101
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Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B. Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Cell Host Microbe 2023; 31:1007-1020.e4. [PMID: 37279755 DOI: 10.1016/j.chom.2023.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 03/11/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.
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Affiliation(s)
- Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Claudia Eberl
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Simon Woelfel
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Diana Ring
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany
| | - Simone Herp
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Iris Lade
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; German Center for Infection Research, Partner site LMU Munich, Munich, Germany.
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102
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Garcia MM, Romero AS, Merkley SD, Meyer-Hagen JL, Forbes C, Hayek EE, Sciezka DP, Templeton R, Gonzalez-Estrella J, Jin Y, Gu H, Benavidez A, Hunter RP, Lucas S, Herbert G, Kim KJ, Cui JY, Gullapalli R, In JG, Campen MJ, Castillo EF. In Vivo Tissue Distribution of Microplastics and Systemic Metabolomic Alterations After Gastrointestinal Exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.542598. [PMID: 37398080 PMCID: PMC10312509 DOI: 10.1101/2023.06.02.542598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Global plastic use has consistently increased over the past century with several different types of plastics now being produced. Much of these plastics end up in oceans or landfills leading to a substantial accumulation of plastics in the environment. Plastic debris slowly degrades into microplastics (MPs) that can ultimately be inhaled or ingested by both animals and humans. A growing body of evidence indicates that MPs can cross the gut barrier and enter into the lymphatic and systemic circulation leading to accumulation in tissues such as the lungs, liver, kidney, and brain. The impacts of mixed MPs exposure on tissue function through metabolism remains largely unexplored. To investigate the impact of ingested MPs on target metabolomic pathways, mice were subjected to either polystyrene microspheres or a mixed plastics (5 µm) exposure consisting of polystyrene, polyethylene and the biodegradability and biocompatible plastic, poly-(lactic-co-glycolic acid). Exposures were performed twice a week for four weeks at a dose of either 0, 2, or 4 mg/week via oral gastric gavage. Our findings demonstrate that, in mice, ingested MPs can pass through the gut barrier, be translocated through the systemic circulation, and accumulate in distant tissues including the brain, liver, and kidney. Additionally, we report on the metabolomic changes that occur in the colon, liver and brain which show differential responses that are dependent on dose and type of MPs exposure. Lastly, our study provides proof of concept for identifying metabolomic alterations associated with MPs exposure and adds insight into the potential health risks that mixed MPs contamination may pose to humans.
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Affiliation(s)
- Marcus M. Garcia
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Aaron S. Romero
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Seth D. Merkley
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jewel L. Meyer-Hagen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Charles Forbes
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Eliane El Hayek
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - David P. Sciezka
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Rachel Templeton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL, USA
| | - Angelica Benavidez
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM, USA
| | - Russell P. Hunter
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Selita Lucas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Guy Herbert
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Kyle Joohyung Kim
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle WA, USA
| | - Julia Yue Cui
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle WA, USA
| | - Rama Gullapalli
- Department of Pathology, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Julie G. In
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Matthew J. Campen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Eliseo F. Castillo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
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103
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Carrizales-Sánchez AK, Tamez-Rivera O, García-Gamboa R, García-Cayuela T, Rodríguez-Gutiérrez NA, Elizondo-Montemayor L, García-Rivas G, Pacheco A, Hernández-Brenes C, Senés-Guerrero C. Gut microbial composition and functionality of school-age Mexican population with metabolic syndrome and type-2 diabetes mellitus using shotgun metagenomic sequencing. Front Pediatr 2023; 11:1193832. [PMID: 37342535 PMCID: PMC10277889 DOI: 10.3389/fped.2023.1193832] [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] [Received: 03/25/2023] [Accepted: 05/05/2023] [Indexed: 06/23/2023] Open
Abstract
Gut metagenome in pediatric subjects with metabolic syndrome (MetS) and type-2 diabetes mellitus (T2DM) has been poorly studied, despite an alarming worldwide increase in the prevalence and incidence of obesity and MetS within this population. The objective of this study was to characterize the gut microbiome taxonomic composition of Mexican pediatric subjects with MetS and T2DM using shotgun metagenomics and analyze the potential relationship with metabolic changes and proinflammatory effects. Paired-end reads of fecal DNA samples were obtained through the Illumina HiSeq X Platform. Statistical analyses and correlational studies were conducted using gut microbiome data and metadata from all individuals. Gut microbial dysbiosis was observed in MetS and T2DM children compared to healthy subjects, which was characterized by an increase in facultative anaerobes (i.e., enteric and lactic acid bacteria) and a decrease in strict anaerobes (i.e., Erysipelatoclostridium, Shaalia, and Actinomyces genera). This may cause a loss of gut hypoxic environment, increased gut microbial nitrogen metabolism, and higher production of pathogen-associated molecular patterns. These metabolic changes may trigger the activation of proinflammatory activity and impair the host's intermediate metabolism, leading to a possible progression of the characteristic risk factors of MetS and T2DM, such as insulin resistance, dyslipidemia, and an increased abdominal circumference. Furthermore, specific viruses (Jiaodavirus genus and Inoviridae family) showed positive correlations with proinflammatory cytokines involved in these metabolic diseases. This study provides novel evidence for the characterization of MetS and T2DM pediatric subjects in which the whole gut microbial composition has been characterized. Additionally, it describes specific gut microorganisms with functional changes that may influence the onset of relevant health risk factors.
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Affiliation(s)
| | - Oscar Tamez-Rivera
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, Mexico
| | - Ricardo García-Gamboa
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Zapopan, Jalisco, Mexico
- Tecnologico de Monterrey, Escuela de Medicina, Colonia Nuevo México, Zapopan, Jalisco, México
| | - Tomás García-Cayuela
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Zapopan, Jalisco, Mexico
| | - Nora A Rodríguez-Gutiérrez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, Mexico
- Hospital Regional Materno Infantil de Alta Especialidad, Guadalupe, Nuevo Leon, Mexico
| | | | - Gerardo García-Rivas
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, Mexico
- Tecnologico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo Leon, Mexico
| | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Nuevo Leon, Mexico
| | - Carmen Hernández-Brenes
- Tecnologico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo Leon, Mexico
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Nuevo Leon, Mexico
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104
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Panah FM, Lauridsen C, Højberg O, Jensen HE, Nielsen TS. Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation. BMC Microbiol 2023; 23:145. [PMID: 37210480 DOI: 10.1186/s12866-023-02874-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/28/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND In the pig production, diarrhea can occur during different growth stages including the period 4-16 weeks post weaning, during which a diarrheal outbreak also termed as colitis-complex diarrhea (CCD) can occur and it is distinct from post-weaning diarrhea (1-2 weeks post weaning). We hypothesized that CCD in growing pigs is associated with changes in colonic microbiota composition and fermentation patterns, and the aim of the present observational study was to identify changes in digesta-associated bacteria (DAB) and mucus-associated bacteria (MAB) in the colon of growing pigs with and without diarrhea. A total number of 30 pigs (8, 11, and 12 weeks of age) were selected; 20 showed clinical signs of diarrhea and 10 appeared healthy. Based on histopathological examination of colonic tissues, 21 pigs were selected for further studies and classified as follows: without diarrhea, no colon inflammation (NoDiar; n = 5), with diarrhea, without colonic inflammation (DiarNoInfl; n = 4), and with diarrhea, with colonic inflammation (DiarInfl; n = 12). Composition (based on 16S rRNA gene amplicon sequencing) and fermentation pattern (short-chain fatty acids; SCFA profile) of the DAB and MAB communities were characterized. RESULTS The DAB showed higher alpha diversity compared to MAB in all pigs, and both DAB and MAB showed lowest alpha diversity in the DiarNoInfl group. Beta diversity was significantly different between DAB and MAB as well as between diarrheal groups in both DAB and MAB. Compared to NoDiar, DiarInfl showed increased abundance of various taxa, incl. certain pathogens, in both digesta and mucus, as well as decreased digesta butyrate concentration. However, DiarNoInfl showed reduced abundance of different genera (mainly Firmicutes) compared to NoDiar, but still lower butyrate concentration. CONCLUSION Diversity and composition of MAB and DAB changed in diarrheal groups depending on presence/absence of colonic inflammation. We also suggest that DiarNoInfl group was at the earlier stage of diarrhea compared with DiarInfl, with a link to dysbiosis of colonic bacterial composition as well as reduced butyrate concentration, which plays a pivotal role in gut health. This could have led to diarrhea with inflammation due to a dysbiosis, associated with an increase in e.g., Escherichia-Shigella (Proteobacteria), Helicobacter (Campylobacterota), and Bifidobacterium (Actinobacteriota), which may tolerate or utilize oxygen and cause epithelial hypoxia and inflammation. The increased consumption of oxygen in epithelial mucosal layer by infiltrated neutrophils may also have added up to this hypoxia. Overall, the results confirmed that changes in DAB and MAB were associated with CCD and reduced butyrate concentration in digesta. Moreover, DAB might suffice for future community-based studies of CCD.
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Affiliation(s)
- Farhad M Panah
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
| | - Charlotte Lauridsen
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
| | - Ole Højberg
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark.
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tina Skau Nielsen
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
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105
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Nakandalage R, Guan LL, Malmuthuge N. Microbial Interventions to Improve Neonatal Gut Health. Microorganisms 2023; 11:1328. [PMID: 37317302 DOI: 10.3390/microorganisms11051328] [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: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023] Open
Abstract
The diverse pioneer microbial community colonizing the mammalian gastrointestinal tract is critical for the developing immune system. Gut microbial communities of neonates can be affected by various internal and external factors, resulting in microbial dysbiosis. Microbial dysbiosis during early life affects gut homeostasis by changing metabolic, physiological, and immunological status, which increases susceptibility to neonatal infections and long-term pathologies. Early life is crucial for the establishment of microbiota and the development of the host immune system. Therefore, it provides a window of opportunity to reverse microbial dysbiosis with a positive impact on host health. Recent attempts to use microbial interventions during early life have successfully reversed dysbiotic gut microbial communities in neonates. However, interventions with persistent effects on microbiota and host health are still limited. This review will critically discuss microbial interventions, modulatory mechanisms, their limitations, and gaps in knowledge to understand their roles in improving neonatal gut health.
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Affiliation(s)
- Ranga Nakandalage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Nilusha Malmuthuge
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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106
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Martin AJ, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D. Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium. MICROBIOME RESEARCH REPORTS 2023; 2:17. [PMID: 38046822 PMCID: PMC10688804 DOI: 10.20517/mrr.2023.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 12/05/2023]
Abstract
The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.
