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Senanayake T, Makanyengo S, Hoedt EC, Goggins B, Smith SR, Keely S. Influence of the bile acid/microbiota axis in ileal surgery: a systematic review. Colorectal Dis 2024; 26:243-257. [PMID: 38177086 DOI: 10.1111/codi.16837] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
AIM The gastrointestinal bile acid (BA)/microbiota axis has emerged as a potential mediator of health and disease, particularly in relation to pathologies such as inflammatory bowel disease (IBD) and colorectal cancer. Whilst it presents an exciting new avenue for therapies, it has not yet been characterized in surgical resection of the ileum, where BA reabsorption occurs. The identification of BA/microbiota signatures may provide future therapies with perioperative personalized medicine. In this work we conduct a systematic review with the aim of investigating the microbiome and BA changes that are associated with resection of the ileum. METHOD The databases included were MEDLINE, EMBASE, Web of Science and Cochrane libraries. The outcomes of interest were faecal microbiome and BA signatures after ileal resection. RESULTS Of the initial 3106 articles, three studies met the inclusion/exclusion criteria for data extraction. A total of 257 patients (46% surgery, 54% nonsurgery controls) were included in the three studies. Two studies included patients with short bowel syndrome and the other included patients with IBD. Large-scale microbiota changes were reported. In general, alpha diversity had decreased amongst patients with ileal surgery. Phylum-level changes included decreased Bacteroidetes and increased Proteobacteria and Fusobacteria in patients with an intestinal resection. Surgery was associated with increased total faecal BAs, cholic acid and chenodeoxycholic acid. There were decreases in deoxycholic acid and glycine and taurine conjugated bile salts. Integrated BA and microbiota data identified correlations with several bacterial families and BA. CONCLUSION The BA/microbiota axis is still a novel area with minimal observational data in surgery. Further mechanistic research is necessary to further explore this and identify its role in improving perioperative outcomes.
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Affiliation(s)
- Tharindu Senanayake
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Samwel Makanyengo
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Emily C Hoedt
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Bridie Goggins
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Stephen R Smith
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Simon Keely
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
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Nieva C, Pryor J, Williams GM, Hoedt EC, Burns GL, Eslick GD, Talley NJ, Duncanson K, Keely S. The Impact of Dietary Interventions on the Microbiota in Inflammatory Bowel Disease: A Systematic Review. J Crohns Colitis 2023:jjad204. [PMID: 38102104 DOI: 10.1093/ecco-jcc/jjad204] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND AND AIMS Diet plays an integral role in the modulation of the intestinal environment, with the potential to be modified for management of individuals with inflammatory bowel disease (IBD). It has been hypothesised that poor "Western-style" dietary patterns select for a microbiota that drives IBD inflammation and that through dietary intervention, a healthy microbiota may be restored. This study aimed to systematically review the literature and assess current available evidence regarding the influence of diet on the intestinal microbiota composition in IBD patients and how this may affect disease activity. METHODS MEDLINE, EMBASE, Scopus, Web of Science and Cochrane Library were searched from January 2013 to June 2023, to identify studies investigating diet and microbiota in IBD. RESULTS Thirteen primary studies met the inclusion criteria and were selected for narrative synthesis. Reported associations between diet and microbiota in IBD were conflicting due to the considerable degree of heterogeneity between studies. Nine intervention studies trialled specific diets and did not demonstrate significant shifts in the diversity and abundance of intestinal microbial communities or improvement in disease outcomes, whilst the remaining four cross-sectional studies did not find a specific microbial signature associated with habitual dietary patterns in IBD patients. CONCLUSIONS Diet modulates the gut microbiota, and this may have implications for IBD; however, the body of evidence does not currently support clear dietary patterns or food constituents that are associated with a specific microbiota profile or disease marker in IBD patients. Further research is required with a focus on robust and consistent methodology to achieve improved identification of associations.
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Affiliation(s)
- Cheenie Nieva
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jennifer Pryor
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Georgina M Williams
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Emily C Hoedt
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Grace L Burns
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Guy D Eslick
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J Talley
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Kerith Duncanson
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Simon Keely
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- National Health and Medical Research Council (NHMRC), Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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Talley NJ, Burns GL, Hoedt EC, Duncanson K, Keely S. Beyond Eosinophilic Esophagitis: Eosinophils in Gastrointestinal Disease-New Insights, "New" Diseases. J Can Assoc Gastroenterol 2023; 6:199-211. [PMID: 38106480 PMCID: PMC10723938 DOI: 10.1093/jcag/gwad046] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Functional dyspepsia (FD) is a highly prevalent disorder. Upper endoscopy is normal, and according to the Rome IV criteria, there is no established pathology. Data accumulated over the last 15 years has challenged the notion FD is free of relevant pathology, and in particular, increased duodenal eosinophils have been observed. Intestinal eosinophils play important roles in microbial defence, immune regulation, tissue regeneration and remodelling, and maintaining tissue homeostasis and metabolism; degranulation of eosinophils releases toxic granule products (e.g., major basic protein, eosinophil-derived neurotoxin) which can damage nerves. Normal cut-offs for eosinophil infiltration into the duodenum histologically are less than five eosinophils per high power field (<25 per five high power fields). In clinical practice there is evidence that pathologically increased intestinal eosinophils may often be overlooked. In a meta-analysis duodenal eosinophils were significantly increased in FD although there was substantial heterogeneity; degranulation of duodenal eosinophils was also significantly higher in FD without significant heterogeneity. In addition, increased duodenal permeability, systemic immune activation, and an altered mucosa-associated duodenal microbiome have been identified that may help explain why symptoms arise, often occur after food with exposure to food antigens, and typically fluctuate. Several potentially reversible risk factors for FD have now been identified. We evaluate the current evidence linking duodenal microinflammation and immune activation with FD and disorders of gut-brain interactions that overlap with FD. We propose a two-hit disease model for eosinophilic functional dyspepsia (EoFD) with management implications.
