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Jang CS, Kim H, Kim D, Han B. MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data. Genes Genomics 2024; 46:701-712. [PMID: 38700829 PMCID: PMC11102407 DOI: 10.1007/s13258-024-01514-w] [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: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND The importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human microbiome are 16S rRNA gene sequencing (16S sequencing) and whole-genome shotgun sequencing (WGS). Owing to the full coverage of the genome in sequencing, WGS has multiple advantages over 16S sequencing, including higher taxonomic profiling resolution at the species-level and functional profiling analysis. However, 16S sequencing remains widely used because of its relatively low cost. Although WGS is the standard method for obtaining accurate species-level data, we found that 16S sequencing data contained rich information to predict high-resolution species-level abundances with reasonable accuracy. OBJECTIVE In this study, we proposed MicroPredict, a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data. METHODS We employed a mixed model using two key strategies: (1) modeling both sample- and species-specific information for predicting WGS abundances, and (2) accounting for the possible correlations among different species. RESULTS We found that MicroPredict outperformed the other machine learning methods. CONCLUSION We expect that our approach will help researchers accurately approximate the species-level abundances of microbiome profiles in datasets for which only cost-effective 16S sequencing has been applied.
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Affiliation(s)
- Chloe Soohyun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hakin Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea
| | - Donghyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea.
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2
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Ambrogi M, Vezina CM. Roles of airway and intestinal epithelia in responding to pathogens and maintaining tissue homeostasis. Front Cell Infect Microbiol 2024; 14:1346087. [PMID: 38736751 PMCID: PMC11082347 DOI: 10.3389/fcimb.2024.1346087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/10/2024] [Indexed: 05/14/2024] Open
Abstract
Epithelial cells form a resilient barrier and orchestrate defensive and reparative mechanisms to maintain tissue stability. This review focuses on gut and airway epithelia, which are positioned where the body interfaces with the outside world. We review the many signaling pathways and mechanisms by which epithelial cells at the interface respond to invading pathogens to mount an innate immune response and initiate adaptive immunity and communicate with other cells, including resident microbiota, to heal damaged tissue and maintain homeostasis. We compare and contrast how airway and gut epithelial cells detect pathogens, release antimicrobial effectors, collaborate with macrophages, Tregs and epithelial stem cells to mount an immune response and orchestrate tissue repair. We also describe advanced research models for studying epithelial communication and behaviors during inflammation, tissue injury and disease.
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Affiliation(s)
| | - Chad M. Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
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3
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Saadh MJ, Ahmed HM, Alani ZK, Al Zuhairi RAH, Almarhoon ZM, Ahmad H, Ubaid M, Alwan NH. The Role of Gut-derived Short-Chain Fatty Acids in Multiple Sclerosis. Neuromolecular Med 2024; 26:14. [PMID: 38630350 DOI: 10.1007/s12017-024-08783-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
Multiple sclerosis (MS) is a chronic condition affecting the central nervous system (CNS), where the interplay of genetic and environmental factors influences its pathophysiology, triggering immune responses and instigating inflammation. Contemporary research has been notably dedicated to investigating the contributions of gut microbiota and their metabolites in modulating inflammatory reactions within the CNS. Recent recognition of the gut microbiome and dietary patterns as environmental elements impacting MS development emphasizes the potential influence of small, ubiquitous molecules from microbiota, such as short-chain fatty acids (SCFAs). These molecules may serve as vital molecular signals or metabolic substances regulating host cellular metabolism in the intricate interplay between microbiota and the host. A current emphasis lies on optimizing the health-promoting attributes of colonic bacteria to mitigate urinary tract issues through dietary management. This review aims to spotlight recent investigations on the impact of SCFAs on immune cells pivotal in MS, the involvement of gut microbiota and SCFAs in MS development, and the considerable influence of probiotics on gastrointestinal disruptions in MS. Comprehending the gut-CNS connection holds promise for the development of innovative therapeutic approaches, particularly probiotic-based supplements, for managing MS.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | - Hani Moslem Ahmed
- Department of Dental Industry Techniques, Al-Noor University College, Nineveh, Iraq
| | - Zaid Khalid Alani
- College of Health and Medical Technical, Al-Bayan University, Baghdad, Iraq
| | | | - Zainab M Almarhoon
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Hijaz Ahmad
- Section of Mathematics, International Telematic University Uninettuno, Corso Vittorio Emanuele II, 39, 00186, Rome, Italy.
- Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Mubarak Al-Abdullah, Kuwait.
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
| | - Mohammed Ubaid
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
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Ciccia F, Dussias NK, Gandolfo S, Rizzello F, Gionchetti P. The effect of anti-TNF drugs on the intestinal microbiota in patients with spondyloarthritis, rheumatoid arthritis, and inflammatory bowel diseases. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2024; 5:27-33. [PMID: 38571933 PMCID: PMC10985709 DOI: 10.1515/rir-2024-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 11/30/2023] [Indexed: 04/05/2024]
Abstract
Spondyloarthritis (SpA), rheumatoid arthritis (RA), and inflammatory bowel diseases (IBD) are chronic inflammatory autoimmune diseases that are associated with alterations in the composition of the intestinal microbiota (i.e., dysbiosis). For SpA and RA, a gut-joint-enthesis axis is hypothesized and recent data suggests that dysbiosis may contribute directly to initiating and perpetuating joint and spine inflammation. Biologic drugs targeting tumor necrosis factor (TNF) are effective in treating these diseases and have been shown to partially restore the disrupted microbiome. Hence, drugs that affect both the intestinal and joint components of these diseases, such as anti-TNF drugs, may act on the intestinal microbiome. However, despite the remarkable efficacy of anti-TNF-α treatments, non-responders are frequent, and predictors of patient outcomes have not been identified. In this narrative review, we summarize recent research on the downstream effects of anti-TNF drugs on the intestinal microbiota in SpA, RA, and IBD. We also discuss whether these changes could have a role as predictive biomarkers of anti-TNF response.
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Affiliation(s)
- Francesco Ciccia
- Rheumatology Unit, Department of Precision Medicine, Università degli Studi della Campania “L. Vanvitelli”, Naples, Italy
| | - Nikolas Konstantine Dussias
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, SSD Malattie Infiammatorie Croniche Intestinali, University of Bologna, BolognaItaly
| | - Saviana Gandolfo
- Rheumatology Unit, Azienda Ospedaliera San Giovanni Bosco, Naples, Italy
| | - Fernando Rizzello
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, SSD Malattie Infiammatorie Croniche Intestinali, University of Bologna, BolognaItaly
| | - Paolo Gionchetti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, SSD Malattie Infiammatorie Croniche Intestinali, University of Bologna, BolognaItaly
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5
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Loch FN, Kamphues C, Menzel P, Schwarzer R, Beyer K, Schineis C. Mucosal microbiome of surgically treated terminal ileal Crohn's disease. Front Cell Infect Microbiol 2024; 13:1324668. [PMID: 38282618 PMCID: PMC10811112 DOI: 10.3389/fcimb.2023.1324668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024] Open
Abstract
Crohn's disease (CD) is associated with changes in the microbiome. The role of these changes and their precise association with disease course and activity remain ambiguous. In this prospective single-center study, the mucosal microbiome of surgical CD and non-CD patients was compared at the time of surgery. Microbial analyses were individually performed for ileal and colonic tissue samples obtained during surgery using 16S-rRNA-gene amplicon sequencing. Three groups out of the 46 included patients were formed: 1) a study group of CD of patients who received ileocecal resection due to CD involvement (CD study, n=10); 2) a control group of non-CD of patients who received intestinal resection due to indications other than CD (non-CD control, n=27); and 3) a second control group of CD who underwent resection of the intestine not affected by CD (CD non-affected control, n=9). Species richness and Shannon diversity were not different between all formed groups and regions analyzed (p>0.05). Several significant taxonomic differences were seen at the phylum-, order-, and genus-levels between the formed groups, such as a decrease of Firmicutes (phylum-level) and an increase of Bacteroides and Escherichia/Shigella/Pseudescherichia (genus-level) in CD study - colon vs. the non-CD control - colon (p ≤ 0.05). The CD non-affected control presented the largest amount of differentially abundant taxa in comparison to the other groups. These results underline that CD is accompanied by changes in affected and non-affected intestinal regions compared to non-CD controls. This study contributes the mucosal microbiome of a well-defined subset of surgical CD patients without confounding aspects of the fecal microbiome or regional microbial differences to the existing literature.
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Affiliation(s)
- Florian N. Loch
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Peter Menzel
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | | | - Katharina Beyer
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Schineis
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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K I, Y M, A N, D S, G G, R S, D G, V SN, O S, M F, S R, S O, J MG, A M. Cognitive behavioral and mindfulness with daily exercise intervention is associated with changes in intestinal microbial taxa and systemic inflammation in patients with Crohn's disease. Gut Microbes 2024; 16:2337269. [PMID: 38591914 PMCID: PMC11005811 DOI: 10.1080/19490976.2024.2337269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease associated with psychological distress and intestinal microbial changes. Here, we examined whether a 3-month period of Cognitive Behavioral and Mindfulness with Daily Exercise (COBMINDEX) intervention, which improves the wellbeing and inflammatory state of CD patients, may also affect their gut microbiome. Gut microbiota, circulating inflammatory markers and hormones were analyzed in 24 CD patients before (T1) and after 3 months of COBMINDEX (T2), and in 25 age- and sex-matched wait-list control patients at the corresponding time-points. Microbiota analysis examined relative taxonomical abundance, alpha and beta diversity, and microbiome correlations with inflammatory and psychological parameters. At T1, CD patients exhibited a characteristic microbial profile mainly constituted of Proteobacteria (17.71%), Firmicutes (65.56%), Actinobacteria (8.46%) and Bacteroidetes (6.24%). Baseline bacterial abundances showed significant correlations with psychological markers of distress and with IFNγ . Following COBMINDEX, no significant changes in alpha and beta diversity were observed between both study groups, though a trend change in beta diversity was noted. Significant changes occurred in the abundance of phyla, families and genera only among the COBMINDEX group. Furthermore, abundance of phyla, families and genera that were altered following COBMNIDEX, significantly correlated with levels of cytokines and psychological parameters. Our results demonstrated that a short-term intervention of COBMINDEX was associated with changes in microbial indices, some of which are linked to psychological manifestations and systemic inflammation in CD patients. Psychological interventions to reduce chronic stress, such as COBMINDEX, appear to be beneficial in mitigating the pathobiology of CD patients, and may thus provide a useful adjunct to pharmacological therapy.