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Affiliation(s)
- Alberto J.M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 8580702, Chile
| | - Kineret Serebrinsky-Duek
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
| | - Erick Riquelme
- Department of Respiratory Diseases, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Pedro A. Saa
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
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107
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Zhou C, Gao P, Wang J. Comprehensive Analysis of Microbiome, Metabolome, and Transcriptome Revealed the Mechanisms of Intestinal Injury in Rainbow Trout under Heat Stress. Int J Mol Sci 2023; 24:ijms24108569. [PMID: 37239914 DOI: 10.3390/ijms24108569] [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: 04/04/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Global warming is one of the most common environmental challenges faced by cold-water fish farming. Intestinal barrier function, gut microbiota, and gut microbial metabolites are significantly altered under heat stress, posing serious obstacles to the healthy artificial culture of rainbow trout. However, the molecular mechanisms underlying intestinal injury in rainbow trout under heat stress remain unclear. In the present study, the optimal growth temperature for rainbow trout (16 °C) was used for the control group, and the maximum temperature tolerated by rainbow trout (24 °C) was used for the heat stress group, which was subjected to heat stress for 21 days. The mechanism of intestinal injury in rainbow trout under heat stress was explored by combining animal histology, 16S rRNA gene amplicon sequencing, ultra-high performance liquid chromatography-mass spectrometry, and transcriptome sequencing. The results showed that the antioxidant capacity of rainbow trout was enhanced under heat stress, the levels of stress-related hormones were significantly increased, and the relative expression of genes related to heat stress proteins was significantly increased, indicating that the heat stress model of rainbow trout was successfully established. Secondly, the intestinal tract of rainbow trout showed inflammatory pathological characteristics under heat stress, with increased permeability, activation of the inflammatory factor signaling pathway, and increased relative expression of inflammatory factor genes, suggesting that the intestinal barrier function was impaired. Thirdly, heat stress caused an imbalance of intestinal commensal microbiota and changes in intestinal metabolites in rainbow trout, which participated in the stress response mainly by affecting lipid metabolism and amino acid metabolism. Finally, heat stress promoted intestinal injury in rainbow trout by activating the peroxisome proliferator-activated receptor-α signaling pathway. These results not only expand the understanding of fish stress physiology and regulation mechanisms, but also provide a scientific basis for healthy artificial culture and the reduction of rainbow trout production costs.
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Affiliation(s)
- Changqing Zhou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Pan Gao
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Jianlin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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108
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Christopoulou I, Kostopoulou E, Matzarapi K, Chasapi SA, Spyroulias GA, Varvarigou A. Identification of Novel Biomarkers in Late Preterm Neonates with Respiratory Distress Syndrome (RDS) Using Urinary Metabolomic Analysis. Metabolites 2023; 13:metabo13050644. [PMID: 37233686 DOI: 10.3390/metabo13050644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Urine metabolomics is gaining traction as a means of identifying metabolic signatures associated with health and disease states. Thirty-one (31) late preterm (LP) neonates admitted to the neonatal intensive care unit (NICU) and 23 age-matched healthy LPs admitted to the maternity ward of a tertiary hospital were included in the study. Proton nuclear magnetic resonance (1H NMR) spectroscopy was employed for urine metabolomic analysis on the 1st and 3rd days of life of the neonates. The data were analyzed using univariate and multivariate statistical analysis. A unique metabolic pattern of enhanced metabolites was identified in the NICU-admitted LPs from the 1st day of life. Metabolic profiles were distinct in LPs presenting with respiratory distress syndrome (RDS). The discrepancies likely reflect differences in the gut microbiota, either due to variations in nutrient intake or as a result of medical interventions, such as the administration of antibiotics and other medications. Altered metabolites could potentially serve as biomarkers for identifying critically ill LP neonates or those at high risk for adverse outcomes later in life, including metabolic risks. The discovery of novel biomarkers may uncover potential targets for drug discovery and optimal periods for effective intervention, offering a personalized approach.
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Affiliation(s)
- Irene Christopoulou
- Department of Paediatrics, University of Patras Medical School, General University Hospital, 26500 Patras, Greece
| | - Eirini Kostopoulou
- Department of Paediatrics, University of Patras Medical School, General University Hospital, 26500 Patras, Greece
| | | | | | | | - Anastasia Varvarigou
- Department of Paediatrics, University of Patras Medical School, General University Hospital, 26500 Patras, Greece
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109
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Seelbinder B, Lohinai Z, Vazquez-Uribe R, Brunke S, Chen X, Mirhakkak M, Lopez-Escalera S, Dome B, Megyesfalvi Z, Berta J, Galffy G, Dulka E, Wellejus A, Weiss GJ, Bauer M, Hube B, Sommer MOA, Panagiotou G. Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions. Nat Commun 2023; 14:2673. [PMID: 37160893 PMCID: PMC10169812 DOI: 10.1038/s41467-023-38058-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
Candida species overgrowth in the human gut is considered a prerequisite for invasive candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is still limited. By integrating cross-sectional mycobiome and shotgun metagenomics data from the stool of 75 male and female cancer patients at risk but without systemic candidiasis, bacterial communities in high Candida samples display higher metabolic flexibility yet lower contributional diversity than those in low Candida samples. We develop machine learning models that use only bacterial taxa or functional relative abundances to predict the levels of Candida genus and species in an external validation cohort with an AUC of 78.6-81.1%. We propose a mechanism for intestinal Candida overgrowth based on an increase in lactate-producing bacteria, which coincides with a decrease in bacteria that regulate short chain fatty acid and oxygen levels. Under these conditions, the ability of Candida to harness lactate as a nutrient source may enable Candida to outcompete other fungi in the gut.
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Affiliation(s)
- Bastian Seelbinder
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Zoltan Lohinai
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sascha Brunke
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Xiuqiang Chen
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Mohammad Mirhakkak
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Silvia Lopez-Escalera
- Chr. Hansen A/S, Human Health Innovation, Hoersholm, Denmark
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Balazs Dome
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - Judit Berta
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | | | - Edit Dulka
- County Hospital of Torokbalint, Torokbalint, Hungary
| | - Anja Wellejus
- Chr. Hansen A/S, Human Health Innovation, Hoersholm, Denmark
| | - Glen J Weiss
- Department of Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Bernhard Hube
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Gianni Panagiotou
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany.
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
- Department of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
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110
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Sharma R, Mishanina TV. A riboswitch-controlled manganese exporter (Alx) tunes intracellular Mn 2+ concentration in E. coli at alkaline pH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539761. [PMID: 37214827 PMCID: PMC10197570 DOI: 10.1101/2023.05.07.539761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells use transition metal ions as structural components of biomolecules and cofactors in enzymatic reactions, making transition metals vital cellular components. The buildup of a particular metal ion in certain stress conditions becomes harmful to the organism due to the misincorporation of the excess ion into biomolecules, resulting in perturbed enzymatic activity or metal-catalyzed formation of reactive oxygen species. Organisms optimize metal concentration by regulating the expression of proteins that import and export that metal, often in a metal concentration-dependent manner. One such regulation mechanism is via riboswitches, which are 5'-untranslated regions (UTR) of an mRNA that undergo conformational changes to promote or inhibit the expression of the downstream gene, commonly in response to a ligand. The yybP-ykoY family of bacterial riboswitches shares a conserved aptamer domain that binds manganese (Mn2+). In E. coli, the yybP-ykoY riboswitch precedes and regulates the expression of two genes: mntP, which based on extensive genetic evidence encodes an Mn2+ exporter, and alx, which encodes a putative metal ion transporter whose cognate ligand is currently in question. Expression of alx is upregulated by both elevated intracellular concentrations of Mn2+ and alkaline pH. With metal ion measurements and gene expression studies, we demonstrate that the alkalinization of media increases cytoplasmic Mn2+ content, which in turn enhances alx expression. Alx then exports excess Mn2+ to prevent toxic buildup of the metal inside the cell, with the export activity maximal at alkaline pH. Using mutational and complementation experiments, we pinpoint a set of acidic residues in the predicted transmembrane segments of Alx that play a crucial role in its Mn2+ export. We propose that Alx-mediated Mn2+ export provides a primary protective layer that fine-tunes the cytoplasmic Mn2+ levels, especially during alkaline stress.
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Affiliation(s)
- Ravish Sharma
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Tatiana V. Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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111
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Fusco W, Lorenzo MB, Cintoni M, Porcari S, Rinninella E, Kaitsas F, Lener E, Mele MC, Gasbarrini A, Collado MC, Cammarota G, Ianiro G. Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota. Nutrients 2023; 15:2211. [PMID: 37432351 DOI: 10.3390/nu15092211] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 07/12/2023] Open
Abstract
Short-chain fatty acids (SCFAs) play a key role in health and disease, as they regulate gut homeostasis and their deficiency is involved in the pathogenesis of several disorders, including inflammatory bowel diseases, colorectal cancer, and cardiometabolic disorders. SCFAs are metabolites of specific bacterial taxa of the human gut microbiota, and their production is influenced by specific foods or food supplements, mainly prebiotics, by the direct fostering of these taxa. This Review provides an overview of SCFAs' roles and functions, and of SCFA-producing bacteria, from their microbiological characteristics and taxonomy to the biochemical process that lead to the release of SCFAs. Moreover, we will describe the potential therapeutic approaches to boost the levels of SCFAs in the human gut and treat different related diseases.
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Affiliation(s)
- William Fusco
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Manuel Bernabeu Lorenzo
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), 46022 Valencia, Spain
| | - Marco Cintoni
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Serena Porcari
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Emanuele Rinninella
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Francesco Kaitsas
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Elena Lener
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Maria Cristina Mele
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), 46022 Valencia, Spain
| | - Giovanni Cammarota
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
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112
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Liu XF, Shao JH, Liao YT, Wang LN, Jia Y, Dong PJ, Liu ZZ, He DD, Li C, Zhang X. Regulation of short-chain fatty acids in the immune system. Front Immunol 2023; 14:1186892. [PMID: 37215145 PMCID: PMC10196242 DOI: 10.3389/fimmu.2023.1186892] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
A growing body of research suggests that short-chain fatty acids (SCFAs), metabolites produced by intestinal symbiotic bacteria that ferment dietary fibers (DFs), play a crucial role in the health status of symbiotes. SCFAs act on a variety of cell types to regulate important biological processes, including host metabolism, intestinal function, and immune function. SCFAs also affect the function and fate of immune cells. This finding provides a new concept in immune metabolism and a better understanding of the regulatory role of SCFAs in the immune system, which impacts the prevention and treatment of disease. The mechanism by which SCFAs induce or regulate the immune response is becoming increasingly clear. This review summarizes the different mechanisms through which SCFAs act in cells. According to the latest research, the regulatory role of SCFAs in the innate immune system, including in NLRP3 inflammasomes, receptors of TLR family members, neutrophils, macrophages, natural killer cells, eosinophils, basophils and innate lymphocyte subsets, is emphasized. The regulatory role of SCFAs in the adaptive immune system, including in T-cell subsets, B cells, and plasma cells, is also highlighted. In addition, we discuss the role that SCFAs play in regulating allergic airway inflammation, colitis, and osteoporosis by influencing the immune system. These findings provide evidence for determining treatment options based on metabolic regulation.