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Affiliation(s)
- Nicholas J Talley
- University of Newcastle, University Drive, Callaghan NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, Locked Bag 1000, New Lambton NSW 2305, Australia
| | - Grace L Burns
- University of Newcastle, University Drive, Callaghan NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, Locked Bag 1000, New Lambton NSW 2305, Australia
| | - Emily C Hoedt
- University of Newcastle, University Drive, Callaghan NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, Locked Bag 1000, New Lambton NSW 2305, Australia
| | - Kerith Duncanson
- University of Newcastle, University Drive, Callaghan NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, Locked Bag 1000, New Lambton NSW 2305, Australia
| | - Simon Keely
- University of Newcastle, University Drive, Callaghan NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, Locked Bag 1000, New Lambton NSW 2305, Australia
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Eslick GD, Fan K, Nair PM, Burns GL, Hoedt EC, Keely S, Talley NJ. Clinical and Pathologic Factors Associated With Colonic Spirochete (Brachyspira pilosicoli and Brachyspira aalborgi) Infection: A Comprehensive Systematic Review and Pooled Analysis. Am J Clin Pathol 2023; 160:335-340. [PMID: 37289435 PMCID: PMC10682506 DOI: 10.1093/ajcp/aqad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/04/2023] [Indexed: 06/09/2023] Open
Abstract
OBJECTIVES This study aims to determine what pathologic and clinical factors differentiate Brachyspira species that may be useful to clinicians and pathologists. METHODS We identified 21 studies of Brachyspira infection with individual patient information (n = 113) and conducted a pooled analysis comparing each species. RESULTS There were differences in the pathologic and clinical profiles of each Brachyspira species. Patients infected with Brachyspira pilosicoli infection were more likely to have diarrhea, fever, HIV, and immunocompromised conditions. Those patients infected with Brachyspira aalborgi were more likely to have lamina propria inflammation. CONCLUSIONS Our novel data provide potential insights into the pathogenic mechanism(s) and the specific risk factor profile of Brachyspira species. This may be clinically useful when assessing and managing patients.
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Affiliation(s)
- Guy D Eslick
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Kening Fan
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Prema M Nair
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Grace L Burns
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Emily C Hoedt
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Simon Keely
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
| | - Nicholas J Talley
- NHMRC Centre for Research Excellence in Digestive Health, The University of Newcastle, Hunter Medical Research Institute (HMRI), Callaghan, Australia
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Vishnoi V, Hoedt EC, Gould T, Carroll G, Carroll R, Lott N, Pockney P, Smith SR, Keely S. A pilot study: intraoperative 16S rRNA sequencing versus culture in predicting colorectal incisional surgical site infection. ANZ J Surg 2023; 93:2464-2472. [PMID: 37025037 DOI: 10.1111/ans.18455] [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: 01/27/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Surgical Site Infection (SSI) of the abdominal incision is a dreaded complication following colorectal surgery. Identifying the intraoperative surgical site microbes may provide clarity in the pathogenesis of SSIs. Genomic sequencing has revolutionized the ability to identify microbes from clinical samples. Utilization of 16S rRNA amplicon sequencing to characterize the intraoperative surgical site may provide the critical information required to predict and prevent infection in colorectal surgery. METHODS This is a pilot, prospective observational study of 50 patients undergoing elective colorectal resection. At completion of surgery, prior to skin closure, swabs were taken from the subcutaneous tissue of the abdominal incision to investigate the microbial profile. Dual swabs were taken to compare standard culture technique and 16S rRNA sequencing to establish if a microbial profile was associated with postoperative SSI. RESULTS 8/50 patients developed an SSI, which was more likely in those undergoing open surgery (5/15 33.3% versus 3/35, 8.6%; P = 0.029). 16S rRNA amplicon sequencing was more sensitive in microbial detection compared to traditional culture. Both culture and 16S rRNA demonstrated contamination of the surgical site, predominantly with anaerobes. Culture was not statistically predictive of infection. 16S rRNA amplicon sequencing was not statistically predictive of infection, however, it demonstrated patients with an SSI had an increased biodiversity (not significant) and a greater relative abundance (not significant) of pathogens such as Bacteroidacaea and Enterobacteriaceae within the intraoperative site. CONCLUSIONS 16S rRNA amplicon sequencing has demonstrated a potential difference in the intraoperative microbial profile of those that develop an infection. These findings require validation through powered experiments to determine the overall clinical significance.
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Affiliation(s)
- Veral Vishnoi
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Emily C Hoedt
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Tiffany Gould
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Georgia Carroll
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Rosemary Carroll
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Natalie Lott
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Peter Pockney
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Stephen R Smith
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
- Department of Surgical Services, Calvary Mater Hospital, Newcastle, New South Wales, Australia
| | - Simon Keely
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
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Hoedt EC, Hueston CM, Cash N, Bongers RS, Keane JM, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge. Microbiome 2023; 11:168. [PMID: 37528457 PMCID: PMC10394833 DOI: 10.1186/s40168-023-01595-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/09/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment. RESULTS In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3 weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention. CONCLUSION Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. Video Abstract.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
- Current address: NHMRC CRE in Digestive Health, HMRI, Newcastle, NSW, Australia
| | - Cara M Hueston
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Nora Cash
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | | | - Jonathan M Keane
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - John MacSharry
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
- School of Medicine, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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Cameron R, Duncanson K, Hoedt EC, Eslick GD, Burns GL, Nieva C, Keely S, Walker MM, Talley NJ. Does the microbiome play a role in the pathogenesis of colonic diverticular disease? A systematic review. J Gastroenterol Hepatol 2023; 38:1028-1039. [PMID: 36775316 PMCID: PMC10946483 DOI: 10.1111/jgh.16142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 02/14/2023]
Abstract
BACKGROUND AND AIMS The role of the microbiota in diverticulosis and diverticular disease is underexplored. This systematic review aimed to assess all literature pertaining to the microbiota and metabolome associations in asymptomatic diverticulosis, symptomatic uncomplicated diverticular disease (SUDD), and diverticulitis pathophysiology. METHODS Seven databases were searched for relevant studies published up to September 28, 2022. Data were screened in Covidence and extracted to Excel. Critical appraisal was undertaken using the Newcastle Ottawa Scale for case/control studies. RESULTS Of the 413 papers screened by title and abstract, 48 full-text papers were reviewed in detail with 12 studies meeting the inclusion criteria. Overall, alpha and beta diversity were unchanged in diverticulosis; however, significant changes in alpha diversity were evident in diverticulitis. A similar Bacteroidetes to Firmicutes ratio compared with controls was reported across studies. The genus-level comparisons showed no relationship with diverticular disease. Butyrate-producing microbial species were decreased in abundance, suggesting a possible contribution to the pathogenesis of diverticular disease. Comamonas species was significantly increased in asymptomatic diverticulosis patients who later developed diverticulitis. Metabolome analysis reported significant differences in diverticulosis and SUDD, with upregulated uracil being the most consistent outcome in both. No significant differences were reported in the mycobiome. CONCLUSION Overall, there is no convincing evidence of microbial dysbiosis in colonic diverticula to suggest that the microbiota contributes to the pathogenesis of asymptomatic diverticulosis, SUDD, or diverticular disease. Future research investigating microbiota involvement in colonic diverticula should consider an investigation of mucosa-associated microbial changes within the colonic diverticulum itself.
