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Uehara M, Inoue T, Hase S, Sasaki E, Toyoda A, Sakakibara Y. Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine. mSystems 2024; 9:e0140523. [PMID: 38557130 PMCID: PMC11097647 DOI: 10.1128/msystems.01405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
The gut microbiome affects the health status of the host through complex interactions with the host's intestinal wall. These host-microbiome interactions may spatially vary along the physical and chemical environment of the intestine, but these changes remain unknown. This study investigated these intricate relationships through a gene co-expression network analysis based on dual transcriptome profiling of different intestinal sites-cecum, transverse colon, and rectum-of the primate common marmoset. We proposed a gene module extraction algorithm based on the graph theory to find tightly interacting gene modules of the host and the microbiome from a vast co-expression network. The 27 gene modules identified by this method, which include both host and microbiome genes, not only produced results consistent with previous studies regarding the host-microbiome relationships, but also provided new insights into microbiome genes acting as potential mediators in host-microbiome interplays. Specifically, we discovered associations between the host gene FBP1, a cancer marker, and polysaccharide degradation-related genes (pfkA and fucI) coded by Bacteroides vulgatus, as well as relationships between host B cell-specific genes (CD19, CD22, CD79B, and PTPN6) and a tryptophan synthesis gene (trpB) coded by Parabacteroides distasonis. Furthermore, our proposed module extraction algorithm surpassed existing approaches by successfully defining more functionally related gene modules, providing insights for understanding the complex relationship between the host and the microbiome.IMPORTANCEWe unveiled the intricate dynamics of the host-microbiome interactions along the colon by identifying closely interacting gene modules from a vast gene co-expression network, constructed based on simultaneous profiling of both host and microbiome transcriptomes. Our proposed gene module extraction algorithm, designed to interpret inter-species interactions, enabled the identification of functionally related gene modules encompassing both host and microbiome genes, which was challenging with conventional modularity maximization algorithms. Through these identified gene modules, we discerned previously unrecognized bacterial genes that potentially mediate in known relationships between host genes and specific bacterial species. Our findings underscore the spatial variations in host-microbiome interactions along the colon, rather than displaying a uniform pattern throughout the colon.
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Affiliation(s)
- Mika Uehara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Takashi Inoue
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Erika Sasaki
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa, Japan
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
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2
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Kolli U, Jalodia R, Moidunny S, Singh PK, Ban Y, Tao J, Cantu GN, Valdes E, Ramakrishnan S, Roy S. Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use. Gut Microbes 2023; 15:2246184. [PMID: 37610102 PMCID: PMC10448978 DOI: 10.1080/19490976.2023.2246184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Opioid crisis is an ongoing epidemic since the past several decades in the United States. Opioid use-associated microbial dysbiosis is emerging as a key regulator of intestinal homeostasis and behavioral responses to opioid. However, the mechanistic insight into the role of microbial community in modulating host response is unavailable. To uncover the role of opioid-induced dysbiosis in disrupting intestinal homeostasis we utilized whole genome sequencing, untargeted metabolomics, and mRNA sequencing to identify changes in microbiome, metabolome, and host transcriptome respectively. Morphine treatment resulted in significant expansion of Parasuterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and depletion of Lactobacillus johnsonii. These changes correlated with alterations in lipid metabolites and flavonoids. Significant alteration in microbial metabolism (metabolism of lipids, amino acids, vitamins and cofactors) and increased expression of virulence factors and biosynthesis of lipopolysaccharides (LPS) and lipoteichoic acid (LTA) were observed in microbiome of morphine-treated animals. In concurrence with changes in microbiome and metabolome extensive changes in innate and adaptive immune response, lipid metabolism, and gut barrier dysfunction were observed in the host transcriptome. Microbiome depleted mice displayed lower levels of inflammation, immune response and tissue destruction compared to mice harboring a dysbiotic microbiome in response to morphine treatment, thus establishing dysbiotic microbiome as mediator of morphine gut pathophysiology. Integrative analysis of multi-omics data highlighted the associations between Parasutterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and altered levels of riboflavin, flavonoids, and lipid metabolites including phosphocholines, carnitines, bile acids, and ethanolamines with host gene expression changes involved in inflammation and barrier integrity of intestine. Omic analysis also highlighted the role of probiotic bacteria Lactobacillus johnsonii, metabolites flavonoids and riboflavin that were depleted with morphine as important factors for intestinal homeostasis. This study presents for the first time ever an interactive view of morphine-induced changes in microbial metabolism, strain level gut microbiome analysis and comprehensive view of changes in gut transcriptome. We also identified areas of potential therapeutic interventions to limit microbial dysbiosis and present a unique resource to the opioid research community.