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Affiliation(s)
- Xiao-feng Liu
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Jia-hao Shao
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Yi-Tao Liao
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Li-Ning Wang
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuan Jia
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Peng-jun Dong
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Zhi-zhong Liu
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Dan-dan He
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Chao Li
- Department of Spine, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Xian Zhang
- Department of Spine, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
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113
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Zhang C, Liu H, Sun L, Wang Y, Chen X, Du J, Sjöling Å, Yao J, Wu S. An overview of host-derived molecules that interact with gut microbiota. IMETA 2023; 2:e88. [PMID: 38868433 PMCID: PMC10989792 DOI: 10.1002/imt2.88] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 06/14/2024]
Abstract
The gut microbiota comprises bacteria, archaea, fungi, protists, and viruses that live together and interact with each other and with host cells. A stable gut microbiota is vital for regulating host metabolism and maintaining body health, while a disturbed microbiota may induce different kinds of disease. In addition, diet is also considered to be the main factor that influences the gut microbiota. The host could shape the gut microbiota through other factors. Here, we reviewed the mechanisms that mediate host regulation on gut microbiota, involved in gut-derived molecules, including gut-derived immune system molecules (secretory immunoglobulin A, antimicrobial peptides, cytokines, cluster of differentiation 4+ effector T cell, and innate lymphoid cells), sources related to gut-derived mucosal molecules (carbon sources, nitrogen sources, oxygen sources, and electron respiratory acceptors), gut-derived exosomal noncoding RNA (ncRNAs) (microRNAs, circular RNA, and long ncRNA), and molecules derived from organs other than the gut (estrogen, androgen, neurohormones, bile acid, and lactic acid). This study provides a systemic overview for understanding the interplay between gut microbiota and host, a comprehensive source for potential ways to manipulate gut microbiota, and a solid foundation for future personalized treatment that utilizes gut microbiota.
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Affiliation(s)
- Chenguang Zhang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Huifeng Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Lei Sun
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Yue Wang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Xiaodong Chen
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Juan Du
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Åsa Sjöling
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Junhu Yao
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Shengru Wu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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114
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Shon WJ, Song JW, Oh SH, Lee KH, Seong H, You HJ, Seong JK, Shin DM. Gut taste receptor type 1 member 3 is an intrinsic regulator of Western diet-induced intestinal inflammation. BMC Med 2023; 21:165. [PMID: 37118698 PMCID: PMC10148556 DOI: 10.1186/s12916-023-02848-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/24/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Long-term intake of a Western diet (WD), characterized by a high-fat content and sugary drinks, is hypothesized to contribute to the development of inflammatory bowel disease (IBD). Despite the identified clinical association, the molecular mechanisms by which dietary changes contribute to IBD development remain unknown. Therefore, we examined the influence of long-term intake of a WD on intestinal inflammation and the mechanisms by which WD intake affects IBD development. METHODS Mice fed normal diet or WD for 10 weeks, and bowel inflammation was evaluated through pathohistological and infiltrated inflammatory cell assessments. To understand the role of intestinal taste receptor type 1 member 3 (TAS1R3) in WD-induced intestinal inflammation, cultured enteroendocrine cells harboring TAS1R3, subjected to RNA interference or antagonist treatment, and Tas1r3-deficient mice were used. RNA-sequencing, flow cytometry, 16S metagenomic sequencing, and bioinformatics analyses were performed to examine the involved mechanisms. To demonstrate their clinical relevance, intestinal biopsies from patients with IBD and mice with dextran sulfate sodium-induced colitis were analyzed. RESULTS Our study revealed for the first time that intestinal TAS1R3 is a critical mediator of WD-induced intestinal inflammation. WD-fed mice showed marked TAS1R3 overexpression with hallmarks of serious bowel inflammation. Conversely, mice lacking TAS1R3 failed to exhibit inflammatory responses to WD. Mechanistically, intestinal transcriptome analysis revealed that Tas1r3 deficiency suppressed mTOR signaling, significantly increasing the expression of PPARγ (a major mucosal defense enhancer) and upregulating the expression of PPARγ target-gene (tight junction protein and antimicrobial peptide). The gut microbiota of Tas1r3-deficient mice showed expansion of butyrate-producing Clostridia. Moreover, an increased expression of host PPARγ-signaling pathway proteins was positively correlated with butyrate-producing microbes, suggesting that intestinal TAS1R3 regulates the relationship between host metabolism and gut microflora in response to dietary factors. In cultured intestinal cells, regulation of the TAS1R3-mTOR-PPARγ axis was critical for triggering an inflammatory response via proinflammatory cytokine production and secretion. Abnormal regulation of the axis was observed in patients with IBD. CONCLUSIONS Our findings suggest that the TAS1R3-mTOR-PPARγ axis in the gut links Western diet consumption with intestinal inflammation and is a potential therapeutic target for IBD.
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Affiliation(s)
- Woo-Jeong Shon
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea.
- Research Institute of Human Ecology, Seoul National University, Seoul, Republic of Korea.
| | - Jae Won Song
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Seung Hoon Oh
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Keon-Hee Lee
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Hobin Seong
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Hyun Ju You
- Bio-MAX/N-Bio, Seoul National University, Seoul, Republic of Korea
| | - Je Kyung Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Korea Mouse Phenotyping Center, Seoul, Republic of Korea
| | - Dong-Mi Shin
- Department of Food and Nutrition, Seoul National University College of Human Ecology, Gwanak-Gu, Seoul, 08826, Republic of Korea
- Research Institute of Human Ecology, Seoul National University, Seoul, Republic of Korea
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115
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Wei Y, Zhou M, Fang W, Liu Q, Mao H, Chen B, Zhang T, Xu Y, Zhang W, Zheng Y, Hu X. Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus). Appl Microbiol Biotechnol 2023; 107:3257-3271. [PMID: 37071138 DOI: 10.1007/s00253-023-12524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023]
Abstract
Previous studies regarding the gastrointestinal biogeography of microbiomes generally focused on longitudinal comparisons, whereas few studies have compared luminal and mucosal microbiomes. Investigations of the snake gut microbiome have attracted interest because of the unique digestive physiology and hibernation behavior, but adequate sampling methods must be developed. Here, we used an omics approach combining 16S rRNA gene sequencing with untargeted metabolomics to profile the luminal and mucosal gut microbiomes and metabolomes in oriental rat snakes, with the goal of revealing the heterogeneity and co-occurrence at these sites. The α-diversity of the gut microbiome was significantly higher at mucosal sites than at luminal sites. Microbial composition also differed according to sampling site, with significant differences in the abundances of dominant phyla and genera, as well as β-diversity clustering and distribution. Metabolome profiling revealed differences that were mainly related to cholinergic substances and nucleic acids. Analysis of variations in Kyoto Encyclopedia of Genes and Genomes functions of microbes and metabolites showed that the mucosal microbiome was more frequently involved in genetic information processing and cellular processes, whereas the luminal microbiome generally participated in metabolic regulation. Notably, we found a greater abundance of the opportunistic pathogen genus Escherichia-Shigella at luminal sites and higher levels of the lipid-regulator metabolite fenfluramine at mucosal sites. Despite the extensive differences between the two sampling sites, the results revealed similarities in terms of amplicon sequence variant composition and dominant core microbes. This pilot exploration of luminal and mucosal microbiomes and metabolites provides key insights to guide future research. KEY POINTS: • Snake luminal and mucosal microbiota was distinct in composition and function. • Metabolome profiling revealed differences related to different metabolites. • The pathogenic microbes are more likely to colonize the gut lumina.
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Affiliation(s)
- Yuting Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mingfang Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenjie Fang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qiuhong Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Biao Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tianxiang Zhang
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, 330045, China
| | - Yongtao Xu
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Weiwei Zhang
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yunlin Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaolong Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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116
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Zhu L, Xie C, Chen L, Dai X, Zhou Y, Pan H, Tian K. Transport of microplastics in the body and interaction with biological barriers, and controlling of microplastics pollution. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114818. [PMID: 36958263 DOI: 10.1016/j.ecoenv.2023.114818] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/05/2023] [Accepted: 03/19/2023] [Indexed: 06/18/2023]
Abstract
Microplastics (MPs) are one novel environmental pollutant sized < 5 mm that is ubiquitously present in numerous environmental media and particularly susceptible to interact with various toxic chemicals. Importantly, MPs can enter the food chain, and are bio-enriched and bio-accumulated with trophic levels, eventually endangering ecosystems and human health. However, there need to be more understanding regarding the bio-interaction of MPs with the host, particularly for biological barriers. This review aimed to summarize the latest findings regarding the main exposure routes of MPs that generated health burdens on humans. Furthermore, their interactions with biological barriers that generate adverse health effects and the underlying mechanisms were also reviewed. Additionally, we provided a comprehensive overview of recent advances regarding the removing and controlling of MPs. Finally, we discussed the future directions for MPs hazard prevention to provide helpful information for regulating decision-making and guiding safer plastics applications.
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Affiliation(s)
- Lin Zhu
- Department of Occupational and Environmental Health, Zunyi Medical University, Zunyi 563000, China
| | - Caiyan Xie
- Department of Occupational and Environmental Health, Zunyi Medical University, Zunyi 563000, China
| | - Liangkai Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xingyu Dai
- Department of Clinical Medicine, Zunyi Medical University, Zunyi 563000, China
| | - Yuanzhong Zhou
- Department of Occupational and Environmental Health, Zunyi Medical University, Zunyi 563000, China
| | - Hong Pan
- Department of Occupational and Environmental Health, Zunyi Medical University, Zunyi 563000, China.
| | - Kunming Tian
- Department of Occupational and Environmental Health, Zunyi Medical University, Zunyi 563000, China.
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117
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Xu C, Gu L, Hu L, Jiang C, Li Q, Sun L, Zhou H, Liu Y, Xue H, Li J, Zhang Z, Zhang X, Xu Q. FADS1-arachidonic acid axis enhances arachidonic acid metabolism by altering intestinal microecology in colorectal cancer. Nat Commun 2023; 14:2042. [PMID: 37041160 PMCID: PMC10090135 DOI: 10.1038/s41467-023-37590-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
Colonocyte metabolism shapes the microbiome. Metabolites are the main mediators of information exchange between intestine and microbial communities. Arachidonic acid (AA) is an essential polyunsaturated fatty acid and its role in colorectal cancer (CRC) remains unexplored. In this study, we show that AA feeding promotes tumor growth in AOM/DSS and intestinal specific Apc-/- mice via modulating the intestinal microecology of increased gram-negative bacteria. Delta-5 desaturase (FADS1), a rate-limiting enzyme, is upregulated in CRC and effectively mediates AA synthesis. Functionally, FADS1 regulates CRC tumor growth via high AA microenvironment-induced enriched gram-negative microbes. Elimination of gram-negative microbe abolishes FADS1 effect. Mechanistically, gram-negative microbes activate TLR4/MYD88 pathway in CRC cells that contributes FADS1-AA axis to metabolize to prostaglandin E2 (PGE2). Cumulatively, we report a potential cancer-promoting mechanism of FADS1-AA axis in CRC that converts raising synthesized AA to PGE2 via modulating the intestinal microecology of gram-negative.