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Affiliation(s)
- Raquel Cameron
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Kerith Duncanson
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Emily C Hoedt
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Guy D Eslick
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Grace L Burns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Cheenie Nieva
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Marjorie M Walker
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
| | - Nicholas J Talley
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNSWAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleNSWAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleAustralia
- Immune Health Research ProgramHunter Medical Research InstituteNewcastleAustralia
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Vishnoi V, Morey T, Hoedt EC, Keely S, Pockney P, Smith SR. A Systematic Review and Meta-Analysis of Intra-Operative Surgical Site Sampling: Culture versus Culture-Independent Techniques in Predicting Downstream Surgical Site Infection. Surg Infect (Larchmt) 2023; 24:293-302. [PMID: 36961409 DOI: 10.1089/sur.2023.012] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Background: Surgical site infection remains a significant cause of morbidity and mortality. Traditionally, the causation has been inferred from the organism(s) detected in the post-operative setting. However, the intra-operative surgical site and the bacteria it harbors have been scarcely studied. Compared with culture-dependent methods, the development of genomic technology provides a new sensitive tool that could aid in characterizing the bacteria within the surgical site. The purpose of this literature review is to establish if there is a predictive role of sampling the intra-operative surgical site. Methods: A systematic literature review was conducted identifying relevant literature reporting on studies that sampled the intra-operative surgical site of any specialty, using either traditional culture or a culture-independent genomic sequencing-based technique and correlation with infection was attempted. The review identified studies between 1959 and 2021 in MEDLINE, EMBASE and Cochrane. Results: The initial search identified 7,835 articles; 36 remained after screening. Thirty-one articles focused on culture-dependent techniques, five on culture-independent. Subgroup meta-analysis demonstrates that a positive intra-operative culture carries a risk of downstream infection with an odds ratio of 8.6, however limited by a high false-positive and inability to correlate the intra-operative culture with the post-operative infection. In contrast, culture-independent studies through genomic sequencing are not predictive but suggest that the surgical incision is a complex microbial community with a shift toward dysbiosis in certain patients. Conclusion: The intra-operative surgical site clearly harbors bacteria. Both techniques give rise to separate explanations underpinning the role of bacteria in surgical site infection. It is possible there is a more complex dynamic community within the incision that makes a patient susceptible to infection. Characterizing this microbial community in large scale studies, including patients with infections may enhance our ability to predict and prevent incisional surgical site infections in patients undergoing surgical procedures.
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Affiliation(s)
- Veral Vishnoi
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Department of Surgery, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Tristan Morey
- School of Dentistry, University of Adelaide, South Australia, Australia
| | - Emily C Hoedt
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Peter Pockney
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Department of Surgery, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Stephen R Smith
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Department of Surgery, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
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9
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Volmer JG, Soo RM, Evans PN, Hoedt EC, Astorga Alsina AL, Woodcroft BJ, Tyson GW, Hugenholtz P, Morrison M. Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biol 2023; 21:59. [PMID: 36949471 PMCID: PMC10035134 DOI: 10.1186/s12915-023-01524-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts. RESULTS Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.). CONCLUSIONS Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.
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Affiliation(s)
- James G Volmer
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Rochelle M Soo
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Paul N Evans
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Current Address: NHMRC Centre of Research Excellence (CRE) in Digestive Health, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia
| | - Ana L Astorga Alsina
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
| | - Benjamin J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia.
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10
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Brown G, Hoedt EC, Keely S, Shah A, Walker MM, Holtmann G, Talley NJ. Role of the duodenal microbiota in functional dyspepsia. Neurogastroenterol Motil 2022; 34:e14372. [PMID: 35403776 PMCID: PMC9786680 DOI: 10.1111/nmo.14372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Functional dyspepsia (FD) is a common and debilitating gastrointestinal disorder attributed to altered gut-brain interactions. While the etiology of FD remains unknown, emerging research suggests the mechanisms are likely multifactorial and heterogenous among patient subgroups. Small bowel motor disturbances, visceral hypersensitivity, chronic microinflammation, and increased intestinal tract permeability have all been linked to the pathogenesis of FD. Recently, alterations to the gut microbiome have also been implicated to play an important role in the disease. Changes to the duodenal microbiota may either trigger or be a consequence of immune and neuronal disturbances observed in the disease, but the mechanisms of influence of small intestinal flora on gastrointestinal function and symptomatology are unknown. PURPOSE This review summarizes and synthesizes the literature on the link between the microbiota, low-grade inflammatory changes in the duodenum and FD. This review is not intended to provide a complete overview of FD or the small intestinal microbiota, but instead outline some of the key conceptual advances in understanding the interactions between altered gastrointestinal bacterial communities; dietary factors; host immune activation; and stimulation of the gut-brain axes in patients with FD versus controls. Current and emerging treatment approaches such as dietary interventions and antibiotic or probiotic use that have demonstrated symptom benefits for patients are reviewed, and their role in modulating the host-microbiota is discussed. Finally, suggested opportunities for diagnostic and therapeutic improvements for patients with this condition are presented.
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Affiliation(s)
- Georgia Brown
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Emily C. Hoedt
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Simon Keely
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Ayesha Shah
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Marjorie M. Walker
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Gerald Holtmann
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia,Department of Gastroenterology & HepatologyPrincess Alexandra HospitalWoolloongabbaQueenslandAustralia
| | - Nicholas J. Talley
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
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11
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Angerami Almeida K, de Queiroz Andrade E, Burns G, Hoedt EC, Mattes J, Keely S, Collison A. The microbiota in eosinophilic esophagitis: A systematic review. J Gastroenterol Hepatol 2022; 37:1673-1684. [PMID: 35730344 PMCID: PMC9544137 DOI: 10.1111/jgh.15921] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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] [Received: 02/21/2022] [Revised: 05/14/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Eosinophilic esophagitis (EoE) is an atopic disease of the esophagus that has shown a significant increase in incidence and prevalence in the last 20 years. The etiology of EoE is unclear, and few studies explore the esophageal microbiota in EoE. The local microbiome has been implicated in the pathogenesis of several allergic and inflammatory diseases, such as asthma and eczema. In this study, we performed a systematic review to evaluate differences in the microbiota profile of patients with EoE compared with controls. MEDLINE, Embase, Cochrane Library, Scopus, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) databases were searched to identify studies investigating the microbiota composition in EoE. Three reviewers screened the articles for eligibility and quality. Seven articles underwent full-text review, and a narrative synthesis was undertaken. The microbiota of the mouth and esophagus are correlated. Patients with active EoE present increased esophageal microbial load and increased abundance in particular species, such as Haemophilus and Aggregatibacter. On the other hand, EoE patients present a decrease in Firmicutes. High microbial load and abundance of Haemophilus are observed in EoE patients, but little evidence exists to demonstrate their influence on inflammation and disease. Understanding microbial signatures in EoE might contribute to the development of novel therapeutic strategies.