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Affiliation(s)
- Udhghatri Kolli
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Richa Jalodia
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shamsudheen Moidunny
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Praveen Kumar Singh
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yuguang Ban
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Fl, USA
| | - Junyi Tao
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Eridania Valdes
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sundaram Ramakrishnan
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
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KleinJan H, Frioux C, Califano G, Aite M, Fremy E, Karimi E, Corre E, Wichard T, Siegel A, Boyen C, Dittami SM. Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation. Mol Ecol 2023; 32:703-723. [PMID: 36326449 PMCID: PMC10099861 DOI: 10.1111/mec.16766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Microbes can modify their hosts' stress tolerance, thus potentially enhancing their ecological range. An example of such interactions is Ectocarpus subulatus, one of the few freshwater-tolerant brown algae. This tolerance is partially due to its (un)cultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. Low salinity acclimation of these algal-bacterial associations was then compared. Salinity significantly impacted bacterial and viral gene expression, albeit in different ways across algal-bacterial communities. In contrast, gene expression of the host and metabolite profiles were affected almost exclusively in the freshwater-intolerant algal-bacterial communities. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, vitamin K synthesis is one possible bacterial service missing specifically in freshwater-intolerant cultures in low salinity. In this condition, we also observed a relative increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a quorum-sensing regulator. This could have resulted in dysbiosis by causing a shift in bacterial behaviour in the intolerant algal-bacterial community. Together, these results provide two promising hypotheses to be examined by future targeted experiments. Although they apply only to the specific study system, they offer an example of how bacteria may impact their host's stress response.
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Affiliation(s)
- Hetty KleinJan
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
- CEBEDEAU, Research and Expertise Centre for WaterQuartier Polytech 1LiègeBelgium
| | - Clémence Frioux
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
- InriaUniversity of Bordeaux, INRAETalenceFrance
| | - Gianmaria Califano
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller University JenaJenaGermany
| | - Méziane Aite
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Enora Fremy
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Elham Karimi
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
| | - Erwan Corre
- Station BiologiqueFR2424, ABiMS, Sorbonne Université, CNRSRoscoffFrance
| | - Thomas Wichard
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller University JenaJenaGermany
| | - Anne Siegel
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Catherine Boyen
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
| | - Simon M. Dittami
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
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Sadeghpour Heravi F, Hu H. Bifidobacterium: Host-Microbiome Interaction and Mechanism of Action in Preventing Common Gut-Microbiota-Associated Complications in Preterm Infants: A Narrative Review. Nutrients 2023; 15:nu15030709. [PMID: 36771414 PMCID: PMC9919561 DOI: 10.3390/nu15030709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The development and health of infants are intertwined with the protective and regulatory functions of different microorganisms in the gut known as the gut microbiota. Preterm infants born with an imbalanced gut microbiota are at substantial risk of several diseases including inflammatory intestinal diseases, necrotizing enterocolitis, late-onset sepsis, neurodevelopmental disorders, and allergies which can potentially persist throughout adulthood. In this review, we have evaluated the role of Bifidobacterium as commonly used probiotics in the development of gut microbiota and prevention of common diseases in preterm infants which is not fully understood yet. The application of Bifidobacterium as a therapeutical approach in the re-programming of the gut microbiota in preterm infants, the mechanisms of host-microbiome interaction, and the mechanism of action of this bacterium have also been investigated, aiming to provide new insights and opportunities in microbiome-targeted interventions in personalized medicine.
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Affiliation(s)
- Fatemah Sadeghpour Heravi
- Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia
- Correspondence: (F.S.H.); (H.H.)
| | - Honghua Hu
- Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia
- Innovation Center of Translational Pharmacy, Jinhua Institute of Zhejiang University, Jinhua 321016, China
- Correspondence: (F.S.H.); (H.H.)
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5
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Xue L, Ding Y, Qin Q, Liu L, Ding X, Zhou Y, Liu K, Singla RK, Shen K, Din AU, Zhang Y, Shen Z, Shen B, Miao L. Assessment of the impact of intravenous antibiotics treatment on gut microbiota in patients: Clinical data from pre-and post-cardiac surgery. Front Cell Infect Microbiol 2023; 12:1043971. [PMID: 36741975 PMCID: PMC9896080 DOI: 10.3389/fcimb.2022.1043971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 01/21/2023] Open
Abstract
Background and aims Surgical site infection is a common complication after surgery. Periprocedural antibiotics are necessary to prescribe for preventing or treating infections. The present study aimed to explore the effect of intravenous antibiotics on gut microbiota and menaquinone biosynthesis in patients, especially in elderly patients undergoing cardiac surgery. Methods A total of 388 fecal samples were collected from 154 cardiac surgery patients. The V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced on a MiSeq PE300. The gut microbiota diversity of samples was analyzed in terms of α- and β-diversity at the OTU level. The different groups were classified according to antibiotics in combinations and single antibiotics. PICRUSt2 was used for preliminary prediction of the gut microbiota function for menaquinone biosynthesis. Results The intravenously administered antibiotics which are excreted via bile represents the main antibiotics that could disturb the gut microbiota's composition in cardiac surgery patients, especially for elderly patients. The effect of antibiotics on gut microbiota is produced after antibiotics treatments over one week. The recovery of gut microbiota to the state of pre-antibiotics may require over two weeks of antibiotics withdrawal. Sex factor doesn't represent as an influencer in gut microbiota composition. Long-term use of cefoperazone-sulbactam may affect coagulation function. Conclusions The composition of the gut microbiota had a significant change post-intravenous antibiotics treatment in cardiac surgery patients. The richness and diversity of gut microbiota are increased in elderly patients.