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Affiliation(s)
- Ilan K
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Motro Y
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Nemirovsky A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Schwartz D
- Department of Gastroenterology and Hepatology, Soroka Medical Center, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Goren G
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sergienko R
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Greenberg D
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Slonim-Nevo V
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sarid O
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Friger M
- Department of Epidemiology, Biostatistics and Community Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Regev S
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Odes S
- Department of Gastroenterology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moran-Gilad J
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Monsonego A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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7
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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. mSystems 2023; 8:e0068823. [PMID: 37942948 PMCID: PMC10734470 DOI: 10.1128/msystems.00688-23] [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: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE To our knowledge, IL-10-KO mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD. We showed that a diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane and protected mice to varying degrees against disease symptoms, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet, further reducing symptoms, as well as increased gut bacterial richness, increased bacterial community similarity to each other, and more location-specific communities than older mice on the diet intervention. Crohn's disease disrupts the lives of patients and requires people to alter dietary and lifestyle habits to manage symptoms. The current medical treatment is expensive with significant side effects, and a dietary intervention represents an affordable, accessible, and simple strategy to reduce the burden of symptoms.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
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Elzayat H, Malik T, Al-Awadhi H, Taha M, Elghazali G, Al-Marzooq F. Deciphering salivary microbiome signature in Crohn's disease patients with different factors contributing to dysbiosis. Sci Rep 2023; 13:19198. [PMID: 37932491 PMCID: PMC10628307 DOI: 10.1038/s41598-023-46714-8] [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: 06/14/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral dysbiosis in CD is poorly understood. We aimed to explore microbiome signature and dysbiosis of the salivary microbiome in CD patients, and correlate microbiota changes to the level of inflammation. Saliva samples were collected from healthy controls (HC) and CD patients (n = 40 per group). Salivary microbiome was analyzed by sequencing the entire 16S rRNA gene. Inflammatory biomarkers (C-reactive protein and calprotectin) were measured and correlated with microbiome diversity. Five dominant species were significantly enriched in CD, namely Veillonella dispar, Megasphaera stantonii, Prevotella jejuni, Dolosigranulum pigrum and Lactobacillus backii. Oral health had a significant impact on the microbiome since various significant features were cariogenic as Streptococcus mutans or periopathogenic such as Fusobacterium periodonticum. Furthermore, disease activity, duration and frequency of relapses impacted the oral microbiota. Treatment with monoclonal antibodies led to the emergence of a unique species called Simonsiella muelleri. Combining immunomodulatory agents with monoclonal antibodies significantly increased multiple pathogenic species such as Salmonella enterica, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Loss of diversity in CD was shown by multiple diversity indices. There was a significant negative correlation between gut inflammatory biomarkers (particularly calprotectin) and α-diversity, suggesting more inflammation associated with diversity loss in CD. Salivary dysbiosis was evident in CD patients, with unique microbiota signatures and perturbed species that can serve as disease biomarkers or potential targets for microbiota modulation. The interplay of various factors collectively contributed to dysbiosis, although each factor probably had a unique effect on the microbiome. The emergence of pathogenic bacteria in the oral cavity of CD patients is alarming since they can disturb gut homeostasis and induce inflammation by swallowing, or hematogenous spread of microbiota, their metabolites, or generated inflammatory mediators.
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Affiliation(s)
- Hala Elzayat
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 15551, Al Ain, UAE
| | - Talha Malik
- Department of Medicine, Sheikh Shakhbout Medical City, Abu Dhabi, UAE
| | - Haifa Al-Awadhi
- Department of Pediatric Gastroenterology, Tawam Hospital, Al Ain, UAE
| | - Mazen Taha
- Department of Internal Medicine, Tawam Hospital, Al Ain, UAE
| | - Gehad Elghazali
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 15551, Al Ain, UAE
- Department of Immunology, Sheikh Khalifa Medical City, Union71-Purehealth, Abu Dhabi, UAE
| | - Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 15551, Al Ain, UAE.
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, UAE.
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Cai X, Zhou N, Zou Q, Peng Y, Xu L, Feng L, Liu X. Integration of taxa abundance and occurrence frequency to identify key gut bacteria correlated to clinics in Crohn's disease. BMC Microbiol 2023; 23:247. [PMID: 37661264 PMCID: PMC10476393 DOI: 10.1186/s12866-023-02999-3] [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: 11/15/2022] [Accepted: 08/29/2023] [Indexed: 09/05/2023] Open
Abstract
Bacteria abundance alternation in the feces or mucosa of Crohn's disease (CD) patients has long been applied to identify potential biomarkers for this disease, while the taxa occurrence frequency and their correlations with clinical traits were understudied. A total of 97 samples from the feces and gut mucosa were collected from CD patients and healthy controls (HCs), 16S rRNA-based analyses were performed to determine the changes in taxa abundance and occurrence frequency along CD and to correlate them with clinical traits. The results showed that bacteria communities were divergent between feces and mucosa, while the taxa abundance and occurrence frequency in both partitions showed similar exponential correlations. The decrease of specific fecal bacteria was much more effective in classifying the CD and HCs than that of the mucosal bacteria. Among them, Christensenellaceae_R-7_group and Ruminococcus were predicted as biomarkers by using random forest algorithm, which were persistently presented (> 71.40% in frequency) in the feces of the HCs with high abundance, whereas transiently presented in the feces (< 5.5% in frequency) and mucosa (< 18.18% in frequency) of CD patients with low abundance. Co-occurrence network analysis then identified them as hub taxa that drive the alternations of other bacteria and were positively correlated to the circuiting monocytes. The loss of specific bacteria in the healthy gut may cause great disturbance of gut microbiota, causing gut bacteria dysbiosis and correlated to immune disorders along CD, which might not only be developed as effective noninvasive biomarkers but also as therapy targets.
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Affiliation(s)
- Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Nan Zhou
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Zou
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Lijuan Feng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China.
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, 410008, China.
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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525953. [PMID: 36747766 PMCID: PMC9900910 DOI: 10.1101/2023.01.27.525953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Crohn's Disease (CD) is a presentation of Inflammatory Bowel Disease (IBD) that manifests in childhood and adolescence, and involves chronic and severe enterocolitis, immune and gut microbiome dysregulation, and other complications. Diet and gut-microbiota-produced metabolites are sources of anti-inflammatories which could ameliorate symptoms. However, questions remain on how IBD influences biogeographic patterns of microbial location and function in the gut, how early life transitional gut communities are affected by IBD and diet interventions, and how disruption to biogeography alters disease mediation by diet components or microbial metabolites. Many studies on diet and IBD use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated CD model. Interleukin-10-knockout (IL-10-KO) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed a control diet or one containing 10% (w/w) raw broccoli sprouts, which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to, and for 2 weeks after inoculation with Helicobacter hepaticus, which triggers Crohn's-like symptoms in these immune-impaired mice. The broccoli sprout diet increased sulforaphane in plasma; decreased weight stagnation, fecal blood, and diarrhea associated; and increased microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacteria in younger mice, and reduced the prevalence and abundance of pathobiont bacteria which trigger inflammation in the IL-10-KO mouse, for example; Escherichia coli and Helicobacter. Overall, the IL-10-KO mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA 04401
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
- Finch Therapeutics, Somerville, Massachusetts, USA 02143
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA 04469
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
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11
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Ordoñez-Rodriguez A, Roman P, Rueda-Ruzafa L, Campos-Rios A, Cardona D. Changes in Gut Microbiota and Multiple Sclerosis: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20054624. [PMID: 36901634 PMCID: PMC10001679 DOI: 10.3390/ijerph20054624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 05/13/2023]
Abstract
INTRODUCTION Multiple sclerosis (MS) is a chronic inflammatory neurodegenerative disease mediated by autoimmune reactions against myelin proteins and gangliosides in the grey and white matter of the brain and spinal cord. It is considered one of the most common neurological diseases of non-traumatic origin in young people, especially in women. Recent studies point to a possible association between MS and gut microbiota. Intestinal dysbiosis has been observed, as well as an alteration of short-chain fatty acid-producing bacteria, although clinical data remain scarce and inconclusive. OBJECTIVE To conduct a systematic review on the relationship between gut microbiota and multiple sclerosis. METHOD The systematic review was conducted in the first quarter of 2022. The articles included were selected and compiled from different electronic databases: PubMed, Scopus, ScienceDirect, Proquest, Cochrane, and CINAHL. The keywords used in the search were: "multiple sclerosis", "gut microbiota", and "microbiome". RESULTS 12 articles were selected for the systematic review. Among the studies that analysed alpha and beta diversity, only three found significant differences with respect to the control. In terms of taxonomy, the data are contradictory, but confirm an alteration of the microbiota marked by a decrease in Firmicutes, Lachnospiraceae, Bifidobacterium, Roseburia, Coprococcus, Butyricicoccus, Lachnospira, Dorea, Faecalibacterium, and Prevotella and an increase in Bacteroidetes, Akkermansia, Blautia, and Ruminocococcus. As for short-chain fatty acids, in general, a decrease in short-chain fatty acids, in particular butyrate, was observed. CONCLUSIONS Gut microbiota dysbiosis was found in multiple sclerosis patients compared to controls. Most of the altered bacteria are short-chain fatty acid (SCFA)-producing, which could explain the chronic inflammation that characterises this disease. Therefore, future studies should consider the characterisation and manipulation of the multiple sclerosis-associated microbiome as a focus of both diagnostic and therapeutic strategies.
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Affiliation(s)
| | - Pablo Roman
- Faculty of Health Sciences, Department of Nursing, Physiotherapy and Medicine, University of Almeria, 04120 Almeria, Spain
- Health Research Center, University of Almería, 04120 Almeria, Spain
| | - Lola Rueda-Ruzafa
- Faculty of Health Sciences, Department of Nursing, Physiotherapy and Medicine, University of Almeria, 04120 Almeria, Spain
- Correspondence:
| | - Ana Campos-Rios
- Laboratory of Neuroscience, CINBIO, University of Vigo, 36310 Vigo, Spain
- Laboratory of Neuroscience, Galicia Sur Health Research Institute (IISGS), 15706 Vigo, Spain
| | - Diana Cardona
- Faculty of Health Sciences, Department of Nursing, Physiotherapy and Medicine, University of Almeria, 04120 Almeria, Spain
- Health Research Center, University of Almería, 04120 Almeria, Spain
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12
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [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: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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Ma X, Lu X, Zhang W, Yang L, Wang D, Xu J, Jia Y, Wang X, Xie H, Li S, Zhang M, He Y, Jin P, Sheng J. Gut microbiota in the early stage of Crohn’s disease has unique characteristics. Gut Pathog 2022; 14:46. [DOI: 10.1186/s13099-022-00521-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Emerging evidence suggests that gut microbiota plays a predominant role in Crohn’s disease (CD). However, the microbiome alterations in the early stage of CD patients still remain unclear. The present study aimed to identify dysbacteriosis in patients with early CD and explore specific gut bacteria related to the progression of CD.