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Affiliation(s)
- Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Longci Sun
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhou
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hanbing Xue
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhigang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China.
| | - Xueli Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China.
| | - Qing Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Ducatelle R, Goossens E, Eeckhaut V, Van Immerseel F. Poultry gut health and beyond. ANIMAL NUTRITION 2023; 13:240-248. [PMID: 37168453 PMCID: PMC10164775 DOI: 10.1016/j.aninu.2023.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Intestinal health is critically important for the digestion and absorption of nutrients and thus is a key factor in determining performance. Intestinal health issues are very common in high performing poultry lines due to the high feed intake, which puts pressure on the physiology of the digestive system. Excess nutrients which are not digested and absorbed in the small intestine may trigger dysbiosis, i.e. a shift in the microbiota composition in the intestinal tract. Dysbiosis as well as other stressors elicit an inflammatory response and loss of integrity of the tight junctions between the epithelial cells, leading to gut leakage. In this paper, key factors determining intestinal health and the most important nutritional tools which are available to support intestinal health are reviewed.
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119
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Lv W, Zhang D, He T, Liu Y, Shao L, Lv Z, Pu X, Wang Y, Liu L. Combination of Lactobacillus plantarum improves the effects of tacrolimus on colitis in a mouse model. Front Cell Infect Microbiol 2023; 13:1130820. [PMID: 36992690 PMCID: PMC10040537 DOI: 10.3389/fcimb.2023.1130820] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/06/2023] [Indexed: 03/14/2023] Open
Abstract
The gut microbiome has been considered to play an important role in inflammatory bowel disease (IBD). Our previous study reported that tacrolimus-altered gut microbiota elicited immunoregulatory effects in both colonic mucosa and circulation, contributing to an increased allograft survival rate in mice. Here, we aimed to observe the changes in the tacrolimus-induced microbiome in a dextran sulfate sodium (DSS)-induced colitis mouse model and explore the possibility and efficacy of combination therapy with tacrolimus and the microbiome on colitis. Mice were divided into the control, DSS, tacrolimus monotherapy and tacrolimus plus Lactobacillus plantarum 550 (Lacto)-treated groups. The body weight, stool consistency, hematochezia and survival of mice were observed daily. Total RNA from colonic mucosa was extracted and subjected to transcriptome sequencing. Cecal contents were collected and the 16S rRNA sequencing was performed to characterize the gut microbiome and the ultrahigh- performance liquid chromatography-MS/MS (UHPLC-MS/MS) was used for targeted quantification of bile acids. The results confirmed that tacrolimus significantly ameliorated DSS-induced colitis in mice. Beneficial alterations of the gut microbiome characterized by a remarkable expansion of the genus Lactobacillus were induced by tacrolimus treatment. Oral supplementation with Lacto further improved the tacrolimus-mediated suppression of body weight loss in colitis, while the survival time of mice was further prolonged and the inflammation of colonic mucosa was obviously relieved. The immune and inflammation-related signaling pathways, including IFN-γ and IFN-α response, allograft rejection, IL2 STAT5 signaling and the inflammatory response pathways, were further downregulated in the tacrolimus plus Lacto cotreatment group. Cotreatment also improved the diversity of the gut microbiome and rescued the concentration of taurochenodeoxycholic acid (TCDCA) in colitis. The latter was positively correlated with the abundance of Lactobacillus but negatively related to the disease activity index score. Overall, our results indicated that Lactobacillus plantarum promoted the therapeutic effect of tacrolimus in experimental colitis, offering a promising strategy to combine tacrolimus and Lactobacillus in the treatment of colitis patients.
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Affiliation(s)
- Wei Lv
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Di Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Tian He
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yingying Liu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Limei Shao
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongping Lv
- Technology Research Institute of Shuxi Condiments of Sichuan Cuisine Co. LTD, Chengdu, Sichuan, China
| | - Xiaoping Pu
- Technology Research Institute of Shuxi Condiments of Sichuan Cuisine Co. LTD, Chengdu, Sichuan, China
| | - Yufang Wang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yufang Wang, ; Ling Liu,
| | - Ling Liu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yufang Wang, ; Ling Liu,
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Feng R, Zhu Q, Li Q, Zhai Y, Wang J, Qin C, Liang D, Zhang R, Tian H, Liu H, Chen Y, Fu Y, Wang X, Ding X. Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses. Front Immunol 2023; 14:1117726. [PMID: 36969214 PMCID: PMC10033601 DOI: 10.3389/fimmu.2023.1117726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/03/2023] [Indexed: 03/12/2023] Open
Abstract
IntroductionGeneralized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.Materials and methodsWe characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.ResultsOur findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.ConclusionsThese findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.
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Affiliation(s)
- Renyi Feng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Qingyong Zhu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Qingchen Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanping Zhai
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiuqi Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Chi Qin
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Dongxiao Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Rui Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Tian
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Han Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Yongkang Chen
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Fu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
| | - Xuejing Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Xuebing Ding, ; Xuejing Wang,
| | - Xuebing Ding
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Xuebing Ding, ; Xuejing Wang,
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Casto-Rebollo C, Argente MJ, García ML, Blasco A, Ibáñez-Escriche N. Effect of environmental variance-based resilience selection on the gut metabolome of rabbits. Genet Sel Evol 2023; 55:15. [PMID: 36894894 PMCID: PMC9996918 DOI: 10.1186/s12711-023-00791-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Gut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resilience because of its influence on host immunity. Environmental variance (VE), specifically the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie differences in the resilience potential of animals originating from a divergent selection for VE of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n = 13) and high (n = 13) VE of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations. RESULTS We identified 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, five that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabolism were low in the resilient population and these pathways can, therefore impact the inflammatory response and health status of animals. CONCLUSIONS This is the first study to identify gut metabolites that could act as potential resilience biomarkers. The results support differences in resilience between the two studied rabbit populations that were generated by selection for VE of LS. Furthermore, selection for VE of LS modified the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and disease.
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Affiliation(s)
- Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - María José Argente
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - María Luz García
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO_UMH), Miguel Hernández University, 03312, Orihuela, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain.
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Wu S, Wang J, Fu Z, Familiari G, Relucenti M, Aschner M, Li X, Chen H, Chen R. Matairesinol Nanoparticles Restore Chemosensitivity and Suppress Colorectal Cancer Progression in Preclinical Models: Role of Lipid Metabolism Reprogramming. NANO LETTERS 2023; 23:1970-1980. [PMID: 36802650 DOI: 10.1021/acs.nanolett.3c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Oncogenic-driven lipogenic metabolism is a common hallmark of colorectal cancer (CRC) progression. Therefore, there is an urgent need to develop novel therapeutic strategies for metabolic reprogramming. Herein, the metabolic profiles in the plasma between CRC patients and paired healthy controls were compared using metabolomics assays. Matairesinol downregulation was evident in CRC patients, and matairesinol supplementation significantly represses CRC tumorigenesis in azoxymethane/dextran sulfate sodium (AOM/DSS) colitis-associated CRC mice. Matairesinol rewired lipid metabolism to improve the therapeutic efficacy in CRC by inducing mitochondrial damage and oxidative damage and blunting ATP production. Finally, matairesinol-loaded liposomes significantly promoted the enhanced antitumor activity of 5-Fu/leucovorin combined with oxaliplatin (FOLFOX) in CDX and PDX mouse models by restoring chemosensitivity to the FOLFOX regimen. Collectively our findings highlight matairesinol-mediated lipid metabolism reprogramming as a novel druggable strategy to restore CRC chemosensitivity, and this nanoenabled approach for matairesinol will improve the chemotherapeutic efficacy with good biosafety.
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Affiliation(s)
- Shenshen Wu
- School of Public Health, Capital Medical University, Beijing 100069, P.R. China
| | - Jiajia Wang
- School of Public Health, Capital Medical University, Beijing 100069, P.R. China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P.R. China
| | - Giuseppe Familiari
- Department of Anatomical, Histological, Medical and Legal Locomotive Apparatus, Section of Human Anatomy Via Alfonso Borelli, Sapienza University of Rome, Roma 5000161, Italia
| | - Michela Relucenti
- Department of Anatomical, Histological, Forensic Medicine and Orthopedic Science, Sapienza University of Rome, Roma 5000161, Italia
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Xiaobo Li
- School of Public Health, Capital Medical University, Beijing 100069, P.R. China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, P.R. China
| | - Hanqing Chen
- Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, P.R. China
| | - Rui Chen
- School of Public Health, Capital Medical University, Beijing 100069, P.R. China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, P. R. China
- Beijing Laboratory of Allergic Diseases, Capital Medical University, Beijing 100069, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
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Su Y, Liang J, Zhang M, Zhao M, Xie X, Wang X, Pan Z, Huang S, Yan R, Wang Q, Zhou L, Luo X. Wogonin regulates colonocyte metabolism via PPARγ to inhibit Enterobacteriaceae against dextran sulfate sodium-induced colitis in mice. Phytother Res 2023; 37:872-884. [PMID: 36451541 DOI: 10.1002/ptr.7677] [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: 05/19/2022] [Revised: 10/04/2022] [Accepted: 11/01/2022] [Indexed: 12/02/2022]
Abstract
To investigate the potential effects and mechanism of wogonin on dextran sulfate sodium (DSS)-induced colitis, 70 male mice were administered wogonin (12.5, 25, 50 mg·kg-1 ·d-1 , i.g.) for 10 days, meanwhile, in order to induce colitis, the mice were free to drink 3% DSS for 6 days. We found that wogonin could obviously ameliorate DSS-induced colitis, including preventing colon shortening and inhibiting pathological damage. In addition, wogonin could increase the expression of PPARγ, which not only restores intestinal epithelial hypoxia but also inhibits iNOS protein to reduce intestinal nitrite levels. All these effects facilitated a reduction in the abundance of Enterobacteriaceae in DSS-induced colitis mice. Therefore, compared with the DSS group, the number of Enterobacteriaceae in the intestinal flora was significantly reduced after administration of wogonin or rosiglitazone by 16s rDNA technology. We also verified that wogonin could promote the expression of PPARγ mRNA and protein in Caco-2 cells, and this effect disappeared when PPARγ signal was inhibited. In conclusion, our study suggested that wogonin can activate the PPARγ signal of the Intestinal epithelium to ameliorate the Intestinal inflammation caused by Enterobacteriaceae bacteria expansion.
