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Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024; 74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment.
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Affiliation(s)
- Pritam Kundu
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Satyajit Beura
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Suman Mondal
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Kumar Das
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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2
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Moreira de Gouveia MI, Bernalier-Donadille A, Jubelin G. Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease. BIOLOGY 2024; 13:142. [PMID: 38534413 DOI: 10.3390/biology13030142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.
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Affiliation(s)
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000 Clermont-Ferrand, France
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3
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Fachi JL, Pral LP, Assis HC, Oliveira S, Rodovalho VR, dos Santos JAC, Fernandes MF, Matheus VA, Sesti-Costa R, Basso PJ, Flóro e Silva M, Câmara NOS, Giorgio S, Colonna M, Vinolo MAR. Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3. Gut Microbes 2024; 16:2297872. [PMID: 38165200 PMCID: PMC10763646 DOI: 10.1080/19490976.2023.2297872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and is typically used for the treatment of various inflammatory conditions, including infectious diseases. However, its effect on the intestinal mucosa, a microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily treatment with hyperbaric oxygen affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible to Clostridioides difficile infection (CDI), an enteric pathogen highly associated with antibiotic-induced colitis. These observations were closely linked with a decline in the level of microbiota-derived short-chain fatty acids (SCFAs). Butyrate, a SCFA produced primarily by anaerobic microbial species, mitigated HBO-induced susceptibility to CDI and increased epithelial barrier integrity by improving group 3 innate lymphoid cell (ILC3) responses. Mice displaying tissue-specific deletion of HIF-1 in RORγt-positive cells exhibited no protective effect of butyrate during CDI. In contrast, the reinforcement of HIF-1 signaling in RORγt-positive cells through the conditional deletion of VHL mitigated disease outcome, even after HBO therapy. Taken together, we conclude that HBO induces intestinal dysbiosis and impairs the production of SCFAs affecting the HIF-1α-IL-22 axis in ILC3 and worsening the response of mice to subsequent C. difficile infection.
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Affiliation(s)
- José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Laís. P. Pral
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Helder C. Assis
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Sarah Oliveira
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vinícius R. Rodovalho
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Jefferson A. C. dos Santos
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Mariane F. Fernandes
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Valquíria A. Matheus
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renata Sesti-Costa
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Paulo J. Basso
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina Flóro e Silva
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Niels O. S. Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco A. R. Vinolo
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, Institute of Biology, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
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Deng ZL, Pieper DH, Stallmach A, Steube A, Vital M, Reck M, Wagner-Döbler I. Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics. MICROBIOME 2023; 11:269. [PMID: 38037086 PMCID: PMC10691019 DOI: 10.1186/s40168-023-01713-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the backbone of treatment of pouchitis; however, antibiotic-resistant pouchitis develops in 5-10% of those patients. It has been shown that fecal microbiota transplantation (FMT) is an effective treatment for UC, but results for FMT antibiotic-resistant pouchitis are inconsistent. METHODS To uncover which metabolic activities were transferred to the recipients during FMT and helped the remission, we performed a longitudinal case study of the gut metatranscriptomes from three patients and their donors. The patients were treated by two to three FMTs, and stool samples were analyzed for up to 140 days. RESULTS Reduced expression in pouchitis patients compared to healthy donors was observed for genes involved in biosynthesis of amino acids, cofactors, and B vitamins. An independent metatranscriptome dataset of UC patients showed a similar result. Other functions including biosynthesis of butyrate, metabolism of bile acids, and tryptophan were also much lower expressed in pouchitis. After FMT, these activities transiently increased, and the overall metatranscriptome profiles closely mirrored those of the respective donors with notable fluctuations during the subsequent weeks. The levels of the clinical marker fecal calprotectin were concordant with the metatranscriptome data. Faecalibacterium prausnitzii represented the most active species contributing to butyrate synthesis via the acetyl-CoA pathway. Remission occurred after the last FMT in all patients and was characterized by a microbiota activity profile distinct from donors in two of the patients. CONCLUSIONS Our study demonstrates the clear but short-lived activity engraftment of donor microbiota, particularly the butyrate biosynthesis after each FMT. The data suggest that FMT triggers shifts in the activity of patient microbiota towards health which need to be repeated to reach critical thresholds. As a case study, these insights warrant cautious interpretation, and validation in larger cohorts is necessary for generalized applications. In the long run, probiotics with high taxonomic diversity consisting of well characterized strains could replace FMT to avoid the costly screening of donors and the risk of transferring unwanted genetic material. Video Abstract.
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Affiliation(s)
- Zhi-Luo Deng
- Group Computational Biology for Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany.
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Andreas Stallmach
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Arndt Steube
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Reck
- Group Microbial Communication, Helmholtz Center for Infection Research, Brunswick, Germany
- TÜV Rheinland, Cologne, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Brunswick, Germany
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Gomez D, Toribio R, Caddey B, Costa M, Vijan S, Dembek K. Longitudinal effects of oral administration of antimicrobial drugs on fecal microbiota of horses. J Vet Intern Med 2023; 37:2562-2572. [PMID: 37681574 PMCID: PMC10658497 DOI: 10.1111/jvim.16853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available. OBJECTIVE Investigate changes of the fecal microbiota in response to oral administration of antimicrobials. ANIMALS Twenty healthy horses. METHODS Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP); and group 5 (control). Antimicrobials were administered for 5 days. Fecal samples were obtained before (day 0) and at 1, 2, 3, 4, 5, 6, and 30 days of the study period. Fecal microbiota was characterized by high throughput sequencing of the V4 region of the 16S rRNA. RESULTS Horses remained healthy throughout the study. Richness and diversity in doxycycline, erythromycin, and metronidazole, but not SMZ-TMP groups, was significantly lower (P < .05) at multiple time points after administration of antimicrobials compared with samples from day 0. Main changes in the microbiota were observed during the time of antimicrobial administration (day 2-5; weighted and unweighted UniFrac PERMANOVA P < .05). Administration of erythromycin, doxycycline and, to a lesser extent, metronidazole produced a pronounced alteration in the microbiota compared with day 0 samples by decreasing the abundance of Treponema, Fibrobacter, and Lachnospiraceae and increasing Fusobacterium and Escherichia-Shigella. CONCLUSIONS AND CLINICAL IMPORTANCE Oral administration of antimicrobials alters the intestinal microbiota of healthy horses resembling horses with dysbiosis, potentially resulting in intestinal inflammation and predisposition to diarrhea.
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Affiliation(s)
- Diego Gomez
- Department of Clinical Studies, Ontario Veterinary CollegeUniversity of GuelphGuelphOntarioCanada
| | - Ramiro Toribio
- Department of Clinical SciencesThe Ohio State University, College of Veterinary MedicineColumbusOhioUSA
| | - Benjamin Caddey
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | - Marcio Costa
- Faculté de Médecine Vétérinaire – Département de Biomédecine VétérinaireUniversity of MontrealSaint‐HyacintheQuebecCanada
| | - Stephanie Vijan
- Department of Clinical SciencesThe Ohio State University, College of Veterinary MedicineColumbusOhioUSA
| | - Katarzyna Dembek
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
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Sahakian L, Robinson AM, Sahakian L, Stavely R, Kelley MR, Nurgali K. APE1/Ref-1 as a Therapeutic Target for Inflammatory Bowel Disease. Biomolecules 2023; 13:1569. [PMID: 38002251 PMCID: PMC10669584 DOI: 10.3390/biom13111569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic relapsing inflammation of the gastrointestinal tract. The prevalence of IBD is increasing with approximately 4.9 million cases reported worldwide. Current therapies are limited due to the severity of side effects and long-term toxicity, therefore, the development of novel IBD treatments is necessitated. Recent findings support apurinic/apyrimidinic endonuclease 1/reduction-oxidation factor 1 (APE1/Ref-1) as a target in many pathological conditions, including inflammatory diseases, where APE1/Ref-1 regulation of crucial transcription factors impacts significant pathways. Thus, a potential target for a novel IBD therapy is the redox activity of the multifunctional protein APE1/Ref-1. This review elaborates on the status of conventional IBD treatments, the role of an APE1/Ref-1 in intestinal inflammation, and the potential of a small molecule inhibitor of APE1/Ref-1 redox activity to modulate inflammation, oxidative stress response, and enteric neuronal damage in IBD.