Methods
This study was nested within a longitudinal prospective Chinese CD cohort, and it included 18 early CD patients, 22 advanced CD patients and 30 healthy controls. The microbiota communities were investigated using high-throughput Illumina HiSeq sequencing targeting the V3–V4 region of 16S ribosomal DNA (rDNA) gene. The relationship between the gut microbiota and clinical characteristics of CD was analyzed.
Results
Differential microbiota compositions were observed in CD samples (including early and advanced CD samples) and healthy controls samples. Notably, Lachnospiracea_incertae_sedis and Parabacteroides were enriched in the early CD patients, Escherichia/Shigella, Enterococcus and Proteus were enriched in the advanced CD patients, and Roseburia, Gemmiger, Coprococcus, Ruminococcus 2, Butyricicoccus, Dorea, Fusicatenibacter, Anaerostipes, Clostridium IV were enriched in the healthy controls [LDA score (log10) > 2]. Furthermore, Kruskal–Wallis Rank sum test results showed that Blautia, Clostridium IV, Coprococcus, Dorea, Fusicatenibacter continued to significantly decrease in early and advanced CD patients, and Escherichia/Shigella and Proteus continued to significantly increase compared with healthy controls (P < 0.05). The PICRUSt analysis identified 16 remarkably different metabolic pathways [LDA score (log10) > 2]. Some genera were significantly correlated with various clinical parameters, such as fecal calprotectin, erythrocyte sedimentation rate, C-reactive protein, gland reduce, goblet cells decreased, clinical symptoms (P < 0.05).
Conclusions
Dysbacteriosis occurs in the early stage of CD and is associated with the progression of CD. This data provides a foundation that furthers the understanding of the role of gut microbiota in CD’s pathogenesis.
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14
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The Crosstalk between the Gut Microbiota Composition and the Clinical Course of Allergic Rhinitis: The Use of Probiotics, Prebiotics and Bacterial Lysates in the Treatment of Allergic Rhinitis. Nutrients 2022; 14:nu14204328. [PMID: 36297012 PMCID: PMC9607052 DOI: 10.3390/nu14204328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2022] Open
Abstract
Although massive progress in discovering allergic rhinitis (AR) aetiology has been made in recent years, its prevalence is still rising and it significantly impacts patients' lives. That is why further and non-conventional research elucidating the role of new factors in AR pathogenesis is needed, facilitating discoveries of new treatment approaches. One of these factors is the gut microbiota, with its specific roles in health and disease. This review presents the process of gut microbiota development, especially in early life, focusing on its impact on the immune system. It emphasizes the link between the gut microbiota composition and immune changes involved in AR development. Specifically, it elucidates the significant link between bacteria colonizing the gut and the Th1/Th2 imbalance. Probiotics, prebiotics and bacterial lysates, which are medications that restore the composition of intestinal bacteria and indirectly affect the clinical course of AR, are also discussed.
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15
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Chai Y, Ding S, Jiang L, Wang S, Yuan X, Jiang H, Fang J. The mitigative effect of ovotransferrin-derived peptide IQW on DSS-induced colitis via alleviating intestinal injury and reprogramming intestinal microbes. Front Nutr 2022; 9:927363. [PMID: 36118755 PMCID: PMC9478110 DOI: 10.3389/fnut.2022.927363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with multiple complications during its development, and it is difficult to cure. The aim of this study was to evaluate the alleviating effect of different concentrations of the bioactive peptide IQW (Ile-Gln-Trp) on dextran sodium sulfate (DSS)-induced colitis in mice. For this study, we randomly divided 56 ICR mice into seven groups: the (I) control (CON), (II) dextran sodium sulfate treatment (2.5% DSS), (III) IQW-DSS (20 μg/ml) treatment, (IV) IQW-DSS (40 μg/ml) treatment, (V) IQW-DSS (60 μg/ml) treatment, (VI) IQW-DSS (80 μg/ml) treatment, and (VII) IQW-DSS (100 μg/ml) groups. The results showed that IQW at 60 μg/ml alleviated body weight loss, improved the liver index (p < 0.05), and improved histomorphological and pathological changes in the colon compared to the DSS-treated group. IQW at 60 μg/ml and IQW at 80 μg/ml modified intestinal microbial disorders. In addition, IQW at 60 μg/ml significantly increased butyric acid levels and decreased valeric acid levels, while IQW at 80 μg/ml significantly increased isobutyric acid and isovaleric acid levels. Hence, IQW at a concentration of 60 μg/ml alleviates DSS-induced colitis by enhancing the body's anti-inflammatory ability and regulating intestinal flora and metabolic changes. In the above context, IQW at 60 μg/ml could be a potential candidate for IBD prevention and treatment.
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Affiliation(s)
- Yajuan Chai
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Sujuan Ding
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Lihong Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shuangshuang Wang
- Department of Cardiology, Wenling First People's Hospital (The Affiliated Wenling Hospital of Wenzhou Medical University), Wenling, China
| | - Xiangnan Yuan
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hongmei Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- *Correspondence: Hongmei Jiang
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Jun Fang
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16
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Yang Z, Yu R, Deng W, Wang W. Roles of 21 Genera of Human Gut Microbiota in Barrett's Esophagus Risk: A Mendelian Randomization Study. Front Genet 2022; 13:894900. [PMID: 35754845 PMCID: PMC9219910 DOI: 10.3389/fgene.2022.894900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Lack of definitive evidence supports the putative hypothesis that gut microbiota dysbiosis is associated with Barrett’s esophagus (BE). We conducted a two-sample Mendelian randomization study to assess the associations of 21 genera of human gut microbiota with BE. Methods: We identified independent genetic instruments for 21 genera of gut microbiota (including nine dominant genera, four core genera among individuals of European ancestry, and eight esophagus-specific genera of gut microbiota) from MiBioGen (up to 18,340 participants). We applied them to summary statistics from the largest publicly available genome-wide association study on BE (9,680 cases and 31,211 controls). We obtained the causal estimates of genetically predicted higher genera of gut microbiota and BE using the inverse variance weighting method. Sensitivity analyses included weighted median, MR-Egger, MR-RAPS, and MR-PRESSO. Results: We found that genetically predicted higher Actinomyces (OR: 0.76 per unit increase in log odds of having BE, 95% CI: 0.70–0.83) and higher Ruminiclostridium (OR: 0.75, 95% CI: 0.63–0.90) were significantly associated with a lower risk of BE. No associations of other genera of gut microbiota with BE were noted, apart from suggestive associations of higher Alistipes (OR: 0.77; 95% CI: 0.61–0.99), higher Eubacterium (OR: 0.89; 95% CI: 0.80–0.99), and higher Veillonella (OR: 0.76; 95% CI: 0.56–1.02) with a lower risk of BE, and higher Faecalibacterium (OR: 1.15; 95% CI: 0.99–1.33) with a higher risk of BE. Conclusion: This study suggests that higher Actinomyces and higher Ruminiclostridium might protect against BE.
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Affiliation(s)
- Zhao Yang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rong Yu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wei Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Weihu Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
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17
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Explainable Machine Learning for Longitudinal Multi-Omic Microbiome. MATHEMATICS 2022. [DOI: 10.3390/math10121994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the years, research studies have shown there is a key connection between the microbial community in the gut, genes, and immune system. Understanding this association may help discover the cause of complex chronic idiopathic disorders such as inflammatory bowel disease. Even though important efforts have been put into the field, the functions, dynamics, and causation of dysbiosis state performed by the microbial community remains unclear. Machine learning models can help elucidate important connections and relationships between microbes in the human host. Our study aims to extend the current knowledge of associations between the human microbiome and health and disease through the application of dynamic Bayesian networks to describe the temporal variation of the gut microbiota and dynamic relationships between taxonomic entities and clinical variables. We develop a set of preprocessing steps to clean, filter, select, integrate, and model informative metagenomics, metatranscriptomics, and metabolomics longitudinal data from the Human Microbiome Project. This study accomplishes novel network models with satisfactory predictive performance (accuracy = 0.648) for each inflammatory bowel disease state, validating Bayesian networks as a framework for developing interpretable models to help understand the basic ways the different biological entities (taxa, genes, metabolites) interact with each other in a given environment (human gut) over time. These findings can serve as a starting point to advance the discovery of novel therapeutic approaches and new biomarkers for precision medicine.
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18
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Does Anti-TNF-α Therapy Affect the Bacteriological Profile of Specimens Collected from Perianal Lesions? A Retrospective Analysis in Patients with Crohn's Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052892. [PMID: 35270584 PMCID: PMC8910208 DOI: 10.3390/ijerph19052892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023]
Abstract
Anal abscesses and fistulas are potential complications of Crohn’s disease (CD). Chronic immunosuppression, loose stools, and poor wound healing in this population present challenges to the management of perianal diseases. The purpose of the study was to determine the predominant bacterial species found in specimens from perianal lesions causing anal abscess and/or fistula drainage in hospitalized patients, and to compare the number and type of microorganisms isolated from samples taken from patients undergoing biological therapy or traditionally treated. The outcomes of studies of patients treated for anal abscesses or fistulas from 2017 to 2019 were evaluated. Data obtained from medical records included culture and antibiotic sensitivity results of swabs from perianal lesions of isolated microorganisms. A total of 373 swabs were collected from perianal lesions during the analysis period, including 51 (49 positive samples) from patients with CD. The predominant pathogen was Escherichia coli (55%, p < 0.001), the second most common microorganism was Staphylococcus aureus (14.3%, p < 0.001). In vitro susceptibility testing showed E. coli, ESBL (strain with Extended Spectrum Beta-Lactamase) in five cases, S. aureus, MRSA (methicillin-resistant S. aureus -resistant to all beta-lactam antibiotics: penicillins with inhibitors, cephalosporins, monobactams, carbapenems, except for ceftaroline) in one sample. Biologic therapy does not affect the type of microorganisms isolated from perianal abscesses in patients with CD.