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Affiliation(s)
- Yulin Su
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junjie Liang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meiling Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meng Zhao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xueqian Xie
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaojing Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zengfeng Pan
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaowei Huang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Rong Yan
- Department of Gastroenterology, The Fourth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qing Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lian Zhou
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xia Luo
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
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Chen L, Mao M, Liu D, Liu W, Wang Y, Xie L, Deng Y, Lin Y, Xu Y, Zhong X, Cao W. HC067047 as a potent TRPV4 inhibitor repairs endotoxemia colonic injury. Int Immunopharmacol 2023; 116:109648. [PMID: 36706595 DOI: 10.1016/j.intimp.2022.109648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/13/2022] [Accepted: 12/24/2022] [Indexed: 01/26/2023]
Abstract
Colonic injury causes severe inflammation during systemic infections in patients with endotoxemia. The prevention of colonic injury could effectively reduce the progression of endotoxemia. We investigated the protective effects and detailed mechanisms of the TRPV4 inhibitor HC067047 in the treatment of colonic injury caused by endotoxemia. An LPS-induced endotoxemia colonic injury model was used to assess the in vivo effects of HC067047. Colon slices were detected by hematoxylin and eosin (HE) staining and immunofluorescence assays. Spectrophotometry was used to determine the levels of MDA, calcium, GSH, and GSSG. Alterations in oxidative stress/mitophagy/inflammatory pyroptosis-related markers were evaluated by Q-PCR and western blot assays. HC067047 reduced the body weight loss and spleen weight index of endotoxemic mice and partly recovered the normal morphology of the colonic mucous layer. As an inhibitor of the calcium permeant cation channel, HC067047 suppressed the phosphorylation of the CAMKIIɑ protein and levels of MDA and calcium, upregulated the ratio of GSH/GSSG, shortened the expression of oxidative stress-related proteins, and enhanced the expression of the anti-oxidative protein CAT in damaged colon tissues. Additionally, HC067047 maintained normal mitochondrial functions in endotoxemia colons by promoting mitochondrial fusion and biosynthesis and suppressing mitochondrial fission and the PINK/Parkin/mitophagy pathway. HC067047 potently blocked inflammatory pyroptosis and protected the colonic tight junction barrier. HC067047 restores endotoxemia colons against oxidative stress, mitophagy, inflammatory pyroptosis, and colonic barrier dysfunction. Hence, HC067047 therapy may be potentially useful in the treatment of colonic injury in endotoxemia.
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Affiliation(s)
- Ling Chen
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Mingli Mao
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Dandan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Wenjia Liu
- Department of Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yajuan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Lihua Xie
- Department of Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yingcheng Deng
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yi Lin
- Cancer Research Institute, Key Laboratory of Cancer Cellular and Molecular Pathology of Hunan Provincial, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yang Xu
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xiaolin Zhong
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Wenyu Cao
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang 421001, China.
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Inchingolo AM, Patano A, Di Pede C, Inchingolo AD, Palmieri G, de Ruvo E, Campanelli M, Buongiorno S, Carpentiere V, Piras F, Settanni V, Viapiano F, Hazballa D, Rapone B, Mancini A, Di Venere D, Inchingolo F, Fatone MC, Palermo A, Minetti E, Lorusso F, Scarano A, Sauro S, Tartaglia GM, Bordea IR, Dipalma G, Malcangi G. Autologous Tooth Graft: Innovative Biomaterial for Bone Regeneration. Tooth Transformer® and the Role of Microbiota in Regenerative Dentistry. A Systematic Review. J Funct Biomater 2023; 14:jfb14030132. [PMID: 36976056 PMCID: PMC10058341 DOI: 10.3390/jfb14030132] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023] Open
Abstract
Different biomaterials, from synthetic products to autologous or heterologous grafts, have been suggested for the preservation and regeneration of bone. The aim of this study is to evaluate the effectiveness of autologous tooth as a grafting material and examine the properties of this material and its interactions with bone metabolism. PubMed, Scopus, Cochrane Library, and Web of Science were searched to find articles addressing our topic published from 1 January 2012 up to 22 November 2022, and a total of 1516 studies were identified. Eighteen papers in all were considered in this review for qualitative analysis. Demineralized dentin can be used as a graft material, since it shows high cell compatibility and promotes rapid bone regeneration by striking an ideal balance between bone resorption and production; it also has several benefits, such as quick recovery times, high-quality newly formed bone, low costs, no risk of disease transmission, the ability to be performed as an outpatient procedure, and no donor-related postoperative complications. Demineralization is a crucial step in the tooth treatment process, which includes cleaning, grinding, and demineralization. Since the presence of hydroxyapatite crystals prevents the release of growth factors, demineralization is essential for effective regenerative surgery. Even though the relationship between the bone system and dysbiosis has not yet been fully explored, this study highlights an association between bone and gut microbes. The creation of additional scientific studies to build upon and enhance the findings of this study should be a future objective of scientific research.
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Affiliation(s)
| | - Assunta Patano
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Chiara Di Pede
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | | | - Giulia Palmieri
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Elisabetta de Ruvo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Merigrazia Campanelli
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Silvio Buongiorno
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Vincenzo Carpentiere
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Fabio Piras
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Vito Settanni
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Fabio Viapiano
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Denisa Hazballa
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Biagio Rapone
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Daniela Di Venere
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Correspondence: (F.I.); (M.C.F.); Tel.: +39-331-211-1104 (F.I.); +39-3479914635 (M.C.F.)
| | - Maria Celeste Fatone
- PTA Trani-ASL BT, Viale Padre Pio, 76125 Trani, Italy
- Correspondence: (F.I.); (M.C.F.); Tel.: +39-331-211-1104 (F.I.); +39-3479914635 (M.C.F.)
| | - Andrea Palermo
- College of Medicine and Dentistry Birmingham, University of Birmingham, Birmingham B4 6BN, UK
| | - Elio Minetti
- Department of Biomedical, Surgical, and Dental Science, Università Degli Studi di Milano, 20122 Milan, Italy
| | - Felice Lorusso
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Antonio Scarano
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Salvatore Sauro
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Dental Biomaterials and Minimally Invasive Dentistry, Department of Dentistry, Cardenal Herrera-CEU University, CEU Universities, C/Santiago Ramón y Cajal, s/n., Alfara del Patriarca, 46115 Valencia, Spain
| | - Gianluca Martino Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20100 Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
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The Colorectal Cancer Microbiota Alter Their Transcriptome To Adapt to the Acidity, Reactive Oxygen Species, and Metabolite Availability of Gut Microenvironments. mSphere 2023; 8:e0062722. [PMID: 36847536 PMCID: PMC10117117 DOI: 10.1128/msphere.00627-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The gut microbiome is implicated in the pathology of colorectal cancer (CRC). However, the mechanisms by which the microbiota actively contribute to disease onset and progression remain elusive. In this pilot study, we sequenced fecal metatranscriptomes of 10 non-CRC and 10 CRC patient gut microbiomes and conducted differential gene expression analyses to assess any changed functionality in disease. We report that oxidative stress responses were the dominant activity across cohorts, an overlooked protective housekeeping role of the human gut microbiome. However, expression of hydrogen peroxide and nitric oxide-scavenging genes was diminished and augmented, respectively, positing that these regulated microbial responses have implications for CRC pathology. CRC microbes enhanced expression of genes for host colonization, biofilm formation, genetic exchange, virulence determinants, antibiotic, and acid resistances. Moreover, microbes promoted transcription of genes involved in metabolism of several beneficial metabolites, suggesting their contribution to patient metabolite deficiencies previously solely attributed to tumor cells. We showed in vitro that expression of genes involved in amino acid-dependent acid resistance mechanisms of meta-gut Escherichia coli responded differently to acid, salt, and oxidative pressures under aerobic conditions. These responses were mostly dictated by the host health status of origin of the microbiota, suggesting their exposure to fundamentally different gut conditions. These findings for the first time highlight mechanisms by which the gut microbiota can either protect against or drive colorectal cancer and provide insights into the cancerous gut environment that drives functional characteristics of the microbiome. IMPORTANCE The human gut microbiota has the genetic potential to drive colorectal cancer onset and progression; however, the expression of this genetic potential during the disease has not been investigated. We found that microbial expression of genes that detoxify DNA-damaging reactive oxygen species, which drive colorectal cancer, is compromised in cancer. We observed a greater activation of expression of genes involved in virulence, host colonization, exchange of genetic material, metabolite utilization, defense against antibiotics, and environmental pressures. Culturing gut Escherichia coli of cancerous and noncancerous metamicrobiota revealed different regulatory responses of amino acid-dependent acid resistance mechanisms in a health-dependent manner under environmental acid, oxidative, and osmotic pressures. Here, for the first time, we demonstrate that the activity of microbial genomes is regulated by the health status of the gut in vivo and in vitro and provides new insights for shifts in microbial gene expression in colorectal cancer.
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127
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Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates. Infect Immun 2023; 91:e0057022. [PMID: 36692308 PMCID: PMC9933713 DOI: 10.1128/iai.00570-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A disrupted "dysbiotic" gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota-accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome is short-chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known to decrease the fitness of C. difficile in vitro, and high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI than in those from healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations. IMPORTANCE Clostridioides difficile is a leading cause of infectious diarrhea in humans, and it imposes a tremendous burden on the health care system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted "dysbiotic" gut microbiota is the primary risk factor for CDI, but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.
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Seike K, Kiledal A, Fujiwara H, Henig I, Burgos da Silva M, van den Brink MRM, Hein R, Hoostal M, Liu C, Oravecz-Wilson K, Lauder E, Li L, Sun Y, Schmidt TM, Shah YM, Jenq RR, Dick G, Reddy P. Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation. Immunity 2023; 56:353-368.e6. [PMID: 36736321 PMCID: PMC11098523 DOI: 10.1016/j.immuni.2023.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
The severity of T cell-mediated gastrointestinal (GI) diseases such as graft-versus-host disease (GVHD) and inflammatory bowel diseases correlates with a decrease in the diversity of the host gut microbiome composition characterized by loss of obligate anaerobic commensals. The mechanisms underpinning these changes in the microbial structure remain unknown. Here, we show in multiple specific pathogen-free (SPF), gnotobiotic, and germ-free murine models of GI GVHD that the initiation of the intestinal damage by the pathogenic T cells altered ambient oxygen levels in the GI tract and caused dysbiosis. The change in oxygen levels contributed to the severity of intestinal pathology in a host intestinal HIF-1α- and a microbiome-dependent manner. Regulation of intestinal ambient oxygen levels with oral iron chelation mitigated dysbiosis and reduced the severity of the GI GVHD. Thus, targeting ambient intestinal oxygen levels may represent a novel, non-immunosuppressive strategy to mitigate T cell-driven intestinal diseases.
