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Simpson RC, Shanahan ER, Scolyer RA, Long GV. Towards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors. Nat Rev Clin Oncol 2023; 20:697-715. [PMID: 37488231 DOI: 10.1038/s41571-023-00803-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
The gut microbiota modulates immune processes both locally and systemically. This includes whether and how the immune system reacts to emerging tumours, whether antitumour immune responses are reactivated during treatment with immune-checkpoint inhibitors (ICIs), and whether unintended destructive immune pathologies accompany such treatment. Advances over the past decade have established that the gut microbiota is a promising target and that modulation of the microbiota might overcome resistance to ICIs and/or improve the safety of treatment. However, the specific mechanisms through which the microbiota modulates antitumour immunity remain unclear. Understanding the biology underpinning microbial associations with clinical outcomes in patients receiving ICIs, as well as the landscape of a 'healthy' microbiota would provide a critical foundation to facilitate opportunities to effectively manipulate the microbiota and thus improve patient outcomes. In this Review, we explore the role of diet and the gut microbiota in shaping immune responses during treatment with ICIs and highlight the key challenges in attempting to leverage the gut microbiome as a practical tool for the clinical management of patients with cancer.
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Affiliation(s)
- Rebecca C Simpson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Erin R Shanahan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
- Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia.
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2
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Fernandes KE, Stanfield B, Frost EA, Shanahan ER, Susantio D, Dong AZ, Tran TD, Cokcetin NN, Carter DA. Low Levels of Hive Stress Are Associated with Decreased Honey Activity and Changes to the Gut Microbiome of Resident Honey Bees. Microbiol Spectr 2023; 11:e0074223. [PMID: 37289060 PMCID: PMC10434159 DOI: 10.1128/spectrum.00742-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
Honey bees (Apis mellifera) face increasing threats to their health, particularly from the degradation of floral resources and chronic pesticide exposure. The properties of honey and the bee gut microbiome are known to both affect and be affected by bee health. Using samples from healthy hives and hives showing signs of stress from a single apiary with access to the same floral resources, we profiled the antimicrobial activity and chemical properties of honey and determined the bacterial and fungal microbiome of the bee gut and the hive environment. We found honey from healthy hives was significantly more active than honey from stressed hives, with increased phenolics and antioxidant content linked to higher antimicrobial activity. The bacterial microbiome was more diverse in stressed hives, suggesting they may have less capacity to exclude potential pathogens. Finally, bees from healthy and stressed hives had significant differences in core and opportunistically pathogenic taxa in gut samples. Our results emphasize the need for understanding and proactively managing bee health. IMPORTANCE Honey bees serve as pollinators for many plants and crops worldwide and produce valuable hive products such as honey and wax. Various sources of stress can disrupt honey bee colonies, affecting their health and productivity. Growing evidence suggests that honey is vitally important to hive functioning and overall health. In this study, we determined the antimicrobial activity and chemical properties of honey from healthy hives and hives showing signs of stress, finding that honey from healthy hives was significantly more antimicrobial, with increased phenolics and antioxidant content. We next profiled the bacterial and fungal microbiome of the bee gut and the hive environment, finding significant differences between healthy and stressed hives. Our results underscore the need for greater understanding in this area, as we found even apparently minor stress can have implications for overall hive fitness as well as the economic potential of hive products.