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19
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Lampejo T. The significance of the gut microbiome in post-COVID-19 gastrointestinal symptoms. Clin Med (Lond) 2022; 22:189-190. [PMID: 38589193 DOI: 10.7861/clinmed.let.22.2.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Temi Lampejo
- Consultant in infectious diseases and virology, Kingʼns College Hospital, London, UK
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20
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The Nutrition-Microbiota-Physical Activity Triad: An Inspiring New Concept for Health and Sports Performance. Nutrients 2022; 14:nu14050924. [PMID: 35267899 PMCID: PMC8912693 DOI: 10.3390/nu14050924] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiota is currently the focus of converging interest in many diseases and sports performance. This review presents gut microbiota as a real “orchestra conductor” in the host’s physio(patho)logy due to its implications in many aspects of health and disease. Reciprocally, gut microbiota composition and activity are influenced by many different factors, such as diet and physical activity. Literature data have shown that macro- and micro-nutrients influence gut microbiota composition. Cumulative data indicate that gut bacteria are sensitive to modulation by physical activity, as shown by studies using training and hypoactivity models. Sports performance studies have also presented interesting and promising results. Therefore, gut microbiota could be considered a “pivotal” organ for health and sports performance, leading to a new concept: the nutrition-microbiota-physical activity triad. The next challenge for the scientific and medical communities is to test this concept in clinical studies. The long-term aim is to find the best combination of the three elements of this triad to optimize treatments, delay disease onset, or enhance sports performance. The many possibilities offered by biotic supplementation and training modalities open different avenues for future research.
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21
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de Sire A, de Sire R, Curci C, Castiglione F, Wahli W. Role of Dietary Supplements and Probiotics in Modulating Microbiota and Bone Health: The Gut-Bone Axis. Cells 2022; 11:cells11040743. [PMID: 35203401 PMCID: PMC8870226 DOI: 10.3390/cells11040743] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Osteoporosis is characterized by an alteration of bone microstructure with a decreased bone mineral density, leading to the incidence of fragility fractures. Around 200 million people are affected by osteoporosis, representing a major health burden worldwide. Several factors are involved in the pathogenesis of osteoporosis. Today, altered intestinal homeostasis is being investigated as a potential additional risk factor for reduced bone health and, therefore, as a novel potential therapeutic target. The intestinal microflora influences osteoclasts’ activity by regulating the serum levels of IGF-1, while also acting on the intestinal absorption of calcium. It is therefore not surprising that gut dysbiosis impacts bone health. Microbiota alterations affect the OPG/RANKL pathway in osteoclasts, and are correlated with reduced bone strength and quality. In this context, it has been hypothesized that dietary supplements, prebiotics, and probiotics contribute to the intestinal microecological balance that is important for bone health. The aim of the present comprehensive review is to describe the state of the art on the role of dietary supplements and probiotics as therapeutic agents for bone health regulation and osteoporosis, through gut microbiota modulation.
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Affiliation(s)
- Alessandro de Sire
- Physical Medicine and Rehabilitation Unit, Department of Medical and Surgical Sciences, University of Catanzaro “Magna Graecia”, 88100 Catanzaro, Italy
- Correspondence: (A.d.S.); (W.W.)
| | - Roberto de Sire
- Gastroenterology Unit, Department of Clinical Medicine and Surgery, University Federico II of Naples, 80126 Naples, Italy; (R.d.S.); (F.C.)
| | - Claudio Curci
- Physical Medicine and Rehabilitation Unit, Department of Neurosciences, ASST Carlo Poma, 46100 Mantova, Italy;
| | - Fabiana Castiglione
- Gastroenterology Unit, Department of Clinical Medicine and Surgery, University Federico II of Naples, 80126 Naples, Italy; (R.d.S.); (F.C.)
| | - Walter Wahli
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, Singapore 308232, Singapore
- Toxalim Research Center in Food Toxicology (UMR 1331), French National Research Institute for Agriculture, Food, and the Environment (INRAE), F-31300 Toulouse, France
- Center for Integrative Genomics, University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
- Correspondence: (A.d.S.); (W.W.)
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22
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Yan Z, Zhang K, Zhang K, Wang G, Wang L, Zhang J, Qiu Z, Guo Z, Song X, Li J. Integrated 16S rDNA Gene Sequencing and Untargeted Metabolomics Analyses to Investigate the Gut Microbial Composition and Plasma Metabolic Phenotype in Calves With Dampness-Heat Diarrhea. Front Vet Sci 2022; 9:703051. [PMID: 35242833 PMCID: PMC8885629 DOI: 10.3389/fvets.2022.703051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/10/2022] [Indexed: 12/26/2022] Open
Abstract
Dampness-heat diarrhea (DHD), a common syndrome in Chinese dairy farms, is mainly resulted from digestive system disorders, and accompanied with metabolic disorders in some cases. However, the underlying mechanisms in the intestinal microbiome and plasma metabolome in calves with DHD remain unclear. In order to investigate the pathogenesis of DHD in calves, multi-omics techniques including the 16S rDNA gene sequencing and metabolomics were used to analyze gut microbial compositions and plasma metabolic changes in calves. The results indicated that DHD had a significant effect on the intestinal microbial compositions in calves, which was confirmed by changes in microbial population and distribution. A total of 14 genera were changed, including Escherichia-Shigella, Bacteroides, and Fournierella, in calves with DHD (P < 0.05). Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated that 11 metabolic functions (level 2) were significantly enriched in DHD cases. The untargeted metabolomics analysis showed that 440 metabolites including bilineurin, phosphatidylcholine, and glutamate were significantly different between two groups (VIP > 1 and P < 0.05), and they were related to 67 signal pathways. Eight signal pathways including alpha-linolenic acid, linoleic acid, and glycerophospholipid metabolism were significantly enriched (P < 0.05), which may be potential biomarkers of plasma in calves with DHD. Further, 107 pairs of intestinal microbiota-plasma metabolite correlations were determined, e.g., Escherichia-Shigella was significantly associated with changes of sulfamethazine, butyrylcarnitine, and 14 other metabolites, which reflected that metabolic activity was influenced by the microbiome. These microbiota-metabolite pairs might have a relationship with DHD in calves. In conclusion, the findings revealed that DHD had effect on intestinal microbial compositions and plasma metabolome in calves, and the altered metabolic pathways and microorganisms might serve as diagnostic markers and potential therapeutic targets for DHD in calves.
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Affiliation(s)
- Zunxiang Yan
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Kang Zhang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Kai Zhang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Guibo Wang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Lei Wang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Jingyan Zhang
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Zhengying Qiu
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Zhiting Guo
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Xiaoping Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Xiaoping Song
| | - Jianxi Li
- Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- *Correspondence: Jianxi Li
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23
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Xiong J, Hu H, Xu C, Yin J, Liu M, Zhang L, Duan Y, Huang Y. Development of gut microbiota along with its metabolites of preschool children. BMC Pediatr 2022; 22:25. [PMID: 34991497 PMCID: PMC8734072 DOI: 10.1186/s12887-021-03099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Background To reveal the changes of intestinal microbial abundance and composition, as well as the microbiota metabolic levels of bile acids and short chain fatty acids of healthy preschool children during their growth. Methods Feces of 120 healthy newborns and 150 healthy children aged 6 months to 6 years were collected. Then the composition of intestinal flora was analyzed by 16S rRNA, and the contents of bile acids and short chain fatty acids in feces were detected by LC-MS and GS methods, respectively. Results The composition and function of intestinal microflora were not stable in neonatal period but significantly improved at 6 months after birth, and gradually stabilized and tended to adult-like formation after 2–3 years old. The levels of short chain fatty acids and secondary bile acids were consistent with the development of gut microbiota. Conclusion The age of 6 months may be a critical period for the development of intestinal microflora in children. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-021-03099-9.
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Affiliation(s)
- Jingjing Xiong
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Xishan District, Kunming, 650032, China
| | - Hongwei Hu
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Xishan District, Kunming, 650032, China
| | - Chuanzhi Xu
- Department of Statistics, School of Public Health, Kunming Medical University, Kunming, 650000, China
| | - Jianwen Yin
- Yunnan Center for Disease Control and Prevention, 158 Dongsi Street, Xishan District, Kunming, 650022, Yunnan, China
| | - Mei Liu
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Xishan District, Kunming, 650032, China
| | - Lizhi Zhang
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Xishan District, Kunming, 650032, China
| | - Yong Duan
- Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Yongkun Huang
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Xishan District, Kunming, 650032, China.
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24
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Mosby CA, Bhar S, Phillips MB, Edelmann MJ, Jones MK. Interaction with mammalian enteric viruses alters outer membrane vesicle production and content by commensal bacteria. J Extracell Vesicles 2022; 11:e12172. [PMID: 34981901 PMCID: PMC8725172 DOI: 10.1002/jev2.12172] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 01/22/2023] Open
Abstract
Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The importance of these organisms is further demonstrated by the widespread ability of enteric viruses to exploit commensal bacteria to enhance viral infection. These viruses interact directly with commensal bacteria, and while the impact of this interaction on viral infection is well described for several viruses, the impact on the commensal bacteria has yet to be explored. In this article, we demonstrate, for the first time, that enteric viruses alter the gene expression and phenotype of individual commensal bacteria. Human and murine norovirus interaction with bacteria resulted in genome-wide differential gene expression and marked changes in the surface architecture of the bacterial cells. Furthermore, the interaction of the virus with bacteria led to increased production of smaller outer membrane vesicles (OMVs). Enhanced production of smaller vesicles was also observed when noroviruses were incubated with other commensal bacteria, indicating a potentially broad impact of norovirus interaction. The vesicle production observed in the in vivo model followed a similar trend where an increased quantity of smaller bacterial vesicles was observed in stool collected from virus-infected mice compared to mock-infected mice. Furthermore, changes in vesicle size were linked to changes in protein content and abundance, indicating that viral binding induced a shift in the mechanism of the OMV biogenesis. Collectively, these data demonstrate that enteric viruses induce specific changes in bacterial gene expression, leading to changes in bacterial extracellular vesicle production that can potentially impact host responses to infection.
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Affiliation(s)
- Chanel A. Mosby
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Sutonuka Bhar
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Matthew B. Phillips
- Department of Molecular Genetics and MicrobiologyCollege of MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Mariola J. Edelmann
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Melissa K. Jones
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
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25
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A Comprehensive Evaluation of Enterobacteriaceae Primer Sets for Analysis of Host-Associated Microbiota. Pathogens 2021; 11:pathogens11010017. [PMID: 35055964 PMCID: PMC8780275 DOI: 10.3390/pathogens11010017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Enterobacteriaceae is one of the most important bacterial groups within the Proteobacteria phylum. This bacterial group includes pathogens, commensal and beneficial populations. Numerous 16S rRNA gene PCR-based assays have been designed to analyze Enterobacteriaceae diversity and relative abundance, and, to the best of our knowledge, 16 primer pairs have been validated, published and used since 2003. Nonetheless, a comprehensive performance analysis of these primer sets has not yet been carried out. This information is of particular importance due to the recent taxonomic restructuration of Enterobacteriaceae into seven bacterial families. To overcome this lack of information, the identified collection of primer pairs (n = 16) was subjected to primer performance analysis using multiple bioinformatics tools. Herein it was revealed that, based on specificity and coverage of the 16S rRNA gene, these 16 primer sets could be divided into different categories: Enterobacterales-, multi-family-, multi-genus- and Enterobacteriaceae-specific primers. These results highlight the impact of taxonomy changes on performance of molecular assays and data interpretation. Moreover, they underline the urgent need to revise and update the molecular tools used for molecular microbial analyses.