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Affiliation(s)
- Keisuke Seike
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Anders Kiledal
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hideaki Fujiwara
- Department of Hematology and Oncology, Okayama University Hospital, 2-5-1, Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Israel Henig
- Department of Hematology, Rambam Health Care Campus, Haifa, Israel
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marcel R M van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert Hein
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Hoostal
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan Health System, Ann Arbor, MI, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Katherine Oravecz-Wilson
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Emma Lauder
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Lu Li
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Yaping Sun
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan Health System, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Health System, Ann Arbor, MI, USA; Department of Molecular and Integrative Physiology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Gregory Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pavan Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Kasprzak A. Autophagy and the Insulin-like Growth Factor (IGF) System in Colonic Cells: Implications for Colorectal Neoplasia. Int J Mol Sci 2023; 24:ijms24043665. [PMID: 36835075 PMCID: PMC9959216 DOI: 10.3390/ijms24043665] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common human malignancies worldwide. Along with apoptosis and inflammation, autophagy is one of three important mechanisms in CRC. The presence of autophagy/mitophagy in most normal mature intestinal epithelial cells has been confirmed, where it has mainly protective functions against reactive oxygen species (ROS)-induced DNA and protein damage. Autophagy regulates cell proliferation, metabolism, differentiation, secretion of mucins and/or anti-microbial peptides. Abnormal autophagy in intestinal epithelial cells leads to dysbiosis, a decline in local immunity and a decrease in cell secretory function. The insulin-like growth factor (IGF) signaling pathway plays an important role in colorectal carcinogenesis. This is evidenced by the biological activities of IGFs (IGF-1 and IGF-2), IGF-1 receptor type 1 (IGF-1R) and IGF-binding proteins (IGF BPs), which have been reported to regulate cell survival, proliferation, differentiation and apoptosis. Defects in autophagy are found in patients with metabolic syndrome (MetS), inflammatory bowel diseases (IBD) and CRC. In neoplastic cells, the IGF system modulates the autophagy process bidirectionally. In the current era of improving CRC therapies, it seems important to investigate the exact mechanisms not only of apoptosis, but also of autophagy in different populations of tumor microenvironment (TME) cells. The role of the IGF system in autophagy in normal as well as transformed colorectal cells still seems poorly understood. Hence, the aim of the review was to summarize the latest knowledge on the role of the IGF system in the molecular mechanisms of autophagy in the normal colon mucosa and in CRC, taking into account the cellular heterogeneity of the colonic and rectal epithelium.
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Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland
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130
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Claudino Dos Santos JC, Lima MPP, Brito GADC, Viana GSDB. Role of enteric glia and microbiota-gut-brain axis in parkinson disease pathogenesis. Ageing Res Rev 2023; 84:101812. [PMID: 36455790 DOI: 10.1016/j.arr.2022.101812] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The microbiota-gut-brain axis or simple gut-brain axis (GBA) is a complex and interactive bidirectional communication network linking the gut to the brain. Alterations in the composition of the gut microbiome have been linked to GBA dysfunction, central nervous system (CNS) inflammation, and dopaminergic degeneration, as those occurring in Parkinson's disease (PD). Besides inflammation, the activation of brain microglia is known to play a central role in the damage of dopaminergic neurons. Inflammation is attributed to the toxic effect of aggregated α-synuclein, in the brain of PD patients. It has been suggested that the α-synuclein misfolding might begin in the gut and spread "prion-like", via the vagus nerve into the lower brainstem and ultimately to the midbrain, known as the Braak hypothesis. In this review, we discuss how the microbiota-gut-brain axis and environmental influences interact with the immune system to promote a pro-inflammatory state that is involved in the initiation and progression of misfolded α-synuclein proteins and the beginning of the early non-motor symptoms of PD. Furthermore, we describe a speculative bidirectional model that explains how the enteric glia is involved in the initiation and spreading of inflammation, epithelial barrier disruption, and α-synuclein misfolding, finally reaching the central nervous system and contributing to neuroinflammatory processes involved with the initial non-motor symptoms of PD.
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Affiliation(s)
- Júlio César Claudino Dos Santos
- Medical School of the Christus University Center - UNICHRISTUS, Fortaleza, CE, Brazil; Graduate Program in Morphofunctional Sciences, Federal University of Ceará - UFC, Fortaleza, CE, Brazil.
| | | | - Gerly Anne de Castro Brito
- Physiology and Pharmacology Department of the Federal University of Ceará - UFC, Fortaleza, CE, Brazil; Morphology Department of the Federal University of Ceará - UFC, Fortaleza, CE, Brazil
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Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, Mack D, Stintzi A. Butyrate's role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clin Nutr 2023; 42:61-75. [PMID: 36502573 DOI: 10.1016/j.clnu.2022.10.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/17/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
Butyrate is a key energy source for colonocytes and is produced by the gut microbiota through fermentation of dietary fiber. Butyrate is a histone deacetylase inhibitor and also signals through three G-protein coupled receptors. It is clear that butyrate has an important role in gastrointestinal health and that butyrate levels can impact both host and microbial functions that are intimately coupled with each other. Maintaining optimal butyrate levels improves gastrointestinal health in animal models by supporting colonocyte function, decreasing inflammation, maintaining the gut barrier, and promoting a healthy microbiome. Butyrate has also shown protective actions in the context of intestinal diseases such as inflammatory bowel disease, graft-versus-host disease of the gastrointestinal tract, and colon cancer, whereas lower levels of butyrate and/or the microbes which are responsible for producing this metabolite are associated with disease and poorer health outcomes. However, clinical efforts to increase butyrate levels in humans and reverse these negative outcomes have generated mixed results. This article discusses our current understanding of the molecular mechanisms of butyrate action with a focus on the gastrointestinal system, the links between host and microbial factors, and the efforts that are currently underway to apply the knowledge gained from the bench to bedside.
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Affiliation(s)
- Kendra Hodgkinson
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Faiha El Abbar
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Peter Dobranowski
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Juliana Manoogian
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - David Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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132
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Romero-Figueroa MDS, Ramírez-Durán N, Montiel-Jarquín AJ, Horta-Baas G. Gut-joint axis: Gut dysbiosis can contribute to the onset of rheumatoid arthritis via multiple pathways. Front Cell Infect Microbiol 2023; 13:1092118. [PMID: 36779190 PMCID: PMC9911673 DOI: 10.3389/fcimb.2023.1092118] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/14/2023] Open
Abstract
Rheumatoid Arthritis (RA) is an autoimmune disease characterized by loss of immune tolerance and chronic inflammation. It is pathogenesis complex and includes interaction between genetic and environmental factors. Current evidence supports the hypothesis that gut dysbiosis may play the role of environmental triggers of arthritis in animals and humans. Progress in the understanding of the gut microbiome and RA. has been remarkable in the last decade. In vitro and in vivo experiments revealed that gut dysbiosis could shape the immune system and cause persistent immune inflammatory responses. Furthermore, gut dysbiosis could induce alterations in intestinal permeability, which have been found to predate arthritis onset. In contrast, metabolites derived from the intestinal microbiota have an immunomodulatory and anti-inflammatory effect. However, the precise underlying mechanisms by which gut dysbiosis induces the development of arthritis remain elusive. This review aimed to highlight the mechanisms by which gut dysbiosis could contribute to the pathogenesis of RA. The overall data showed that gut dysbiosis could contribute to RA pathogenesis by multiple pathways, including alterations in gut barrier function, molecular mimicry, gut dysbiosis influences the activation and the differentiation of innate and acquired immune cells, cross-talk between gut microbiota-derived metabolites and immune cells, and alterations in the microenvironment. The relative weight of each of these mechanisms in RA pathogenesis remains uncertain. Recent studies showed a substantial role for gut microbiota-derived metabolites pathway, especially butyrate, in the RA pathogenesis.
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Affiliation(s)
| | - Ninfa Ramírez-Durán
- Laboratory of Medical and Environmental Microbiology, Department of Medicine, Autonomous University of the State of Mexico, Toluca, Mexico
| | - Alvaro José Montiel-Jarquín
- Dirección de Educación e Investigación en Salud, Hospital de Especialidades de Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Gabriel Horta-Baas
- Rheumatology Service, Internal Medicine Department, Instituto Mexicano del Seguro Social, Merida, Mexico,*Correspondence: Gabriel Horta-Baas,
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133
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Singh V, Lee G, Son H, Koh H, Kim ES, Unno T, Shin JH. Butyrate producers, "The Sentinel of Gut": Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front Microbiol 2023; 13:1103836. [PMID: 36713166 PMCID: PMC9877435 DOI: 10.3389/fmicb.2022.1103836] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Gut-microbial butyrate is a short-chain fatty acid (SCFA) of significant physiological importance than the other major SCFAs (acetate and propionate). Most butyrate producers belong to the Clostridium cluster of the phylum Firmicutes, such as Faecalibacterium, Roseburia, Eubacterium, Anaerostipes, Coprococcus, Subdoligranulum, and Anaerobutyricum. They metabolize carbohydrates via the butyryl-CoA: acetate CoA-transferase pathway and butyrate kinase terminal enzymes to produce most of butyrate. Although, in minor fractions, amino acids can also be utilized to generate butyrate via glutamate and lysine pathways. Butyrogenic microbes play a vital role in various gut-associated metabolisms. Butyrate is used by colonocytes to generate energy, stabilizes hypoxia-inducible factor to maintain the anaerobic environment in the gut, maintains gut barrier integrity by regulating Claudin-1 and synaptopodin expression, limits pro-inflammatory cytokines (IL-6, IL-12), and inhibits oncogenic pathways (Akt/ERK, Wnt, and TGF-β signaling). Colonic butyrate producers shape the gut microbial community by secreting various anti-microbial substances, such as cathelicidins, reuterin, and β-defensin-1, and maintain gut homeostasis by releasing anti-inflammatory molecules, such as IgA, vitamin B, and microbial anti-inflammatory molecules. Additionally, butyrate producers, such as Roseburia, produce anti-carcinogenic metabolites, such as shikimic acid and a precursor of conjugated linoleic acid. In this review, we summarized the significance of butyrate, critically examined the role and relevance of butyrate producers, and contextualized their importance as microbial therapeutics.
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Affiliation(s)
- Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - HyunWoo Son
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Tatsuya Unno
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, Republic of Korea,*Correspondence: Tatsuya Unno, ✉
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea,Department of Integrative Biotechnology, Kyungpook National University, Daegu, Republic of Korea,Jae-Ho Shin, ✉
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134
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Seymour DJ, Winia PA, Uittenbogaard G, Carson M, Doelman J. Supplementation of hydrogenated fat-embedded calcium gluconate improves milk fat content and yield in multiparous Holstein dairy cattle. J DAIRY RES 2023; 90:1-3. [PMID: 36632800 DOI: 10.1017/s0022029922000851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This research communication reports the responses to supplementing dairy cattle with a hydrogenated fat-embedded calcium gluconate feed additive. The role of hindgut health in ruminant performance and wellbeing is an area of growing interest. Various prebiotic compounds have been used to promote lower gut health in various non-ruminant species. Calcium gluconate, a prebiotic compound, has previously been observed to increase milk fat yield when fed to ruminants in a form capable of resisting fermentation in the rumen, though the mechanism(s) behind this response remain unclear. The objective of this study was to compare the responses of lactating cattle to two different supplementation levels of a hydrogenated fat-embedded calcium gluconate (HFCG) product to evaluate a potential linear dose response. Forty-six lactating Holstein dairy cattle were used in a 3 × 3 replicated Latin square design with 28 d periods to evaluate a previously used dose of HFCG (approximately 16 g/d) with both a negative control and a dose of 25 g/d. Supplementation of multiparous animals with 16 g/d HFCG significantly (P < 0.05) increased milk fat yield and content relative to the negative control, and subsequently improved gross feed efficiency (P < 0.05); additionally, the presence of a potential non-linear dose response was observed for these parameters. Responses when supplemented with 25 g/d HFCG did not differ from the negative control. No production responses were observed in primiparous animals. The mode of action of HFCG, in addition to the potential differential response in primiparous animals remains unclear and warrants further investigation.