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Affiliation(s)
- Kaylani Angerami Almeida
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,Priority Research Centre GrowUpWell, Hunter Medical Research InstituteUniversity of NewcastleNewcastleNew South WalesAustralia,Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) ProgramHunter Medical Research Institute (HMRI)New Lambton HeightsNew South WalesAustralia,NHMRC Centre of Research Excellence (CRE) in Digestive HealthThe University of NewcastleCallaghanNew South WalesAustralia
| | - Ediane de Queiroz Andrade
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,Priority Research Centre GrowUpWell, Hunter Medical Research InstituteUniversity of NewcastleNewcastleNew South WalesAustralia,Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) ProgramHunter Medical Research Institute (HMRI)New Lambton HeightsNew South WalesAustralia
| | - Grace Burns
- NHMRC Centre of Research Excellence (CRE) in Digestive HealthThe University of NewcastleCallaghanNew South WalesAustralia,School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingThe University of NewcastleCallaghanNew South WalesAustralia
| | - Emily C Hoedt
- NHMRC Centre of Research Excellence (CRE) in Digestive HealthThe University of NewcastleCallaghanNew South WalesAustralia,School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingThe University of NewcastleCallaghanNew South WalesAustralia
| | - Joerg Mattes
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,Priority Research Centre GrowUpWell, Hunter Medical Research InstituteUniversity of NewcastleNewcastleNew South WalesAustralia,Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) ProgramHunter Medical Research Institute (HMRI)New Lambton HeightsNew South WalesAustralia
| | - Simon Keely
- NHMRC Centre of Research Excellence (CRE) in Digestive HealthThe University of NewcastleCallaghanNew South WalesAustralia,School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingThe University of NewcastleCallaghanNew South WalesAustralia
| | - Adam Collison
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,Priority Research Centre GrowUpWell, Hunter Medical Research InstituteUniversity of NewcastleNewcastleNew South WalesAustralia,Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) ProgramHunter Medical Research Institute (HMRI)New Lambton HeightsNew South WalesAustralia
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12
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Cuskelly A, Hoedt EC, Harms L, Talley NJ, Tadros MA, Keely S, Hodgson DM. Neonatal immune challenge influences the microbiota and behaviour in a sexually dimorphic manner. Brain Behav Immun 2022; 103:232-242. [PMID: 35491004 DOI: 10.1016/j.bbi.2022.04.023] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/31/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022] Open
Abstract
There is comorbidity between anxiety disorders and gastrointestinal disorders, with both linked to adverse early life events. The microbiome gut-brain-axis, a bidirectional communication system, is plastic throughout the neonatal period and is a possible mediator of this relationship. Here, we used a well-established neonatal rodent immune activation model to investigate the long-term effect of neonatal lipopolysaccharide (LPS) exposure on adult behaviour and the relationship to microbiome composition. Wistar rats were injected with LPS (0.05 mg/kg) or saline (equivolume) on postnatal days 3 and 5. In adulthood, behavioural tests were performed to assess anxiety-like behaviour, and microbiota sequencing was performed on stool samples. There were distinctly different behavioural phenotypes for LPS-exposed males and females. LPS-exposed males displayed typical anxiety-like behaviours with significantly decreased social interaction (F(1,22) = 7.576, p = 0.009) and increased defecation relative to saline controls (F(1,23) = 8.623, p = 0.005). LPS-exposed females displayed a different behavioural phenotype with significantly increased social interaction (F(1,22) = 6.094, p = 0.018), and exploration (F(1,24) = 6.359, p = 0.015), compared to saline controls. With respect to microbiota profiling data, Bacteroidota was significantly increased for LPS-exposed females (F(1,14) = 4.931p = 0.035) and Proteobacteria was decreased for LPS-exposed rats of both sexes versus controls (F(1,30) = 4.923p = 0.035). Furthermore, alterations in predicted functional pathways for neurotransmitters in faeces were observed with a decrease in the relative abundance of D-glutamine and D-glutamate metabolism in LPS exposed females compared to control females (p < 0.05). This suggests that neonatal immune activation alters both later life behaviour and adult gut microbiota in sex-specific ways. These findings highlight the importance of sex in determining the impact of neonatal immune activation on social behaviour and the gut microbiota.
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Affiliation(s)
- A Cuskelly
- School of Psychological Sciences, University of Newcastle, Callaghan, NSW, Australia; Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia.
| | - E C Hoedt
- Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia; NHMRC Centre of Research Excellence (CRE) in Digestive Health, HMRI, Newcastle, NSW, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, Australia
| | - L Harms
- School of Medicine and Public Health, University of Newcastle, New Lambton, NSW, Australia
| | - N J Talley
- Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia; NHMRC Centre of Research Excellence (CRE) in Digestive Health, HMRI, Newcastle, NSW, Australia; School of Medicine and Public Health, University of Newcastle, New Lambton, NSW, Australia
| | - M A Tadros
- School of Medicine and Public Health, University of Newcastle, New Lambton, NSW, Australia
| | - S Keely
- Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia; NHMRC Centre of Research Excellence (CRE) in Digestive Health, HMRI, Newcastle, NSW, Australia; School of Medicine and Public Health, University of Newcastle, New Lambton, NSW, Australia
| | - D M Hodgson
- School of Psychological Sciences, University of Newcastle, Callaghan, NSW, Australia; Viruses, Infection, Immunity, Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia
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13
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Fan K, Eslick GD, Nair PM, Burns GL, Walker MM, Hoedt EC, Keely S, Talley NJ. Human intestinal spirochetosis, irritable bowel syndrome, and colonic polyps: A systematic review and meta-analysis. J Gastroenterol Hepatol 2022; 37:1222-1234. [PMID: 35385602 PMCID: PMC9545717 DOI: 10.1111/jgh.15851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/24/2022] [Indexed: 12/09/2022]
Abstract
Human colonic spirochetosis (CS) is usually due toBrachyspira pilosicolior Brachyspira aalborgiinfection. While traditionally considered to be commensal bacteria, there are scattered case reports and case series of gastrointestinal (GI) symptoms in CS and reports of colonic polyps with adherent spirochetes. We performed a systematic review and meta-analysis investigating the association between CS and GI symptoms and conditions including the irritable bowel syndrome (IBS) and colonic polyps. Following PRISMA 2020 guidelines, a systematic search of Medline, CINAHL, EMBASE, and Web of Science was performed using specific keywords for CS and GI disease. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model. Of 75 studies identified in the search, 8 case-control studies met the inclusion criteria for meta-analysis and 67 case series studies met the inclusion criteria for pooled prevalence analysis. CS was significantly associated with diarrhea (n = 141/127, cases/controls, OR: 4.19, 95% CI: 1.72-10.21, P = 0.002) and abdominal pain (n = 64/65, OR: 3.66, 95% CI: 1.43-9.35, P = 0.007). CS cases were significantly more likely to have Rome III-diagnosed IBS (n = 79/48, OR: 3.84, 95% CI: 1.44-10.20, P = 0.007), but not colonic polyps (n = 127/843, OR: 8.78, 95% CI: 0.75-103.36, P = 0.084). In conclusion, we found evidence of associations between CS and both diarrhea and IBS, but not colonic polyps. CS is likely underestimated due to suboptimal diagnostic methods and may be an overlooked risk factor for a subset of IBS patients with diarrhea.