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26
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Jinnouchi M, Miyahara T, Suzuki Y. Coix Seed Consumption Affects the Gut Microbiota and the Peripheral Lymphocyte Subset Profiles of Healthy Male Adults. Nutrients 2021; 13:nu13114079. [PMID: 34836336 PMCID: PMC8618347 DOI: 10.3390/nu13114079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 01/01/2023] Open
Abstract
A systematic examination of the effects of traditional herbal medicines including their mechanisms could allow for their effective use and provide opportunities to develop new medicines. Coix seed has been suggested to promote spontaneous regression of viral skin infection. Purified oil from coix seed has also been suggested to increase the peripheral CD4+ lymphocytes. We, herein, attempt to shed more light on the way through which coix seed affects the human systemic immune function by hypothesizing that a central role to these changes could be played through changes in the gut microbiota. To that end, healthy adult males (n = 19) were divided into two groups; 11 of them consumed cooked coix seed (160 g per day) for 7 days (intervention), while the other eight were given no intervention. One week of coix seed consumption lead to an increase of the intestinal Faecalibacterium abundance and of the abundance (as % presence of overall peripheral lymphocytes) of CD3+CD8+ cells, CD4+ cells, CD4+CD25+ cells, and naïve/memory T cell ratio. As the relationship of microbiota and skin infection has not been clarified, our findings could provide a clue to a mechanism through which coix seed could promote the spontaneous regression of viral skin infections.
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27
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Hu T, Dong Y, Yang C, Zhao M, He Q. Pathogenesis of Children's Allergic Diseases: Refocusing the Role of the Gut Microbiota. Front Physiol 2021; 12:749544. [PMID: 34721073 PMCID: PMC8551706 DOI: 10.3389/fphys.2021.749544] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Allergic diseases comprise a genetically heterogeneous cluster of immunologically mediated diseases, including asthma, food allergy (FA), allergic rhinitis (AR) and eczema, that have become major worldwide health problems. Over the past few decades, the spread of allergic diseases has displayed an increasing trend, and it has been reported that 22% of 1.39 billion people in 30 countries have a type of allergic disease. Undoubtedly, allergic diseases, which can be chronic, with significant morbidity, mortality and dynamic progression, impose major economic burdens on society and families; thus, exploring the cause of allergic diseases and reducing their prevalence is a top priority. Recently, it has been reported that the gastrointestinal (GI) microbiota can provide vital signals for the development, function, and regulation of the immune system, and the above-mentioned contributions make the GI microbiota a key player in allergic diseases. Notably, the GI microbiota is highly influenced by the mode of delivery, infant diet, environment, antibiotic use and so on. Specifically, changes in the environment can result in the dysbiosis of the GI microbiota. The proper function of the GI microbiota depends on a stable cellular composition which in the case of the human microbiota consists mainly of bacteria. Large shifts in the ratio between these phyla or the expansion of new bacterial groups lead to a disease-promoting imbalance, which is often referred to as dysbiosis. And the dysbiosis can lead to alterations of the composition of the microbiota and subsequent changes in metabolism. Further, the GI microbiota can affect the physiological characteristics of the human host and modulate the immune response of the host. The objectives of this review are to evaluate the development of the GI microbiota, the main drivers of the colonization of the GI tract, and the potential role of the GI microbiota in allergic diseases and provide a theoretical basis as well as molecular strategies for clinical practice.
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Affiliation(s)
- Tingting Hu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yinmiao Dong
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Chenghao Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingnan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
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28
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Sultan S, El-Mowafy M, Elgaml A, Ahmed TAE, Hassan H, Mottawea W. Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease. Front Physiol 2021; 12:715506. [PMID: 34646151 PMCID: PMC8502967 DOI: 10.3389/fphys.2021.715506] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H2S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.
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Affiliation(s)
- Salma Sultan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Tamer A E Ahmed
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hebatoallah Hassan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Walid Mottawea
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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29
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Kriaa A, Jablaoui A, Rhimi S, Soussou S, Mkaouar H, Mariaule V, Gruba N, Gargouri A, Maguin E, Lesner A, Rhimi M. SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice. Cells 2021; 10:2658. [PMID: 34685638 PMCID: PMC8534766 DOI: 10.3390/cells10102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/20/2022] Open
Abstract
Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.
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Affiliation(s)
- Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Souha Soussou
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Ali Gargouri
- Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax Bp ‘1177’ 3018, Tunisia;
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
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30
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Kouzu K, Tsujimoto H, Kishi Y, Ueno H, Shinomiya N. Role of Microbial Infection-Induced Inflammation in the Development of Gastrointestinal Cancers. MEDICINES 2021; 8:medicines8080045. [PMID: 34436224 PMCID: PMC8400127 DOI: 10.3390/medicines8080045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022]
Abstract
There has been increasing evidence that a local inflammatory response stimulates tumor cells to acquire metastatic potential, and the concept of inflammatory oncotaxis has been spreading in recent years. However, the interaction between microbial inflammation and the development of gastrointestinal cancer is still unclear. This review summarizes the present knowledge on the role of microbial inflammation in the development of gastrointestinal cancers from the perspective of molecular biological findings. Chronic inflammation caused by bacterial infection is known to induce cancers as exemplified by Helicobacter pylori, which is associated with the development of gastric cancer via the activation of the TLR4 pathway by bacterial lipopolysaccharide followed by cancer growth through CagA-MET signaling. In addition, the development of inflammatory bowel diseases has been known to become a risk factor for colorectal cancers, where inflammation caused by certain bacterial infections plays a key role. It is also known that the cancer microenvironment is associated with cancer growth. Moreover, infectious complication after surgery for gastrointestinal cancers may promote tumor progression via the stimulation of pathogen-associated molecular patterns and various inflammatory mediators secreted by immunocytes. Further research on the link between microbial inflammation and cancer progression is needed to drive a paradigm shift in cancer treatment.
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Affiliation(s)
- Keita Kouzu
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
| | - Hironori Tsujimoto
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
- Correspondence: ; Tel.: +81-4-2995-1637
| | - Yoji Kishi
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
| | - Hideki Ueno
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
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31
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Alshehri D, Saadah O, Mosli M, Edris S, Alhindi R, Bahieldin A. Dysbiosis of gut microbiota in inflammatory bowel disease: Current therapies and potential for microbiota-modulating therapeutic approaches. Bosn J Basic Med Sci 2021; 21:270-283. [PMID: 33052081 PMCID: PMC8112554 DOI: 10.17305/bjbms.2020.5016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
There is a growing body of evidence reinforcing the unique connections between the host microbiome, health, and diseases. Due to the extreme importance of the symbiotic relationship between the intestinal microbiome and the host, it is not surprising that any alteration in the gut microbiota would result in various diseases, including inflammatory bowel disease (IBD), Crohn's disease, (CD) and ulcerative colitis (UC). IBD is a chronic, relapsing-remitting condition that is associated with significant morbidity, mortality, compromised quality of life, and costly medical care. Dysbiosis is believed to exacerbate the progression of IBD. One of the currently used treatments for IBD are anti-tumor necrosis factor (TNF) drugs, representing a biologic therapy that is reported to have an impact on the gut microbiota composition. The efficacy of anti-TNF agents is hindered by the possibility of non-response, which occurs in 10-20% of treated patients, and secondary loss of response, which occurs in up to 30% of treated patients. This underscores the need for novel therapies and studies that evaluate the role of the gut microbiota in these conditions. The success of any therapeutic strategy for IBD depends on our understanding of the interactions that occur between the gut microbiota and the host. In this review, the health and disease IBD-associated microbiota patterns will be discussed, in addition to the effect of currently used therapies for IBD on the gut microbiota composition, as well as new therapeutic approaches that can be used to overcome the current treatment constraints.
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Affiliation(s)
- Dikhnah Alshehri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Biology, Faculty of Science, Tabuk University, Tabuk, Saudi Arabia
| | - Omar Saadah
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; Inflammatory Bowel Disease Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmoud Mosli
- Inflammatory Bowel Disease Research Group, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt; Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rashad Alhindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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32
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Dionizio A, Uyghurturk DA, Melo CGS, Sabino-Arias IT, Araujo TT, Ventura TMS, Perles JVCM, Zanoni JN, Den Besten P, Buzalaf MAR. Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses. CHEMOSPHERE 2021; 273:129607. [PMID: 33508686 PMCID: PMC8076095 DOI: 10.1016/j.chemosphere.2021.129607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 05/10/2023]
Abstract
Gastrointestinal signs and symptoms are the first signs of toxicity due to exposure to fluoride (F). This suggests the possibility that lower levels of subchronic F exposure may affect the gut. The aim of this study was to evaluate changes in the morphology, proteome and microbiome of the ileum of rats, after subchronic exposure to F. Male rats ingested water with 0, 10, or 50 mgF/L for thirty days. Treatment with F, regardless of the dose, significantly decreased the density of HuC/D-IR neurons, whereas CGRP-IR and SP-IR varicosities were significantly increased compared to the control group. Increased VIP-IR varicosities were significantly increased only in the group treated with 50 mgF/L. A significant increase in thickness of the tunica muscularis, as well as in the total thickness of the ileum wall was observed at both F doses when compared to controls. In proteomics analysis, myosin isoforms were increased, and Gastrotopin was decreased in F-exposed mice. In the microbiome metagenomics analysis, Class Clostridia was significantly reduced upon exposure to 10 mgF/L. At the higher F dose of 50 mg/L, genus Ureaplasma was significantly reduced in comparison with controls. Morphological and proteomics alterations induced by F were marked by changes associated with inflammation, and alterations in the gut microbiome. Further studies are needed to determine whether F exposure increases inflammation with secondary effects of the gut microbiome, and/or whether primary effects of F on the gut microbiome enhance changes associated with inflammation.
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Affiliation(s)
- Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - Dawud Abduweli Uyghurturk
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, USA
| | | | | | - Tamara Teodoro Araujo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | | | | | | | - Pamela Den Besten
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, USA.
