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BMJ Open Is Committed to Open Peer Review. As Part of This Commitment We Make the Peer Review History of Every Article We Publish Publicly Available BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from BMJ Open is committed to open peer review. As part of this commitment we make the peer review history of every article we publish publicly available. When an article is published we post the peer reviewers’ comments and the authors’ responses online. We also post the versions of the paper that were used during peer review. These are the versions that the peer review comments apply to. The versions of the paper that follow are the versions that were submitted during the peer review process. They are not the versions of record or the final published versions. They should not be cited or distributed as the published version of this manuscript. BMJ Open is an open access journal and the full, final, typeset and author-corrected version of record of the manuscript is available on our site with no access controls, subscription charges or pay-per-view fees (http://bmjopen.bmj.com). If you have any questions on BMJ Open’s open peer review process please email [email protected] http://bmjopen.bmj.com/ on October 1, 2021 by guest. Protected copyright. BMJ Open BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from The Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study. Journal: BMJ Open ManuscriptFor ID peerbmjopen-2020-042493 review only Article Type: Protocol Date Submitted by the 07-Jul-2020 Author: Complete List of Authors: Williams, Astrid-Jane; Liverpool Hospital, Department of Gastroenterology; Ingham Institute, Paramsothy, Ramesh; Blacktown Hospital, Department of Gastroenterology & Hepatology Wu, Nan; University of New South Wales, St George and Sutherland Clinical School Ghaly, Simon; St Vincent's Hospital Sydney, Gastroenterology Leach, Steven; Sydney Children's Hospital Randwick, Westfield Research Laboratories Paramsothy, Sudarshan; Macquarie University Faculty of Medicine and Health Sciences; The University of Sydney, Concord Clinical School Corte, Crispin; Royal Prince Alfred Hospital, AW Morrow Gastroenterology and Liver Centre O'Brien, Claire; University of Canberra, Faculty of Science and Technology http://bmjopen.bmj.com/ Burke, Catherine; University of Technology Sydney, School of Life Sciences Wark, Gabrielle; St Vincent's Hospital Sydney, Gastroenterology Samocha-Bonet, Dorit; Garvan Institute of Medical Research, Diabetes Division Lambert, Kelly; University of Wollongong Faculty of Business, Centre for Health Research Illawarra Shoalhaven Population; Illawarra Shoalhaven Local Health District Ahlenstiel, Golo; Blacktown & Mount Druitt Hospital on October 1, 2021 by guest. Protected copyright. Wasinger, Valerie; University of New South Wales, Bioanalytical Mass Spectrometry Facility Dutt, Shoma; The Sydney Children's Hospitals Network Randwick and Westmead, Department of Gastroenterology Pavli, Paul; Canberra Hospital, Gastroenterology Unit Grimm, Michael; University of New South Wales, St George and Sutherland Clinical School Lemberg, Daniel; Sydney Children's Hospital Randwick, Department of Gastroenterology Connor, Susan; University of New South Wales, South Western Sydney Clinical School; Liverpool Hospital, Department of Gastroenterology Leong, Rupert; Concord Repatriation General Hospital, Gastroenterology and Liver Services Hold, Georgina; University of New South Wales, Microbiome Research Centre Keywords: Inflammatory bowel disease < GASTROENTEROLOGY, Adult For peer review only - http://bmjopen.bmj.com/site/about/guidelines.xhtml Page 1 of 22 BMJ Open BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from 1 2 3 gastroenterology < GASTROENTEROLOGY, Paediatric gastroenterology < 4 GASTROENTEROLOGY 5 6 7 8 9 10 11 12 13 14 15 16 For peer review only 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 http://bmjopen.bmj.com/ 35 36 37 38 39 40 41 42 on October 1, 2021 by guest. Protected copyright. 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 For peer review only - http://bmjopen.bmj.com/site/about/guidelines.xhtml BMJ Open Page 2 of 22 1 2 3 4 BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from 5 6 7 8 9 I, the Submitting Author has the right to grant and does grant on behalf of all authors of the Work (as defined 10 in the below author licence), an exclusive licence and/or a non-exclusive licence for contributions from authors 11 who are: i) UK Crown employees; ii) where BMJ has agreed a CC-BY licence shall apply, and/or iii) in accordance 12 with the terms applicable for US Federal Government officers or employees acting as part of their official 13 duties; on a worldwide, perpetual, irrevocable, royalty-free basis to BMJ Publishing Group Ltd (“BMJ”) its 14 licensees and where the relevant Journal is co-owned by BMJ to the co-owners of the Journal, to publish the 15 Work in this journal and any other BMJ products and to exploit all rights, as set out in our licence. 