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Affiliation(s)
- Kenya E Fernandes
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Bridie Stanfield
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth A Frost
- ABGU, A Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, New South Wales, Australia
- NSW Department of Primary Industries, Paterson, New South Wales, Australia
| | - Erin R Shanahan
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Susantio
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew Z Dong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Trong D Tran
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Nural N Cokcetin
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, New South Wales, Australia
| | - Dee A Carter
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia
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Shah A, Kang S, Talley NJ, Do A, Walker MM, Shanahan ER, Koloski NA, Jones MP, Keely S, Morrison M, Holtmann GJ. The duodenal mucosa associated microbiome, visceral sensory function, immune activation and psychological comorbidities in functional gastrointestinal disorders with and without self-reported non-celiac wheat sensitivity. Gut Microbes 2022; 14:2132078. [PMID: 36303431 PMCID: PMC9621048 DOI: 10.1080/19490976.2022.2132078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Frequently, patients with functional gastrointestinal disorders (FGIDs) report intolerance of wheat products. We compared gastrointestinal symptoms, sensory function, psychiatric comorbidities, gut-homing immune cells, and duodenal mucosa-associated microbiome (d-MAM) in FGID patients and controls with and without self-reported wheat sensitivity (SR-NCWS). We recruited 40 FGID patients and 20 controls referred by GPs for treatment. Gastrointestinal/extraintestinal symptoms, visceral sensory function, psychological comorbidities, and SR-NCWS were assessed in a standardized approach. Peripheral gut homing T-cells (CD4+α4+β7+CCR9+/CD8+α4+β7+CCR9+) were quantified, and the d-MAM was assessed by DNA sequencing for 46 subjects. Factors of bacterial genera were extracted utilizing factor analysis with varimax rotation and factors univariately associated with FGID or SR-NCWS included in a subsequent multivariate analysis of variance to identify statistically independent discriminators. Anxiety scores (p < .05) and increased symptom responses to a nutrient challenge (p < .05) were univariately associated with FGID. Gut homing T-cells were increased in FGID patients with SR-NCWS compared to other groups (p all <0.05). MANOVA revealed that anxiety (p = .03), visceral sensory function (p = 0.007), and a d-MAM factor comprise members of the Alloprevotella, Prevotella, Peptostreptococcus, Leptotrichia, and Veillonella lineages were significantly (p = .001) associated with FGID, while gut homing CD4+α4+ β7+CCR9+ T-cells were associated (p = .002) with SR-NCWS. Compared to controls, patients with and without SR-NCWS show that there are shifts in the amplicon sequence variants within specific bacterial genera between the FGID subgroups (particularly Prevotella and Streptococcus) as well as distinct bacterial taxa discriminatory for the two different FGID subtypes. Compared to controls, both FGID patients with and without SR-NCWS have an increased symptom response to a standardized nutrient challenge and increased anxiety scores. The FGID patients with SR-NCWS - as compared to FGID without SR-NCWS (and controls without SR-NCWS) - have increased gut homing T-cells. The d-MAM profiles suggest species and strain-based variations between the two FGID subtypes and in comparison to controls.
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Affiliation(s)
- Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Translational Research Institute Queensland, Australia,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Seungha Kang
- Faculty of Medicine, University of Queensland, Brisbane, Australia,University of Queensland Diamantina Institute, Woolloongabba, Australia
| | - Nicholas J Talley
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, and Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Anh Do
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Marjorie M Walker
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, and Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Erin R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Translational Research Institute Queensland, Australia
| | - Natasha A Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Translational Research Institute Queensland, Australia,Faculty of Medicine, University of Queensland, Brisbane, Australia,College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, and Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Michael P Jones
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, and Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, and Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Mark Morrison
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Faculty of Medicine, University of Queensland, Brisbane, Australia,University of Queensland Diamantina Institute, Woolloongabba, Australia,CONTACT Mark Morrison
| | - Gerald J Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Australia,Translational Research Institute Queensland, Australia,Faculty of Medicine, University of Queensland, Brisbane, Australia,Gerald J Holtmann Princess Alexandra Hospital, Brisbane Department of Gastroenterology and Hepatology & University of Queensland 199 Ipswich Road, Woolloongabba, Queensland, Australia