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Affiliation(s)
- Lauren Sahakian
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Ainsley M. Robinson
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Linda Sahakian
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
| | - Rhian Stavely
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mark R. Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kulmira Nurgali
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Regenerative Medicine and Stem Cells Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Gao X, Ye T, Lei Y, Zhang Q, Luo Y, Yang H, Zeng X, Zhou W, Wen Q, Liu J, Xiong H, Wan R. Dendrobium officinale aqueous extract influences the immune response following vaccination against SARS-CoV-2. Biomed Pharmacother 2023; 162:114702. [PMID: 37062221 PMCID: PMC10099150 DOI: 10.1016/j.biopha.2023.114702] [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: 02/08/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Vaccination is the most effective way to prevent coronavirus disease 2019 (COVID-19). However, it is often less protective and does not significantly increase antibody levels, especially in individuals with impaired immune systems. Nevertheless, the immunocompetence can be enhanced using a natural immunomodulator, such as Dendrobium officinale aqueous extract (DoAE). METHODS To determine whether DoAE promotes antibody production, we treated healthy volunteers with DoAE during COVID-19 vaccination. Meanwhile, the control volunteers were given a placebo (cornstarch) during the vaccination. Antibody levels were measured at three-week intervals in the DoAE and control groups. RESULTS DoAE enhanced immunity and preserved immune cell homeostasis. However, the neutralizing antibody (nAb) levels in the DoAE group were lower than those in the control group. Analysis of the gut microbiota revealed that the abundance of anti-inflammatory flora was increased, while the pro-inflammatory flora was reduced in the DoAE group. CONCLUSION DoAE has immunomodulatory and anti-inflammatory properties. Therefore, DoAE has the potential for COVID-19 prophylaxis, treatment, and recovery from the adverse effects of COVID-19. However, its anti-inflammatory activity affects the production of nAbs. Thus, DoAE may not be recommended for consumption during COVID-19 vaccination.
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Affiliation(s)
- Xiaoping Gao
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Ting Ye
- Medical Laboratory Department, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yu Lei
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Qi Zhang
- Hejiang County Hospital of Traditional Chinese Medicine, Luzhou, Sichuan 646000, China
| | - Yuanning Luo
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Haiyan Yang
- Department of Respiratory and Critical Care Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiaochun Zeng
- Department of Respiratory and Critical Care Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Wen Zhou
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Qinglian Wen
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jingbo Liu
- Medical Laboratory Department, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Hong Xiong
- Department of Respiratory and Critical Care Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Runlan Wan
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China.
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9
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Ma Z, Bolinger AA, Zhou J, Tian B. Bromodomain-containing protein 4 (BRD4): a key player in inflammatory bowel disease and potential to inspire epigenetic therapeutics. Expert Opin Ther Targets 2023; 27:1-7. [PMID: 36710583 PMCID: PMC11092387 DOI: 10.1080/14728222.2023.2175317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Inflammatory bowel diseases (IBDs) are debilitating chronic inflammatory disorders with increasing prevalence worldwide. Epigenetic regulator bromodomain-containing protein 4 (BRD4) is critical in controlling gene expression of IBD-associated inflammatory cytokine networks. BRD4 as a promising therapeutic target is also tightly associated with many other diseases, such as airway inflammation and fibrosis, cancers, infectious diseases and central nervous system disorders. AREAS COVERED This review briefly summarized the critical role of BRD4 in the pathogenesis of IBDs and the current clinical landscape of developing bromodomain and extra terminal domain (BET) inhibitors. The challenges and opportunities as well as future directions of targeting BRD4 inhibition for potential IBD medications were also discussed. EXPERT OPINION Targeting BRD4 with potent and specific inhibitors may offer novel effective therapeutics for IBD patients, particularly those who are refractory to anti-TNFα therapy and IBD-related profibrotic. Developing highly specific BRD4 inhibitors for IBD medications may help erase the drawbacks of most current pan-BET/BRD4 inhibitors, such as off-target effects, poor oral bioavailability, and low gut mucosal absorbance. Novel strategies such as combinatorial therapy, BRD4-based dual inhibitors and proteolysis targeting chimeras (PROTACs) may also have great potential to mitigate side effects and overcome drug resistance during IBD treatment.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
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10
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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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11
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Daoust L, Choi BSY, Agrinier AL, Varin TV, Ouellette A, Mitchell PL, Samson N, Pilon G, Levy E, Desjardins Y, Laplante M, Anhê FF, Houde VP, Marette A. Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity. Gut 2022; 72:896-905. [PMID: 36881441 DOI: 10.1136/gutjnl-2021-326475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/20/2022] [Indexed: 03/08/2023]
Abstract
OBJECTIVE Faecal microbiota transplantation (FMT) in germ-free (GF) mice is a common approach to study the causal role of the gut microbiota in metabolic diseases. Lack of consideration of housing conditions post-FMT may contribute to study heterogeneity. We compared the impact of two housing strategies on the metabolic outcomes of GF mice colonised by gut microbiota from mice treated with a known gut modulator (cranberry proanthocyanidins (PAC)) or vehicle. DESIGN High-fat high-sucrose diet-fed GF mice underwent FMT-PAC colonisation in sterile individual positive flow ventilated cages under rigorous housing conditions and then maintained for 8 weeks either in the gnotobiotic-axenic sector or in the specific pathogen free (SPF) sector of the same animal facility. RESULTS Unexpectedly, 8 weeks after colonisation, we observed opposing liver phenotypes dependent on the housing environment of mice. Mice housed in the GF sector receiving the PAC gut microbiota showed a significant decrease in liver weight and hepatic triglyceride accumulation compared with control group. Conversely, exacerbated liver steatosis was observed in the FMT-PAC mice housed in the SPF sector. These phenotypic differences were associated with housing-specific profiles of colonising bacterial in the gut and of faecal metabolites. CONCLUSION These results suggest that the housing environment in which gnotobiotic mice are maintained post-FMT strongly influences gut microbiota composition and function and can lead to distinctive phenotypes in recipient mice. Better standardisation of FMT experiments is needed to ensure reproducible and translatable results.
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Affiliation(s)
- Laurence Daoust
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Béatrice S-Y Choi
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Anne-Laure Agrinier
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Thibault V Varin
- Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Adia Ouellette
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Patricia L Mitchell
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | | | - Genevieve Pilon
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Emile Levy
- Institute of Nutrition and Functional Foods, Quebec, Québec, Canada.,CHU Ste-Justine Research Center, Université de Montréal, Montreal, Quebec, Canada
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | | | - Fernando F Anhê
- Department of Biochemistry and Biomedical Sciences; Farncombe Family Digestive Health Research Institute and Centre for Metabolsim, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
| | - Vanessa P Houde
- Quebec Heart and Lung Institute, Quebec, Québec, Canada.,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
| | - Andre Marette
- Quebec Heart and Lung Institute, Quebec, Québec, Canada .,Institute of Nutrition and Functional Foods, Quebec, Québec, Canada
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12
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Peña-Ocaña BA, Hoshiko Y, Silva-Flores M, Maeda T, Pérez-Torres I, García-Contreras R, Gutiérrez-Sarmiento W, Hernández-Esquivel L, Marín-Hernández Á, Sánchez-Thomas R, Saavedra E, Rodríguez-Zavala JS, Jasso-Chávez R. Cultivation of gastrointestinal microbiota in a new growth system revealed dysbiosis and metabolic disruptions in carcinoma-bearing rats. Front Microbiol 2022; 13:949272. [PMID: 36118191 PMCID: PMC9479207 DOI: 10.3389/fmicb.2022.949272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
A challenge in the study of gastrointestinal microbiota (GITm) is the validation of the genomic data with metabolic studies of the microbial communities to understand how the microbial networks work during health and sickness. To gain insights into the metabolism of the GITm, feces from healthy and sick rats with cancer were inoculated in a defined synthetic medium directed for anaerobic prokaryote growth (INC-07 medium). Significant differences between cultures of healthy and sick individuals were found: 1) the consumption of the carbon source and the enzyme activity involved in their catabolism (e.g., sucrase, lactase, lipases, aminotransferases, and dehydrogenases); 2) higher excretion of acetic, propionic, isobutyric, butyric, valeric, and isovaleric acids; 3) methane production; 4) ability to form biofilms; and 5) up to 500 amplicon sequencing variants (ASVs) identified showed different diversity and abundance. Moreover, the bowel inflammation induced by cancer triggered oxidative stress, which correlated with deficient antioxidant machinery (e.g., NADPH-producing enzymes) determined in the GITm cultures from sick individuals in comparison with those from control individuals. Altogether, the data suggested that to preserve the microbial network between bacteria and methanogenic archaea, a complete oxidation of the carbon source may be essential for healthy microbiota. The correlation of 16S rRNA gene metabarcoding between cultures and feces, as well as metabolomic data found in cultures, suggest that INC-07 medium may be a useful tool to understand the metabolism of microbiota under gut conditions.
