Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context
Summary: Background: Large-scale multicentre studies are needed to understand complex relationships between the gut microbiota, health and disease. Interrogating the mucosal microbiota may identify important biology not captured by stool analysis. Gold standard tissue cryopreservation (‘flash freez...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-02-01
|
| Series: | EBioMedicine |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352396424005863 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850051125999304704 |
|---|---|
| author | Nicola J. Wyatt Hannah Watson Gregory R. Young Mary Doona Ned Tilling Dean Allerton Andrea C. Masi Tariq Ahmad Jennifer A. Doyle Katherine Frith Ailsa Hart Victoria Hildreth Peter M. Irving Claire Jones Nicholas A. Kennedy Sarah Lawrence Charlie W. Lees Robert Lees Trevor Liddle James O. Lindsay Julian R. Marchesi Miles Parkes Nick Powell Natalie J. Prescott Tim Raine Jack Satsangi Kevin Whelan Ruth Wood Andrew King Luke Jostins-Dean R. Alexander Speight Naomi McGregor Christopher J. Stewart Christopher A. Lamb |
| author_facet | Nicola J. Wyatt Hannah Watson Gregory R. Young Mary Doona Ned Tilling Dean Allerton Andrea C. Masi Tariq Ahmad Jennifer A. Doyle Katherine Frith Ailsa Hart Victoria Hildreth Peter M. Irving Claire Jones Nicholas A. Kennedy Sarah Lawrence Charlie W. Lees Robert Lees Trevor Liddle James O. Lindsay Julian R. Marchesi Miles Parkes Nick Powell Natalie J. Prescott Tim Raine Jack Satsangi Kevin Whelan Ruth Wood Andrew King Luke Jostins-Dean R. Alexander Speight Naomi McGregor Christopher J. Stewart Christopher A. Lamb |
| author_sort | Nicola J. Wyatt |
| collection | DOAJ |
| description | Summary: Background: Large-scale multicentre studies are needed to understand complex relationships between the gut microbiota, health and disease. Interrogating the mucosal microbiota may identify important biology not captured by stool analysis. Gold standard tissue cryopreservation (‘flash freezing’) limits large-scale study feasibility. We aimed to compare gut microbiota in gold standard and pragmatic mucosal biopsy storage conditions. Methods: We collected endoscopic recto-sigmoid biopsies from 20 adults with inflammatory bowel disease. Biopsies were preserved using three methods: (i) flash freezing (most proximal and distal biopsy sites); (ii) nucleic acid preservative reagents (QIAGEN Allprotect®, Invitrogen RNAlater™, and Zymo DNA/RNA Shield™); and (iii) formalin fixation with paraffin embedding (FFPE), which is used to preserve tissue for clinical histopathology within healthcare settings. Microbiota were sequenced on the MiSeq platform (V4 region, 16S rRNA gene). Findings: Tissue microbiota were consistent between most proximal and distal tissue suggesting any within-patient variation observed reflected storage condition, not biopsy location. There was no significant difference in alpha-diversity or microbial community profiles of reagent-preserved versus gold standard tissue. FFPE community structure was significantly dissimilar to other tissue samples, driven by differential relative abundance of obligate gut anaerobes; Faecalibacterium, Anaerostipes and Lachnospiraceae. Despite these differences, tissue microbiota grouped by participant regardless of preservation and storage conditions. Interpretation: Preservative reagents offer a convenient alternative to flash freezing tissue in prospective large-scale mucosal microbiota studies. Whilst less comparable, FFPE provides potential for retrospective microbiota studies using historical samples. Funding: Medical Research Council (MR/T032162/1) and The Leona M. and Harry B. Helmsley Charitable Trust (G-2002-04255). |
| format | Article |
| id | doaj-art-ae405a42171a4f22bd811dcbd8a50f8a |
| institution | DOAJ |
| issn | 2352-3964 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EBioMedicine |
| spelling | doaj-art-ae405a42171a4f22bd811dcbd8a50f8a2025-08-20T02:53:15ZengElsevierEBioMedicine2352-39642025-02-0111210555010.1016/j.ebiom.2024.105550Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in contextNicola J. Wyatt0Hannah Watson1Gregory R. Young2Mary Doona3Ned Tilling4Dean Allerton5Andrea C. Masi6Tariq Ahmad7Jennifer A. Doyle8Katherine Frith9Ailsa Hart10Victoria Hildreth11Peter M. Irving12Claire Jones13Nicholas A. Kennedy14Sarah Lawrence15Charlie W. Lees16Robert Lees17Trevor Liddle18James O. Lindsay19Julian R. Marchesi20Miles Parkes21Nick Powell22Natalie J. Prescott23Tim Raine24Jack Satsangi25Kevin Whelan26Ruth Wood27Andrew King28Luke Jostins-Dean29R. Alexander Speight30Naomi McGregor31Christopher J. Stewart32Christopher A. Lamb33Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, St Marks Hospital and Academic Institute, Gastroenterology, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom; School of Immunology & Microbial Sciences, King's College London, London, United KingdomDepartment of Histopathology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomInstitute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom; Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, United KingdomDepartment of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomResearch Informatics Team, Clinical Research, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, Barts Health NHS Trust, The Royal London Hospital, London, United Kingdom; Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United KingdomDivision of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, United KingdomDepartment of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United KingdomDivision of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, United Kingdom; Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, United KingdomDepartment of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, United KingdomDepartment of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United KingdomNuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United KingdomDepartment of Nutritional Sciences, King's College London, London, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomDepartment of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomKennedy Institute of Rheumatology, University of Oxford, Oxford, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United KingdomNewcastle Clinical Trials Unit (NCTU), Newcastle University, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United