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Affiliation(s)
- Dave J Seymour
- Trouw Nutrition R&D, PO Box 299, 3800 Amersfoort AG, the Netherlands
| | - Pieter A Winia
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 Wageningen AH, the Netherlands
| | - Gera Uittenbogaard
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 Wageningen AH, the Netherlands
| | - Michelle Carson
- Trouw Nutrition Canada, 7504 McLean Rd E., Puslinch, Ontario, Canada N0B 2J0
| | - John Doelman
- Trouw Nutrition R&D, PO Box 299, 3800 Amersfoort AG, the Netherlands
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135
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Shouval R, Waters NR, Gomes ALC, Zuanelli Brambilla C, Fei T, Devlin SM, Nguyen CL, Markey KA, Dai A, Slingerland JB, Clurman AG, Fontana E, Amoretti LA, Wright RJ, Hohl TM, Taur Y, Sung AD, Weber D, Hashimoto D, Teshima T, Chao NJ, Holler E, Scordo M, Giralt SA, Perales MA, Peled JU, van den Brink MRM. Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation. Clin Cancer Res 2023; 29:165-173. [PMID: 36322005 PMCID: PMC9812902 DOI: 10.1158/1078-0432.ccr-22-1254] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022]
Abstract
PURPOSE The gut microbiota is subject to multiple insults in allogeneic hematopoietic cell transplantation (allo-HCT) recipients. We hypothesized that preparative conditioning regimens contribute to microbiota perturbation in allo-HCT. EXPERIMENTAL DESIGN This was a retrospective study that evaluated the relationship between conditioning regimens exposure in 1,188 allo-HCT recipients and the gut microbiome. Stool samples collected from 20 days before transplantation up to 30 days after were profiled using 16S rRNA sequencing. Microbiota injury was quantified by changes in α-diversity. RESULTS We identified distinct patterns of microbiota injury that varied by conditioning regimen. Diversity loss was graded into three levels of conditioning-associated microbiota injury (CMBI) in a multivariable model that included antibiotic exposures. High-intensity regimens, such as total body irradiation (TBI)-thiotepa-cyclophosphamide, were associated with the greatest injury (CMBI III). In contrast, the nonmyeloablative regimen fludarabine-cyclophosphamide with low-dose TBI (Flu/Cy/TBI200) had a low-grade injury (CMBI I). The risk of acute GVHD correlated with CMBI degree. Pretransplant microbial compositions were best preserved with Flu/Cy/TBI200, whereas other regimens were associated with loss of commensal bacteria and expansion of Enterococcus. CONCLUSIONS Our findings support an interaction between conditioning at the regimen level and the extent of microbiota injury.
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Affiliation(s)
- Roni Shouval
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nicholas R. Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio L. C. Gomes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corrado Zuanelli Brambilla
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Hematology Unit, Department of Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chi L. Nguyen
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kate A. Markey
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John B Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Annelie G Clurman
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Fontana
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luigi A Amoretti
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta J Wright
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias M Hohl
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Taur
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony D. Sung
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Daniela Weber
- Department of Internal Medicine, University Medical Center, University of Regensburg, Regensburg, Germany
| | - Daigo Hashimoto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Nelson J. Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ernst Holler
- Department of Internal Medicine, University Medical Center, University of Regensburg, Regensburg, Germany
| | - Michael Scordo
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sergio A. Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jonathan U. Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marcel R. M. van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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136
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Wu A, Gao Y, Kan R, Ren P, Xue C, Kong B, Tang Q. Alginate Oligosaccharides Prevent Dextran-Sulfate-Sodium-Induced Ulcerative Colitis via Enhancing Intestinal Barrier Function and Modulating Gut Microbiota. Foods 2023; 12:foods12010220. [PMID: 36613442 PMCID: PMC9818813 DOI: 10.3390/foods12010220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
Alginate oligosaccharides are degradation products of alginate and have attracted increasing attention due to their versatile biological functions. In the present study, C57BL/6 mice were used to assess the ameliorative effects and mechanisms of guluronate oligosaccharides (GAOS), mannuronic oligosaccharides (MAOS), and heterozygous alginate oligosaccharides (HAOS), which are the three alginate oligosaccharides of dextran sulfate sodium (DSS)-induced ulcerative colitis. The study showed that alginate oligosaccharides alleviated pathological histological damage by slowing down weight loss, inhibiting colonic length shortening, and reducing disease activity index (DAI) and histopathological scores. Alginate oligosaccharides modulated the colonic inflammatory response by reducing colonic MPO levels and downregulating the expression of IL-6 and IL-1β. Alginate oligosaccharides reduced intestinal permeability and reversed intestinal barrier damage by increasing the number of goblet cells, decreasing LPS levels, downregulating Bax protein levels, upregulating Bcl-2 protein levels, and enhancing the expression of the E-cadherin. Furthermore, alginate oligosaccharides modulated the composition of the gut microbiota and restored the production of short-chain fatty acids (SCFAs), especially acetate and butyrate. In conclusion, our study provides a scientific basis for the role of alginate oligosaccharides in relieving ulcerative colitis.
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Affiliation(s)
- Axue Wu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yuan Gao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ruotong Kan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Pengfei Ren
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China
| | - Biao Kong
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
- Correspondence: ; Tel.: +86-13912383919
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137
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Larabi AB, Masson HLP, Bäumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes 2023; 15:2172671. [PMID: 36740850 PMCID: PMC9904317 DOI: 10.1080/19490976.2023.2172671] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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138
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Ferraris L, Balvay A, Bellet D, Delannoy J, Maudet C, Larcher T, Rozé JC, Philippe C, Meylheuc T, Butel MJ, Rabot S, Aires J. Neonatal necrotizing enterocolitis: Clostridium butyricum and Clostridium neonatale fermentation metabolism and enteropathogenicity. Gut Microbes 2023; 15:2172666. [PMID: 36801067 PMCID: PMC9980464 DOI: 10.1080/19490976.2023.2172666] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Bacterial colonization in the gut plays a pivotal role in neonatal necrotizing enterocolitis (NEC) development, but the relationship between bacteria and NEC remains unclear. In this study, we aimed to elucidate whether bacterial butyrate end-fermentation metabolites participate in the development of NEC lesions and confirm the enteropathogenicity of Clostridium butyricum and Clostridium neonatale in NEC. First, we produced C.butyricum and C.neonatale strains impaired in butyrate production by genetically inactivating the hbd gene encoding β-hydroxybutyryl-CoA dehydrogenase that produces end-fermentation metabolites. Second, we evaluated the enteropathogenicty of the hbd-knockout strains in a gnotobiotic quail model of NEC. The analyses showed that animals harboring these strains had significantly fewer and less intense intestinal lesions than those harboring the respective wild-type strains. In the absence of specific biological markers of NEC, the data provide original and new mechanistic insights into the disease pathophysiology, a necessary step for developing potential novel therapies.
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Affiliation(s)
- Laurent Ferraris
- Université Paris Cité, INSERM, UMR-S 1139, 3PHM, Paris, France,FHU PREMA « Fighting prematurity, Paris, France
| | - Aurélie Balvay
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Deborah Bellet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Johanne Delannoy
- Université Paris Cité, INSERM, UMR-S 1139, 3PHM, Paris, France,FHU PREMA « Fighting prematurity, Paris, France
| | - Claire Maudet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Jean-Christophe Rozé
- INRAE, UMR 1280, Physiologie des Adaptations Nutritionnelles (PhAN), Université hospitalière de Nantes, Nantes, France
| | - Catherine Philippe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-José Butel
- Université Paris Cité, INSERM, UMR-S 1139, 3PHM, Paris, France,FHU PREMA « Fighting prematurity, Paris, France
| | - Sylvie Rabot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julio Aires
- Université Paris Cité, INSERM, UMR-S 1139, 3PHM, Paris, France,FHU PREMA « Fighting prematurity, Paris, France,CONTACT Julio Aires Université Paris Cité, INSERM, UMR-S 1139, 3PHM, F-75006Paris, France
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139
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Baltsavias S, Van Treuren W, Sawaby A, Baker SW, Sonnenburg JL, Arbabian A. Gut Microbiome Redox Sensors With Ultrasonic Wake-Up and Galvanic Coupling Wireless Links. IEEE Trans Biomed Eng 2023; 70:76-87. [PMID: 35727787 PMCID: PMC9911315 DOI: 10.1109/tbme.2022.3184972] [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] [Indexed: 11/07/2022]
Abstract
Tools to measure in vivo redox activity of the gut microbiome and its influence on host health are lacking. In this paper, we present the design of new in vivo gut oxidation-reduction potential (ORP) sensors for rodents, to study host-microbe and microbe-environment interactions throughout the gut. These are the first in vivo sensors to combine ultrasonic wake-up and galvanic coupling telemetry, allowing for sensor miniaturization, experiment flexibility, and robust wireless measurements in live rodents. A novel study of in situ ORP along the intestine reveals biogeographical redox features that the ORP sensors can uniquely access in future gut microbiome studies.
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140
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Procházková N, Falony G, Dragsted LO, Licht TR, Raes J, Roager HM. Advancing human gut microbiota research by considering gut transit time. Gut 2023; 72:180-191. [PMID: 36171079 PMCID: PMC9763197 DOI: 10.1136/gutjnl-2022-328166] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/10/2022] [Indexed: 02/04/2023]
Abstract
Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet-microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.
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Affiliation(s)
- Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Gwen Falony
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University, Kgs. Lyngby, Denmark
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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141
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Bonilla-Díaz A, Ordóñez-Morán P. Differentiated Epithelial Cells of the Gut. Methods Mol Biol 2023; 2650:3-16. [PMID: 37310619 DOI: 10.1007/978-1-0716-3076-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The intestine is a prime example of self-renewal where stem cells give rise to progenitor cells called transit-amplifying cells which differentiate into more specialized cells. There are two intestinal lineages: the absorptive (enterocytes and microfold cells) and the secretory (Paneth cells, enteroendocrine, goblet cells, and tuft cells). Each of these differentiated cell types has a role in creating an "ecosystem" to maintain intestinal homeostasis. Here, we summarize the main roles of each cell type.
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Affiliation(s)
- Andrea Bonilla-Díaz
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Institute of Biomedicine , University of Barcelona, Barcelona, Spain
| | - Paloma Ordóñez-Morán
- Translational Medical Sciences Unit, School of Medicine, Centre for Cancer Sciences, Biodiscovery Institute-3, University Park, University of Nottingham, Nottingham, UK.