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Affiliation(s)
- Ling Xue
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China,Department of Pharmacology, Faculty of Medicine, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Yinglong Ding
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiong Qin
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Linsheng Liu
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoliang Ding
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Zhou
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Kun Liu
- Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, China
| | - Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China,School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Ke Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Ahmad Ud Din
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zhang
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenya Shen
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Liyan Miao, ; Bairong Shen, ; Zhenya Shen,
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Liyan Miao, ; Bairong Shen, ; Zhenya Shen,
| | - Liyan Miao
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China,Institute for Interdisciplinary Drug Research and Translational Sciences, Soochow University, Suzhou, China,*Correspondence: Liyan Miao, ; Bairong Shen, ; Zhenya Shen,
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6
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Abstract
The small intestine is a digestive organ that has a complex and dynamic ecosystem, which is vulnerable to the risk of pathogen infections and disorders or imbalances. Many studies have focused attention on intestinal mechanisms, such as host–microbiome interactions and pathways, which are associated with its healthy and diseased conditions. This review highlights the intestine models currently used for simulating such normal and diseased states. We introduce the typical models used to simulate the intestine along with its cell composition, structure, cellular functions, and external environment and review the current state of the art for in vitro cell-based models of the small intestine system to replace animal models, including ex vivo, 2D culture, organoid, lab-on-a-chip, and 3D culture models. These models are described in terms of their structure, composition, and co-culture availability with microbiomes. Furthermore, we discuss the potential application for the aforementioned techniques to these in vitro models. The review concludes with a summary of intestine models from the viewpoint of current techniques as well as their main features, highlighting potential future developments and applications.
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Affiliation(s)
- Sang-Myung Jung
- Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Seonghun Kim
- Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
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7
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Mujagic Z, Kasapi M, Jonkers DMAE, Garcia-Perez I, Vork L, Weerts ZZR, Serrano-Contreras JI, Zhernakova A, Kurilshikov A, Scotcher J, Holmes E, Wijmenga C, Keszthelyi D, Nicholson JK, Posma JM, Masclee AAM. Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome. Gut Microbes 2022; 14:2063016. [PMID: 35446234 PMCID: PMC9037519 DOI: 10.1080/19490976.2022.2063016] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.
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Affiliation(s)
- Zlatan Mujagic
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands,Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK,CONTACT Zlatan Mujagic Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Melpomeni Kasapi
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Daisy MAE Jonkers
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Isabel Garcia-Perez
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK
| | - Lisa Vork
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Zsa Zsa R.M. Weerts
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jose Ivan Serrano-Contreras
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jamie Scotcher
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK,The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Daniel Keszthelyi
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jeremy K Nicholson
- The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Joram M Posma
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Ad AM Masclee
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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Abstract
Every individual harbours a complex, diverse and mutualistic microbial flora in their intestine and over the time it became an integral part of the body, affecting a plethora of activities of the host. Interaction between host and gut-microbiota affects several aspects of host physiology. Gut-microbiota affects host metabolism by fermenting unabsorbed/undigested carbohydrates in the large intestine. Not only the metabolic functions, any disturbances in the composition of the gut-microbiota during first 2-3 years of life may impact on the brain development and later affects cognition and behaviour. Thus, gut-dysbiosis causes certain serious pathological conditions in the host including metabolic disorders, inflammatory bowel disease and mood alterations, etc. Microbial-metabolites in recent times have emerged as key mediators and are responsible for microbiota induced beneficial effects on host. This review provides an overview of the mechanism of microbial-metabolite production, their respective physiological functions and the impact of gut-microbiome in health and diseases. Metabolites from dietary fibres, aromatic amino acids such as tryptophan, primary bile acids and others are the potential substances and link microbiota to host physiology. Many of these metabolites act as signalling molecules to a number of cells types and also help in the secretion of hormones. Moreover, interaction of microbiota derived metabolites with their host, immunity boosting mechanisms, protection against pathogens and modulation of metabolism is also highlighted here. Understanding all these functional attributes of metabolites produced from gut-microbiota may lead to the opening of a new avenue for preventing and developing potent therapies against several diseases.
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Affiliation(s)
- Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu & Kashmir, India
| | | | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Jant-Pali, India
| | - Praveen Kumar Mehta
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu & Kashmir, India
| | - Ashok Kumar Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu & Kashmir, India
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9
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Byrne EH, Farcasanu M, Bloom SM, Xulu N, Xu J, Hykes BL, Mafunda NA, Hayward MR, Dong M, Dong KL, Gumbi T, Ceasar FX, Ismail N, Ndung'u T, Gosmann C, Ghebremichael MS, Handley SA, Mitchell CM, Villani AC, Kwon DS. Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures. Front Cell Infect Microbiol 2021; 11:733619. [PMID: 34604114 PMCID: PMC8482842 DOI: 10.3389/fcimb.2021.733619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023] Open
Abstract
The microbiome of the female genital tract (FGT) is closely linked to reproductive health outcomes. Diverse, anaerobe-dominated communities with low Lactobacillus abundance are associated with a number of adverse reproductive outcomes, such as preterm birth, cervical dysplasia, and sexually transmitted infections (STIs), including HIV. Vaginal dysbiosis is associated with local mucosal inflammation, which likely serves as a biological mediator of poor reproductive outcomes. Yet the precise mechanisms of this FGT inflammation remain unclear. Studies in humans have been complicated by confounding demographic, behavioral, and clinical variables. Specifically, hormonal contraception is associated both with changes in the vaginal microbiome and with mucosal inflammation. In this study, we examined the transcriptional landscape of cervical cell populations in a cohort of South African women with differing vaginal microbial community types. We also investigate effects of reproductive hormones on the transcriptional profiles of cervical cells, focusing on the contraceptive depot medroxyprogesterone acetate (DMPA), the most common form of contraception in sub-Saharan Africa. We found that antigen presenting cells (APCs) are key mediators of microbiome associated FGT inflammation. We also found that DMPA is associated with significant transcriptional changes across multiple cell lineages, with some shared and some distinct pathways compared to the inflammatory signature seen with dysbiosis. These results highlight the importance of an integrated, systems-level approach to understanding host-microbe interactions, with an appreciation for important variables, such as reproductive hormones, in the complex system of the FGT mucosa.