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Affiliation(s)
- Betsy Anaid Peña-Ocaña
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Yuki Hoshiko
- Division of Environment-Conscious Chemistry and Bioengineering, Department of Biological Functions Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Mayel Silva-Flores
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Toshinari Maeda
- Division of Environment-Conscious Chemistry and Bioengineering, Department of Biological Functions Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Israel Pérez-Torres
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wilbert Gutiérrez-Sarmiento
- Instituto Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Luz Hernández-Esquivel
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rosina Sánchez-Thomas
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
- *Correspondence: Ricardo Jasso-Chávez
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13
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Kang GU, Park S, Jung Y, Jee JJ, Kim MS, Lee S, Lee DW, Shin JH, Koh H. Exploration of Potential Gut Microbiota-Derived Biomarkers to Predict the Success of Fecal Microbiota Transplantation in Ulcerative Colitis: A Prospective Cohort in Korea. Gut Liver 2022; 16:775-785. [PMID: 35975640 PMCID: PMC9474483 DOI: 10.5009/gnl210369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/02/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022] Open
Abstract
Background/Aims Although fecal microbiota transplantation (FMT) has been proven as one of the promising treatments for patients with ulcerative colitis (UC), potential prognostic markers regarding the clinical outcomes of FMT remain elusive. Methods We collected fecal samples of 10 participants undergoing FMT to treat UC and those from the corresponding donors. We categorized them into two groups: responders and nonresponders. Sequencing of the bacterial 16S rRNA gene was conducted on the samples to explore bacterial composition. Results Analyzing the gut microbiota of patients who showed different outcomes in FMT presented a distinct microbial niche. Source tracking analysis showed the nonresponder group had a higher rate of preservation of donor microbiota, underscoring that engraftment degrees are not one of the major drivers for the success of FMT. At the phylum level, Bacteroidetes bacteria were significantly depleted (p<0.003), and three genera, including Enterococcus, Rothia, and Pediococcus, were enriched in the responder group before FMT (p=0.003, p=0.025, and p=0.048, respectively). Furthermore, we applied a machine learning algorithm to build a prediction model that might allow the prediction of FMT outcomes, which yielded an area under the receiver operating characteristic (ROC) curve of 0.844. Notably, the microbiota-based model was much better at predicting outcomes than the clinical features model (area under the ROC curve=0.531). Conclusions This study is the first to suggest the significance of indigenous microbiota of recipients as a critical factor. The result highlights that bacterial composition should be evaluated before FMT to select suitable patients and achieve better efficiency.
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Affiliation(s)
- Gi-Ung Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Sowon Park
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yeongyun Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Jai J Jee
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Min-Sueng Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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14
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The Role of the Human Gut Microbiome in Inflammatory Bowel Disease and Radiation Enteropathy. Microorganisms 2022; 10:microorganisms10081613. [PMID: 36014031 PMCID: PMC9415405 DOI: 10.3390/microorganisms10081613] [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: 06/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
The human gut microbiome plays a key role in regulating host physiology. In a stable state, both the microbiota and the gut work synergistically. The overall homeostasis of the intestinal flora can be affected by multiple factors, including disease states and the treatments given for those diseases. In this review, we examine the relatively well-characterised abnormalities that develop in the microbiome in idiopathic inflammatory bowel disease, and compare and contrast them to those that are found in radiation enteropathy. We discuss how these changes may exert their effects at a molecular level, and the possible role of manipulating the microbiome through the use of a variety of therapies to reduce the severity of the underlying condition.
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15
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Abstract
Changes in the composition of the gut microbiota are associated with many human diseases. So far, however, we have failed to define homeostasis or dysbiosis by the presence or absence of specific microbial species. The composition and function of the adult gut microbiota is governed by diet and host factors that regulate and direct microbial growth. The host delivers oxygen and nitrate to the lumen of the small intestine, which selects for bacteria that use respiration for energy production. In the colon, by contrast, the host limits the availability of oxygen and nitrate, which results in a bacterial community that specializes in fermentation for growth. Although diet influences microbiota composition, a poor diet weakens host control mechanisms that regulate the microbiota. Hence, quantifying host parameters that control microbial growth could help define homeostasis or dysbiosis and could offer alternative strategies to remediate dysbiosis.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
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16
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Xue J, Dominguez Rieg JA, Thomas L, White JR, Rieg T. Intestine-Specific NHE3 Deletion in Adulthood Causes Microbial Dysbiosis. Front Cell Infect Microbiol 2022; 12:896309. [PMID: 35719363 PMCID: PMC9204535 DOI: 10.3389/fcimb.2022.896309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
In the intestine, the Na+/H+ exchanger 3 (NHE3) plays a critical role for Na+ and fluid absorption. NHE3 deficiency predisposes patients to inflammatory bowel disease (IBD). In mice, selective deletion of intestinal NHE3 causes various local and systemic pathologies due to dramatic changes in the intestinal environment, which can influence microbiota colonization. By using metagenome shotgun sequencing, we determined the effect of inducible intestinal epithelial cell-specific deletion of NHE3 (NHE3IEC-KO) in adulthood on the gut microbiome in mice. Compared with control mice, NHE3IEC-KO mice show a significantly different gut microbiome signature, with an unexpected greater diversity. At the phylum level, NHE3IEC-KO mice showed a significant expansion in Proteobacteria and a tendency for lower Firmicutes/Bacteroidetes (F/B) ratio, an indicator of dysbiosis. At the family level, NHE3IEC-KO mice showed significant expansions in Bacteroidaceae, Rikenellaceae, Tannerellaceae, Flavobacteriaceae and Erysipelotrichaceae, but had contractions in Lachnospiraceae, Prevotellaceae and Eubacteriaceae. At the species level, after removing those with lowest occurrence and abundance, we identified 23 species that were significantly expanded (several of which are established pro-inflammatory pathobionts); whereas another 23 species were found to be contracted (some of which are potential anti-inflammatory probiotics) in NHE3IEC-KO mice. These results reveal that intestinal NHE3 deletion creates an intestinal environment favoring the competitive advantage of inflammophilic over anti-inflammatory species, which is commonly featured in conventional NHE3 knockout mice and patients with IBD. In conclusion, our study emphasizes the importance of intestinal NHE3 for gut microbiota homeostasis, and provides a deeper understanding regarding interactions between NHE3, dysbiosis, and IBD.
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Affiliation(s)
- Jianxiang Xue
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - Jessica A Dominguez Rieg
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States.,James A. Haley Veterans' Hospital, Tampa, FL, United States
| | - Linto Thomas
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - James R White
- Resphera Biosciences LLC, Baltimore, MD, United States
| | - Timo Rieg
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States.,James A. Haley Veterans' Hospital, Tampa, FL, United States.,Center for Hypertension and Kidney Research, University of South Florida, Tampa, FL, United States
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17
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Ahn SY, Sung DK, Chang YS, Park WS. Intratracheal Transplantation of Mesenchymal Stem Cells Attenuates Hyperoxia-Induced Microbial Dysbiosis in the Lungs, Brain, and Gut in Newborn Rats. Int J Mol Sci 2022; 23:ijms23126601. [PMID: 35743045 PMCID: PMC9223745 DOI: 10.3390/ijms23126601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Accepted: 06/11/2022] [Indexed: 01/25/2023] Open
Abstract
We attempted to determine whether intratracheal (IT) transplantation of mesenchymal stem cells (MSCs) could simultaneously attenuate hyperoxia-induced lung injuries and microbial dysbiosis of the lungs, brain, and gut in newborn rats. Newborn rats were exposed to hyperoxia (90% oxygen) for 14 days. Human umbilical cord blood-derived MSCs (5 × 105) were transplanted via the IT route on postnatal day (P) five. At P14, the lungs were harvested for histological, biochemical, and microbiome analyses. Bacterial 16S ribosomal RNA genes from the lungs, brain, and large intestine were amplified, pyrosequenced, and analyzed. IT transplantation of MSCs simultaneously attenuated hyperoxia-induced lung inflammation and the ensuing injuries, as well as the dysbiosis of the lungs, brain, and gut. In correlation analyses, lung interleukin-6 (IL-6) levels were significantly positively correlated with the abundance of Proteobacteria in the lungs, brain, and gut, and it was significantly inversely correlated with the abundance of Firmicutes in the gut and lungs and that of Bacteroidetes in the lungs. In conclusion, microbial dysbiosis in the lungs, brain, and gut does not cause but is caused by hyperoxic lung inflammation and ensuing injuries, and IT transplantation of MSCs attenuates dysbiosis in the lungs, brain, and gut, primarily by their anti-oxidative and anti-inflammatory effects.
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Affiliation(s)
- So Yoon Ahn
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.Y.A.); (Y.S.C.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
| | - Dong Kyung Sung
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.Y.A.); (Y.S.C.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Won Soon Park
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.Y.A.); (Y.S.C.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology SAIHST, Sungkyunkwan University, Seoul 06351, Korea
- Correspondence: ; Tel.: +82-2-3410-3523; Fax: +82-2-3410-0049
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18
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Gomez DE, Li L, Goetz H, MacNicol J, Gamsjaeger L, Renaud DL. Calf Diarrhea Is Associated With a Shift From Obligated to Facultative Anaerobes and Expansion of Lactate-Producing Bacteria. Front Vet Sci 2022; 9:846383. [PMID: 35392114 PMCID: PMC8981386 DOI: 10.3389/fvets.2022.846383] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/21/2022] [Indexed: 12/29/2022] Open
Abstract
Diarrhea is the leading cause of morbidity, mortality and antimicrobial drug use in calves during the first month of age. Alteration in the bacterial communities of the gastrointestinal tract occurs during diarrhea. Diarrheic calves often develop anion gap (AG) acidosis associated with increased concentrations of unmeasured anions including D- and L-lactate. However, studies investigating the association between gut microbiota alterations and the development of acid-base disorders in diarrheic calves are lacking. We investigated the fecal bacterial alterations of calves with diarrhea and its association with changes in blood pH, and AG. Blood and fecal samples from healthy and diarrheic veal calves were taken 7 days after arrival to the farm. The fecal microbiota of healthy and diarrheic calves was assessed by sequencing of 16S ribosomal RNA gene amplicons. Blood gas analysis was completed using an i-Stat analyzer. In healthy calves, higher richness, evenness, and diversity were observed compared to diarrheic calves. Phocaeicola, Bacteroides, Prevotella, Faecalibacterium, Butyricicoccus, Ruminococcaceae and Lachnospiraceae were enriched in healthy compared with diarrheic calves. Enterococcus, Ligilactobacillus, Lactobacilus, Gallibacterium Streptococcus, and Escherichia/Shigella were enriched in diarrheic calves. In diarrheic calves, an increased abundance of lactate-producing bacteria including Lactobacillus, Streptococcus, Veillonella, Ligilactobacillus and Olsenella was detected. Diarrheic calves had a lower pH and bicarbonate concentration and a higher AG concentration than healthy calves. Together, these results indicate that calf diarrhea is associated with a shift from obligated to facultative anaerobes and expansion of lactate-producing bacteria which are related to acidemia, low bicarbonate and increase AG. Our results highlight the importance of the gastrointestinal microbiota on the clinicopathological changes observed in diarrheic calves.