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Shanahan ER, Kang S, Staudacher H, Shah A, Do A, Burns G, Chachay VS, Koloski NA, Keely S, Walker MM, Talley NJ, Morrison M, Holtmann GJ. Alterations to the duodenal microbiota are linked to gastric emptying and symptoms in functional dyspepsia. Gut 2022; 72:929-938. [PMID: 36167662 DOI: 10.1136/gutjnl-2021-326158] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 08/28/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Functional dyspepsia (FD) is a complex disorder, with debilitating epigastric symptoms. Evidence suggests alterations in gastrointestinal (GI) motility, visceral hypersensitivity, permeability and low-level immune activation in the duodenum may play a role. However, we still have a relatively poor understanding of how these factors interact to precipitate the onset of FD symptoms which are frequently meal related. The duodenal microbiota, in combination with specific dietary substrates, may be important mediators in disease pathophysiology; however, these interlinked factors have not been thoroughly investigated in FD. DESIGN Eighty-six individuals (56 FD, 30 controls) undergoing endoscopy were consecutively recruited and underwent detailed clinical assessment, including upper GI symptoms, gastric emptying and dietary assessment. Duodenal biopsies were obtained aseptically, and the mucosa-associated microbiota (MAM) analysed via 16S rRNA gene amplicon sequencing. RESULTS The relative abundances of predominant members of the Firmicutes, Bacteroidota and Fusobacteriota phyla were linked to symptom burden in FD. Inverse relationships between the relative abundances of Streptococcus and Prevotella, and the relative abundance of Veillonella spp with gastric emptying time, were also observed. No significant differences in long-term nutrient intake or diet quality were found between FD and controls, and there appeared to be limited association between habitual diet and duodenal MAM profiles. CONCLUSION This study suggests a link between the duodenal MAM, gastric emptying and FD symptoms, and this is largely independent of long-term dietary intake.
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Affiliation(s)
- Erin R Shanahan
- Faculty of Medicine and Faculty of Health & Behavioural Sciences, University of Queensland, Brisbane, Queensland, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Seungha Kang
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Heidi Staudacher
- Faculty of Medicine and Faculty of Health & Behavioural Sciences, University of Queensland, Brisbane, Queensland, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,Faculty of Medicine, Faculty of Health & Behavioural Sciences, and NHMRC Centre of Research Excellence Digestive Health, University of Queensland, Brisbane, Queensland, Australia
| | - Anh Do
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Grace Burns
- School of Biomedical Sciences and Pharmacy and NHMRC Centre of Research Excellence Digestive Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia.,Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Veronique S Chachay
- School of Human Movement and Nutrition Sciences, Faculty of Health and Behavioural Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Natasha A Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,Faculty of Medicine, Faculty of Health & Behavioural Sciences, and NHMRC Centre of Research Excellence Digestive Health, University of Queensland, Brisbane, Queensland, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy and NHMRC Centre of Research Excellence Digestive Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia.,Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Marjorie M Walker
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,School of Medicine and Public Health and NHMRC Centre of Research Excellence Digestive Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Nicholas J Talley
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,School of Medicine and Public Health and NHMRC Centre of Research Excellence Digestive Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute and NHMRC Centre of Research Excellence Digestive Health, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Gerald J Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia .,Faculty of Medicine, Faculty of Health & Behavioural Sciences, and NHMRC Centre of Research Excellence Digestive Health, University of Queensland, Brisbane, Queensland, Australia
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5
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Shanahan ER, McMaster JJ, Staudacher HM. Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design. J Hum Nutr Diet 2021; 34:631-644. [PMID: 33639033 DOI: 10.1111/jhn.12868] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.
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Affiliation(s)
- Erin R Shanahan
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | | | - Heidi M Staudacher
- IMPACT (The Institute for Mental and Physical Health and Clinical Translation) Food & Mood Centre, Deakin University, Geelong, VIC, Australia
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Todd E, Elnour R, Simpson R, Castaneda M, Shanahan ER. Munching microbes: diet–microbiome interactions shape gut health and cancer outcomes. Microbiol Aust 2021. [DOI: 10.1071/ma21026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The gut microbiome describes the complex community of microorganisms that populate the gastrointestinal tract. Gut microbes in the large bowel utilise both dietary-derived nutrients, such as host-indigestible carbohydrates (fibre) and excess protein, host-derived nutrients (intestinal mucin), and also interact with the by-products of digestion such as bile acids. They transform these compounds into a series of metabolites that can profoundly shape host physiology both locally and systemically. These metabolites can fundamentally alter host outcomes, promoting either gut health, or sub-optimal conditions in the gut that contribute to poor health, including increased risk of cancer. The microbiome of an individual has also been shown to impact response to cancer treatment strategies, including both treatment efficacy and side-effects in the gut and more systemically. This makes the microbiome a powerful potential tool for therapeutic purposes, once we overcome the challenges associated with individual variation in microbial community composition. As the gut microbial ecosystem is primarily altered by nutrient availability, diet therefore represents an important asset in therapeutically altering the gut microbiome.