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142
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Wang M, Zhang Y, Li C, Chang W, Zhang L. The relationship between gut microbiota and COVID-19 progression: new insights into immunopathogenesis and treatment. Front Immunol 2023; 14:1180336. [PMID: 37205106 PMCID: PMC10185909 DOI: 10.3389/fimmu.2023.1180336] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a global health crisis. Increasing evidence underlines the key role of competent immune responses in resisting SARS-CoV-2 infection and manifests the disastrous consequence of host immune dysregulation. Elucidating the mechanisms responsible for deregulated host immunity in COVID-19 may provide a theoretical basis for further research on new treatment modalities. Gut microbiota comprises trillions of microorganisms colonizing the human gastrointestinal tract and has a vital role in immune homeostasis and the gut-lung crosstalk. Particularly, SARS-CoV-2 infection can lead to the disruption of gut microbiota equilibrium, a condition called gut dysbiosis. Due to its regulatory effect on host immunity, gut microbiota has recently received considerable attention in the field of SARS-CoV-2 immunopathology. Imbalanced gut microbiota can fuel COVID-19 progression through production of bioactive metabolites, intestinal metabolism, enhancement of the cytokine storm, exaggeration of inflammation, regulation of adaptive immunity and other aspects. In this review, we provide an overview of the alterations in gut microbiota in COVID-19 patients, and their effects on individuals' susceptibility to viral infection and COVID-19 progression. Moreover, we summarize currently available data on the critical role of the bidirectional regulation between intestinal microbes and host immunity in SARS-CoV-2-induced pathology, and highlight the immunomodulatory mechanisms of gut microbiota contributing to COVID-19 pathogenesis. In addition, we discuss the therapeutic benefits and future perspectives of microbiota-targeted interventions including faecal microbiota transplantation (FMT), bacteriotherapy and traditional Chinese medicine (TCM) in COVID-19 treatment.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Chunmei Li
- Department of Radiology, Qingdao Municipal Hospital, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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143
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Walaas GA, Gopalakrishnan S, Bakke I, Skovdahl HK, Flatberg A, Østvik AE, Sandvik AK, Bruland T. Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids. Front Immunol 2023; 14:1095812. [PMID: 36793710 PMCID: PMC9922616 DOI: 10.3389/fimmu.2023.1095812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Background The epithelium in the colonic mucosa is implicated in the pathophysiology of various diseases, including inflammatory bowel diseases and colorectal cancer. Intestinal epithelial organoids from the colon (colonoids) can be used for disease modeling and personalized drug screening. Colonoids are usually cultured at 18-21% oxygen without accounting for the physiological hypoxia in the colonic epithelium (3% to <1% oxygen). We hypothesize that recapitulating the in vivo physiological oxygen environment (i.e., physioxia) will enhance the translational value of colonoids as pre-clinical models. Here we evaluate whether human colonoids can be established and cultured in physioxia and compare growth, differentiation, and immunological responses at 2% and 20% oxygen. Methods Growth from single cells to differentiated colonoids was monitored by brightfield images and evaluated with a linear mixed model. Cell composition was identified by immunofluorescence staining of cell markers and single-cell RNA-sequencing (scRNA-seq). Enrichment analysis was used to identify transcriptomic differences within cell populations. Pro-inflammatory stimuli induced chemokines and Neutrophil gelatinase-associated lipocalin (NGAL) release were analyzed by Multiplex profiling and ELISA. Direct response to a lower oxygen level was analyzed by enrichment analysis of bulk RNA sequencing data. Results Colonoids established in a 2% oxygen environment acquired a significantly larger cell mass compared to a 20% oxygen environment. No differences in expression of cell markers for cells with proliferation potential (KI67 positive), goblet cells (MUC2 positive), absorptive cells (MUC2 negative, CK20 positive) and enteroendocrine cells (CGA positive) were found between colonoids cultured in 2% and 20% oxygen. However, the scRNA-seq analysis identified differences in the transcriptome within stem-, progenitor- and differentiated cell clusters. Both colonoids grown at 2% and 20% oxygen secreted CXCL2, CXCL5, CXCL10, CXCL12, CX3CL1 and CCL25, and NGAL upon TNF + poly(I:C) treatment, but there appeared to be a tendency towards lower pro-inflammatory response in 2% oxygen. Reducing the oxygen environment from 20% to 2% in differentiated colonoids altered the expression of genes related to differentiation, metabolism, mucus lining, and immune networks. Conclusions Our results suggest that colonoids studies can and should be performed in physioxia when the resemblance to in vivo conditions is important.
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Affiliation(s)
- Gunnar Andreas Walaas
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Shreya Gopalakrishnan
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Bakke
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Helene Kolstad Skovdahl
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Centre of Molecular Inflammation Research (CEMIR), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Central Administration, St. Olav's University Hospital, Trondheim, Norway
| | - Ann Elisabet Østvik
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Arne Kristian Sandvik
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Centre of Molecular Inflammation Research (CEMIR), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Torunn Bruland
- Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
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144
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Interpreting tree ensemble machine learning models with endoR. PLoS Comput Biol 2022; 18:e1010714. [PMID: 36516158 PMCID: PMC9797088 DOI: 10.1371/journal.pcbi.1010714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 12/28/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022] Open
Abstract
Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.
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145
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Lund PJ, Gates LA, Leboeuf M, Smith SA, Chau L, Lopes M, Friedman ES, Saiman Y, Kim MS, Shoffler CA, Petucci C, Allis CD, Wu GD, Garcia BA. Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation. Cell Rep 2022; 41:111809. [PMID: 36516747 PMCID: PMC9994635 DOI: 10.1016/j.celrep.2022.111809] [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: 07/23/2021] [Revised: 03/09/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota influences acetylation on host histones by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-coenzyme A (CoA), a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah A Gates
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Marylene Leboeuf
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Sarah A Smith
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lillian Chau
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariana Lopes
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elliot S Friedman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yedidya Saiman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Min Soo Kim
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clarissa A Shoffler
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Petucci
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Gary D Wu
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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146
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Wang X, Hu L, Wang C, He B, Fu Z, Jin C, Jin Y. Cross-generational effects of maternal exposure to imazalil on anaerobic components and carnitine absorption associated with OCTN2 expression in mice. CHEMOSPHERE 2022; 308:136542. [PMID: 36150497 DOI: 10.1016/j.chemosphere.2022.136542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Imazalil (IMZ) is a fungicide recommended by the Chinese ministry of agriculture. However, recent study was observed high level of IMZ by dietary exposure in pregnant women. To determine the cross-generational effects, C57BL/6 mice were exposed to IMZ at dietary levels of 0, 0.025‰, and 0.25‰ during the gestation and lactation periods. Then, we assessed the changes in growth phenotypes, carnitine levels, and gut microbiota in F0, F1 or F2 generations. The growth phenotypes of dams didn't observe significant difference, but there were significant changes in the offspring. Plasma samples revealed low levels of free carnitine (C0), long-chain acyl-carnitines and total carnitine. In particular, C0 may be regarded as relatively potential, specific markers by maternal IMZ exposure. Caco2 cell culture and animal experiment confirmed IMZ affected carnitine absorption through the organic cation transporter type-2 (OCTN2) protein encoded by solute carrier family 22A member 5 (SLC22A5) gene in colon. Maternal IMZ exposure also had a greater effect on gut microbiota in offspring, especially anaerobic bacteria, which positively correlated with C0 and acyl-carnitines. These results suggested that maternal IMZ exposure affected carnitine absorption through OCTN2 protein, which led to the decline of anaerobic bacteria and unbalanced intestinal homeostasis.
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Affiliation(s)
- Xiaofang Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Lingyu Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Caiyun Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Bingnan He
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Cuiyuan Jin
- Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, 310015, China.
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China.
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147
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Dodd D, Cann I. Tutorial: Microbiome studies in drug metabolism. Clin Transl Sci 2022; 15:2812-2837. [PMID: 36099474 PMCID: PMC9747132 DOI: 10.1111/cts.13416] [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: 04/16/2022] [Revised: 07/20/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
The human gastrointestinal tract is home to a dense population of microorganisms whose metabolism impacts human health and physiology. The gut microbiome encodes millions of genes, the products of which endow our bodies with unique biochemical activities. In the context of drug metabolism, microbial biochemistry in the gut influences humans in two major ways: (1) by producing small molecules that modulate expression and activity of human phase I and II pathways; and (2) by directly modifying drugs administered to humans to yield active, inactive, or toxic metabolites. Although the capacity of the microbiome to modulate drug metabolism has long been known, recent studies have explored these interactions on a much broader scale and have revealed an unprecedented scope of microbial drug metabolism. The implication of this work is that we might be able to predict the capacity of an individual's microbiome to metabolize drugs and use this information to avoid toxicity and inform proper dosing. Here, we provide a tutorial of how to study the microbiome in the context of drug metabolism, focusing on in vitro, rodent, and human studies. We then highlight some limitations and opportunities for the field.
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Affiliation(s)
- Dylan Dodd
- Department of PathologyStanford University School of MedicineStanfordCaliforniaUSA,Department of Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Isaac Cann
- Department of Animal ScienceUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme)University of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Division of Nutritional SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Center for East Asian & Pacific StudiesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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148
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Dong L, Qin C, Li Y, Wu Z, Liu L. Oat phenolic compounds regulate metabolic syndrome in high fat diet-fed mice via gut microbiota. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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149
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Gustafsson JK, Johansson MEV. The role of goblet cells and mucus in intestinal homeostasis. Nat Rev Gastroenterol Hepatol 2022; 19:785-803. [PMID: 36097076 DOI: 10.1038/s41575-022-00675-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 12/08/2022]
Abstract
The intestinal tract faces numerous challenges that require several layers of defence. The tight epithelium forms a physical barrier that is further protected by a mucus layer, which provides various site-specific protective functions. Mucus is produced by goblet cells, and as a result of single-cell RNA sequencing identifying novel goblet cell subpopulations, our understanding of their various contributions to intestinal homeostasis has improved. Goblet cells not only produce mucus but also are intimately linked to the immune system. Mucus and goblet cell development is tightly regulated during early life and synchronized with microbial colonization. Dysregulation of the developing mucus systems and goblet cells has been associated with infectious and inflammatory conditions and predisposition to chronic disease later in life. Dysfunctional mucus and altered goblet cell profiles are associated with inflammatory conditions in which some mucus system impairments precede inflammation, indicating a role in pathogenesis. In this Review, we present an overview of the current understanding of the role of goblet cells and the mucus layer in maintaining intestinal health during steady-state and how alterations to these systems contribute to inflammatory and infectious disease.
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Affiliation(s)
- Jenny K Gustafsson
- Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemisty and Cell biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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150
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Bekebrede A, Noorman L, Keijer J, de Boer V, Gerrits W. Functional metabolic capacity of pig colonocytes is differentially modulated by fermentable fibre and poorly digestible protein. Animal 2022; 16:100625. [DOI: 10.1016/j.animal.2022.100625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 01/10/2023] Open
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