KingdomTranslational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Gastroenterology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; Corresponding author. M3.054, William Leech Building, Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.Summary: Background: Large-scale multicentre studies are needed to understand complex relationships between the gut microbiota, health and disease. Interrogating the mucosal microbiota may identify important biology not captured by stool analysis. Gold standard tissue cryopreservation (‘flash freezing’) limits large-scale study feasibility. We aimed to compare gut microbiota in gold standard and pragmatic mucosal biopsy storage conditions. Methods: We collected endoscopic recto-sigmoid biopsies from 20 adults with inflammatory bowel disease. Biopsies were preserved using three methods: (i) flash freezing (most proximal and distal biopsy sites); (ii) nucleic acid preservative reagents (QIAGEN Allprotect®, Invitrogen RNAlater™, and Zymo DNA/RNA Shield™); and (iii) formalin fixation with paraffin embedding (FFPE), which is used to preserve tissue for clinical histopathology within healthcare settings. Microbiota were sequenced on the MiSeq platform (V4 region, 16S rRNA gene). Findings: Tissue microbiota were consistent between most proximal and distal tissue suggesting any within-patient variation observed reflected storage condition, not biopsy location. There was no significant difference in alpha-diversity or microbial community profiles of reagent-preserved versus gold standard tissue. FFPE community structure was significantly dissimilar to other tissue samples, driven by differential relative abundance of obligate gut anaerobes; Faecalibacterium, Anaerostipes and Lachnospiraceae. Despite these differences, tissue microbiota grouped by participant regardless of preservation and storage conditions. Interpretation: Preservative reagents offer a convenient alternative to flash freezing tissue in prospective large-scale mucosal microbiota studies. Whilst less comparable, FFPE provides potential for retrospective microbiota studies using historical samples. Funding: Medical Research Council (MR/T032162/1) and The Leona M. and Harry B. Helmsley Charitable Trust (G-2002-04255).http://www.sciencedirect.com/science/article/pii/S2352396424005863Inflammatory bowel diseasePrecision medicineGut microbiomeTissue microbiomeTissue preservative reagentsFormalin fixed paraffin embedded |
| spellingShingle | Nicola J. Wyatt Hannah Watson Gregory R. Young Mary Doona Ned Tilling Dean Allerton Andrea C. Masi Tariq Ahmad Jennifer A. Doyle Katherine Frith Ailsa Hart Victoria Hildreth Peter M. Irving Claire Jones Nicholas A. Kennedy Sarah Lawrence Charlie W. Lees Robert Lees Trevor Liddle James O. Lindsay Julian R. Marchesi Miles Parkes Nick Powell Natalie J. Prescott Tim Raine Jack Satsangi Kevin Whelan Ruth Wood Andrew King Luke Jostins-Dean R. Alexander Speight Naomi McGregor Christopher J. Stewart Christopher A. Lamb Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context EBioMedicine Inflammatory bowel disease Precision medicine Gut microbiome Tissue microbiome Tissue preservative reagents Formalin fixed paraffin embedded |
| title | Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context |
| title_full | Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context |
| title_fullStr | Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context |
| title_full_unstemmed | Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context |
| title_short | Evaluation of intestinal biopsy tissue preservation methods to facilitate large-scale mucosal microbiota researchResearch in context |
| title_sort | evaluation of intestinal biopsy tissue preservation methods to facilitate large scale mucosal microbiota researchresearch in context |
| topic | Inflammatory bowel disease Precision medicine Gut microbiome Tissue microbiome Tissue preservative reagents Formalin fixed paraffin embedded |
| url | http://www.sciencedirect.com/science/article/pii/S2352396424005863 |
| work_keys_str_mv | AT nicolajwyatt evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT hannahwatson evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT gregoryryoung evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT marydoona evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT nedtilling evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT deanallerton evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT andreacmasi evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT tariqahmad evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT jenniferadoyle evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT katherinefrith evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT ailsahart evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT victoriahildreth evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT petermirving evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT clairejones evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT nicholasakennedy evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT sarahlawrence evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT charliewlees evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT robertlees evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT trevorliddle evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT jamesolindsay evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT julianrmarchesi evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT milesparkes evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT nickpowell evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT nataliejprescott evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT timraine evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT jacksatsangi evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT kevinwhelan evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT ruthwood evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT andrewking evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT lukejostinsdean evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT ralexanderspeight evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT naomimcgregor evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT christopherjstewart evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext AT christopheralamb evaluationofintestinalbiopsytissuepreservationmethodstofacilitatelargescalemucosalmicrobiotaresearchresearchincontext |