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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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Shah A, Talley NJ, Koloski N, Macdonald GA, Kendall BJ, Shanahan ER, Walker MM, Keely S, Jones MP, Morrison M, Holtmann GJ. Duodenal bacterial load as determined by quantitative polymerase chain reaction in asymptomatic controls, functional gastrointestinal disorders and inflammatory bowel disease. Aliment Pharmacol Ther 2020; 52:155-167. [PMID: 32412673 DOI: 10.1111/apt.15786] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/12/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Small intestinal bacterial overgrowth may play a role in gastrointestinal and non-gastrointestinal diseases. AIMS To use quantitative polymerase chain reaction (qPCR) to determine and compare bacterial loads of duodenal biopsies in asymptomatic controls, and patients with functional gastrointestinal disorders (FGIDs) and inflammatory bowel disease (IBD) including ulcerative colitis (UC) and Crohn's disease (CD). To define effects of gastric acid inhibition on bacterial load, explore links of bacterial load and gastrointestinal symptoms in response to a standardised nutrient challenge and compare bacterial load with glucose breath test results. METHODS In 237 patients (63 controls, 84 FGID and 90 IBD), we collected mucosal samples under aseptic conditions during endoscopy extracted and total DNA. Bacterial load metric was calculated utilising qPCR measurements of the bacterial 16S rRNA gene, normalised to human beta-actin expression. Standard glucose breath test and nutrient challenge test were performed. RESULTS The duodenal microbial load was higher in patients with FGID (0.22 ± 0.03) than controls (0.07 ± 0.05; P = 0.007) and patients with UC (0.01 ± 0.05) or CD (0.02 ± 0.09), (P = 0.0001). While patients treated with proton pump inhibitors (PPI) had significantly higher bacterial loads than non-users (P < 0.05), this did not explain differences between patient groups and controls. Bacterial load was significantly (r = 0.21, P < 0.016) associated with the symptom response to standardised nutrient challenge test. Methane, but not hydrogen values on glucose breath test were associated with bacterial load measured utilising qPCR. CONCLUSIONS Utilising qPCR, a diagnosis of FGID and treatment with PPI were independently associated with increased bacterial loads. Increased bacterial loads are associated with an augmented symptom response to a standardised nutrient challenge.
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Affiliation(s)
- Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Nicholas J Talley
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Natasha Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Graeme A Macdonald
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Bradley J Kendall
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Erin R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Marjorie M Walker
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Simon Keely
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Michael P Jones
- Psychology Department, Macquarie University, Ryde, NSW, Australia
| | - Mark Morrison
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Diamantina Institute, University of Queensland, Brisbane, Qld, Australia
| | - Gerald J Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
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Batten M, Shanahan ER, Silva IP, Adhikari C, Conway J, Tasker A, Menzies AM, Wilmott JS, Saw RP, Spillane AJ, Shannon KF, Blank CU, Holmes AJ, Scolyer RA, Long GV. Abstract 2822: Low intestinal microbial diversity is associated with severe immune-related adverse events and lack of response to neoadjuvant combination antiPD1, anti-CTLA4 immunotherapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Immunotherapies targeting PD-1/PD-L1 and CTLA4 have revolutionized the treatment of advanced melanoma. Combining the two therapeutics increases the response rates compared to either treatment alone. However, this increased efficacy is accompanied by a higher incidence of severe immune-related adverse events (irAEs). Metrics of the intestinal microbiome are associated with cancer patients’ responses to immunotherapy but the value of microbiome metrics as predictors for irAEs, are unknown. In an effort to reduce irAEs during combination neoadjuvant therapy, the OpACIN-neo trial (Rozeman et al. ESMO 2018) was initiated wherein Stage III melanoma patients were treated with 2 doses each of ipilimumab and nivolumab in the neoadjuvant setting, according to three dosing regimen. Involved lymph nodes were resected after 6 weeks.