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Affiliation(s)
- Elizabeth H Byrne
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Mara Farcasanu
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Seth M Bloom
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Nondumiso Xulu
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jiawu Xu
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Nomfuneko A Mafunda
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Matthew R Hayward
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Mary Dong
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Females Rising Through Education, Support, and Health (FRESH), Durban, South Africa
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,Females Rising Through Education, Support, and Health (FRESH), Durban, South Africa
| | - Thandeka Gumbi
- Females Rising Through Education, Support, and Health (FRESH), Durban, South Africa.,Health Systems Trust, Durban, South Africa
| | - Fransisca Xolisile Ceasar
- Females Rising Through Education, Support, and Health (FRESH), Durban, South Africa.,Health Systems Trust, Durban, South Africa
| | - Nasreen Ismail
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Christina Gosmann
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Musie S Ghebremichael
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Caroline M Mitchell
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, United States
| | - Alexandra-Chloé Villani
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States.,Broad Institute of MIT and Harvard, Immunology Program, Cambridge, MA, United States
| | - Douglas S Kwon
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
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10
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Chen Z, Wong PY, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Wong SH, Wu WKK, Li RJ, Meehan K, Lui VWY, Chow C, Lo KW, Chan ABW, Boon SS, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Cheng ASL, Yu J, Chan PKS, Chan JYK. The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2020; 12:E3425. [PMID: 33218162 DOI: 10.3390/cancers12113425] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Recently, there has been increased recognition of an association between the bacterial microbiome and cancer. In this study, we characterized the non-HPV head and neck squamous cell carcinoma (HNSCC) microbiome. We found a significant enrichment of Fusobacterium, depletion of Streptococcus, and the microbial signatures of twelve bacterial genera distinguishing HNSCC. With increased Fusobacterium—in particular, F. nucleatum—in our HNSCC cohort and its known association with prognosis in colorectal cancers (CRC), we sought to further characterize the association between clinical outcomes and F. nucleatum, and the host interaction with F. nucleatum. We identified a higher abundance of F. nucleatum in non-smokers and an improved survival, in contrast to CRC. An integrative analysis also identified that the enrichment of F. nucleatum was associated with host gene promoter methylation, suggesting that the bacterial mircobiome status may have a potential role as a prognostic biomarker and be involved in the pathogenesis of HNSCC. Abstract The role of oral microbiota in head and neck squamous cell carcinoma (HNSCC) is poorly understood. Here we sought to evaluate the association of the bacterial microbiome with host gene methylation and patient outcomes, and to explore its potential as a biomarker for early detection or intervention. Here we performed 16S rRNA gene amplicon sequencing in sixty-eight HNSCC patients across both tissue and oral rinse samples to identify oral bacteria with differential abundance between HNSCC and controls. A subset of thirty-one pairs of HNSCC tumor tissues and the adjacent normal tissues were characterized for host gene methylation profile using bisulfite capture sequencing. We observed significant enrichments of Fusobacterium and Peptostreptococcus in HNSCC tumor tissues when compared to the adjacent normal tissues, and in HNSCC oral rinses when compared to healthy subjects, while ten other bacterial genera were largely depleted. These HNSCC-related bacteria were discriminative for HNSCC and controls with area under the receiver operating curves (AUCs) of 0.84 and 0.86 in tissue and oral rinse samples, respectively. Moreover, Fusobacterium nucleatum abundance in HNSCC cases was strongly associated with non-smokers, lower tumor stage, lower rate of recurrence, and improved disease-specific survival. An integrative analysis identified that enrichment of F. nucleatum was associated with host gene promoter methylation, including hypermethylation of tumor suppressor genes LXN and SMARCA2, for which gene expressions were downregulated in the HNSCC cohort from The Cancer Genome Atlas. In conclusion, we identified a taxonomically defined microbial consortium associated with HNSCC that may have clinical potential regarding biomarkers for early detection or intervention. Host–microbe interactions between F. nucleatum enrichment and clinical outcomes or host gene methylation imply a potential role of F. nucleatum as a pro-inflammatory driver in initiating HNSCC without traditional risk factors, which warrants further investigation for the underlying mechanisms.