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19
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Somathilaka SS, Martins DP, Barton W, O'Sullivan O, Cotter PD, Balasubramaniam S. A Graph-based Molecular Communications Model Analysis of the Human Gut Bacteriome. IEEE J Biomed Health Inform 2022; 26:3567-3577. [PMID: 35120016 DOI: 10.1109/jbhi.2022.3148672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alterations in the human Gut Bacteriome (GB) can be associated with human health issues, such as type-2 diabetes and obesity. Both external and internal factors can drive changes in the composition and in interactions of the human GB, impacting negatively on the host cells. This paper focuses on the human GB metabolism and proposes a two-layer network system to investigate its dynamics. Furthermore, we develop an in-silico simulation model (virtual GB), allowing us to study the impact of the metabolite exchange through molecular communications in the human GB network system. Our results show that regulation of molecular inputs strongly affect bacterial population growth and create an unbalanced network, as shown by shifts in the node weights based on the produced molecular signals. Additionally, we show that the metabolite molecular communication production is greatly affected when directly manipulating the composition of the human GB network in the virtual GB. These results indicate that our human GB interaction model can help to identify hidden behaviors of the human GB depending on molecular signal interactions. Moreover, the virtual GB can support the research and development of novel medical treatments based on the accurate control of bacterial population growth and exchange of metabolites.
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20
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Frau A, Ijaz UZ, Slater R, Jonkers D, Penders J, Campbell BJ, Kenny JG, Hall N, Lenzi L, Burkitt MD, Pierik M, Darby AC, Probert CSJ. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes 2022; 13:1930871. [PMID: 34241567 PMCID: PMC8274447 DOI: 10.1080/19490976.2021.1930871] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The etiology of Crohn's disease (CD) is multifactorial. Bacterial and fungal microbiota are involved in the onset and/or progression of the disease. A bacterial dysbiosis in CD patients is accepted; however, less is known about the mycobiome and the relationships between the two communities. We investigated the interkingdom relationships, their metabolic consequences, and the changes in the fungal community during relapse and remission in CD.Two cohorts were evaluated: a British cohort (n = 63) comprising CD and ulcerative colitis patients, and controls. The fungal and bacterial communities of biopsy and fecal samples were analyzed, with the fecal volatiles; datasets were also integrated; and a Dutch cohort (n = 41) comprising CD patients and healthy controls was analyzed for stability of the gut mycobiome.A dysbiosis of the bacterial community was observed in biopsies and stool. Results suggest Bacteroides is likely key in CD and may modulate Candida colonization. A dysbiosis of the fungal community was observed only in the Dutch cohort; Malassezia and Candida were increased in patients taking immunosuppressants. Longitudinal analysis showed an increase in Cyberlindnera in relapse. Saccharomyces was dominant in all fecal samples, but not in biopsies, some of which did not yield fungal reads; amino acid degradation was the main metabolic change associated with CD and both bacteria and fungi might be implicated.We have shown that Bacteroides and yeasts may play a role in CD; understanding their role and relationship in the disease would shed new light on the development and treatment of CD.
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Affiliation(s)
- Alessandra Frau
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK,CONTACT Alessandra Frau Department of Molecular and Clinical Cancer Medicine, Nuffield Building, Ashton Street, LiverpoolL69 3GE, UK
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK,Umer Z. Ijaz School of Engineering, University of Glasgow, Glasgow, UK
| | - Rachael Slater
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daisy Jonkers
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Barry J. Campbell
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | | | - Neil Hall
- Earlham Institute, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Luca Lenzi
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Michael D. Burkitt
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Marieke Pierik
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Alistair C. Darby
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | - Christopher S. J. Probert
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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21
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Wei LY, Zhang JK, Zheng L, Chen Y. The functional role of sulforaphane in intestinal inflammation: a review. Food Funct 2021; 13:514-529. [PMID: 34935814 DOI: 10.1039/d1fo03398k] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Intestinal inflammation represented by inflammatory bowel disease (IBD) has become a global epidemic disease and the number of patients with IBD continues to increase. This digestive tract disease not only affects the absorption of food components by destroying the intestinal epithelial structure, but also can induce diseases in remote organs via the gut-organ axis, seriously harming human health. Nowadays, increasing attention is being paid to the nutritional and medicinal value of food components with increasing awareness among the general public regarding health. As an important member of the isothiocyanates, sulforaphane (SFN) is abundant in cruciferous plants and is famous for its excellent anti-cancer effects. With the development of clinical research, more physiological activities of SFN, such as antidepressant, hypoglycemic and anti-inflammatory activities, have been discovered, supporting the fact that SFN and SFN-rich sources have great potential to be dietary supplements that are beneficial to health. This review summarizes the characteristics of intestinal inflammation, the anti-inflammatory mechanism of SFN and its various protective effects on intestinal inflammation, and the possible future applications of SFN for promoting intestinal health have also been discussed.
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Affiliation(s)
- Li-Yang Wei
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, People's Republic of China. .,School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Jiu-Kai Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, People's Republic of China.
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, People's Republic of China.
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22
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Chang CS, Liao YC, Huang CT, Lin CM, Cheung CHY, Ruan JW, Yu WH, Tsai YT, Lin IJ, Huang CH, Liou JS, Chou YH, Chien HJ, Chuang HL, Juan HF, Huang HC, Chan HL, Liao YC, Tang SC, Su YW, Tan TH, Bäumler AJ, Kao CY. Identification of a gut microbiota member that ameliorates DSS-induced colitis in intestinal barrier enhanced Dusp6-deficient mice. Cell Rep 2021; 37:110016. [PMID: 34818535 DOI: 10.1016/j.celrep.2021.110016] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/30/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Strengthening the gut epithelial barrier is a potential strategy for management of gut microbiota-associated illnesses. Here, we demonstrate that dual-specificity phosphatase 6 (Dusp6) knockout enhances baseline colon barrier integrity and ameliorates dextran sulfate sodium (DSS)-induced colonic injury. DUSP6 mutation in Caco-2 cells enhances the epithelial feature and increases mitochondrial oxygen consumption, accompanied by altered glucose metabolism and decreased glycolysis. We find that Dusp6-knockout mice are more resistant to DSS-induced dysbiosis, and the cohousing and fecal microbiota transplantation experiments show that the gut/fecal microbiota derived from Dusp6-knockout mice also confers protection against colitis. Further culturomics and mono-colonialization experiments show that one gut microbiota member in the genus Duncaniella confers host protection from DSS-induced injury. We identify Dusp6 deficiency as beneficial for shaping the gut microbiota eubiosis necessary to protect against gut barrier-related diseases.
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Affiliation(s)
- Cherng-Shyang Chang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Yi-Chu Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chih-Ting Huang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chiao-Mei Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | | | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Wen-Hsuan Yu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Ting Tsai
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - I-Jung Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062, Taiwan
| | - Ya-Hsien Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hung-Jen Chien
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hsiao-Li Chuang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, 11571, Taiwan
| | - Hsueh-Fen Juan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan; Center for Computational and Systems Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology and Department of Medical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Shiue-Cheng Tang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Cheng-Yuan Kao
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan; Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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23
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Esvap E, Ulgen KO. Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome. ACS Synth Biol 2021; 10:2121-2137. [PMID: 34402617 DOI: 10.1021/acssynbio.1c00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A genome-scale metabolic model (GEM) represents metabolic pathways of an organism in a mathematical form and can be built using biochemistry and genome annotation data. GEMs are invaluable for understanding organisms since they analyze the metabolic capabilities and behaviors quantitatively and can predict phenotypes. The development of high-throughput data collection techniques led to an immense increase in omics data such as metagenomics, which expand our knowledge on the human microbiome, but this also created a need for systematic analysis of these data. In recent years, GEMs have also been reconstructed for microbial species, including human gut microbiota, and methods for the analysis of microbial communities have been developed to examine the interaction between the organisms or the host. The purpose of this review is to provide a comprehensive guide for the applications of GEMs in microbial community analysis. Starting with GEM repositories, automatic GEM reconstruction tools, and quality control of models, this review will give insights into microbe-microbe and microbe-host interaction predictions and optimization of microbial community models. Recent studies that utilize microbial GEMs and personalized models to infer the influence of microbiota on human diseases such as inflammatory bowel diseases (IBD) or Parkinson's disease are exemplified. Being powerful system biology tools for both species-level and community-level analysis of microbes, GEMs integrated with omics data and machine learning techniques will be indispensable for studying the microbiome and their effects on human physiology as well as for deciphering the mechanisms behind human diseases.