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33
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Maldonado-Arriaga B, Sandoval-Jiménez S, Rodríguez-Silverio J, Lizeth Alcaráz-Estrada S, Cortés-Espinosa T, Pérez-Cabeza de Vaca R, Licona-Cassani C, Gámez-Valdez JS, Shaw J, Mondragón-Terán P, Hernández-Cortez C, Suárez-Cuenca JA, Castro-Escarpulli G. Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis. Microbiologyopen 2021; 10:e1181. [PMID: 33970546 PMCID: PMC8087925 DOI: 10.1002/mbo3.1181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 12/22/2022] Open
Abstract
Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical‐endoscopic evidenced pancolitis (active phase n = 9 and remission phase n = 9), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus Roseburia and Faecalibacterium were enriched in remission pancolitis, and genera Bilophila and Fusobacterium were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.
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Affiliation(s)
- Brenda Maldonado-Arriaga
- Laboratorio de Metabolismo Experimental e Investigación Clínica, División de Investigación Clínica, C.M.N. "20 de Noviembre", ISSSTE and Hospital General de 2A Troncoso, Instituto Mexicano del Seguro Social, Ciudad de México, México.,Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Sergio Sandoval-Jiménez
- Laboratorio de Metabolismo Experimental e Investigación Clínica, División de Investigación Clínica, C.M.N. "20 de Noviembre", ISSSTE and Hospital General de 2A Troncoso, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | | | - Tomás Cortés-Espinosa
- Clínica de Enfermedad Inflamatoria Intestinal, Servicio de Gastroenterología, C.M.N. "20 de Noviembre", ISSSTE, Ciudad de México, México
| | - Rebeca Pérez-Cabeza de Vaca
- Coordinación de Investigación y División de Investigación Biomédica, C.M.N. "20 de Noviembre", ISSSTE, Ciudad de México, México
| | - Cuauhtémoc Licona-Cassani
- Laboratorio de Genómica Industrial, Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Monterrey, NL, Mexico
| | - July Stephany Gámez-Valdez
- Laboratorio de Genómica Industrial, Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Monterrey, NL, Mexico
| | - Jonathan Shaw
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - Paul Mondragón-Terán
- Coordinación de Investigación y División de Investigación Biomédica, C.M.N. "20 de Noviembre", ISSSTE, Ciudad de México, México
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Juan Antonio Suárez-Cuenca
- Laboratorio de Metabolismo Experimental e Investigación Clínica, División de Investigación Clínica, C.M.N. "20 de Noviembre", ISSSTE and Hospital General de 2A Troncoso, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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Jalanka J, Lam C, Bennett A, Hartikainen A, Crispie F, Finnegan LA, Cotter PD, Spiller R. Colonic Gene Expression and Fecal Microbiota in Diarrhea-predominant Irritable Bowel Syndrome: Increased Toll-like Receptor 4 but Minimal Inflammation and no Response to Mesalazine. J Neurogastroenterol Motil 2021; 27:279-291. [PMID: 33795545 PMCID: PMC8026366 DOI: 10.5056/jnm20205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Background/Aims Diarrhea-predominant irritable bowel syndrome (IBS-D) has been previously associated with evidence of immune activation and altered microbiota. Our aim is to assess the effect of the anti-inflammatory agent, mesalazine, on inflammatory gene expression and microbiota composition in IBS-D. Methods We studied a subset of patients (n = 43) from a previously published 12-week radomized placebo-controlled trial of mesalazine. Mucosal biopsies were assessed by immunohistochemistry and reverse transcription-polymerase chain reaction for a range of markers of inflammation, altered permeability, and sensory receptors including Toll-like receptors (TLRs) at randomization after treatment. All biopsy data were compared to 21 healthy controls. Patient’s stool microbiota composition was analysed through 16S ribosomal RNA sequencing. Results We found no evidence of increased immune activation compared to healthy controls. However, we did find increased expression of receptors in both sensory pathways and innate immune response including TLR4. Higher TLR4 expression was associated with greater urgency. TLR4 expression correlated strongly with the expression of the receptors bradykinin receptor B2, chemerin chemokine-like receptor 1, and transient receptor potential cation channel, subfamily A, member 1 as well as TLR4’s downstream adaptor myeloid differentiation factor 88. Mesalazine had minimal effect on either gene expression or microbiota composition. Conclusions Biopsies from a well-characterized IBS-D cohort showed no substantial inflammation. Mesalazine has little effect on gene expression and its previous reported effect on fecal microbiota associated with much greater inflammation found in inflammatory bowel diseases is likely secondary to reduced inflammation. Increased expression of TLR4 and correlated receptors in IBS may mediate a general increase in sensitivity to external stimuli, particularly those that signal via the TLR system.
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Affiliation(s)
- Jonna Jalanka
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Nottingham Digestive Diseases Center and NIHR Nottingham Biomedical Research Center at Nottingham University Hospitals NHS Trust, the University of Nottingham, Nottingham, Notts, UK
| | - Ching Lam
- Nottingham Digestive Diseases Center and NIHR Nottingham Biomedical Research Center at Nottingham University Hospitals NHS Trust, the University of Nottingham, Nottingham, Notts, UK
| | - Andrew Bennett
- Nottingham Digestive Diseases Center and NIHR Nottingham Biomedical Research Center at Nottingham University Hospitals NHS Trust, the University of Nottingham, Nottingham, Notts, UK.,FRAME Alternatives Laboratory, School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham, Notts, UK
| | - Anna Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fiona Crispie
- Teagasc Food Research Center, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Laura A Finnegan
- Teagasc Food Research Center, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Center, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Robin Spiller
- Nottingham Digestive Diseases Center and NIHR Nottingham Biomedical Research Center at Nottingham University Hospitals NHS Trust, the University of Nottingham, Nottingham, Notts, UK
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35
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Elhenawy W, Hordienko S, Gould S, Oberc AM, Tsai CN, Hubbard TP, Waldor MK, Coombes BK. High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. Nat Commun 2021; 12:2032. [PMID: 33795670 PMCID: PMC8016931 DOI: 10.1038/s41467-021-22306-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn's disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. Here, we conduct a high-resolution, in vivo genetic screen to map AIEC genes required for intestinal colonization of mice. In addition, we use in vivo RNA-sequencing to define the host-associated AIEC transcriptome. We identify diverse metabolic pathways required for efficient gut colonization by AIEC and show that a type IV secretion system (T4SS) is required to form biofilms on the surface of epithelial cells, thereby promoting AIEC persistence in the gut. E. coli isolated from CD patients are enriched for a T4SS, suggesting a possible connection to disease activity. Our findings establish the T4SS as a principal AIEC colonization factor and highlight the use of genome-wide screens in decoding the infection biology of CD-associated bacteria that otherwise lack a defined genetic signature.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Sarah Hordienko
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Steven Gould
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexander M Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Troy P Hubbard
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada.
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada.
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36
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Yersiniabactin Siderophore of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Is Involved in Autophagy Activation in Host Cells. Int J Mol Sci 2021; 22:ijms22073512. [PMID: 33805299 PMCID: PMC8037853 DOI: 10.3390/ijms22073512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/18/2023] Open
Abstract
Background: Adherent-invasive Escherichia coli (AIEC) have been implicated in the etiology of Crohn’s disease. The AIEC reference strain LF82 possesses a pathogenicity island similar to the high pathogenicity island of Yersinia spp., which encodes the yersiniabactin siderophore required for iron uptake and growth of the bacteria in iron-restricted environment. Here, we investigated the role of yersiniabactin during AIEC infection. Methods: Intestinal epithelial T84 cells and CEABAC10 transgenic mice were infected with LF82 or its mutants deficient in yersiniabactin expression. Autophagy was assessed by Western blot analysis for p62 and LC3-II expression. Results: Loss of yersiniabactin decreased the growth of LF82 in competitive conditions, reducing the ability of LF82 to adhere to and invade T84 cells and to colonize the intestinal tract of CEABAC10 mice. However, yersiniabactin deficiency increased LF82 intracellular replication. Mechanistically, a functional yersiniabactin is necessary for LF82-induced expression of HIF-1α, which is implicated in autophagy activation in infected cells. Conclusion: Our study highlights a novel role for yersiniabactin siderophore in AIEC–host interaction. Indeed, yersiniabactin, which is an advantage for AIEC to growth in a competitive environment, could be a disadvantage for the bacteria as it activates autophagy, a key host defense mechanism, leading to bacterial clearance.
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37
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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38
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Ming S, Zhang M, Liang Z, Li C, He J, Chen P, Zhang S, Niu X, Deng S, Geng L, Zhang G, Gong S, Wu Y. OX40L/OX40 Signal Promotes IL-9 Production by Mucosal MAIT Cells During Helicobacter pylori Infection. Front Immunol 2021; 12:626017. [PMID: 33777009 PMCID: PMC7990886 DOI: 10.3389/fimmu.2021.626017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Mucosal associated invariant T (MAIT) cells play a critical role in Helicobacter pylori (H. pylori)-induced gastritis by promoting mucosal inflammation and aggravating mucosal injuries (1, 2). However, the underlying mechanism and key molecules involved are still uncertain. Here we identified OX40, a co-stimulatory molecule mainly expressed on T cells, as a critical regulator to promote proliferation and IL-9 production by MAIT cells and facilitate mucosal inflammation in H. pylori-positive gastritis patients. Serum examination revealed an increased level of IL-9 in gastritis patients. Meanwhile, OX40 expression was increased in mucosal MAIT cells, and its ligand OX40L was also up-regulated in mucosal dendritic cells (DCs) of gastritis patients, compared with healthy controls. Further results demonstrated that activation of the OX40/OX40L pathway promoted IL-9 production by MAIT cells, and MAIT cells displayed a highly-activated phenotype after the cross-linking of OX40 and OX40L. Moreover, the level of IL-9 produced by MAIT cells was positively correlated with inflammatory indexes in the gastric mucosa, suggesting the potential role of IL-9-producing MAIT cells in mucosal inflammation. Taken together, we elucidated that OX40/OX40L axis promoted mucosal MAIT cell proliferation and IL-9 production in H. pylori-induced gastritis, which may provide potential targeting strategies for gastritis treatment.
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Affiliation(s)
- Siqi Ming
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China.,Center for Infection and Immunity, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Mei Zhang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Zibin Liang
- Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Chunna Li
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jianzhong He
- Department of Pathology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Peiyu Chen
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Shunxian Zhang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Xiaoli Niu
- Center for Infection and Immunity, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shimei Deng
- Center for Infection and Immunity, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lanlan Geng
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Sitang Gong
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Yongjian Wu
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China.,Center for Infection and Immunity, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Iljazovic A, Roy U, Gálvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, Schmidt-Hohagen K, Neumann-Schaal M, Strowig T. Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Mucosal Immunol 2021; 14:113-124. [PMID: 32433514 PMCID: PMC7790746 DOI: 10.1038/s41385-020-0296-4] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Diverse microbial signatures within the intestinal microbiota have been associated with intestinal and systemic inflammatory diseases, but whether these candidate microbes actively modulate host phenotypes or passively expand within the altered microbial ecosystem is frequently not known. Here we demonstrate that colonization of mice with a member of the genus Prevotella, which has been previously associated to colitis in mice, exacerbates intestinal inflammation. Our analysis revealed that Prevotella intestinalis alters composition and function of the ecosystem resulting in a reduction of short-chain fatty acids, specifically acetate, and consequently a decrease in intestinal IL-18 levels during steady state. Supplementation of IL-18 to Prevotella-colonized mice was sufficient to reduce intestinal inflammation. Hence, we conclude that intestinal Prevotella colonization results in metabolic changes in the microbiota, which reduce IL-18 production and consequently exacerbate intestinal inflammation, and potential systemic autoimmunity.