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11
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Abstract
Microbes are the most prevalent form of life yet also the least well-understood in terms of their diversity. Due to a greater appreciation of their role in modulating host physiology, microbes have come to the forefront of biological investigation of human health and disease. Despite this, capturing the heterogeneity of microbes, and that of the host responses they induce, has been challenging due to the bulk methods of nucleic acid and cellular analysis. One of the greatest recent advancements in our understanding of complex organisms has happened in the field of single-cell analysis through genomics, transcriptomics, and spatial resolution. While significantly advancing our understanding of host biology, these techniques have only recently been applied to microbial systems to shed light on their diversity as well as interactions with host cells in both commensal and pathogenic contexts. In this review, we highlight emerging technologies that are poised to provide key insights into understanding how microbe heterogeneity can be studied. We then take a detailed look into how host single-cell analysis has uncovered the impact of microbes on host heterogeneity and the effect of host biology on microorganisms. Most of these insights would have been challenging, and in some cases impossible, without the advent of single-cell analysis, suggesting the importance of the single-cell paradigm for progressing the microbiology field forward through a host-microbiome perspective and applying these insights to better understand and treat human disease.
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Affiliation(s)
| | - Christoph A. Thaiss
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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12
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Abstract
Once referred to as “normal commensal flora” the human microbiome plays an integral role between health and disease. The host mucosal surface replete with a multitude of immune cells is a vast arena constantly sensing and responding to antigen presentation and microbial by-products. It is this key role that may allow the microbiome to prime or protect the host from autoimmune disease. Rheumatoid arthritis (RA) is a chronic, disabling inflammatory condition characterized by a complex multifactorial etiology. The presence of certain genetic markers has been proven to increase susceptibility to RA however it does not guarantee disease development. Given low concordance rates demonstrated in monozygotic twin studies there is a clear implication for the involvement of external players in RA pathogenesis. Since the historical description of rheumatoid factor, numerous additional autoantibodies have been described in the sera of RA patients. The presence of anti-cyclic citrullinated protein antibody is now a standard test, and is associated with a more severe disease course. Interestingly these antibodies are detectable in patient’s sera long before the clinical signs of RA occur. The production of autoantibodies is driven by the lack of tolerance of the immune system, and how tolerance is broken is a crucial question for understanding RA development. Here we review current literature on the role of the microbiome in RA development including periodontal, gut and lung mucosa, with particular focus on proposed mechanisms of host microbiome interactions. We discuss the use of Mendelian randomization to assign causality to the microbiome and present considerations for future studies.
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Affiliation(s)
- Cristopher M Rooney
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, United Kingdom
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, United Kingdom.,Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Leeds, United Kingdom
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, United Kingdom.,Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Leeds, United Kingdom
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13
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Li L, Figeys D. Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface. Mol Cell Proteomics 2020; 19:1409-1417. [PMID: 32581040 PMCID: PMC8143649 DOI: 10.1074/mcp.r120.002051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.
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Affiliation(s)
- Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.
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14
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Yang B, Zhang G, Elias M, Zhu Y, Wang J. The role of cytokine and immune responses in intestinal fibrosis. J Dig Dis 2020; 21:308-314. [PMID: 32410365 DOI: 10.1111/1751-2980.12879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/11/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022]
Abstract
The rapidly increasing incidence of inflammatory bowel disease (IBD) in South America, eastern Europe, Asia, and Africa has resulted in a global public health challenge. Intestinal fibrosis is a common complication in patients with long-term IBD, which may develop into stenosis and subsequent obstruction. Hitherto, the origin of IBD is unclear and several factors may be involved, including genetic, immune, environmental and microbial influences. Little is known about how the recurrent inflammation in patients with IBD develops into intestinal fibrosis and currently, there is no suitable treatment to reverse intestinal fibrosis in these patients. Here, we review the role of immune components in the pathogenesis of IBD and intestinal fibrosis, including cytokine networks, host-microbiome interactions, and immune cell trafficking.
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Affiliation(s)
- Bo Yang
- School of Laboratory Medicine, Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Ge Zhang
- School of Laboratory Medicine, Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Michael Elias
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Yijun Zhu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA.,Department of Gastroenterology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jie Wang
- School of Laboratory Medicine, Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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15
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Zhou X, Devescovi V, Liu Y, Dent JE, Nardini C. Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis. Biomolecules 2019; 9:biom9040144. [PMID: 30970641 PMCID: PMC6523851 DOI: 10.3390/biom9040144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022] Open
Abstract
Chronic inflammatory autoimmune disorders are systemic diseases with increasing incidence and still lack a cure. More recently, attention has been placed in understanding gastrointestinal (GI) dysbiosis and, although important progress has been made in this area, it is currently unclear to what extent microbiome manipulation can be used in the treatment of autoimmune disorders. Via the use of appropriate models, rheumatoid arthritis (RA), a well-known exemplar of such pathologies, can be exploited to shed light on the currently overlooked effects of existing therapies on the GI microbiome. In this direction, we here explore the crosstalk between the GI microbiome and the host immunity in model arthritis (collagen induced arthritis, CIA). By exploiting omics from samples of limited invasiveness (blood and stools), we assess the host-microbiome responses to standard therapy (methotrexate, MTX) combined with mechanical subcutaneous stimulation (MS) and to mechanical stimulation alone. When MS is involved, results reveal the sphingolipid metabolism as the trait d’union among known hallmarks of (model) RA, namely: Imbalance in the S1P-S1PR1 axis, expansion of Prevotella sp., and invariant Natural Killer T (iNKT)-penia, thus offering the base of a rationale to mechanically modulate this pathway as a therapeutic target in RA.