Aims: (1) To determine whether intestinal microbial components are associated with response to antiPD1/anti-CTLA4 immunotherapy in the neoadjuvant setting or with the development of severe irAEs. (2) To determine the effects of antiPD1/anti-CTLA4 immunotherapy on the microbiome over the 6 week course of treatment.
Methods: Of Melanoma Institute Australia patients enrolled in the OpACIN-neo trial (n=38), 68% of patients experienced complete, or near complete pathological responses and 61% experienced at least one irAE of grade 3 or more. Faecal microbiomes at baseline, and at resection (6 weeks immunotherapy), were analyzed using 16S ribosomal gene and metagenomic sequencing and the results compared with patient response and development of G3-G5 irAEs. Results: In baseline samples, Inverse Simpson’s diversity index indicated significantly lower overall microbial diversity in non-responders (p=.014), as well as those who went on to experience severe irAEs (p=.002). Importantly, the group of patients who were both non-responders and experienced severe irAEs had the lowest microbial diversity of all patients (p=.0033). Specific taxa associated with irAEs are distinct from those described for response. The 6 week course of immunotherapy led to a slight increase in microbial diversity but few specific taxa were observed to be significantly altered between the timepoints.
Conclusions: The findings suggest that not only are patients with extremely low microbial diversity predisposed to develop severe irAEs but they are also unlikely to respond to combination immunotherapy. Thus, microbial diversity may delineate patients who are likely to have poor outcomes and would benefit from microbial modulation.
Citation Format: Marcel Batten, Erin R. Shanahan, Ines P. Silva, Chandra Adhikari, Jordan Conway, Annie Tasker, Alexander M. Menzies, James S. Wilmott, Robyn P. Saw, Andrew J. Spillane, Kerwin F. Shannon, Christian U. Blank, Andrew J. Holmes, Richard A. Scolyer, Georgina V. Long. Low intestinal microbial diversity is associated with severe immune-related adverse events and lack of response to neoadjuvant combination antiPD1, anti-CTLA4 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2822.
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Affiliation(s)
| | | | | | | | | | - Annie Tasker
- 1Melanoma Institute Australia, Sydney, Australia
| | | | | | - Robyn P. Saw
- 1Melanoma Institute Australia, Sydney, Australia
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Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M, Holtmann GJ. Influence of cigarette smoking on the human duodenal mucosa-associated microbiota. Microbiome 2018; 6:150. [PMID: 30157953 PMCID: PMC6116507 DOI: 10.1186/s40168-018-0531-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cigarette smoking is a known risk factor in a number of gastrointestinal (GI) diseases in which the microbiota is implicated, including duodenal ulcer and Crohn's disease. Smoking has the potential to alter the microbiota; however, to date, the impact of smoking on the mucosa-associated microbiota (MAM), and particularly that of the upper GI tract, remains very poorly characterised. Thus, we investigated the impact of smoking on the upper small intestinal MAM. A total of 102 patients undergoing upper GI endoscopy for the assessment of GI symptoms, iron deficiency, or Crohn's disease, but without identifiable lesions in the duodenum, were recruited. Smoking status was determined during clinical assessment and patients classified as current (n = 21), previous smokers (n = 40), or having never smoked (n = 41). The duodenal (D2) MAM was profiled via 16S rRNA gene amplicon sequencing. RESULTS Smoking, both current and previous, is associated with significantly reduced bacterial diversity in the upper small intestinal mucosa, as compared to patients who had never smoked. This was accompanied by higher relative abundance of Firmicutes, specifically Streptococcus and Veillonella spp. The relative abundance of the genus Rothia was also observed to be greater in current smokers; while in contrast, levels of Prevotella and Neisseria were lower. The MAM profiles and diversity of previous smokers were observed to be intermediate between current and never smokers. Smoking did not impact the total density of bacteria present on the mucosa. CONCLUSIONS These data indicate the duodenal MAM of current smokers is characterised by reduced bacterial diversity, which is partially but not completely restored in previous smokers. While the precise mechanisms remain to be elucidated, these microbiota changes may in some part explain the adverse effects of smoking on mucosa-associated diseases of the GI tract. Smoking status requires consideration when interpreting MAM data.