16 17 The Submitting Author accepts and understands that any supply made under these terms is made by BMJ to 18 the Submitting Author Forunless you peer are acting as review an employee on behalf only of your employer or a postgraduate 19 student of an affiliated institution which is paying any applicable article publishing charge (“APC”) for Open 20 Access articles. Where the Submitting Author wishes to make the Work available on an Open Access basis (and 21 intends to pay the relevant APC), the terms of reuse of such Open Access shall be governed by a Creative 22 Commons licence – details of these licences and which Creative Commons licence will apply to this Work are set 23 out in our licence referred to above. 24 25 Other than as permitted in any relevant BMJ Author’s Self Archiving Policies, I confirm this Work has not been 26 accepted for publication elsewhere, is not being considered for publication elsewhere and does not duplicate 27 material already published. I confirm all authors consent to publication of this Work and authorise the granting 28 of this licence. 29 30 31 32 33 34 35 36 37 38 http://bmjopen.bmj.com/ 39 40 41 42 43 44 45 46 on October 1, 2021 by guest. Protected copyright. 47 48 49 50 51 52 53 54 55 56 57 58 59 60 For peer review only - http://bmjopen.bmj.com/site/about/guidelines.xhtml Page 3 of 22 BMJ Open 1 2 3 The Australia IBD Microbiome (AIM) Study: protocol for a multicentre 4 BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from 5 longitudinal prospective cohort study. 6 7 8 Running title: The Australian Inflammatory Bowel Disease Microbiome Study 9 10 11 12 Astrid-Jane Williams*, Ramesh Paramsothy*, Nan Wu*, Simon Ghaly*, Steven 13 14 Leach*, Sudarshan Paramsothy*, Crispin Corte, Claire O’Brien, Catherine Burke, 15 Gabrielle Wark, Dorit Samocha-Bonet, Kelly Lambert, Golo Ahlenstiel, Valerie 16 17 Wasinger, Shoma Dutt, Paul Pavli, Michael Grimm, Daniel Lemberg, Susan Connor, 18 For peer review only 19 Rupert Leong, Georgina Hold, on behalf of the Sydney+ IBD Research Consortium 20 21 22 * = denotes equal contribution 23 24 25 26 Name: Astrid-Jane Williams 27 Institutional address: Department of Gastroenterology & Hepatology, Liverpool 28 29 Hospital, Elizabeth St, Liverpool, Sydney, New South Wales 1871 Australia. 30 31 ORCID ID: https//orcid.org/0000-0002-1756-5329 32 33 Email address: [email protected] 34 35 36 Name: Dr Ramesh Paramsothy 37 38 Institutional address: Department of Gastroenterology & Hepatology, Blacktown http://bmjopen.bmj.com/ 39 40 Hospital, Sydney, New South Wales 2148 Australia 41 ORCID ID: https//orcid.org/0000-0002-1757-4129 42 43 Email address: [email protected] 44 45 on October 1, 2021 by guest. Protected copyright. 46 Name: Dr Nan Wu 47 48 Institutional address: Microbiome Research Centre, St George and Sutherland Clinical 49 50 School, University of New South Wales, Level 2 Pitney Building, St George Hospital, 51 52 Short St, Kogarah, New South Wales 2217 Australia 53 ORCID ID: https//orcid.org/0000-0003-1446-6656 54 55 Email address: [email protected] 56 57 58 Name: Dr Simon Ghaly 59 60 For peer review only - http://bmjopen.bmj.com/site/about/guidelines.xhtml BMJ Open Page 4 of 22 1 2 3 Institutional address: Department of Gastroenterology, St. Vincent’s Hospital, 390 4 BMJ Open: first published as 10.1136/bmjopen-2020-042493 on 16 February 2021. Downloaded from 5 Victoria St, Darlinghurst, New South Wales 2010 Australia 6 7 ORCID ID: https//orcid.org/0000-0003-2489-6430 8 Email Address: [email protected] 9 10 11 12 Name: Dr Steven Leach 13 14 Institutional address: Westfield Research Laboratories, Level 2 Sydney Children’s 15 Hospital, High Street, Randwick, New South Wales 2031 Australia 16 17 ORCID ID: https//orcid.org/0000-0001-9704-1666 18 For peer review only 19 Email address: [email protected] 20 21 22 Name: Dr Sudarshan Paramsothy 23 24 Institutional address: 1 Faculty of Medicine and Health Sciences, Macquarie 25 26 University, Sydney, NSW, Australia. 2 Department of Gastroenterology, Macquarie 27 University Hospital, Sydney, NSW, Australia. 3 Concord Clinical School, University of 28 29 Sydney, Sydney, Australia 30 31 ORCID ID: https//orcid.org/0000-0002-9097-6028 32 33 Email address: [email protected] 34 35 36 Name: Dr Crispin Corte 37 38 Institutional address: AW Morrow Gastroenterology and Liver Centre, Royal Prince http://bmjopen.bmj.com/ 39 40 Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050 Australia 41 ORCID ID: https//orcid.org/0000-0003-1286-8459 42 43 Email address: [email protected] 44 45 on October 1, 2021 by guest.
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