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Affiliation(s)
- Xiaoyuan Zhou
- Department of Neurology, University of California, San Francisco, CA 94158, USA.
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
| | - Valentina Devescovi
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
| | - Yuanhua Liu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
- Bioinformatics Platform, Institut Pasteur of Shanghai, CAS, Shanghai 200031, China.
| | - Jennifer E Dent
- NORSAS Consultancy Ltd., Hoveton, Norwich, Norfolk, NR128QP, UK.
| | - Christine Nardini
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
- Department of Laboratory Medicine, Division of Clinical Chemistry Karolinska Institute, 17177 Stockholm, Sweden.
- Scientific and Medical Direction, SOL Group S.r.l, 20900 Monza, Italy.
- CNR IAC "Mauro Picone", 00185 Roma, Italy.
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16
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Shin W, Wu A, Massidda MW, Foster C, Thomas N, Lee DW, Koh H, Ju Y, Kim J, Kim HJ. A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic Interface-on-a-Chip. Front Bioeng Biotechnol 2019; 7:13. [PMID: 30792981 PMCID: PMC6374617 DOI: 10.3389/fbioe.2019.00013] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging a modified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen microchannel is necessary and sufficient to create the steady-state vertical oxygen gradient in the AOI Chip. We confirmed that the created AOI does not compromise the viability, barrier function, mucin production, and the expression and localization of tight junction proteins in the 3D intestinal epithelial layer. Two obligate anaerobic commensal gut microbiome, Bifidobacterium adolescentis and Eubacterium hallii, that exert metabolic cross-feeding in vivo, were independently co-cultured with epithelial cells in the AOI Chip for up to a week without compromising any cell viability. Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells associated with intestinal metabolism, homeostasis, and immune regulation.
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Affiliation(s)
- Woojung Shin
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Alexander Wu
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Miles W Massidda
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Charles Foster
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Newin Thomas
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Dong-Woo Lee
- Department of Biotechnology, College of Life Science and Technology, Yonsei University, Seoul, South Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Youngwon Ju
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Joohoon Kim
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States.,Department of Medical Engineering, Yonsei University College of Medicine, Seoul, South Korea
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17
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Paller AS, Kong HH, Seed P, Naik S, Scharschmidt TC, Gallo RL, Luger T, Irvine AD. The microbiome in patients with atopic dermatitis. J Allergy Clin Immunol 2018; 143:26-35. [PMID: 30476499 PMCID: PMC7163929 DOI: 10.1016/j.jaci.2018.11.015] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/15/2022]
Abstract
As an interface with the environment, the skin is a complex ecosystem colonized by many microorganisms that coexist in an established balance. The cutaneous microbiome inhibits colonization with pathogens, such as Staphylococcus aureus, and is a crucial component for function of the epidermal barrier. Moreover, crosstalk between commensals and the immune system is now recognized because microorganisms can modulate both innate and adaptive immune responses. Host-commensal interactions also have an effect on the developing immune system in infants and, subsequently, the occurrence of diseases, such as asthma and atopic dermatitis (AD). Later in life, the cutaneous microbiome contributes to the development and course of skin disease. Accordingly, in patients with AD, a decrease in microbiome diversity correlates with disease severity and increased colonization with pathogenic bacteria, such as S aureus. Early clinical studies suggest that topical application of commensal organisms (eg, Staphylococcus hominis or Roseomonas mucosa) reduces AD severity, which supports an important role for commensals in decreasing S aureus colonization in patients with AD. Advancing knowledge of the cutaneous microbiome and its function in modulating the course of skin disorders, such as AD, might result in novel therapeutic strategies.
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Affiliation(s)
- Amy S Paller
- Dermatology and Infectious Disease, Northwestern University Feinberg School of Medicine and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Ill.
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskletal and Skin Diseases, Bethesda, Md
| | - Patrick Seed
- Dermatology and Infectious Disease, Northwestern University Feinberg School of Medicine and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Shruti Naik
- Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY
| | | | | | - Thomas Luger
- Dermatology, University of Muenster, Munster, Germany
| | - Alan D Irvine
- Paediatric Dermatology, Our Lady's Children's Hospital Crumlin, National Children's Research Centre and Trinity College, Dublin, Ireland.
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18
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Kokou F, Sasson G, Nitzan T, Doron-Faigenboim A, Harpaz S, Cnaani A, Mizrahi I. Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature. eLife 2018; 7:e36398. [PMID: 30454554 PMCID: PMC6277203 DOI: 10.7554/elife.36398] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023] Open
Abstract
The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.