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Affiliation(s)
- Aida Iljazovic
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Urmi Roy
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- Hannover Medical School, Hannover, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Bei Zhao
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Achim Gronow
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Sabine E Will
- Bacterial Metabolomics, Leibniz institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia D Hofmann
- Department of Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marina C Pils
- Mouse Pathology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Hannover Medical School, Hannover, Germany.
- Centre for Individualised Infection Medicine, Hannover, Germany.
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40
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Olaisen M, Flatberg A, Granlund AVB, Røyset ES, Martinsen TC, Sandvik AK, Fossmark R. Bacterial Mucosa-associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients With Crohn's Disease. Inflamm Bowel Dis 2021; 27:12-24. [PMID: 32448900 PMCID: PMC7737161 DOI: 10.1093/ibd/izaa107] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Microbiota is most likely essential in the pathogenesis of Crohn's disease (CD). Fecal diversion after ileocecal resection (ICR) protects against CD recurrence, whereas infusion of fecal content triggers inflammation. After ICR, the majority of patients experience endoscopic recurrence in the neoterminal ileum, and the ileal microbiome is of particular interest. We have assessed the mucosa-associated microbiome in the inflamed and noninflamed ileum in patients with CD. METHODS Mucosa-associated microbiome was assessed by 16S rRNA sequencing of biopsies sampled 5 and 15 cm orally of the ileocecal valve or ileocolic anastomosis. RESULTS Fifty-one CD patients and forty healthy controls (HCs) were included in the study. Twenty CD patients had terminal ileitis, with endoscopic inflammation at 5 cm, normal mucosa at 15 cm, and no history of upper CD involvement. Crohn's disease patients (n = 51) had lower alpha diversity and separated clearly from HC on beta diversity plots. Twenty-three bacterial taxa were differentially represented in CD patients vs HC; among these, Tyzzerella 4 was profoundly overrepresented in CD. The microbiome in the inflamed and proximal noninflamed ileal mucosa did not differ according to alpha diversity or beta diversity. Additionally, no bacterial taxa were differentially represented. CONCLUSIONS The microbiome is similar in the inflamed and proximal noninflamed ileal mucosa within the same patients. Our results support the concept of CD-specific microbiota alterations and demonstrate that neither ileal sublocation nor endoscopic inflammation influence the mucosa-associated microbiome.
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Affiliation(s)
- Maya Olaisen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav’s Hospital, Trondheim University Hospital, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elin Synnøve Røyset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pathology, St. Olav’s Hospital, Trondheim University Hospital, Norway
| | - Tom Christian Martinsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav’s Hospital, Trondheim University Hospital, Norway
| | - Arne Kristian Sandvik
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav’s Hospital, Trondheim University Hospital, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Reidar Fossmark
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav’s Hospital, Trondheim University Hospital, Norway
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Osaki H, Jodai Y, Koyama K, Omori T, Horiguchi N, Kamano T, Funasaka K, Nagasaka M, Nakagawa Y, Shibata T, Ohmiya N. Clinical response and changes in the fecal microbiota and metabolite levels after fecal microbiota transplantation in patients with inflammatory bowel disease and recurrent Clostridioides difficile infection. FUJITA MEDICAL JOURNAL 2021; 7:87-98. [PMID: 35111551 PMCID: PMC8749495 DOI: 10.20407/fmj.2020-021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/20/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES We determined the efficacy of fecal microbiota transplantation (FMT) and subsequent changes in fecal microbiota and short-chain fatty acid (SCFA) levels in patients with ulcerative colitis (UC), Crohn's disease (CD), and recurrent Clostridioides difficile infection (rCDI). METHODS A filtered solution of Japanese donor feces was endoscopically administered. The efficacy of FMT was evaluated after 8 weeks using the Mayo score, Crohn's Disease Activity Index (CDAI), and the absence of diarrhea with stool toxin negativity in patients with active UC, CD, and rCDI, respectively. For fecal microbiota analysis, the 16S ribosomal RNA gene was sequenced, and fecal SCFA levels were measured. RESULTS Clinical response was achieved in 5/20 (25%), 3/4 (75%), and 4/4 (100%) patients with UC, CD, and rCDI, respectively. Clinical remission was achieved in 4/20 (20%) and 1/4 (25%) patients with UC and CD, respectively. Linear discriminant analysis illustrated that UC responders had lower counts of Clostridium cluster XIVa before FMT and higher counts after FMT. Higher Fusicatenibacter saccharivorans counts in donors were significantly correlated with 8-week clinical remission. Patients with CD exhibited lower Blautia, Dorea, and Eubacterium counts before FMT and higher Collinsella, Dorea, and Eubacterium counts after FMT, accompanied by functional profiles predictive of SCFA fermentation and elevated fecal butyrate concentrations. Patients with rCDI displayed significantly lower abundances of Clostridium clusters IV and XIVa before FMT and higher abundances after FMT accompanied by elevated fecal propionate concentrations. CONCLUSIONS FMT exhibited various efficacy against UC, CD, and rCDI by altering the gut microbiota and SCFA production.
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Affiliation(s)
- Hayato Osaki
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Yasutaka Jodai
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Keishi Koyama
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Takafumi Omori
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Toshiaki Kamano
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Mitsuo Nagasaka
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
| | - Naoki Ohmiya
- Department of Gastroenterology, Fujita Health University, School of
Medicine, Toyoake, Aichi, Japan
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42
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Szałwińska P, Włodarczyk J, Spinelli A, Fichna J, Włodarczyk M. IBS-Symptoms in IBD Patients-Manifestation of Concomitant or Different Entities. J Clin Med 2020; 10:jcm10010031. [PMID: 33374388 PMCID: PMC7794700 DOI: 10.3390/jcm10010031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a functional heterogenous disease with a multifactorial pathogenesis. It is characterized by abdominal pain, discomfort, and alteration in gut motility. The occurrence of similar symptoms was observed in patients in clinical remission of inflammatory bowel diseases (IBD) that is Crohn's disease (CD) and ulcerative colitis (UC), which pathogenesis is also not fully understood. Hence, arose the question if these symptoms are "true IBS" imposed on IBD, or is it a subclinical form of IBD or even pre-IBD? In this article, based on a narrative overview of the literature, we try to find an answer to this query by discussing the pathogenesis and overlaps between these conditions.
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Affiliation(s)
- Patrycja Szałwińska
- Department of Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (P.S.); (J.W.); (J.F.)
| | - Jakub Włodarczyk
- Department of Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (P.S.); (J.W.); (J.F.)
- Department of General and Colorectal Surgery, Medical University of Lodz, Haller Square 1, 90-624 Lodz, Poland
| | - Antonino Spinelli
- Colon and Rectal Surgery Division, Humanitas Clinical and Research Center IRCCS, Rozzano, 20089 Milano, Italy;
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090 Milano, Italy
| | - Jakub Fichna
- Department of Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (P.S.); (J.W.); (J.F.)
| | - Marcin Włodarczyk
- Department of General and Colorectal Surgery, Medical University of Lodz, Haller Square 1, 90-624 Lodz, Poland
- Correspondence:
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Zhang W, Zou G, Li B, Du X, Sun Z, Sun Y, Jiang X. Fecal Microbiota Transplantation (FMT) Alleviates Experimental Colitis in Mice by Gut Microbiota Regulation. J Microbiol Biotechnol 2020; 30:1132-1141. [PMID: 32423189 PMCID: PMC9728197 DOI: 10.4014/jmb.2002.02044] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/10/2020] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel disease (IBD) is an increasing global burden and a predisposing factor to colorectal cancer. Although a number of treatment options are available, the side effects could be considerable. Studies on fecal microbiota transplantation (FMT) as an IBD intervention protocol require further validation as the underlying mechanisms for its attenuating effects remain unclear. This study aims to demonstrate the ameliorative role of FMT in an ulcerative colitis (UC) model induced by dextran sulfate sodium (DSS) and elucidate its relative mechanisms in a mouse model. It was shown that FMT intervention decreased disease activity index (DAI) levels and increased the body weight, colon weight and colon length of experimental animals. It also alleviated histopathological changes, reduced key cytokine expression and oxidative status in the colon. A down-regulated expression level of genes associated with NF-κB signaling pathway was also observed. The results of 16S rRNA gene sequencing showed that FMT intervention restored the gut microbiota to the pattern of the control group by increasing the relative abundance of Firmicutes and decreasing the abundances of Bacteroidetes and Proteobacteria. The relative abundances of the genera Lactobacillus, Butyricicoccus, Lachnoclostridium, Olsenella and Odoribacter were upregulated but Helicobacter, Bacteroides and Clostridium were reduced after FMT administration. Furthermore, FMT administration elevated the concentrations of SCFAs in the colon. In conclusion, FMT intervention could be suitable for UC control, but further validations via clinical trials are recommended.