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Affiliation(s)
- Elif Esvap
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
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24
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Le Guern R, Stabler S, Gosset P, Pichavant M, Grandjean T, Faure E, Karaca Y, Faure K, Kipnis E, Dessein R. Colonization resistance against multi-drug-resistant bacteria: a narrative review. J Hosp Infect 2021; 118:48-58. [PMID: 34492304 DOI: 10.1016/j.jhin.2021.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Colonization resistance by gut microbiota is a fundamental phenomenon in infection prevention and control. Hospitalized patients may be exposed to multi-drug-resistant bacteria when hand hygiene compliance among healthcare workers is not adequate. An additional layer of defence is provided by the healthy gut microbiota, which helps clear the exogenous bacteria and acts as a safety net when hand hygiene procedures are not followed. This narrative review focuses on the role of the gut microbiota in colonization resistance against multi-drug-resistant bacteria, and its implications for infection control. The review discusses the underlying mechanisms of colonization resistance (direct or indirect), the concept of resilience of the gut microbiota, the link between the antimicrobial spectrum and gut dysbiosis, and possible therapeutic strategies. Antimicrobial stewardship is crucial to maximize the effects of colonization resistance. Avoiding unnecessary antimicrobial therapy, shortening the antimicrobial duration as much as possible, and favouring antibiotics with low anti-anaerobe activity may decrease the acquisition and expansion of multi-drug-resistant bacteria. Even after antimicrobial therapy, the resilience of the gut microbiota often occurs spontaneously. Spontaneous resilience explains the existence of a window of opportunity for colonization of multi-drug-resistant bacteria during or just after antimicrobial therapy. Strategies favouring resilience of the gut microbiota, such as high-fibre diets or precision probiotics, should be evaluated.
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Affiliation(s)
- R Le Guern
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France.
| | - S Stabler
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - P Gosset
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - M Pichavant
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - T Grandjean
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - E Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - Y Karaca
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - K Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - E Kipnis
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Réanimation Chirurgicale, CHU Lille, Lille, France
| | - R Dessein
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France
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25
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Chamorro N, Montero DA, Gallardo P, Farfán M, Contreras M, De la Fuente M, Dubois K, Hermoso MA, Quera R, Pizarro-Guajardo M, Paredes-Sabja D, Ginard D, Rosselló-Móra R, Vidal R. Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:223-238. [PMID: 34527721 PMCID: PMC8404152 DOI: 10.15698/mic2021.09.760] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 06/02/2021] [Accepted: 06/13/2021] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn's disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.
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Affiliation(s)
- Nayaret Chamorro
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
| | - David A. Montero
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
| | - Pablo Gallardo
- Facultad de Medicina, Departamento de Pediatría y Cirugía Infantil, Campus Oriente-Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Chile
| | - Mauricio Farfán
- Facultad de Medicina, Departamento de Pediatría y Cirugía Infantil, Campus Oriente-Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Chile
| | - Mauricio Contreras
- Facultad de Ciencias Básicas, Departamento de Física, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
| | - Marjorie De la Fuente
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
| | - Karen Dubois
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
| | - Marcela A. Hermoso
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
| | - Rodrigo Quera
- Programa Enfermedad Inflamatoria Intestinal. Servicio de Gastroenterología, Clínica Las Condes, Santiago, Chile
- Gastroenterología, Clínica Universidad de Los Andes, Santiago, Chile
| | - Marjorie Pizarro-Guajardo
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Daniel Ginard
- Department of Gastroenterology and Palma Health Research Institute, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Chile
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26
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Antunes JC, Seabra CL, Domingues JM, Teixeira MO, Nunes C, Costa-Lima SA, Homem NC, Reis S, Amorim MTP, Felgueiras HP. Drug Targeting of Inflammatory Bowel Diseases by Biomolecules. NANOMATERIALS 2021; 11:nano11082035. [PMID: 34443866 PMCID: PMC8401460 DOI: 10.3390/nano11082035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel disease (IBD) is a group of disabling, destructive and incurable immune-mediated inflammatory diseases comprising Crohn’s disease (CD) and ulcerative colitis (UC), disorders that are highly prevalent worldwide and demand a large investment in healthcare. A persistent inflammatory state enables the dysfunction and destruction of healthy tissue, hindering the initiation and endurance of wound healing. Current treatments are ineffective at counteracting disease progression. Further, increased risk of serious side effects, other comorbidities and/or opportunistic infections highlight the need for effective treatment options. Gut microbiota, the key to preserving a healthy state, may, alternatively, increase a patient’s susceptibility to IBD onset and development given a relevant bacterial dysbiosis. Hence, the main goal of this review is to showcase the main conventional and emerging therapies for IBD, including microbiota-inspired untargeted and targeted approaches (such as phage therapy) to infection control. Special recognition is given to existing targeted strategies with biologics (via monoclonal antibodies, small molecules and nucleic acids) and stimuli-responsive (pH-, enzyme- and reactive oxygen species-triggered release), polymer-based nanomedicine that is specifically directed towards the regulation of inflammation overload (with some nanosystems additionally functionalized with carbohydrates or peptides directed towards M1-macrophages). The overall goal is to restore gut balance and decrease IBD’s societal impact.
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Affiliation(s)
- Joana Costa Antunes
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
- Correspondence: ; Tel.: +351-253-510-289
| | - Catarina Leal Seabra
- Laboratório Associado para a Química Verde (LAQV), Network of Chemistry and Technology (REQUIMTE), Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (C.L.S.); (C.N.); (S.A.C.-L.); (S.R.)
| | - Joana Margarida Domingues
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
| | - Marta Oliveira Teixeira
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
| | - Cláudia Nunes
- Laboratório Associado para a Química Verde (LAQV), Network of Chemistry and Technology (REQUIMTE), Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (C.L.S.); (C.N.); (S.A.C.-L.); (S.R.)
| | - Sofia Antunes Costa-Lima
- Laboratório Associado para a Química Verde (LAQV), Network of Chemistry and Technology (REQUIMTE), Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (C.L.S.); (C.N.); (S.A.C.-L.); (S.R.)
| | - Natália Cândido Homem
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
| | - Salette Reis
- Laboratório Associado para a Química Verde (LAQV), Network of Chemistry and Technology (REQUIMTE), Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (C.L.S.); (C.N.); (S.A.C.-L.); (S.R.)
| | - Maria Teresa Pessoa Amorim
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
| | - Helena Prado Felgueiras
- Centre for Textile Science and Technology (2C2T), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal; (J.M.D.); (M.O.T.); (N.C.H.); (M.T.P.A.); (H.P.F.)
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27
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Patel A, Carlson RP, Henson MA. In silico analysis of synthetic multispecies biofilms for cellobiose-to-isobutanol conversion reveals design principles for stable and productive communities. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Morvan C, Folgosa F, Kint N, Teixeira M, Martin-Verstraete I. Responses of Clostridia to oxygen: from detoxification to adaptive strategies. Environ Microbiol 2021; 23:4112-4125. [PMID: 34245087 DOI: 10.1111/1462-2920.15665] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022]
Abstract
Clostridia comprise bacteria of environmental, biotechnological and medical interest and many commensals of the gut microbiota. Because of their strictly anaerobic lifestyle, oxygen is a major stress for Clostridia. However, recent data showed that these bacteria can cope with O2 better than expected for obligate anaerobes through their ability to scavenge, detoxify and consume O2 . Upon O2 exposure, Clostridia redirect their central metabolism onto pathways less O2 -sensitive and induce the expression of genes encoding enzymes involved in O2 -reduction and in the repair of oxidized damaged molecules. While Faecalibacterium prausnitzii efficiently consumes O2 through a specific extracellular electron shuttling system requiring riboflavin, enzymes such as rubrerythrins and flavodiiron proteins with NAD(P)H-dependent O2 - and/or H2 O2 -reductase activities are usually encoded in other Clostridia. These two classes of enzymes play indeed a pivotal role in O2 tolerance in Clostridioides difficile and Clostridium acetobutylicum. Two main signalling pathways triggering O2 -induced responses have been described so far in Clostridia. PerR acts as a key regulator of the O2 - and/or reactive oxygen species-defence machinery while in C. difficile, σB , the sigma factor of the general stress response also plays a crucial role in O2 tolerance by controlling the expression of genes involved in O2 scavenging and repair systems.