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Affiliation(s)
- Fotini Kokou
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Goor Sasson
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
| | - Tali Nitzan
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Institute of Plant ScienceAgricultural Research OrganizationRishon LeZionIsrael
| | - Sheenan Harpaz
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
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19
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Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P. The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster. FEBS Lett 2018; 592:4078-4086. [PMID: 30372516 PMCID: PMC6587461 DOI: 10.1002/1873-3468.13278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 02/01/2023]
Abstract
Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germline although microbiota is also passed on to the offspring. Thus, we inspected the involvement of the gut microbiome in transgenerational inheritance of environmental exposures in Drosophila melanogaster. We grew flies in the cold versus control temperatures and compared their transcriptional patterns in both conditions as well as in their offspring. F2 flies grew in control temperature, while we controlled their microbiota acquisition from either F1 sets. Transcriptional status of some genes was conserved transgenerationally, and a subset of these genes, mainly expressed in the gut, was transcriptionally dependent on the acquired microbiome.
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Affiliation(s)
- Aman Zare
- Department of Molecular Biology, Umeå University, Sweden
| | | | - Edvin Karlsson
- Department of Molecular Biology, Umeå University, Sweden.,Division of CBRN Security and Defence, FOI-Swedish, Defence Research Agency, Umeå, Sweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Sweden.,Division of CBRN Security and Defence, FOI-Swedish, Defence Research Agency, Umeå, Sweden.,Department of Ecology and Environmental Science (EMG), Umeå University, Sweden
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20
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Cope EK. Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies. mSystems 2018; 3:e00158-17. [PMID: 29556535 DOI: 10.1128/mSystems.00158-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/27/2017] [Indexed: 12/27/2022] Open
Abstract
Despite growing efforts to understand the role of the microbiota in airway disease, mechanisms that link microbial community dysbiosis to chronic inflammation remain elusive. Our laboratory is interested in how altered microbiota composition or function influences airway inflammatory diseases, including chronic rhinosinusitis, asthma, and cystic fibrosis. Despite growing efforts to understand the role of the microbiota in airway disease, mechanisms that link microbial community dysbiosis to chronic inflammation remain elusive. Our laboratory is interested in how altered microbiota composition or function influences airway inflammatory diseases, including chronic rhinosinusitis, asthma, and cystic fibrosis. Given the tight interplay between host-associated microbes and host immunity, the potential for translational microbiome research to guide clinical decisions and novel therapeutics is becoming better appreciated. We hope to advance our understanding of the ecology of airway disease through integrating multiple omics assays and in vitro and in vivo experimental validation. An increased understanding of the role of the microbiota in chronic airway inflammation will ultimately lead to the rational development of therapeutics aimed at manipulation of microbiota composition or activity to treat these important and costly diseases. In this perspective, I discuss our current research investigating the microbiology and ecology of the airway microbiome.
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21
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Lozupone CA. Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease. mSystems 2018; 3:e00183-17. [PMID: 29556546 DOI: 10.1128/mSystems.00183-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023] Open
Abstract
In recent years, there has been a deluge of papers linking altered microbiome compositions to a myriad of diseases. Mechanistic insight into microbial drivers of disease phenotypes is essential for translation to novel therapies. In recent years, there has been a deluge of papers linking altered microbiome compositions to a myriad of diseases. Mechanistic insight into microbial drivers of disease phenotypes is essential for translation to novel therapies. A key mechanism by which microbes influence health is immune modulation by components of their capsule and cell envelope and their metabolites. A major research focus of my laboratory is to gain mechanistic insight into which microbes modulate host immunity generally and in the context of disease. Using 16S rRNA-targeted sequencing, we have established associations between gut microbiome composition and immune-modulated disease phenotypes in diseases such as graft-versus-host disease in cancer patients undergoing stem cell transplantation. By integrating omics and computational approaches with laboratory experiments, we have expanded knowledge of mechanisms used by host-associated microbes to dampen inflammatory responses. This work has promise for development of novel microbiome-targeted therapeutics.
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22
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Wichert R, Ermund A, Schmidt S, Schweinlin M, Ksiazek M, Arnold P, Knittler K, Wilkens F, Potempa B, Rabe B, Stirnberg M, Lucius R, Bartsch JW, Nikolaus S, Falk-Paulsen M, Rosenstiel P, Metzger M, Rose-John S, Potempa J, Hansson GC, Dempsey PJ, Becker-Pauly C. Mucus Detachment by Host Metalloprotease Meprin β Requires Shedding of Its Inactive Pro-form, which Is Abrogated by the Pathogenic Protease RgpB. Cell Rep 2017; 21:2090-2103. [PMID: 29166602 DOI: 10.1016/j.celrep.2017.10.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/22/2017] [Accepted: 10/24/2017] [Indexed: 12/26/2022] Open
Abstract
The host metalloprotease meprin β is required for mucin 2 (MUC2) cleavage, which drives intestinal mucus detachment and prevents bacterial overgrowth. To gain access to the cleavage site in MUC2, meprin β must be proteolytically shed from epithelial cells. Hence, regulation of meprin β shedding and activation is important for physiological and pathophysiological conditions. Here, we demonstrate that meprin β activation and shedding are mutually exclusive events. Employing ex vivo small intestinal organoid and cell culture experiments, we found that ADAM-mediated shedding is restricted to the inactive pro-form of meprin β and is completely inhibited upon its conversion to the active form at the cell surface. This strict regulation of meprin β activity can be overridden by pathogens, as demonstrated for the bacterial protease Arg-gingipain (RgpB). This secreted cysteine protease potently converts membrane-bound meprin β into its active form, impairing meprin β shedding and its function as a mucus-detaching protease.