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Affiliation(s)
- Kening Fan
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
| | - Guy D Eslick
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
| | - Prema M Nair
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
| | - Grace L Burns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
| | - Marjorie M Walker
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
| | - Emily C Hoedt
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
| | - Nicholas J Talley
- Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- NHMRC Centre for Research Excellence in Digestive Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
- Australian Gastrointestinal Research Alliance (AGIRA)NewcastleNew South WalesAustralia
- School of Medicine and Public Health, College of Health, Medicine and WellbeingUniversity of NewcastleNewcastleNew South WalesAustralia
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14
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Hari S, Burns GL, Hoedt EC, Keely S, Talley NJ. Eosinophils, Hypoxia-Inducible Factors, and Barrier Dysfunction in Functional Dyspepsia. Front Allergy 2022; 3:851482. [PMID: 35769556 PMCID: PMC9234913 DOI: 10.3389/falgy.2022.851482] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Functional dyspepsia (FD) is a highly prevalent disorder of gut-brain interaction (DGBI), previously known as a functional gastrointestinal disorder. Characterized by early satiety, postprandial fullness, and/or epigastric pain or burning, diagnosis depends on positive symptomatology and exclusion of obvious structural diseases. A subtle inflammatory phenotype has been identified in FD patients, involving an increase in duodenal mucosal eosinophils, and imbalances in the duodenal gut microbiota. A dysregulated epithelial barrier has also been well described in FD and is thought to be a contributing factor to the low-grade duodenal inflammation observed, however the mechanisms underpinning this are poorly understood. One possible explanation is that alterations in the microbiota and increased immune cells can result in the activation of cellular stress response pathways to perpetuate epithelial barrier dysregulation. One such cellular response pathway involves the stabilization of hypoxia-inducible factors (HIF). HIF, a transcriptional protein involved in the cellular recognition and adaptation to hypoxia, has been identified as a critical component of various pathologies, from cancer to inflammatory bowel disease (IBD). While the contribution of HIF to subtle inflammation, such as that seen in FD, is unknown, HIF has been shown to have roles in regulating the inflammatory response, particularly the recruitment of eosinophils, as well as maintaining epithelial barrier structure and function. As such, we aim to review our present understanding of the involvement of eosinophils, barrier dysfunction, and the changes to the gut microbiota including the potential pathways and mechanisms of HIF in FD. A combination of PubMed searches using the Mesh terms functional dyspepsia, functional gastrointestinal disorders, disorders of gut-brain interaction, duodenal eosinophilia, barrier dysfunction, gut microbiota, gut dysbiosis, low-grade duodenal inflammation, hypoxia-inducible factors (or HIF), and/or intestinal inflammation were undertaken in the writing of this narrative review to ensure relevant literature was included. Given the findings from various sources of literature, we propose a novel hypothesis involving a potential role for HIF in the pathophysiological mechanisms underlying FD.
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Affiliation(s)
- Suraj Hari
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
| | - Grace L. Burns
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
| | - Emily C. Hoedt
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
| | - Simon Keely
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J. Talley
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
- *Correspondence: Nicholas J. Talley
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15
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Fan K, Gottstein M, Walker MM, Hoedt EC, Talley NJ, Keely S. Mucosal Immune Characterization of Colonic Spirochetosis. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4289] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Hoedt EC, Fan K, Burns GL, Kang S, Morrison M, Talley NJ, Keely S. Functional Dyspepsia Duodeum Mucosal Associated Microbiota: Comparison Between Fresh Biopsy and Historical Formalin‐fixed Paraffin‐embedded Biopsies Is Viable. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4272] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Seungha Kang
- Diamantina InstituteFaculty of MedicineThe University of QueenslandBrisbane
| | - Mark Morrison
- Diamantina InstituteFaculty of MedicineThe University of QueenslandBrisbane
| | | | - Simon Keely
- School of Biomedical Sciences & PharmacyCollege of Health, Medicine and WellbeingUniversity of NewcastleNewcastle
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17
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Burns GL, Hoedt EC, Jamaluddin MFB, Shanahan E, Lim Y, Teh JJ, Bruce J, Almazi J, Woldu A, Dun MD, Tanwar P, Potter M, Minahan K, Horvat J, Foster PS, Holtmann G, Veysey M, Walker MM, Morrison M, Talley NJ, Keely S. Seroreactivity to mucosa associated microbiota is associated with T cell gut‐homing in functional dyspepsia patients. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4212] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Yenkai Lim
- University of Queensland Diamantina InstituteBrisbane
| | - Jing Jie Teh
- University of Queensland Diamantina InstituteBrisbane
| | | | | | | | | | | | | | | | - Jay Horvat
- University of NewcastleNew Lambton Heights
| | | | | | | | | | - Mark Morrison
- University of Queensland Diamantina InstituteBrisbane
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18
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Giri R, Hoedt EC, Khushi S, Salim AA, Bergot AS, Schreiber V, Thomas R, McGuckin MA, Florin TH, Morrison M, Capon RJ, Ó Cuív P, Begun J. Secreted NF-κB suppressive microbial metabolites modulate gut inflammation. Cell Rep 2022; 39:110646. [PMID: 35417687 DOI: 10.1016/j.celrep.2022.110646] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 05/09/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence suggests that microbiome-host crosstalk regulates intestinal immune activity and predisposition to inflammatory bowel disease (IBD). NF-κB is a master regulator of immune function and a validated target for the treatment of IBD. Here, we identify five Clostridium strains that suppress immune-mediated NF-κB activation in epithelial cell lines, PBMCs, and gut epithelial organoids from healthy human subjects and patients with IBD. Cell-free culture supernatant from Clostridium bolteae AHG0001 strain, but not the reference C. bolteae BAA-613 strain, suppresses inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice. The in vivo responses to Clostridium bolteae AHG0001 and BAA-613 mirror the in vitro activity. Thus, using our in vitro screening of bacteria capable of suppressing NF-κB in the context of IBD and using an ex vivo organoid-based approach, we identify a strain capable of alleviating colitis in a relevant pre-clinical animal model of IBD.
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Affiliation(s)
- Rabina Giri
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Shamsunnahar Khushi
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela A Salim
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Veronika Schreiber
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Michael A McGuckin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Timothy H Florin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Robert J Capon
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Páraic Ó Cuív
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia.