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Affiliation(s)
- Claire Morvan
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Nicolas Kint
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
- Institut Universitaire de France, Paris, France
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29
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Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine. Annu Rev Microbiol 2021; 75:199-222. [PMID: 34314593 DOI: 10.1146/annurev-micro-060221-012134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human microbiome plays an important role in human health and disease. Meta-omics analyses provide indispensable data for linking changes in microbiome composition and function to disease etiology. Yet, the lack of a mechanistic understanding of, e.g., microbiome-metabolome links hampers the translation of these findings into effective, novel therapeutics. Here, we propose metabolic modeling of microbial communities through constraint-based reconstruction and analysis (COBRA) as a complementary approach to meta-omics analyses. First, we highlight the importance of microbial metabolism in cardiometabolic diseases, inflammatory bowel disease, colorectal cancer, Alzheimer disease, and Parkinson disease. Next, we demonstrate that microbial community modeling can stratify patients and controls, mechanistically link microbes with fecal metabolites altered in disease, and identify host pathways affected by the microbiome. Finally, we outline our vision for COBRA modeling combined with meta-omics analyses and multivariate statistical analyses to inform and guide clinical trials, yield testable hypotheses, and ultimately propose novel dietary and therapeutic interventions. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Arianna Basile
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Department of Psychiatry and Psychotherapy, University of Greifswald, 17489 Greifswald, Germany
| | - Cyrille Thinnes
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Division of Microbiology, National University of Ireland, Galway, H91 TK33, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
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30
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Breban M, Beaufrère M, Glatigny S. Intestinal dysbiosis in spondyloarthritis - chicken or egg? Curr Opin Rheumatol 2021; 33:341-347. [PMID: 33973546 DOI: 10.1097/bor.0000000000000800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
PURPOSE OF REVIEW The well-established link between intestinal inflammation and spondyloarthritis (SpA) remains largely unexplained. Recent sequencing technologies have given access to a thorough characterization of the gut microbiota in healthy and disease conditions. This showed that inflammatory bowel disease (IBD) is associated with dysbiosis - i.e., disturbed gut microbiota composition - which may contribute to disease pathogenesis. Whether gut dysbiosis exists in SpA and could contribute to disease development or be a bystander consequence of chronic inflammation is a question of major interest. RECENT FINDINGS Several metagenomic studies have been performed in SpA. Most of them concerned faecal samples and showed dysbiosis consisting in a reduction of microbial biodiversity in a way similar to what has been described in IBD. They also highlighted changes in microbial taxa composition that could contribute to the inflammatory process. Likewise, healthy carriers of human leukocyte antigen (HLA)-B27 exhibited gut dysbiosis, indicating that this predisposing allele could exert its pathogenic effect by influencing microbiota composition, and possibly by driving antigen-specific cross-reactive immune response. On the other hand, SpA treatments were associated with a reduction of dysbiosis, showing that it is at least in part a consequence of inflammation. SUMMARY Recent insights from metagenomic studies warrant further investigations to identify the mechanisms by which microbial dysbiosis could contribute to SpA development. This would bring novel therapeutic opportunities aiming at correcting detrimental changes.
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Affiliation(s)
- Maxime Breban
- Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, Montigny-le-Bretonneux
- Service de Rhumatologie, Hôpital Ambroise Paré, AP-HP, Boulogne
- Laboratoire d'Excellence Inflamex, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marie Beaufrère
- Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, Montigny-le-Bretonneux
- Service de Rhumatologie, Hôpital Ambroise Paré, AP-HP, Boulogne
- Laboratoire d'Excellence Inflamex, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Simon Glatigny
- Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, Montigny-le-Bretonneux
- Laboratoire d'Excellence Inflamex, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Rahman S, Davids M, van Hamersveld PHP, Welting O, Rahaoui H, Schuren F, Meijer SL, van den Wijngaard RM, Hakvoort TBM, de Jonge WJ, Heinsbroek SEM. Dietary Curdlan Enhances Bifidobacteria and Reduces Intestinal Inflammation in Mice. Nutrients 2021; 13:1305. [PMID: 33920960 PMCID: PMC8071228 DOI: 10.3390/nu13041305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
β-glucan consumption is known for its beneficial health effects, but the mode of action is unclear. While humans and mice lack the required enzymes to digest β-glucans, certain intestinal microbes can digest β-glucans, triggering gut microbial changes. Curdlan, a particulate β-glucan isolated from Alcaligenes faecalis, is used as a food additive. In this study we determined the effect of curdlan intake in mice on the intestinal microbiota and dextran sodium sulfate (DSS)-induced intestinal inflammation. The effect of curdlan on the human intestinal microbiota was assessed using i-screen, an assay for studying anaerobic microbial interactions. Mice received oral gavage with vehicle or curdlan for 14 days followed by DSS for 7 days. The curdlan-fed group showed reduced weight loss and colonic inflammation compared to the vehicle-fed group. Curdlan intake did not induce general microbiota community changes, although a specific Bifidobacterium, closely related to Bifidobacterium choerinum, was observed to be 10- to 100-fold more prevalent in the curdlan-fed group under control and colitis conditions, respectively. When tested in i-screen, curdlan induced a global change in the microbial composition of the healthy intestinal microbiota from a human. Overall, these results suggest that dietary curdlan induces microbiota changes that could reduce intestinal inflammation.
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Affiliation(s)
- Shafaque Rahman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
| | - Mark Davids
- Department of Vascular Medicine, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Patricia H. P. van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
| | - Olaf Welting
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
| | - Hakim Rahaoui
- The Netherlands Organization for Applied Scientific Research (TNO), 3704 HE Zeist, The Netherlands; (H.R.); (F.S.)
| | - Frank Schuren
- The Netherlands Organization for Applied Scientific Research (TNO), 3704 HE Zeist, The Netherlands; (H.R.); (F.S.)
| | - Sybren L. Meijer
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - René M. van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
| | - Theodorus B. M. Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
- Department of Surgery, University of Bonn, 53113 Bonn, Germany
| | - Sigrid E. M. Heinsbroek
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (O.W.); (R.M.v.d.W.); (T.B.M.H.); (W.J.d.J.)
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Dissecting Individual Interactions between Pathogenic and Commensal Bacteria within a Multispecies Gut Microbial Community. mSphere 2021; 6:6/2/e00013-21. [PMID: 33762315 PMCID: PMC8546675 DOI: 10.1128/msphere.00013-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.
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Jiang Y, Yuan Z, Shen Y, Rosa BA, Martin J, Cao S, Zhou Y, Mitreva M, Cao J. Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection. ACTA ACUST UNITED AC 2021; 28:1. [PMID: 33416489 PMCID: PMC7792497 DOI: 10.1051/parasite/2020074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022]
Abstract
Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype.
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Affiliation(s)
- Yanyan Jiang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Zhongying Yuan
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - John Martin
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - Shengkui Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, 06023 CT, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA - Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, 63001 MO, USA
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
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Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. Int J Mol Sci 2020; 21:ijms21249770. [PMID: 33371435 PMCID: PMC7767453 DOI: 10.3390/ijms21249770] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Damage to the tissue and the ruining of functions characterize autoimmune syndromes. This review centers around leaky gut syndromes and how they stimulate autoimmune pathogenesis. Lymphoid tissue commonly associated with the gut, together with the neuroendocrine network, collaborates with the intestinal epithelial wall, with its paracellular tight junctions, to maintain the balance, tolerance, and resistance to foreign/neo-antigens. The physiological regulator of paracellular tight junctions plays a vital role in transferring macromolecules across the intestinal barrier and thereby maintains immune response equilibrium. A new paradigm has explained the intricacies of disease development and proposed that the processes can be prevented if the interaction between the genetic factor and environmental causes is barred by re-instituting the intestinal wall function. The latest clinical evidence and animal models reinforce this current thought and offer the basis for innovative methodologies to thwart and treat autoimmune syndromes.
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35
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Tan P, Li X, Shen J, Feng Q. Fecal Microbiota Transplantation for the Treatment of Inflammatory Bowel Disease: An Update. Front Pharmacol 2020; 11:574533. [PMID: 33041818 PMCID: PMC7530266 DOI: 10.3389/fphar.2020.574533] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/20/2020] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has successfully been applied for the treatment of recurrent Clostridioides difficile infection (CDI), which has led to studies on its application to other gastrointestinal diseases and extraintestinal diseases associated with gut microbiota dysbiosis. Recently, the results of FMT for patients with inflammatory bowel disease (IBD) have been encouraging. However, studies have not fully clarified the clinical application of this emerging therapy. Here, we aimed to review the current knowledge in this fast-growing field and characterize the effectiveness, safety and mechanisms of FMT for the treatment of IBD patients.
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Affiliation(s)
- Pufang Tan
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaogang Li
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Feng
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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36
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Bilski J, Wojcik D, Danielak A, Mazur-Bialy A, Magierowski M, Tønnesen K, Brzozowski B, Surmiak M, Magierowska K, Pajdo R, Ptak-Belowska A, Brzozowski T. Alternative Therapy in the Prevention of Experimental and Clinical Inflammatory Bowel Disease. Impact of Regular Physical Activity, Intestinal Alkaline Phosphatase and Herbal Products. Curr Pharm Des 2020; 26:2936-2950. [DOI: 10.2174/1381612826666200427090127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are multifactorial, chronic, disabling, and progressive diseases characterised by cyclical nature, alternating between active and quiescent states. While the aetiology of IBD is not fully understood, this complex of diseases involve a combination of factors including the genetic predisposition and changes in microbiome as well as environmental risk factors such as high-fat and low-fibre diets, reduced physical activity, air pollution and exposure to various toxins and drugs such as antibiotics. The prevalence of both IBD and obesity is increasing in parallel, undoubtedly proving the existing interactions between these risk factors common to both disorders to unravel poorly recognized cell signaling and molecular alterations leading to human IBD. Therefore, there is still a significant and unmet need for supportive and adjunctive therapy for IBD patients directed against the negative consequences of visceral obesity and bacterial dysbiosis. Among the alternative therapies, a moderate-intensity exercise can benefit the health and well-being of IBD patients and improve both the healing of human IBD and experimental animal colitis. Intestinal alkaline phosphatase (IAP) plays an essential role in the maintenance of intestinal homeostasis intestinal and the mechanism of mucosal defence. The administration of exogenous IAP could be recommended as a therapeutic strategy for the cure of diseases resulting from the intestinal barrier dysfunction such as IBD. Curcumin, a natural anti-inflammatory agent, which is capable of stimulating the synthesis of endogenous IAP, represents another alternative approach in the treatment of IBD. This review was designed to discuss potential “nonpharmacological” alternative and supplementary therapeutic approaches taking into account epidemiological and pathophysiological links between obesity and IBD, including changes in the functional parameters of the intestinal mucosa and alterations in the intestinal microbiome.
