outcomes of mothers of inappropriate age, describe the increased health risks of newborns, help us examine the importance of age-appropriate birth from a broader perspective, and contribute to the discovery of mother-child bonds for a better understanding of healthy reproduction. IMPORTANCE In this study, we demonstrated that physiological indicators and the gut microbiome fluctuate drastically among parturients of different reproductive ages and that there is a significant correlation between the two changes. Mothers of different ages had different gut microbes, and the gut microbiota varied as the childbearing age became too high. Changes in the gut microbiome with maternal reproductive age affected the offspring, and the influence of reproductive age on the intestinal flora had a synergistic effect between mother and child that was revealed for the first time. The maternal childbearing age might affect the colonization of the offspring's initial flora. The results provide new evidence to explain the increased adverse pregnancy outcomes of mothers of inappropriate age, describe the increased health risks of newborns, and contribute to the discovery of mother-child bonds for a better understanding of healthy reproduction.
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25
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Shaikh FY, Gills JJ, Mohammad F, White JR, Stevens CM, Ding H, Fu J, Tam A, Blosser RL, Domingue JC, Larman TC, Chaft JE, Spicer JD, Reuss JE, Naidoo J, Forde PM, Ganguly S, Housseau F, Pardoll DM, Sears CL. Murine fecal microbiota transfer models selectively colonize human microbes and reveal transcriptional programs associated with response to neoadjuvant checkpoint inhibitors. Cancer Immunol Immunother 2022; 71:2405-2420. [PMID: 35217892 PMCID: PMC9411268 DOI: 10.1007/s00262-022-03169-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/02/2022] [Indexed: 10/19/2022]
Abstract
Human gut microbial species found to associate with clinical responses to immune checkpoint inhibitors (ICIs) are often tested in mice using fecal microbiota transfer (FMT), wherein tumor responses in recipient mice may recapitulate human responses to ICI treatment. However, many FMT studies have reported only limited methodological description, details of murine cohorts, and statistical methods. To investigate the reproducibility and robustness of gut microbial species that impact ICI responses, we performed human to germ-free mouse FMT using fecal samples from patients with non-small cell lung cancer who had a pathological response or nonresponse after neoadjuvant ICI treatment. R-FMT mice yielded greater anti-tumor responses in combination with anti-PD-L1 treatment compared to NR-FMT, although the magnitude varied depending on mouse cell line, sex, and individual experiment. Detailed investigation of post-FMT mouse microbiota using 16S rRNA amplicon sequencing, with models to classify and correct for biological variables, revealed a shared presence of the most highly abundant taxa between the human inocula and mice, though low abundance human taxa colonized mice more variably after FMT. Multiple Clostridium species also correlated with tumor outcome in individual anti-PD-L1-treated R-FMT mice. RNAseq analysis revealed differential expression of T and NK cell-related pathways in responding tumors, irrespective of FMT source, with enrichment of these cell types confirmed by immunohistochemistry. This study identifies several human gut microbial species that may play a role in clinical responses to ICIs and suggests attention to biological variables is needed to improve reproducibility and limit variability across experimental murine cohorts.
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Affiliation(s)
- Fyza Y Shaikh
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joell J Gills
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fuad Mohammad
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Courtney M Stevens
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hua Ding
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Juan Fu
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ada Tam
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard L Blosser
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jada C Domingue
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tatianna C Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Jonathan D Spicer
- Department of Surgery, Division of Thoracic Surgery, Faculty of Medicine, Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Joshua E Reuss
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Jarushka Naidoo
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Beaumont Hospital and RCSI University of Health Sciences, Dublin, Ireland
| | - Patrick M Forde
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sudipto Ganguly
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Franck Housseau
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 1550 Orleans Street CRB2 Bldg, Suite 1M.05, Baltimore, MD, 21231, USA
| | - Cynthia L Sears
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, 1550 Orleans Street CRB2 Bldg, Suite 1M.05, Baltimore, MD, 21231, USA.