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Affiliation(s)
- Erin R. Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
- Faculty of Medicine, The University of Queensland Diamantina Institute, The University of Queensland, Saint Lucia, Queensland 4072 Australia
- Present address: School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales Australia
| | - Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
| | - Natasha Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Marjorie M. Walker
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Nicholas J. Talley
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Mark Morrison
- Translational Research Institute, Woolloongabba, Queensland Australia
- Faculty of Medicine, The University of Queensland Diamantina Institute, The University of Queensland, Saint Lucia, Queensland 4072 Australia
| | - Gerald J. Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
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So D, Whelan K, Rossi M, Morrison M, Holtmann G, Kelly JT, Shanahan ER, Staudacher HM, Campbell KL. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr 2018; 107:965-983. [PMID: 29757343 DOI: 10.1093/ajcn/nqy041] [Citation(s) in RCA: 345] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/14/2018] [Indexed: 12/17/2022] Open
Abstract
Background Dysfunction of the gut microbiota is frequently reported as a manifestation of chronic diseases, and therefore presents as a modifiable risk factor in their development. Diet is a major regulator of the gut microbiota, and certain types of dietary fiber may modify bacterial numbers and metabolism, including short-chain fatty acid (SCFA) generation. Objective A systematic review and meta-analysis were undertaken to assess the effect of dietary fiber interventions on gut microbiota composition in healthy adults. Design A systematic search was conducted across MEDLINE, EMBASE, CENTRAL, and CINAHL for randomized controlled trials using culture and/or molecular microbiological techniques evaluating the effect of fiber intervention on gut microbiota composition in healthy adults. Meta-analyses via a random-effects model were performed on alpha diversity, prespecified bacterial abundances including Bifidobacterium and Lactobacillus spp., and fecal SCFA concentrations comparing dietary fiber interventions with placebo/low-fiber comparators. Results A total of 64 studies involving 2099 participants were included. Dietary fiber intervention resulted in higher abundance of Bifidobacterium spp. (standardized mean difference (SMD): 0.64; 95% CI: 0.42, 0.86; P < 0.00001) and Lactobacillus spp. (SMD: 0.22; 0.03, 0.41; P = 0.02) as well as fecal butyrate concentration (SMD: 0.24; 0.00, 0.47; P = 0.05) compared with placebo/low-fiber comparators. Subgroup analysis revealed that fructans and galacto-oligosaccharides led to significantly greater abundance of both Bifidobacterium spp. and Lactobacillus spp. compared with comparators (P < 0.00001 and P = 0.002, respectively). No differences in effect were found between fiber intervention and comparators for α-diversity, abundances of other prespecified bacteria, or other SCFA concentrations. Conclusions Dietary fiber intervention, particularly involving fructans and galacto-oligosaccharides, leads to higher fecal abundance of Bifidobacterium and Lactobacillus spp. but does not affect α-diversity. Further research is required to better understand the role of individual fiber types on the growth of microbes and the overall gut microbial community. This review was registered at PROSPERO as CRD42016053101.