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Affiliation(s)
- Rielana Wichert
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Anna Ermund
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | | | - Matthias Schweinlin
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
| | - Miroslaw Ksiazek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | | | | | | | - Barbara Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Björn Rabe
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | | | - Ralph Lucius
- Anatomical Institute, University of Kiel, Kiel, Germany
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Marburg, Germany
| | - Susanna Nikolaus
- I. Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Marco Metzger
- Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Translational Center "Regenerative Therapies for Oncology and Musculoskeletal Diseases" - Würzburg Branch, Würzburg, Germany
| | | | - Jan Potempa
- Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA
| | - Gunnar C Hansson
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Peter J Dempsey
- Department of Pediatrics, University of Colorado Medical School, Aurora, CO 80045, USA
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23
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Manes NP, Shulzhenko N, Nuccio AG, Azeem S, Morgun A, Nita-Lazar A. Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota. mSystems 2017; 2:e00107-17. [PMID: 29085914 DOI: 10.1128/mSystems.00107-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023] Open
Abstract
Multiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different levels will lead to a complete understanding of the complex relationships between the host and the microbiota. Therefore, our results demonstrate the importance of using an integrative approach to study host-microbiota interaction at the molecular level. The bodies of mammals are hosts to vast microbial communities composed of trillions of bacteria from thousands of species, whose effects on health and development have begun to be appreciated only recently. In this investigation, an integrated analysis combining proteomics and transcriptomics was used to quantitatively compare the terminal ilia from conventional and germfree mice. Female and male mice responded similarly to the microbiota, but C57BL/10A mice responded more strongly than BALB/c mice at both the transcriptome and proteome levels. The microbiota primarily caused upregulation of immunological pathways and downregulation of metabolic pathways in the conventional mice. Many of the affected pathways were altered only at either the transcriptome or proteome level. Of the pathways that were affected at both levels, most were affected concordantly. The discordant pathways were not principally involved in the immune system but instead were related to metabolism, oxidative phosphorylation, protein translation, transport, and turnover. To broaden the discovery of affected host pathways, a meta-analysis was performed using intestinal transcriptomics data from previously published studies of germfree versus conventional mice with diverse microbiota populations. Similar transcript-level responses to the microbiota were found, and many additional affected host pathways were discovered. IMPORTANCE Multiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different levels will lead to a complete understanding of the complex relationships between the host and the microbiota. Therefore, our results demonstrate the importance of using an integrative approach to study host-microbiota interaction at the molecular level.
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24
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Pomowski A, Usón I, Nowakowska Z, Veillard F, Sztukowska MN, Guevara T, Goulas T, Mizgalska D, Nowak M, Potempa B, Huntington JA, Potempa J, Gomis-Rüth FX. Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome. J Biol Chem 2017; 292:5724-5735. [PMID: 28196869 DOI: 10.1074/jbc.m117.776724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Indexed: 01/11/2023] Open
Abstract
Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as Porphyromonas gingivalis, the main etiological agent of periodontitis. P. gingivalis secretes proteolytic gingipains (Kgp and RgpA/B) as zymogens inhibited by a pro-domain that is removed during extracellular activation. Unraveling the molecular mechanism of Kgp zymogenicity is essential to design inhibitors blocking its activity. Here, we found that the isolated 209-residue Kgp pro-domain is a boomerang-shaped all-β protein similar to the RgpB pro-domain. Using composite structural information of Kgp and RgpB, we derived a plausible homology model and mechanism of Kgp-regulating zymogenicity. Accordingly, the pro-domain would laterally attach to the catalytic moiety in Kgp and block the active site through an exposed inhibitory loop. This loop features a lysine (Lys129) likely occupying the S1 specificity pocket and exerting latency. Lys129 mutation to glutamate or arginine led to misfolded protein that was degraded in vivo Mutation to alanine gave milder effects but still strongly diminished proteolytic activity, without affecting the subcellular location of the enzyme. Accordingly, the interactions of Lys129 within the S1 pocket are also essential for correct folding. Uniquely for gingipains, the isolated Kgp pro-domain dimerized through an interface, which partially overlapped with that between the catalytic moiety and the pro-domain within the zymogen, i.e. both complexes are mutually exclusive. Thus, pro-domain dimerization, together with partial rearrangement of the active site upon activation, explains the lack of inhibition of the pro-domain in trans. Our results reveal that the specific latency mechanism of Kgp differs from those of Rgps.
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Affiliation(s)
- Anja Pomowski
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Isabel Usón
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain.,the Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Catalonia, Spain
| | - Zuzanna Nowakowska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Florian Veillard
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Maryta N Sztukowska
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Tibisay Guevara
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Theodoros Goulas
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Danuta Mizgalska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Magdalena Nowak
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Barbara Potempa
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - James A Huntington
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and .,the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - F Xavier Gomis-Rüth
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain,
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