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19
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Fowler S, Hoedt EC, Talley NJ, Keely S, Burns GL. Circadian Rhythms and Melatonin Metabolism in Patients With Disorders of Gut-Brain Interactions. Front Neurosci 2022; 16:825246. [PMID: 35356051 PMCID: PMC8959415 DOI: 10.3389/fnins.2022.825246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/30/2021] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Circadian rhythms are cyclic patterns of physiological, behavioural and molecular events that occur over a 24-h period. They are controlled by the suprachiasmatic nucleus (SCN), the brain’s master pacemaker which governs peripheral clocks and melatonin release. While circadian systems are endogenous, there are external factors that synchronise the SCN to the ambient environment including light/dark cycles, fasting/fed state, temperature and physical activity. Circadian rhythms also provide internal temporal organisation which ensures that any internal changes that take place are centrally coordinated. Melatonin synchronises peripheral clocks to the external time and circadian rhythms are regulated by gene expression to control physiological function. Synchronisation of the circadian system with the external environment is vital for the health and survival of an organism and as circadian rhythms play a pivotal role in regulating GI physiology, disruption may lead to gastrointestinal (GI) dysfunction. Disorders of gut-brain interactions (DGBIs), also known as functional gastrointestinal disorders (FGIDs), are a group of diseases where patients experience reoccurring gastrointestinal symptoms which cannot be explained by obvious structural abnormalities and include functional dyspepsia (FD) and irritable bowel syndrome (IBS). Food timing impacts on the production of melatonin and given the correlation between food intake and symptom onset reported by patients with DGBIs, chronodisruption may be a feature of these conditions. Recent advances in immunology implicate circadian rhythms in the regulation of immune responses, and DGBI patients report fatigue and disordered sleep, suggesting circadian disruption. Further, melatonin treatment has been demonstrated to improve symptom burden in IBS patients, however, the mechanisms underlying this efficacy are unclear. Given the influence of circadian rhythms on gastrointestinal physiology and the immune system, modulation of these rhythms may be a potential therapeutic option for reducing symptom burden in these patients.
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Affiliation(s)
- Sophie Fowler
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Emily C. Hoedt
- NHMRC Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J. Talley
- NHMRC Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Grace L. Burns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia
- NHMRC Centre of Research Excellence in Digestive Health, The University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- *Correspondence: Grace L. Burns,
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20
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Pryor J, Eslick GD, Talley NJ, Duncanson K, Keely S, Hoedt EC. Clinical medicine journals lag behind science journals with regards to "microbiota sequence" data availability. Clin Transl Med 2021; 11:e656. [PMID: 34870904 PMCID: PMC8647683 DOI: 10.1002/ctm2.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jennifer Pryor
- School of Biomedical Sciences and PharmacyCollege of HealthMedicine and WellbeingUniversity of NewcastleNewcastleAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
| | - Guy D. Eslick
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- School of Medicine and Public HealthCollege of HealthMedicine and WellbeingUniversity of NewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
| | - Nicholas J. Talley
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- School of Medicine and Public HealthCollege of HealthMedicine and WellbeingUniversity of NewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
| | - Kerith Duncanson
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- School of Medicine and Public HealthCollege of HealthMedicine and WellbeingUniversity of NewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
| | - Simon Keely
- School of Biomedical Sciences and PharmacyCollege of HealthMedicine and WellbeingUniversity of NewcastleNewcastleAustralia
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
| | - Emily C. Hoedt
- NHMRC Centre for Research Excellence in Digestive HealthUniversity of NewcastleNewcastleAustralia
- School of Medicine and Public HealthCollege of HealthMedicine and WellbeingUniversity of NewcastleAustralia
- Hunter Medical Research InstituteNewcastleAustralia
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21
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Burns GL, Hoedt EC, Walker MM, Talley NJ, Keely S. Physiological mechanisms of unexplained (functional) gastrointestinal disorders. J Physiol 2021; 599:5141-5161. [PMID: 34705270 DOI: 10.1113/jp281620] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Functional gastrointestinal disorders (FGIDs) encompass a range of complex conditions with similar clinical characteristics and no overt pathology. Recent recognition of sub-clinical pathologies in FGIDs, in conjunction with physiological and biochemical abnormalities including increased intestinal permeability, microbial profile alterations, differences in metabolites and extra-intestinal manifestations of disease, call into question the designation of these conditions as 'functional'. This is despite significant heterogeneity in both symptom profile and specifics of reported physiological abnormalities hampering efforts to determine defined mechanisms that drive onset and chronicity of symptoms. Instead, the literature demonstrates these conditions are disorders of homeostatic imbalance, with disruptions in both host and microbial function and metabolism. This imbalance is also associated with extraintestinal abnormalities including psychological comorbidities and fatigue that may be a consequence of gastrointestinal disruption. Given the exploitation of such abnormalities will be crucial for improved therapeutic selection, an enhanced understanding of the relationship between alterations in function of the gastrointestinal tract and the response of the immune system is of interest in identifying mechanisms that drive FGID onset and chronicity. Considerations for future research should include the role of sex hormones in regulating physiological functions and treatment responses in patients, as well as the importance of high-level phenotyping of clinical, immune, microbial and physiological parameters in study cohorts. There is opportunity to examine the functional contribution of the microbiota and associated metabolites as a source of mechanistic insight and targets for therapeutic modulation.
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Affiliation(s)
- Grace L Burns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia.,NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia.,New Lambton Heights, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Emily C Hoedt
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia.,New Lambton Heights, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Marjorie M Walker
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia.,New Lambton Heights, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J Talley
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia.,New Lambton Heights, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia.,NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia.,New Lambton Heights, Hunter Medical Research Institute, Newcastle, NSW, Australia
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22
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Burns GL, Hoedt EC, Keely S. Spore-forming probiotics for functional dyspepsia. Lancet Gastroenterol Hepatol 2021; 6:772-773. [PMID: 34358485 DOI: 10.1016/s2468-1253(21)00260-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Grace L Burns
- School of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2305, Australia; Viruses, Infection, Immunity, Vaccine and Asthma Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
| | - Emily C Hoedt
- School of Medicine and Public Health, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2305, Australia; Viruses, Infection, Immunity, Vaccine and Asthma Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2305, Australia; Viruses, Infection, Immunity, Vaccine and Asthma Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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23
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Feng G, Mikkelsen D, Hoedt EC, Williams BA, Flanagan BM, Morrison M, Gidley MJ. In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry. Food Funct 2021; 11:7892-7904. [PMID: 32813756 DOI: 10.1039/d0fo01103g] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Using in vitro fermentation conditions, this study investigated the fermentation characteristics of arabinoxylan (AX) and xyloglucan (XG) with a fecal inoculum that was collected either from humans consuming unrestricted diets or pigs fed a semi-defined diet with cellulose being the sole non-starch polysaccharide for 10 days prior to fecal collection. Metagenomic analysis revealed that microbial communities in the two types of inoculum were distinctively different, which led to distinct fermentation characteristics with the polysaccharides. The microbial communities fermented with the porcine fecal inoculum were clustered according to the fermentation time, while those fermented with the human fecal inoculum were differentiated by the substrates. Using the porcine fecal inoculum, irrespective of the substrates, Prevotella copri and the unclassified lineage rc4-4 were the dominant operational taxonomic units (OTUs) promoted during fermentation. Fermentation of wheat AX (WAX) and galacto-XG (GXG) with the human fecal inoculum, however, promoted different OTUs, except for a shared OTU belonging to Lachnospiraceae. Specifically, WAX promoted the growth of Bacteroides plebeius and a Blautia sp., while GXG promoted an unclassified Bacteroidales, Parabacteroides distasonis, Bacteroides uniformis and Bacteroides sp. 2. These changes in bacterial communities were in accordance with the short chain fatty acid (SCFA) production, where comparable SCFA profiles were obtained from the porcine fecal fermentation while different amounts and proportions of SCFA were acquired from fermentation of WAX and GXG with the human fecal inoculum. Altogether, this study indicated that the starting inoculum composition had a greater effect than polysaccharide chemistry in driving fermentation outcomes.