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Affiliation(s)
- Daniel So
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Megan Rossi
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Gerald Holtmann
- Faculty of Medicine, University of Queensland, Brisbane, Australia.,Department of Gastroenterology & Hepatology
| | - Jaimon T Kelly
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Erin R Shanahan
- The University of Queensland Diamantina Institute, Translational Research Institute.,Department of Gastroenterology & Hepatology
| | | | - Katrina L Campbell
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia.,Department of Nutrition and Dietetics, Princess Alexandra Hospital, Brisbane, Australia
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Zhong L, Shanahan ER, Raj A, Koloski NA, Fletcher L, Morrison M, Walker MM, Talley NJ, Holtmann G. Dyspepsia and the microbiome: time to focus on the small intestine. Gut 2017; 66:1168-1169. [PMID: 27489239 DOI: 10.1136/gutjnl-2016-312574] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Laurie Zhong
- School of Population Health, University of Queensland, Brisbane, Queensland, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Erin R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.,Microbial Biology and Metagenomics Research Group, Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ashok Raj
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Natasha A Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Linda Fletcher
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics Research Group, Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Marjorie M Walker
- Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Nicholas J Talley
- Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Gerald Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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Shanahan ER, Holtmann G, Morrison M. Life in the small intestine: the forgotten microbiome? Microbiol Aust 2017. [DOI: 10.1071/ma17045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The gastrointestinal (GI) microbiota is now widely accepted to be an important modulator of our health and well-being. The microbes colonising the GI tract aid in promoting gut and immune homeostasis, while alterations in the composition and/or density of these microbes, often referred to as dysbiosis, have been implicated in many intestinal and extra-intestinal disorders. As a result, the GI microbiota is of increasing interest as a therapeutic target. This is particularly the case in the context of GI disorders linked to chronic inflammation of the mucosa. In this article, we focus on the small intestinal microbiota, which in many senses can be considered the ‘forgotten' gut microbiome.
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Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Letter: investigating the intestinal mucosa-associated microbiota - relevance and potential pitfalls. Authors' reply. Aliment Pharmacol Ther 2016; 44:648-9. [PMID: 27511137 DOI: 10.1111/apt.13741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- E R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia. .,Faculty of Medicine and Biomedical Sciences, Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia. .,Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia. .,Translational Research Institute (TRI), Brisbane, Qld, Australia.
| | - L Zhong
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - N J Talley
- Faculty of Health, The University of Newcastle, Callaghan, NSW, Australia
| | - M Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - G Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
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15
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Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Aliment Pharmacol Ther 2016; 43:1186-96. [PMID: 27086880 DOI: 10.1111/apt.13622] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents. AIM To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota. METHODS A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota. RESULTS Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination. CONCLUSIONS Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions.
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Affiliation(s)
- E R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - L Zhong
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - N J Talley
- Faculty of Health, The University of Newcastle, Callaghan, NSW, Australia
| | - M Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - G Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
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Cuív PÓ, Smith WJ, Pottenger S, Burman S, Shanahan ER, Morrison M. Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating. Sci Rep 2015; 5:13282. [PMID: 26293474 PMCID: PMC4642544 DOI: 10.1038/srep13282] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/16/2015] [Indexed: 01/03/2023] Open
Abstract
Metagenomics has rapidly advanced our inventory and appreciation of the genetic potential inherent to the gut microbiome. However it is widely accepted that two key constraints to further genetic dissection of the gut microbiota and host-microbe interactions have been our inability to recover new isolates from the human gut, and the paucity of genetically tractable gut microbes. To address this challenge we developed a modular RP4 mobilisable recombinant vector system and an approach termed metaparental mating to support the rapid and directed isolation of genetically tractable fastidious gut bacteria. Using this approach we isolated transconjugants affiliated with Clostridium cluster IV (Faecalibacterium and Oscillibacter spp.), Clostridium cluster XI (Anaerococcus) and Clostridium XIVa (Blautia spp.) and group 2 ruminococci amongst others, and demonstrated that the recombinant vectors were stably maintained in their recipient hosts. By a similar approach we constructed fluorescently labelled bacterial transconjugants affiliated with Clostridium cluster IV (including Flavonifractor and Pseudoflavonifractor spp.), Clostridium XIVa (Blautia spp.) and Clostridium cluster XVIII (Clostridium ramosum) that expressed a flavin mononucleotide-based reporter gene (evoglow-C-Bs2). Our approach will advance the integration of bacterial genetics with metagenomics and realize new directions to support a more mechanistic dissection of host-microbe associations relevant to human health and disease.