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26
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Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N, Raine T, Stares MD, Zhu A, De La Revilla Negro J, Lawley TD, Parkes M. Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut 2022; 71:1821-1830. [PMID: 34810234 PMCID: PMC9380505 DOI: 10.1136/gutjnl-2021-325177] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action. DESIGN We used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet. RESULTS Unsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBSP (pathogenic-like) and IBSH (health-like) subtypes. IBSP microbiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBSH microbiomes were similar to controls. On the low FODMAP diet, IBSH and control microbiota were unaffected, but the IBSP signature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalisation of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBSP subjects compared with IBSH (p=0.02). CONCLUSION 50% of IBS cases manifested a 'pathogenic' gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBSP cases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP reduction in IBSP may result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBSP species and metabolic pathways might yield insights regarding IBS pathogenic mechanisms.
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Affiliation(s)
- Kevin Vervier
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen Moss
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Anne Adoum
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Meg Barne
- Department of Dietetics, Addenbrookes Hospital, Cambridge, UK
| | - Hilary Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Christopher J Kiely
- Department of Gastroenterology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Nina Powell
- Department of Dietetics, Addenbrookes Hospital, Cambridge, UK
| | - Tim Raine
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Ana Zhu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
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Sex-Biased Immune Responses to Antibiotics during Anti-PD-L1 Treatment in Mice with Colon Cancer. J Immunol Res 2022; 2022:9202491. [PMID: 35903754 PMCID: PMC9325566 DOI: 10.1155/2022/9202491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Colitis is a frequently occurred side effect of immune checkpoint inhibitors (ICIs), which are increasingly used in cancer treatment, whereas antibiotics are widely used to treat colitis, their effectiveness in ICI-associated colitis remains controversial. In this study, we firstly assessed the effectiveness of several commonly used antibiotics and antibiotic cocktails in alleviating of dextran sulfate sodium- (DSS-) induced colitis. We observed that two narrow-spectrum antibiotics, neomycin and metronidazole, were more effective in alleviating colitis, as evidenced by the remission of loss of the body weight, enlargement of the spleen, shortening of the colon, secretion of proinflammatory cytokines, and histological score of the colon tissue. Moreover, these two antibiotics resulted in better relief of colitis symptoms in the MC38 tumor-bearing male mice receiving the anti-PD-L1 mAb (αPD-L1) treatment, compared to the females. In the meantime, an enhanced response to αPD-L1 efficiency against mice colon cancer was observed in the male mouse group upon the application of these two antibiotics. In contrast, both neomycin and metronidazole showed destructive effects on the antitumor efficiency of αPD-L1 in female mice, despite relief from colitis. We found that antibiotic treatment attenuated the increased infiltration of granulocytes and myeloid cells in colon tissue induced by DSS in female mice, while reducing the proportion of Th17 cells in male mice. These differences were further associated with the sex-biased differences in the gut microbiota. These findings indicated that sex-dependent alterations in the gut microbiota should be considered when applying antibiotics for the treatment of ICI-associated colitis.
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Martin A, Woolbright BL, Umar S, Ingersoll MA, Taylor JA. Bladder cancer, inflammageing and microbiomes. Nat Rev Urol 2022; 19:495-509. [PMID: 35798831 DOI: 10.1038/s41585-022-00611-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 02/08/2023]
Abstract
Ageing is correlated with elevated bladder cancer incidence, morbidity and mortality. Advanced age is also associated with elevated markers of chronic inflammation and perturbations in gut and urinary tract microbiota. One reason for the increased incidence and mortality of bladder cancer in the elderly might be that age-associated changes in multiple microbiomes induce systemic metabolic changes that contribute to immune dysregulation with potentially tumorigenic effects. The gut and urinary microbiomes could be dysregulated in bladder cancer, although the effect of these changes is poorly understood. Each of these domains - the immune system, gut microbiome and urinary microbiome - might also influence the response of patients with bladder cancer to treatment. Improved understanding of age-related alterations to the immune system and gut and urinary microbiomes could provide possible insight into the risk of bladder cancer development and progression in the elderly. In patients with bladder cancer, improved understanding of microbiota might also provide potential targets for therapeutic intervention.