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Affiliation(s)
- Wanying Zhang
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Guiling Zou
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Bin Li
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Xuefei Du
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Zhe Sun
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Yu Sun
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China
| | - Xiaofeng Jiang
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin 150001, P.R. China,Heilongjiang Longwei Precision Medical Laboratory Center, Longchuan Road, Songbei District, Harbin 150028, P.R. China,Corresponding author Phone: +86-0451-85716079 Fax: +86-0451-85716079 E-mail:
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Gut Microbiota Profile in Patients with Type 1 Diabetes Based on 16S rRNA Gene Sequencing: A Systematic Review. DISEASE MARKERS 2020; 2020:3936247. [PMID: 32908614 PMCID: PMC7474751 DOI: 10.1155/2020/3936247] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023]
Abstract
The gut microbiota has been presumed to have a role in the pathogenesis of type 1 diabetes (T1D). Significant changes in the microbial composition of T1D patients have been reported in several case-control studies. This study is aimed at systematically reviewing the existing literature, which has investigated the alterations of the intestinal microbiome in T1D patients compared with healthy controls (HCs) using 16S ribosomal RNA-targeted sequencing. The databases of MEDLINE, EMBASE, Web of Science, and the Cochrane Library were searched until April 2019 for case-control studies comparing the composition of the intestinal microbiome in T1D patients and HCs based on 16S rRNA gene sequencing techniques. The Newcastle-Ottawa Scale was used to assess the methodological quality. Ten articles involving 260 patients with T1D and 276 HCs were included in this systematic review. The quality scores of all included studies were 6–8 points. In summary, a decreased microbiota diversity and a significantly distinct pattern of clustering with regard to β-diversity were observed in T1D patients when compared with HCs. At the phylum level, T1D was characterised by a reduced ratio of Firmicutes/Bacteroidetes in the structure of the gut community, although no consistent conclusion was reached. At the genus or species level, T1D patients had a reduced abundance of Clostridium and Prevotella compared with HCs, whereas Bacteroides and Ruminococcus were found to be more enriched in T1D patients. This systematic review identified that there is a close association between the gut microbiota and development of T1D. Moreover, gut dysbiosis might be involved in the pathogenesis of T1D, although the causative role of gut microbiota remains to be established. Further well-controlled prospective studies are needed to better understand the role of the intestinal microbiome in the pathogenesis of T1D, which may help explore novel microbiota-based strategies to prevent and treat T1D.
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Jensen EA, Young JA, Mathes SC, List EO, Carroll RK, Kuhn J, Onusko M, Kopchick JJ, Murphy ER, Berryman DE. Crosstalk between the growth hormone/insulin-like growth factor-1 axis and the gut microbiome: A new frontier for microbial endocrinology. Growth Horm IGF Res 2020; 53-54:101333. [PMID: 32717585 PMCID: PMC7938704 DOI: 10.1016/j.ghir.2020.101333] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Both the GH/IGF-1 axis and the gut microbiota independently play an important role in host growth, metabolism, and intestinal homeostasis. Inversely, abnormalities in GH action and microbial dysbiosis (or a lack of diversity) in the gut have been implicated in restricted growth, metabolic disorders (such as chronic undernutrition, anorexia nervosa, obesity, and diabetes), and intestinal dysfunction (such as pediatric Crohn's disease, colonic polyps, and colon cancer). Over the last decade, studies have demonstrated that the microbial impact on growth may be mediated through the GH/IGF-1 axis, pointing toward a potential relationship between GH and the gut microbiota. This review covers current research on the GH/IGF-1 axis and the gut microbiome and its influence on overall host growth, metabolism, and intestinal health, proposing a bidirectional relationship between GH and the gut microbiome.
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Affiliation(s)
- Elizabeth A Jensen
- Translational Biomedical Sciences Graduate Program, Graduate College, Ohio University, Athens, OH, United States of America; Ohio University Heritage College of Osteopathic Medicine, Athens, OH, United States of America
| | - Jonathan A Young
- Ohio University Heritage College of Osteopathic Medicine, Athens, OH, United States of America; Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America
| | - Samuel C Mathes
- Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America
| | - Edward O List
- Translational Biomedical Sciences Graduate Program, Graduate College, Ohio University, Athens, OH, United States of America; Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America; The Diabetes Institute, Parks Hall Suite 142, Ohio University, Athens, OH, United States of America
| | - Ronan K Carroll
- Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH, United States of America; Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States of America
| | - Jaycie Kuhn
- Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America
| | - Maria Onusko
- The Diabetes Institute, Parks Hall Suite 142, Ohio University, Athens, OH, United States of America; Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH, United States of America
| | - John J Kopchick
- Translational Biomedical Sciences Graduate Program, Graduate College, Ohio University, Athens, OH, United States of America; Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America; The Diabetes Institute, Parks Hall Suite 142, Ohio University, Athens, OH, United States of America; Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States of America; Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America
| | - Erin R Murphy
- Translational Biomedical Sciences Graduate Program, Graduate College, Ohio University, Athens, OH, United States of America; Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States of America; Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America; Infectious and Tropical Diseases Institute, Irvine Hall, Ohio University, Athens, OH, United States of America
| | - Darlene E Berryman
- Translational Biomedical Sciences Graduate Program, Graduate College, Ohio University, Athens, OH, United States of America; Edison Biotechnology Institute, Konneker Research Labs, Athens, OH, United States of America; The Diabetes Institute, Parks Hall Suite 142, Ohio University, Athens, OH, United States of America; Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States of America; Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America.
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Parker MFL, Flavell RR, Luu JM, Rosenberg OS, Ohliger MA, Wilson DM. Small Molecule Sensors Targeting the Bacterial Cell Wall. ACS Infect Dis 2020; 6:1587-1598. [PMID: 32433879 DOI: 10.1021/acsinfecdis.9b00515] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review highlights recent efforts to detect bacteria using engineered small molecules that are processed and incorporated similarly to their natural counterparts. There are both scientific and clinical justifications for these endeavors. The use of detectable, cell-wall targeted chemical probes has elucidated microbial behavior, with several fluorescent labeling methods in widespread laboratory use. Furthermore, many existing efforts including ours, focus on developing new imaging tools to study infection in clinical practice. The bacterial cell wall, a remarkably rich and complex structure, is an outstanding target for bacteria-specific detection. Several cell wall components are found in bacteria but not mammals, especially peptidoglycan, lipopolysaccharide, and teichoic acids. As this review highlights, the development of laboratory tools for fluorescence microscopy has vastly outstripped related positron emission tomography (PET) or single photon emission computed tomography (SPECT) radiotracer development. However, there is great synergy between these chemical strategies, which both employ mimicry of endogenous substrates to incorporate detectable structures. As the field of bacteria-specific imaging grows, it will be important to understand the mechanisms involved in microbial incorporation of radionuclides. Additionally, we will highlight the clinical challenges motivating this imaging effort.
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Affiliation(s)
- Matthew F. L. Parker
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Robert R. Flavell
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Justin M. Luu
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Oren S. Rosenberg
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
- Department of Radiology, Zuckerberg San Francisco General Hospital, San Francisco, California 94110, United States
| | - David M. Wilson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
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47
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Susin A, Wang Y, Lê Cao KA, Calle ML. Variable selection in microbiome compositional data analysis. NAR Genom Bioinform 2020; 2:lqaa029. [PMID: 33575585 PMCID: PMC7671404 DOI: 10.1093/nargab/lqaa029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/13/2020] [Accepted: 04/29/2020] [Indexed: 12/25/2022] Open
Abstract
Though variable selection is one of the most relevant tasks in microbiome analysis, e.g. for the identification of microbial signatures, many studies still rely on methods that ignore the compositional nature of microbiome data. The applicability of compositional data analysis methods has been hampered by the availability of software and the difficulty in interpreting their results. This work is focused on three methods for variable selection that acknowledge the compositional structure of microbiome data: selbal, a forward selection approach for the identification of compositional balances, and clr-lasso and coda-lasso, two penalized regression models for compositional data analysis. This study highlights the link between these methods and brings out some limitations of the centered log-ratio transformation for variable selection. In particular, the fact that it is not subcompositionally consistent makes the microbial signatures obtained from clr-lasso not readily transferable. Coda-lasso is computationally efficient and suitable when the focus is the identification of the most associated microbial taxa. Selbal stands out when the goal is to obtain a parsimonious model with optimal prediction performance, but it is computationally greedy. We provide a reproducible vignette for the application of these methods that will enable researchers to fully leverage their potential in microbiome studies.
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Affiliation(s)
- Antoni Susin
- Mathematical Department, UPC-Barcelona Tech, 08028 Barcelona, Spain
| | - Yiwen Wang
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - M Luz Calle
- Biosciences Department, Faculty of Sciences and Technology, University of Vic—Central University of Catalonia, Carrer de la Laura, 13, 08500 Vic, Spain
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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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Wang H, Zhou C, Huang J, Kuai X, Shao X. The potential therapeutic role of Lactobacillus reuteri for treatment of inflammatory bowel disease. Am J Transl Res 2020; 12:1569-1583. [PMID: 32509162 PMCID: PMC7270012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal disease of unknown etiology. However, recent studies have established a pathological role of disordered intestinal microbiota and immune dysregulation. Clinical studies have suggested that the reconstruction of the normal intestinal flora in patients with IBD can reverse the dysbiosis caused by genetic, environmental, dietary, or antibiotic factors to ameliorate the symptoms of IBD. Lactobacillus reuteri is widely present in the intestines of healthy individuals and regulates the intestinal immune system, reducing inflammation through multiple mechanisms. This review summarizes the current knowledge of the role of L. reuteri in maintaining intestinal homeostasis and considers its possible value as a new therapeutic agent for patients with IBD.
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Affiliation(s)
- Huiyu Wang
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou, Jiangsu, China
| | - Chunli Zhou
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou, Jiangsu, China
| | - Junxiang Huang
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou, Jiangsu, China
| | - Xiaoyi Kuai
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou, Jiangsu, China
| | - Xinyu Shao
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou, Jiangsu, China
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Strömbeck A, Lasson A, Strid H, Sundin J, Stotzer PO, Simrén M, Magnusson MK, Öhman L. Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn's disease. BMC Gastroenterol 2020; 20:130. [PMID: 32366222 PMCID: PMC7197162 DOI: 10.1186/s12876-020-01281-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Background The role of the fecal microbiota composition for the postoperative disease course of patients with Crohn’s disease (CD) who have undergone ileocecal resection remains to be established. In this study, we investigated if the fecal microbiota composition, determined by a high throughput test quantifying a pre-selected set of bacteria, is associated with the postoperative disease course of CD patients. Methods Fecal samples were obtained from healthy subjects as well as from CD patients, 3–10 weeks and 1 year after ileocaecal resection. The fecal microbial composition was analyzed by Genetic Analysis GA-map Dysbiosis test, targeting ≥300 bacteria on different taxonomic levels. Postoperative disease status was assessed endoscopically according to Rutgeerts scoring system 1 year after surgery. Differences in fecal microbiota composition between groups were analyzed by multivariate factor analyses and cluster analysis. Microbial stability over time was determined using Bray-Curtis dissimilarity. Results One year after surgery, the fecal microbiota composition differed between CD patients (n = 21) and healthy subjects (n = 7). At this time point, the microbiota composition of CD patients was associated with disease course, clearly separating patients with disease relapse (n = 8) and patients in remission (n = 13). Further, the microbial within-patient stability was high during the first year after surgery, irrespective of disease course. Conclusion The fecal microbiota composition of CD patients, analyzed by GA-map Dysbiosis test, is subject to little variation over time, and may potentially be used as a non-invasive diagnostic tool for the postoperative disease course.
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Affiliation(s)
- Anna Strömbeck
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden.
| | - Anders Lasson
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Johanna Sundin
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Per-Ove Stotzer
- Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
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