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Affiliation(s)
- Guangli Feng
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Deirdre Mikkelsen
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Emily C Hoedt
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, 4072, Australia. and APC Microbiome Ireland, University College Cork, Cork, T12, Ireland
| | - Barbara A Williams
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Mark Morrison
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
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24
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Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve. Front Microbiol 2021; 12:636822. [PMID: 33833740 PMCID: PMC8021953 DOI: 10.3389/fmicb.2021.636822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Francesca Bottacini
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Nora Cash
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | | | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - John MacSharry
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland
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25
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Zhang J, Hoedt EC, Liu Q, Berendsen E, Teh JJ, Hamilton A, O' Brien AW, Ching JYL, Wei H, Yang K, Xu Z, Wong SH, Mak JWY, Sung JJY, Morrison M, Yu J, Kamm MA, Ng SC. Elucidation of Proteus mirabilis as a Key Bacterium in Crohn's Disease Inflammation. Gastroenterology 2021; 160:317-330.e11. [PMID: 33011176 DOI: 10.1053/j.gastro.2020.09.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [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: 06/03/2020] [Revised: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Proteus spp, Gram-negative facultative anaerobic bacilli, have recently been associated with Crohn's disease (CD) recurrence after intestinal resection. We investigated the genomic and functional role of Proteus as a gut pathogen in CD. METHODS Proteus spp abundance was assessed by ure gene-specific polymerase chain in 54 pairs of fecal samples and 101 intestinal biopsies from patients with CD and healthy controls. The adherence, invasion, and intracellular presence of 2 distinct isolates of Proteus mirabilis in epithelial cells were evaluated using immunofluorescence and electron microscopy. Intracellular gene expression profiles and regulated pathways were analyzed by RNA sequencing and KEGG pathway analysis. Biologic functions of 2 isolates of P mirabilis were determined by in vitro cell culture, and in vivo using conventional mice and germ-free mice. RESULTS Proteus spp were significantly more prevalent and abundant in fecal samples and colonic tissue of patients with CD than controls. A greater abundance of the genus Fusobacterium and a lesser abundance of the genus Faecalibacterium were seen in patients with CD with a high Proteus spp abundance. All 24 Proteus monoclones isolated from patients with CD belonged to members of P mirabilis lineages and 2 isolates, recovered from stool or mucosa, were used in further studies. Mice gavaged with either P mirabilis strain had more severe colonic inflammation. Co-culture of the isolates with epithelial cell lines showed bacterial adherence, invasion, increased production of pro-inflammatory cytokines IL-18 and IL-1α, and cell necrosis. Both isolates induced key pro-inflammatory pathways, including NOD-like receptor signaling, Jak-STAT signaling, and MAPK signaling, and induced pro-inflammatory genes and activated inflammation-related pathways in gnotobiotic mice. CONCLUSIONS P mirabilis in the gut is associated with CD and can induce inflammation in cells and animal models of colitis. P mirabilis can act as a pathobiont and play a crucial role in the pathogenesis of CD.
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Affiliation(s)
- Jingwan Zhang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Emily C Hoedt
- The University of Queensland Diamantina Institute, Faculty of Medicine, Brisbane, Australia; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Qin Liu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Erwin Berendsen
- The University of Queensland Diamantina Institute, Faculty of Medicine, Brisbane, Australia
| | - Jing Jie Teh
- The University of Queensland Diamantina Institute, Faculty of Medicine, Brisbane, Australia
| | - Amy Hamilton
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Australia; Department of Medicine, The University of Melbourne, Melbourne, Australia
| | - Amy Wilson O' Brien
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Australia; Department of Medicine, The University of Melbourne, Melbourne, Australia
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Hong Wei
- Department of Laboratory Animal Science at the Third Military Medical University in Chongqing, China
| | - Keli Yang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China; Center for Gut Microbiota Research, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Joyce W Y Mak
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Faculty of Medicine, Brisbane, Australia.
| | - Jun Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China; Center for Gut Microbiota Research, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
| | - Michael A Kamm
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Australia; Department of Medicine, The University of Melbourne, Melbourne, Australia.
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China; Center for Gut Microbiota Research, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
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Bui AT, Williams BA, Hoedt EC, Morrison M, Mikkelsen D, Gidley MJ. High amylose wheat starch structures display unique fermentability characteristics, microbial community shifts and enzyme degradation profiles. Food Funct 2020; 11:5635-5646. [DOI: 10.1039/d0fo00198h] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In vitro fermentation of wheat starch depends on amylose content in cooked but not granule forms, and shows that high amylose wheat is a promising source of fermentable carbohydrate in the large intestine.
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Affiliation(s)
- Alexander T. Bui
- Centre for Nutrition and Food Sciences
- Queensland Alliance for Agriculture and Food Innovation
- The University of Queensland
- Brisbane
- Australia
| | - Barbara A. Williams
- Centre for Nutrition and Food Sciences
- Queensland Alliance for Agriculture and Food Innovation
- The University of Queensland
- Brisbane
- Australia
| | - Emily C. Hoedt
- Diamantina Institute
- Faculty of Medicine
- Translational Research Institute
- The University of Queensland
- Brisbane
| | - Mark Morrison
- Diamantina Institute
- Faculty of Medicine
- Translational Research Institute
- The University of Queensland
- Brisbane
| | - Deirdre Mikkelsen
- Centre for Nutrition and Food Sciences
- Queensland Alliance for Agriculture and Food Innovation
- The University of Queensland
- Brisbane
- Australia
| | - Michael J. Gidley
- Centre for Nutrition and Food Sciences
- Queensland Alliance for Agriculture and Food Innovation
- The University of Queensland
- Brisbane
- Australia
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27
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Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME J 2018; 12:2942-2953. [PMID: 30068938 DOI: 10.1038/s41396-018-0225-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/27/2018] [Accepted: 06/03/2018] [Indexed: 11/09/2022]
Abstract
The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.