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Affiliation(s)
- Austin Martin
- Department of Urology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Shahid Umar
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS, USA
| | - Molly A Ingersoll
- Université Paris Cité, Institut Cochin, INSERM U1016, Paris, France.,Mucosal Inflammation and Immunity group, Department of Immunology, Institut Pasteur, Paris, France
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, KS, USA.
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29
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Ferulic acid improves intestinal barrier function through altering gut microbiota composition in high-fat diet-induced mice. Eur J Nutr 2022; 61:3767-3783. [PMID: 35732902 DOI: 10.1007/s00394-022-02927-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/31/2022] [Indexed: 12/16/2022]
Abstract
PURPOSE A high-fat diet (HFD) induces gut microbiota (GM) disorders, leading to intestinal barrier dysfunction and inflammation. Ferulic acid (FA) has shown anti-obesity effects, e.g., reducing body weight and food intake. However, the mechanism linking the anti-obesity effects of FA and GM modulation remains obscure. The present study aimed to clarify the mechanism underlying the anti-obesity effects of FA and modulation of the GM. METHODS C57BL/6 J mice were fed by a low-fat diet (LFD) and HFD with or without FA at a dose of 100 mg/kg of body weight by oral gavage for 12 weeks. Using high-throughput sequencing, gas chromatography, real-time fluorescence quantitative PCR and immunohistochemical staining, the attenuation of obesity by FA were assessed via intestinal barrier integrity, inflammation, and the GM. RESULTS FA reduced weight gain, improved HFD-induced GM imbalance, significantly enhanced intestinal short-chain fatty acid (SCFA)-producing bacteria (e.g., Olsenella, Eisenbergiella, Dubosiella, Clostridiales_unclassified, and Faecalibaculum) along with SCFA accumulation and its receptors' expression, decreased endotoxin-producing bacteria or obesity-related bacterial genera, and serum endotoxin (lipopolysaccharides), and inhibited the colonic TLR4/NF-κB pathway. Thus, FA can mitigate colonic barrier dysfunction and intestinal inflammation, induce the production of SCFAs and inhibit endotoxins by modulating the GM. CONCLUSION These results indicate that enhancement of intestinal barrier by altering the GM may be an anti-obesity target of FA and that FA can be used as a functional compound with great developmental values.
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30
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Su Z, Wen D. Characterization of antibiotic resistance across Earth's microbial genomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151613. [PMID: 34774941 DOI: 10.1016/j.scitotenv.2021.151613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, large-scale investigation on the distribution of antibiotic resistance genes (ARGs) in the microbiomes from most types of ecosystem is still lacking. In this study, we provide a comprehensive characterization of ARGs for 52,515 microbial genomes covering various Earth's ecosystems, and conduct the risk assessment for ARG-carrying species based on further identification of mobile genetic elements (MGEs) and virulence factor genes (VFGs). We identify a total of 6159 ARG-carrying metagenome-assembled genomes (ACMs), and most of them are recovered from human gut and city subway. Our results show that efflux pump is the most common mechanism for bacteria to acquire multidrug resistance genes in Earth's microbiomes. Enterobacteriaceae species are the largest hosts of ARGs, accounting for 14% of total ACMs with 64% of the total ARG hits. Most of ARG-carrying species are unique in the different ecosystem categories, while 33 potential background ARGs are commonly shared by all ecosystem categories. We then detect 36 high-risk ARGs that likely threat public health in all ACMs. Based on ranking the importance of ARG-carrying species in the different ecosystem categories, several bacterial taxa such as Escherichia coli, Enterococcus faecalis, and Pseudomonas_A stutzeri are recognized as priority species for surveillance and control. Overall, our study gives a broad view of ARG-host associations in the environments.