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Affiliation(s)
- Jan Bilski
- Department of Ergonomics and Exercise Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Dagmara Wojcik
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Aleksandra Danielak
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Agnieszka Mazur-Bialy
- Department of Ergonomics and Exercise Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Marcin Magierowski
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Katherine Tønnesen
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Bartosz Brzozowski
- Gastroenterology and Hepatology Clinic, Jagiellonian University Medical College, Cracow, Poland
| | - Marcin Surmiak
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Katarzyna Magierowska
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Robert Pajdo
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Agata Ptak-Belowska
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Tomasz Brzozowski
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
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Charlet R, Bortolus C, Sendid B, Jawhara S. Bacteroides thetaiotaomicron and Lactobacillus johnsonii modulate intestinal inflammation and eliminate fungi via enzymatic hydrolysis of the fungal cell wall. Sci Rep 2020; 10:11510. [PMID: 32661259 PMCID: PMC7359362 DOI: 10.1038/s41598-020-68214-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Alterations to the gut microbiota can cause an amplification of the inflammatory response to intestinal pathogens. We assessed the effect of Bacteroides thetaiotaomicron and Lactobacillus johnsonii on the elimination of Candida species and whether restoration of these two anaerobic bacteria could attenuate the development of colitis in mice. In this study, L. johnsonii and B. thetaiotaomicron interacted directly with Candida species and induced a degradation of the fungal cell wall, mediated via chitinase-like and mannosidase-like activities, which promoted the inhibition of Candida species growth. In the DSS-induced colitis model, oral administration of L. johnsonii and B. thetaiotaomicron to mice reduced the overgrowth of Escherichia coli, Enterococcus faecalis and Candida glabrata populations and resulted in a significant reduction in inflammatory parameters. L. johnsonii and B. thetaiotaomicron decreased pro-inflammatory mediators and enhanced the anti-inflammatory cytokine response with high TLR9 expression and chitinase-like protein-1 activation, which promoted the elimination of C. glabrata from the gut. Overall, these findings provide evidence that L. johnsonii and B. thetaiotaomicron decrease the development of colitis mediated by TLR9 and promote the elimination of C. glabrata from the gut via chitinase-like and mannosidase-like activities.
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Affiliation(s)
- Rogatien Charlet
- CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, INSERM U1285, 59000, Lille, France.,University of Lille, 1 place Verdun, 59000, Lille, France.,CHU Lille, Service de Parasitologie Mycologie, Pôle de Biologie Pathologie Génétique, 59000, Lille, France
| | - Clovis Bortolus
- CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, INSERM U1285, 59000, Lille, France.,University of Lille, 1 place Verdun, 59000, Lille, France.,CHU Lille, Service de Parasitologie Mycologie, Pôle de Biologie Pathologie Génétique, 59000, Lille, France
| | - Boualem Sendid
- CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, INSERM U1285, 59000, Lille, France.,University of Lille, 1 place Verdun, 59000, Lille, France.,CHU Lille, Service de Parasitologie Mycologie, Pôle de Biologie Pathologie Génétique, 59000, Lille, France
| | - Samir Jawhara
- CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, INSERM U1285, 59000, Lille, France. .,University of Lille, 1 place Verdun, 59000, Lille, France. .,CHU Lille, Service de Parasitologie Mycologie, Pôle de Biologie Pathologie Génétique, 59000, Lille, France.
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39
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Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis 2020; 26:1843-1855. [PMID: 32469069 PMCID: PMC7676424 DOI: 10.1093/ibd/izaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis. METHODS The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.
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Affiliation(s)
- Nur M Shahir
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy R Wang
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E Ashley Wolber
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew S Schaner
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicole Chaumont
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy S Sadiq
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Koruda
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- Department of Surgery, REX Healthcare of Wakefield, Wakefield, North Carolina, USA
| | - B Darren Nix
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Rodney D Newberry
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shehzad Z Sheikh
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terrence S Furey
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Biology, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Address correspondence to: Terrence S. Furey, PhD, Departments of Genetics and Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 ()
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Chen Y, Zhang L, Hong G, Huang C, Qian W, Bai T, Song J, Song Y, Hou X. Probiotic mixtures with aerobic constituent promoted the recovery of multi-barriers in DSS-induced chronic colitis. Life Sci 2019; 240:117089. [PMID: 31759038 DOI: 10.1016/j.lfs.2019.117089] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/12/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022]
Abstract
AIMS Gut microbiota has been closely linked to the mucosal immune and been regarded as a reliable target for intestinal inflammation. This study aimed to explore the therapeutic roles of probiotic mixtures of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis with (quadruple probiotics, P-qua) or without (triple probiotics, P-tri) aerobic Bacillus cereus in colitis, focusing on the multiple barrier functions. MATERIALS AND METHODS Chronic colitis was induced by dextran sulfate sodium (DSS) in C57BL/6 mice. The probiotic mixtures P-qua or P-tri was gavage administrated respectively, while fecal microbiota transplantation (FMT) as a positive control. The intestinal inflammation and functions of multiple barriers were assessed, including the mucus barrier, epithelial barrier and endothelial barrier known as gut-vascular barrier (GVB). Altered composition and diversity in gut microbiota were observed via sequencing analysis. KEY FINDINGS Both P-qua and P-tri relieved the intestinal inflammation and improved the functions of multiple barriers with increased integrity of mucous layer, enhanced transepithelial electrical resistance, declined epithelial and endothelial permeability to macromolecules in DSS-colitis. Aerobe-contained P-qua revealed a more active role in barrier recovering relative to P-tri, while FMT as a positive control seemed to get better results than pure probiotics. Indeed, P-qua was effective in rebuilding the structure and diversity of gut flora in DSS-colitis, especially increased abundance of Bifidobacterium, Akkermansia, Lactobacillus and Bacteroides. SIGNIFICANCE Aerobe-contained P-qua was a powerful adjuvant therapy for chronic colitis, via restoring the intestinal microflora and recovering the multi-barriers in the inflamed gut.
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Affiliation(s)
- Yuhua Chen
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lei Zhang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Gaichao Hong
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chao Huang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Qian
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jun Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yuhu Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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41
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Montalban-Arques A, Scharl M. Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy. EBioMedicine 2019; 48:648-655. [PMID: 31631043 PMCID: PMC6838386 DOI: 10.1016/j.ebiom.2019.09.050] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/06/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed cancers and leading cause of cancer-related deaths worldwide. In recent years, there has been a growing realisation that lifestyle plays a major role for CRC development and that intestinal microbiota, which are shaped by lifestyle and nutrition habits, may be critically involved in the pathogenesis of CRC. Although the precise mechanisms for how the microbiota contribute to CRC development and progression remain elusive, increasing evidence suggests a direct causative role for the intestinal microbiota in modulating signalling pathways, anti-tumour immune responses and cell proliferation. Recent advances in understanding host-microbe interactions have shed light onto the putative use of intestinal microbiota as a powerful tool in CRC diagnosis and therapy. Here, we will discuss the role of the intestinal microbiota in CRC pathogenesis, their potential utility as diagnostic markers, and consider how microbes could be used in therapeutic approaches for the treatment of CRC.
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Affiliation(s)
- Ana Montalban-Arques
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland.
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42
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Babbar A, Hitch TCA, Pabst O, Clavel T, Hübel J, Eswaran S, Wagner N, Schippers A. The Compromised Mucosal Immune System of β7 Integrin-Deficient Mice Has Only Minor Effects on the Fecal Microbiota in Homeostasis. Front Microbiol 2019; 10:2284. [PMID: 31636620 PMCID: PMC6787405 DOI: 10.3389/fmicb.2019.02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract is an ideal habitat for diverse bacterial species that reside in a homeostatic balance with local tissue and significantly contribute to host health. Negative shifts in gut microbiota profiles, also known as dysbiosis, may be implicated in the development of chronic disorders such as inflammatory bowel diseases (IBD). Adhesion molecule-dependent recruitment of immune cells to the gut is an important step in IBD pathogenesis. The adhesion molecule β7 integrin contributes to the development of the gut-associated lymphoid tissue (GALT), intestinal immune cell homing, and immune responses and is known to promote intestinal inflammation. Although many studies underlined the role of the gut microbiota in shaping the mucosal immune system, studies on the influence of the host immune system on the microbiota are rare, especially in homeostasis. We addressed this question via comparative 16S rRNA gene amplicon analysis of fecal microbial communities from wild-type and β7 integrin-deficient mice, the latter being characterized by a compromised GALT. Besides subtle changes in relative abundances of Muribaculaceae spp. and unknown members of the families Ruminococcaceae and Lachnospiraceae, there was altogether no major difference in microbiota profiles in β7 integrin-deficient mice vs. wild-type littermates. This indicates that, in conditions of homeostasis, there is only a minor influence of the host immune system on the fecal microbiota in our mouse model, stressing the potential importance of pathological factors for dysbiosis development.