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Affiliation(s)
- Emily C Hoedt
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - James G Volmer
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Carly P Rosewarne
- Commonwealth Scientific and Industrial Research Organisation, Kintore Avenue, Adelaide, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Australia
| | - Jane G Muir
- Department of Gastroenterology, Central Clinical School, The Alfred Centre, Monash University, Melbourne, Victoria, Australia
| | - Peter R Gibson
- Department of Gastroenterology, Central Clinical School, The Alfred Centre, Monash University, Melbourne, Victoria, Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.
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Ó Cuív P, Giri R, Hoedt EC, McGuckin MA, Begun J, Morrison M. Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells. Front Immunol 2018; 9:790. [PMID: 29720977 PMCID: PMC5915459 DOI: 10.3389/fimmu.2018.00790] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is an early coloniser of the human infant gut and contributes to the development of intestinal immunity. To better understand the functional capacity of E. faecalis, we constructed a broad host range RP4 mobilizable vector, pEHR513112, that confers chloramphenicol resistance and used a metaparental mating approach to isolate E. faecalis AHG0090 from a fecal sample collected from a healthy human infant. We demonstrated that E. faecalis AHG0090 is genetically tractable and could be manipulated using traditional molecular microbiology approaches. E. faecalis AHG0090 was comparable to the gold-standard anti-inflammatory bacterium Faecalibacterium prausnitzii A2-165 in its ability to suppress cytokine-mediated nuclear factor kappa B (NF-κB) activation in human gut-derived LS174T goblet cell like and Caco-2 enterocyte-like cell lines. E. faecalis AHG0090 and F. prausnitzii A2-165 produced secreted low molecular weight NF-κB suppressive peptidic bioactives. Both bioactives were sensitive to heat and proteinase K treatments although the E. faecalis AHG0090 bioactive was more resilient to both forms of treatment. As expected, E. faecalis AHG0090 suppressed IL-1β-induced NF-κB-p65 subunit nuclear translocation and expression of the NF-κB regulated genes IL-6, IL-8 and CXCL-10. Finally, we determined that E. faecalis AHG0090 is distantly related to other commensal strains and likely encodes niche factors that support effective colonization of the infant gut.
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Affiliation(s)
- Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rabina Giri
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Emily C Hoedt
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Michael A McGuckin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Jakob Begun
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
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29
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Affiliation(s)
- Emily C. Hoedt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072 Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
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30
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Hoedt EC, Cuív PÓ, Evans PN, Smith WJM, McSweeney CS, Denman SE, Morrison M. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J 2016; 10:2376-88. [PMID: 27022996 DOI: 10.1038/ismej.2016.41] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 02/10/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
The Australian macropodids (kangaroos and wallabies) possess a distinctive foregut microbiota that contributes to their reduced methane emissions. However, methanogenic archaea are present within the macropodid foregut, although there is scant understanding of these microbes. Here, an isolate taxonomically assigned to the Methanosphaera genus (Methanosphaera sp. WGK6) was recovered from the anterior sacciform forestomach contents of a Western grey kangaroo (Macropus fuliginosus). Like the human gut isolate Methanosphaera stadtmanae DSMZ 3091(T), strain WGK6 is a methylotroph with no capacity for autotrophic growth. In contrast, though with the human isolate, strain WGK6 was found to utilize ethanol to support growth, but principally as a source of reducing power. Both the WGK6 and DSMZ 3091(T) genomes are very similar in terms of their size, synteny and G:C content. However, the WGK6 genome was found to encode contiguous genes encoding putative alcohol and aldehyde dehydrogenases, which are absent from the DSMZ 3091(T) genome. Interestingly, homologs of these genes are present in the genomes for several other members of the Methanobacteriales. In WGK6, these genes are cotranscribed under both growth conditions, and we propose the two genes provide a plausible explanation for the ability of WGK6 to utilize ethanol for methanol reduction to methane. Furthermore, our in vitro studies suggest that ethanol supports a greater cell yield per mol of methane formed compared to hydrogen-dependent growth. Taken together, this expansion in metabolic versatility can explain the persistence of these archaea in the kangaroo foregut, and their abundance in these 'low-methane-emitting' herbivores.
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Affiliation(s)
- Emily C Hoedt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute (TRI), Brisbane, Queensland, Australia
| | - Paul N Evans
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Wendy J M Smith
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Chris S McSweeney
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute (TRI), Brisbane, Queensland, Australia
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31
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Burman S, Hoedt EC, Pottenger S, Mohd-Najman NS, Ó Cuív P, Morrison M. An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? Dig Dis 2016; 34:64-71. [PMID: 26982568 DOI: 10.1159/000443759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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] [Indexed: 02/02/2023]
Abstract
While it is now accepted that the gut microbiota contribute to the genotype-environment-lifestyle interactions triggering inflammatory bowel disease (IBD) episodes, efforts to identify the pathogen(s) that cause these diseases have met with limited success. The advent of culture-independent techniques for characterizing the structure and/or function of microbial communities (hereafter referred to as metagenomics) has provided new insights into the events associated with the onset, remission and recurrence of IBD. A large number of observational and/or case-control studies of IBD patients have confirmed substantive changes in gut bacterial profiles (dysbiosis) associated with disease. These types of studies have been augmented by new profiling approaches that support the identification of more 'colitogenic' bacteria from numerically predominant taxa. Evidence of alterations in lesser abundant taxa such as the methanogenic archaea, to favor types that are more immunogenic, has also been forthcoming. Several recent longitudinal studies of patients with Crohn's disease have produced additional insights, including evidence for the role of 'anti-inflammatory' microbiota in providing a protective effect and/or promoting remission. In summation, the implications of dysbiosis and restoration of a 'healthy microbiota' in IBD patients requires definition beyond a taxonomic assessment of the changes in the gut microbiota during disease course. The available evidence does suggest that specific members of the gut microbiota can contribute either pro- or anti-inflammatory effects, and their ecological fitness in the large bowel affects the onset and recurrence of IBD. While metagenomics and related approaches offer the potential to provide novel and important insights into these microbiota and thereby the pathophysiology of IBD, we also need to better understand factors affecting the ecological fitness of these microbes, if new treatment of IBD patients are to be delivered.
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Affiliation(s)
- S Burman
- The University of Queensland Diamantina Institute, and Faculty of Medicine and Biomedical Sciences, Translational Research Institute, University of Queensland, St. Lucia, Brisbane, Australia
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