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Affiliation(s)
- Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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31
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McCulloch JA, Davar D, Rodrigues RR, Badger JH, Fang JR, Cole AM, Balaji AK, Vetizou M, Prescott SM, Fernandes MR, Costa RGF, Yuan W, Salcedo R, Bahadiroglu E, Roy S, DeBlasio RN, Morrison RM, Chauvin JM, Ding Q, Zidi B, Lowin A, Chakka S, Gao W, Pagliano O, Ernst SJ, Rose A, Newman NK, Morgun A, Zarour HM, Trinchieri G, Dzutsev AK. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. Nat Med 2022; 28:545-556. [PMID: 35228752 DOI: 10.1038/s41591-022-01698-2] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022]
Abstract
Ample evidence indicates that the gut microbiome is a tumor-extrinsic factor associated with antitumor response to anti-programmed cell death protein-1 (PD-1) therapy, but inconsistencies exist between published microbial signatures associated with clinical outcomes. To resolve this, we evaluated a new melanoma cohort, along with four published datasets. Time-to-event analysis showed that baseline microbiota composition was optimally associated with clinical outcome at approximately 1 year after initiation of treatment. Meta-analysis and other bioinformatic analyses of the combined data show that bacteria associated with favorable response are confined within the Actinobacteria phylum and the Lachnospiraceae/Ruminococcaceae families of Firmicutes. Conversely, Gram-negative bacteria were associated with an inflammatory host intestinal gene signature, increased blood neutrophil-to-lymphocyte ratio, and unfavorable outcome. Two microbial signatures, enriched for Lachnospiraceae spp. and Streptococcaceae spp., were associated with favorable and unfavorable clinical response, respectively, and with distinct immune-related adverse effects. Despite between-cohort heterogeneity, optimized all-minus-one supervised learning algorithms trained on batch-corrected microbiome data consistently predicted outcomes to programmed cell death protein-1 therapy in all cohorts. Gut microbial communities (microbiotypes) with nonuniform geographical distribution were associated with favorable and unfavorable outcomes, contributing to discrepancies between cohorts. Our findings shed new light on the complex interaction between the gut microbiome and response to cancer immunotherapy, providing a roadmap for future studies.
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Affiliation(s)
- John A McCulloch
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Diwakar Davar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard R Rodrigues
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jonathan H Badger
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jennifer R Fang
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alicia M Cole
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ascharya K Balaji
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marie Vetizou
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Stephanie M Prescott
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Miriam R Fernandes
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Raquel G F Costa
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wuxing Yuan
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rosalba Salcedo
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Erol Bahadiroglu
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Soumen Roy
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Richelle N DeBlasio
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert M Morrison
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joe-Marc Chauvin
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Quanquan Ding
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bochra Zidi
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ava Lowin
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Saranya Chakka
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wentao Gao
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ornella Pagliano
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scarlett J Ernst
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amy Rose
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Hassane M Zarour
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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32
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Leigh SJ, Lynch CMK, Bird BRH, Griffin BT, Cryan JF, Clarke G. Gut microbiota-drug interactions in cancer pharmacotherapies: implications for efficacy and adverse effects. Expert Opin Drug Metab Toxicol 2022; 18:5-26. [PMID: 35176217 DOI: 10.1080/17425255.2022.2043849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The gut microbiota is involved in host physiology and health. Reciprocal microbiota-drug interactions are increasingly recognized as underlying some individual differences in therapy response and adverse events. Cancer pharmacotherapies are characterized by a high degree of interpatient variability in efficacy and side effect profile and recently, the microbiota has emerged as a factor that may underlie these differences. AREAS COVERED The effects of cancer pharmacotherapy on microbiota composition and function are reviewed with consideration of the relationship between baseline microbiota composition, microbiota modification, antibiotics exposure and cancer therapy efficacy. We assess the evidence implicating the microbiota in cancer therapy-related adverse events including impaired gut function, cognition and pain perception. Finally, potential mechanisms underlying microbiota-cancer drug interactions are described, including direct microbial metabolism, and microbial modulation of liver metabolism and immune function. This review focused on preclinical and clinical studies conducted in the last 5 years. EXPERT OPINION Preclinical and clinical research supports a role for baseline microbiota in cancer therapy efficacy, with emerging evidence that the microbiota modification may assist in side effect management. Future efforts should focus on exploiting this knowledge towards the development of microbiota-targeted therapies. Finally, a focus on specific drug-microbiota-cancer interactions is warranted.