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Affiliation(s)
- Páraic Ó Cuív
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Wendy J Smith
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia
| | - Sian Pottenger
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Sriti Burman
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
| | - Erin R Shanahan
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Queensland, Australia
| | - Mark Morrison
- CSIRO Preventative Health Flagship Research Program, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Queensland, Australia
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Tyne AS, Chan JGY, Shanahan ER, Atmosukarto I, Chan HK, Britton WJ, West NP. TLR2-targeted secreted proteins from Mycobacterium tuberculosis are protective as powdered pulmonary vaccines. Vaccine 2013; 31:4322-9. [DOI: 10.1016/j.vaccine.2013.07.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 01/08/2023]
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Pinto R, Leotta L, Shanahan ER, West NP, Leyh TS, Britton W, Triccas JA. Host cell-induced components of the sulfate assimilation pathway are major protective antigens of Mycobacterium tuberculosis. J Infect Dis 2012; 207:778-85. [PMID: 23225904 DOI: 10.1093/infdis/jis751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
New therapies to control tuberculosis are urgently required because of the inability of the only available vaccine, BCG, to adequately protect against tuberculosis. Here we demonstrate that proteins of the Mycobacterium tuberculosis sulfate-assimilation pathway (SAP) represent major immunogenic targets of the bacillus, as defined by strong T-cell recognition by both mice and humans infected with M. tuberculosis. SAP proteins displayed increased expression when M. tuberculosis was resident within host cells, which may account in part for their ability to stimulate anti-M. tuberculosis host immunity. Vaccination with the first enzyme in this pathway, adenosine-5'-triphosphate sulfurylase, conferred significant protection against murine tuberculosis and boosted BCG-induced protective immunity in the lung. Therefore, we have identified SAP components as a new family of M. tuberculosis antigens, and we have demonstrated that these components are promising candidate for inclusion in new vaccines to control tuberculosis in humans.
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Affiliation(s)
- Rachel Pinto
- Mycobacterial Research Program, Centenary Institute, Newtown, Australia
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Shanahan ER, Pinto R, Triccas JA, Britton WJ, West NP. Cutinase-like protein-6 of Mycobacterium tuberculosis is recognised in tuberculosis patients and protects mice against pulmonary infection as a single and fusion protein vaccine. Vaccine 2009; 28:1341-6. [PMID: 19941992 DOI: 10.1016/j.vaccine.2009.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/28/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Infection with Mycobacterium tuberculosis continues to be a leading cause of death in many regions of the world, and control of this disease is hampered by the lack of a safe and effective vaccine. Secreted proteins of M. tuberculosis are an important group of antigens for subunit vaccines which target this infection. We have tested three secreted members of the cutinase-like protein (CULP) family of M. tuberculosis for their potential as protein vaccine antigens. Culp6 elicited a strong T lymphocyte response in M. tuberculosis infected mice, and importantly, in tuberculosis (TB) patients tested. Culp1, Culp2 and Culp6 when delivered as protein vaccines to mice, induced potent IFN-gamma responses which in turn translated into a significant level of protection against aerosol M. tuberculosis infection. A Culp1-6 fusion protein provided an increased level of protection against infection compared to Culp1 or Culp6 alone. The data presented here may indicate that the cell wall-associated, putatively essential protein Culp6, shown here for the first time to be recognised in TB patients, is an attractive candidate for inclusion in future subunit vaccines.
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Affiliation(s)
- Erin R Shanahan
- Mycobacterial Research Program, Centenary Institute, New South Wales, Australia
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