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Affiliation(s)
- Anshu Babbar
- Department of Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Jessica Hübel
- Department of Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Sreepradha Eswaran
- Department of Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Norbert Wagner
- Department of Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Angela Schippers
- Department of Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
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43
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Martínez N, Hidalgo-Cantabrana C, Delgado S, Margolles A, Sánchez B. Filling the gap between collection, transport and storage of the human gut microbiota. Sci Rep 2019; 9:8327. [PMID: 31171823 PMCID: PMC6554407 DOI: 10.1038/s41598-019-44888-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.
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Affiliation(s)
- Noelia Martínez
- Microviable Therapeutics SL. Edificio Severo Ochoa, Campus de El Cristo. C/Fernando Bonguera s/n, 33006, Oviedo, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain
| | - Abelardo Margolles
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain
| | - Borja Sánchez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain.
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Patel A, Carlson RP, Henson MA. In Silico Metabolic Design of Two-Strain Biofilm Systems Predicts Enhanced Biomass Production and Biochemical Synthesis. Biotechnol J 2019; 14:e1800511. [PMID: 30927492 DOI: 10.1002/biot.201800511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/20/2019] [Indexed: 11/09/2022]
Abstract
Engineered biofilm consortia have the potential to solve important biotechnological problems that have proved difficult for monoculture biofilms and planktonic consortia, such as conversion of lignocellulosic material to useful biochemicals. While considerable experimental progress has been reported for engineering and characterizing biofilm consortia, the field still lacks in silico tools for simulation, design, and optimization of stable, robust, and productive designed consortia. We developed biofilm consortia metabolic models for two coculture systems centered around the ecological design motif of a primary cell type that utilizes a supplied electron donor and secretes acetate as a byproduct and a secondary cell type that consumes the acetate, relieving byproduct inhibition on the primary cell type and enhancing overall system biomass. The models presented in this paper predict that distinct metabolic niches for the two cell types could be established by supplying electron donors and acceptors at opposite ends of the biofilm and that acetate consumption by the secondary cell type could increase total biomass accumulation and the synthesis of valuable biochemicals, such as isobutanol, by the primary cell type. System tunability is enhanced when each cell type is supplied with a unique terminal electron acceptor at opposite ends of the biofilm rather than competing for a common electron acceptor. Our model provides good qualitative agreement with data for a synthetic Escherichia coli coculture system, suggesting that the proposed design rules may have wide applicability to engineered biofilm consortia.
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Affiliation(s)
- Ayushi Patel
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering Montana State University, Bozeman, MT, 59717, USA
| | - Michael A Henson
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
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An In Vitro Study of the Influence of Curcuma longa Extracts on the Microbiota Modulation Process, In Patients with Hypertension. Pharmaceutics 2019; 11:pharmaceutics11040191. [PMID: 31003502 PMCID: PMC6523074 DOI: 10.3390/pharmaceutics11040191] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
The multiple causes of cardiovascular diseases signify a major incidence and developmental risk of this pathology. One of the processes accountable for this pathologic development is the instauration of dysbiosis and its connection with an inflammatory process. Low antioxidant colonic protection encourages the progression of inflammation, with cardiovascular dysfunctions being a secondary consequence of the dysbiosis. Curcumin is one of the bioactive compounds displaying promising results for the reduction of an inflammatory process. The present study aims at demonstrating the capacity of three extracts drawn from Curcuma (C.) longa through an in vitro simulation process, for microbiota modulation in patients with hypertension. The acidic pH in the extraction process determined a high curcumin content in the extracts. The major phenolic compound identified was curcumin III, 622 ± 6.88 µg/mL for the ethanol/water/acetic acid extract. Low EC50 values were associated (0.2 µg/mL for DPPH scavenging activity) with the presence of curcumin isomers. A metabolic pattern became evident because the relationship between the short-chain fatty acids acted as a clinical biomarker. The curcumin present stimulated the formation of butyric and propionic acids. Microbiota activity control included a high degree of curcumin degradation and biotransformation in the other phenolic compounds. This developmental process was supported by the progression in the enterobacteria with a corresponding escalation in the pH level. The metabolomic pattern demonstrated a performance similar to the administration of dietary fibre, with the positive effects being dose-dependent.
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46
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Byndloss MX, Litvak Y, Bäumler AJ. Microbiota-nourishing Immunity and Its Relevance for Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:811-815. [PMID: 30698700 PMCID: PMC6769399 DOI: 10.1093/ibd/izz004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Indexed: 12/15/2022]
Abstract
An imbalance in our microbiota may contribute to many human diseases, but the mechanistic underpinnings of dysbiosis remain poorly understood. We argue that dysbiosis is secondary to a defect in microbiota-nourishing immunity, a part of our immune system that balances the microbiota to attain colonization resistance against environmental exposure to microorganisms. We discuss this new hypothesis and its implications for ulcerative colitis, an inflammatory bowel disease of the large intestine.
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Affiliation(s)
- Mariana X Byndloss
- Vanderbilt Institute for Infection, Immunology, and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
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47
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Tandon D, Haque MM, Gote M, Jain M, Bhaduri A, Dubey AK, Mande SS. A prospective randomized, double-blind, placebo-controlled, dose-response relationship study to investigate efficacy of fructo-oligosaccharides (FOS) on human gut microflora. Sci Rep 2019; 9:5473. [PMID: 30940833 PMCID: PMC6445088 DOI: 10.1038/s41598-019-41837-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Fructo-oligosaccharides (FOS), a prebiotic supplement, is known for its Bifidogenic capabilities. However, aspects such as effect of variable quantities of FOS intake on gut microbiota, and temporal dynamics of gut microbiota (transitioning through basal, dosage, and follow-up phases) has not been studied in detail. This study investigated these aspects through a randomized, double-blind, placebo-controlled, dose-response relationship study. The study involved 80 participants being administered FOS at three dose levels (2.5, 5, and 10 g/day) or placebo (Maltodextrin 10 g/day) during dosage phase. Microbial DNA extracted from fecal samples collected at 9 intervening time-points was sequenced and analysed. Results indicate that FOS consumption increased the relative abundance of OTUs belonging to Bifidobacterium and Lactobacillus. Interestingly, higher FOS dosage appears to promote, in contrast to Maltodextrin, the selective proliferation of OTUs belonging to Lactobacillus. While consumption of prebiotics increased bacterial diversity, withdrawal led to its reduction. Apart from probiotic bacteria, a significant change was also observed in certain butyrate-producing microbes like Faecalibacterium, Ruminococcus and Oscillospira. The positive impact of FOS on butyrate-producing bacteria and FOS-mediated increased bacterial diversity reinforces the role of prebiotics in conferring beneficial functions to the host.
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Affiliation(s)
- Disha Tandon
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India
| | - Mohammed Monzoorul Haque
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India
| | - Manoj Gote
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Manish Jain
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Anirban Bhaduri
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Ashok Kumar Dubey
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India.
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India.
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48
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Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota. Processes (Basel) 2019. [DOI: 10.3390/pr7020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota and reduce competition for available nutrients, resulting in imbalance among commensal species and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of C. difficile with commensal species from the three dominant phyla in the human gut, we developed a multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile, Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance. We tuned the model to produce species abundances and short-chain fatty acid levels consistent with available data for healthy individuals. The model predicted that experimentally-observed host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels and/or increased primary bile acid levels would induce large increases in C. difficile abundance and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation of increased host nitrate secretion, the model also was able to predict increased E. coli abundance associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient levels and disease progression, the model generated hypotheses for future testing and has the capability to support the development of new treatment strategies for C. difficile gut infections.
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49
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Levy AN, Allegretti JR. Insights into the role of fecal microbiota transplantation for the treatment of inflammatory bowel disease. Therap Adv Gastroenterol 2019; 12:1756284819836893. [PMID: 30906424 PMCID: PMC6421596 DOI: 10.1177/1756284819836893] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 02/16/2019] [Indexed: 02/04/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has changed the treatment landscape of Clostridium difficile infection (CDI). Emerging evidence has shown that FMT can also be an effective and safe treatment strategy in CDI with underlying inflammatory bowel disease (IBD). Recently, randomized controlled trials of FMT in ulcerative colitis support its expanding role in restoring gut homeostasis in this disease. However, heterogeneous study designs leave several questions yet to be answered, including how to best position this novel therapy in the treatment approach of Crohn's disease and pouchitis. Additional studies are needed to validate whether FMT can assume a complementary role in the standard treatment of IBD.
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Affiliation(s)
- Alexander N. Levy
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, USA
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50
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Abstract
An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.
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Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.
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