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Affiliation(s)
| | | | | | | | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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33
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Hanahan D. Hallmarks of Cancer: New Dimensions. Cancer Discov 2022; 12:31-46. [PMID: 35022204 DOI: 10.1158/2159-8290.cd-21-1059] [Citation(s) in RCA: 3274] [Impact Index Per Article: 1637.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023]
Abstract
The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles. As knowledge of cancer mechanisms has progressed, other facets of the disease have emerged as potential refinements. Herein, the prospect is raised that phenotypic plasticity and disrupted differentiation is a discrete hallmark capability, and that nonmutational epigenetic reprogramming and polymorphic microbiomes both constitute distinctive enabling characteristics that facilitate the acquisition of hallmark capabilities. Additionally, senescent cells, of varying origins, may be added to the roster of functionally important cell types in the tumor microenvironment. SIGNIFICANCE: Cancer is daunting in the breadth and scope of its diversity, spanning genetics, cell and tissue biology, pathology, and response to therapy. Ever more powerful experimental and computational tools and technologies are providing an avalanche of "big data" about the myriad manifestations of the diseases that cancer encompasses. The integrative concept embodied in the hallmarks of cancer is helping to distill this complexity into an increasingly logical science, and the provisional new dimensions presented in this perspective may add value to that endeavor, to more fully understand mechanisms of cancer development and malignant progression, and apply that knowledge to cancer medicine.
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Affiliation(s)
- Douglas Hanahan
- Ludwig Institute for Cancer Research - Lausanne Branch, Lausanne, Switzerland. The Swiss Institute for Experimental Cancer Research (ISREC) within the School of Life Sciences at the Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. The Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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34
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Human immune diversity: from evolution to modernity. Nat Immunol 2021; 22:1479-1489. [PMID: 34795445 DOI: 10.1038/s41590-021-01058-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023]
Abstract
The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.
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35
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Knippel RJ, Drewes JL, Sears CL. The Cancer Microbiome: Recent Highlights and Knowledge Gaps. Cancer Discov 2021; 11:2378-2395. [PMID: 34400408 DOI: 10.1158/2159-8290.cd-21-0324] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
Knowledge of the human microbiome, which is likely a critical factor in the initiation, progression, and prognosis of multiple forms of cancer, is rapidly expanding. In this review, we focus on recent investigations to discern putative, causative microbial species and the microbiome composition and structure currently associated with procarcinogenesis and tumorigenesis at select body sites. We specifically highlight forms of cancer, gastrointestinal and nongastrointestinal, that have significant bacterial associations and well-defined experimental evidence with the aim of generating directions for future experimental and translational investigations to develop a clearer understanding of the multifaceted mechanisms by which microbiota affect cancer formation. SIGNIFICANCE: Emerging and, for some cancers, strong experimental and translational data support the contribution of the microbiome to cancer biology and disease progression. Disrupting microbiome features and pathways contributing to cancer may provide new approaches to improving cancer outcomes in patients.
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Affiliation(s)
- Reece J Knippel
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julia L Drewes
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia L Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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36
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Cannarile MA, Gomes B, Canamero M, Reis B, Byrd A, Charo J, Yadav M, Karanikas V. Biomarker Technologies to Support Early Clinical Immuno-oncology Development: Advances and Interpretation. Clin Cancer Res 2021; 27:4147-4159. [PMID: 33766813 DOI: 10.1158/1078-0432.ccr-20-2345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Today, there is a huge effort to develop cancer immunotherapeutics capable of combating cancer cells as well as the biological environment in which they can grow, adapt, and survive. For such treatments to benefit more patients, there is a great need to dissect the complex interplays between tumor cells and the host's immune system. Monitoring mechanisms of resistance to immunotherapeutics can delineate the evolution of key players capable of driving an efficacious antitumor immune response. In doing so, simultaneous and systematic interrogation of multiple biomarkers beyond single biomarker approaches needs to be undertaken. Zooming into cell-to-cell interactions using technological advancements with unprecedented cellular resolution such as single-cell spatial transcriptomics, advanced tissue histology approaches, and new molecular immune profiling tools promises to provide a unique level of molecular granularity of the tumor environment and may support better decision-making during drug development. This review will focus on how such technological tools are applied in clinical settings, to inform the underlying tumor-immune biology of patients and offer a deeper understanding of cancer immune responsiveness to immuno-oncology treatments.
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Affiliation(s)
- Michael A Cannarile
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bruno Gomes
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | - Marta Canamero
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bernhard Reis
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Jehad Charo
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland
| | | | - Vaios Karanikas
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland.
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37
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Li Y, Chen T, Li Y, Tang Y, Huang Z. Gut microbiota are associated with sex and age of host: Evidence from semi-provisioned rhesus macaques in southwest Guangxi, China. Ecol Evol 2021; 11:8096-8122. [PMID: 34188874 PMCID: PMC8216961 DOI: 10.1002/ece3.7643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
Host characteristics, such as sex and age, are closely associated with the structure and function of gut microbiota; however, less is known about the effects of age and sex on the gut microbiota of nonhuman primates, and therefore, our knowledge of interindividual variability in host gut microbiota is limited. In this study, 153 fecal samples from rhesus macaques (Macaca mulatta) were analyzed using high-throughput 16S rRNA sequencing in order to explore associations between age and sex of the host and their gut microbiota. The results indicated that female macaques had higher alpha diversity and a more unique gut microbiota than did males. The proportion of Proteobacteria, Tenericutes, Cyanobacteria, unclassified bacteria, and Verrucomicrobia was higher in females than that in males. We also found that adults of both sexes had a higher alpha diversity, a higher proportion of norank Ruminococcaceae, Oscillospira, norank Lachnospiraceae, norank Clostridiales, and Succinivibrio, and a lower proportion of Enterococcus than immatures. Functional analyses revealed that the richness of metabolic pathways was higher in females than males and in adults compared with immatures. These results could be attributed to differences in the nutritional requirements and hormone levels of macaques of different sex and age classes. We conclude that variation in the gut microbiota of different sex and age classes of rhesus macaques may be linked to age- and sex-specific differences in nutrient requirements and hormone levels. These results highlight the importance of host age and sex on the structure and function of the gut microbiota and the need to consider physiological traits when conducting studies on the gut microbiota.
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Affiliation(s)
- Yuhui Li
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
- College of Life SciencesGuangxi Normal UniversityGuilinChina
| | - Ting Chen
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
- College of Life SciencesGuangxi Normal UniversityGuilinChina
| | - Youbang Li
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
- College of Life SciencesGuangxi Normal UniversityGuilinChina
| | - Yin Tang
- College of ArtsGuilin University of TechnologyGuilinChina
| | - Zhonghao Huang
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
- College of Life SciencesGuangxi Normal UniversityGuilinChina
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Andreu-Sánchez S, Chen L, Wang D, Augustijn HE, Zhernakova A, Fu J. A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing. Front Genet 2021; 12:648229. [PMID: 34040632 PMCID: PMC8141913 DOI: 10.3389/fgene.2021.648229] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/22/2021] [Indexed: 12/25/2022] Open
Abstract
Microbes live in complex communities that are of major importance for environmental ecology, public health, and animal physiology and pathology. Short-read metagenomic shotgun sequencing is currently the state-of-the-art technique for exploring these communities. With the aid of metagenomics, our understanding of the microbiome is moving from composition toward functionality, even down to the genetic variant level. While the exploration of single-nucleotide variation in a genome is a standard procedure in genomics, and many sophisticated tools exist to perform this task, identification of genetic variation in metagenomes remains challenging. Major factors that hamper the widespread application of variant-calling analysis include low-depth sequencing of individual genomes (which is especially significant for the microorganisms present in low abundance), the existence of large genomic variation even within the same species, the absence of comprehensive reference genomes, and the noise introduced by next-generation sequencing errors. Some bioinformatics tools, such as metaSNV or InStrain, have been created to identify genetic variants in metagenomes, but the performance of these tools has not been systematically assessed or compared with the variant callers commonly used on single or pooled genomes. In this study, we benchmark seven bioinformatic tools for genetic variant calling in metagenomics data and assess their performance. To do so, we simulated metagenomic reads to mimic human microbial composition, sequencing errors, and genetic variability. We also simulated different conditions, including low and high depth of coverage and unique or multiple strains per species. Our analysis of the simulated data shows that probabilistic method-based tools such as HaplotypeCaller and Mutect2 from the GATK toolset show the best performance. By applying these tools to longitudinal gut microbiome data from the Human Microbiome Project, we show that the genetic similarity between longitudinal samples from the same individuals is significantly greater than the similarity between samples from different individuals. Our benchmark shows that probabilistic tools can be used to call metagenomes, and we recommend the use of GATK's tools as reliable variant callers for metagenomic samples.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Hannah E. Augustijn
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
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Zhang YK, Zhang Q, Wang YL, Zhang WY, Hu HQ, Wu HY, Sheng XZ, Luo KJ, Zhang H, Wang M, Huang R, Wang GY. A Comparison Study of Age and Colorectal Cancer-Related Gut Bacteria. Front Cell Infect Microbiol 2021; 11:606490. [PMID: 33996615 PMCID: PMC8121496 DOI: 10.3389/fcimb.2021.606490] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
Intestinal microbiota is gaining increasing interest from researchers, and a series of studies proved that gut bacteria plays a significant role in various malignancies, especially in colorectal cancer (CRC). In this study, a cohort of 34 CRC patients (average age=65 years old), 26 young volunteers (below 30 years old), and 26 old volunteers (over 60 years old) was enrolled. 16S ribosomal RNA gene sequencing was used to explore fecal bacteria diversity. The operational taxonomic unit (OTU) clustering analysis and NMDS (non-metric multidimensional scaling) analysis were used to separate different groups. Cluster of ortholog genes (COG) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) were used to detect enriched pathways among three groups. Community separations were observed among the three groups of this cohort. Clostridia, Actinobacteria, Bifidobacterium, and Fusobacteria were the most enriched bacteria in the young group, old group, and CRC group respectively. Also, in the young, old, and CRC group, the ratio of Firmicutes/Bacteroidetes was increased sequentially despite no statistical differences. Further, COG showed that transcription, cell wall/membrane/envelope biogenesis, inorganic ion transport and metabolism, and signal transduction mechanisms were differentially expressed among three groups. KEGG pathways associated with ABC transporters, amino sugar and nucleotide sugar metabolism, arginine and proline metabolism, and aminoacyl-tRNA biosynthesis also showed statistical differences among the three groups. These results indicated that the intestinal bacterial community varied as age changed and was related to CRC, and we discussed that specific bacteria enriched in the young and old group may exert a protective function, while bacteria enriched in the CRC group may promote tumorigenesis.
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Affiliation(s)
- Yu-Kun Zhang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qian Zhang
- Department of Colorectal Cancer, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Yu-Liuming Wang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei-Yuan Zhang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Han-Qing Hu
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong-Yu Wu
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiang-Zong Sheng
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kang-Jia Luo
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hao Zhang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meng Wang
- Department of Colorectal Cancer, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Rui Huang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gui-Yu Wang
- Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Colorectal Cancer, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
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