Research
Print page Print page
Switch language
The Capital Region of Denmark - a part of Copenhagen University Hospital
Published

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing

Research output: Contribution to journalJournal articleResearchpeer-review

  1. Direct exposure of the head to solar heat radiation impairs motor-cognitive performance

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Glycemic control and use of glucose-lowering medications in hospital-admitted type 2 diabetes patients over 80 years

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. CTLA-4 blockade boosts the expansion of tumor-reactive CD8+ tumor-infiltrating lymphocytes in ovarian cancer

    Research output: Contribution to journalJournal articleResearchpeer-review

  1. Sexual Function and Quality of Life in a National Cohort of Survivors of Bilateral Testicular Cancer

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Compassionate Use of Remdesivir in Covid-19

    Research output: Contribution to journalLetterResearchpeer-review

  3. Interstitial lung abnormalities in people with HIV infection and uninfected controls

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Luteinizing Hormone Receptor Is Expressed in Testicular Germ Cell Tumors: Possible Implications for Tumor Growth and Prognosis

    Research output: Contribution to journalJournal articleResearchpeer-review

View graph of relations

Collection of faecal samples for microbiome analysis in acutely sick patients is logistically difficult, particularly if immediate freezing is required (i.e. fresh-frozen, or FF sampling). Previous studies in healthy/non-hospitalized volunteers have shown that chemical stabilization (i.e. stabilized-frozen, or SF sampling) allows room-temperature storage with comparable results to FF samples. To test this in a hospital setting we compared FF and SF approaches across 17 patients undergoing haematopoietic stem cell transplantation (HSCT) using both 16S rRNA gene and shotgun metagenomic sequencing. A paired (same stool specimen) comparison of FF and SF samples was made, with an overall comparable level in relative taxonomic abundances between the two sampling techniques. Though shotgun metagenomic sequencing found significant differences for certain bacterial genera (P < 0.001), these were considered minor methodological effects. Within-sample diversity of either method was not significantly different (Shannon diversity P16SrRNA = 0.68 and Pshotgun = 0.89) and we could not reject the null hypothesis that between-sample variation in FF and SF were equivalent (P16SrRNA = 0.98 and Pshotgun = 1.0). This indicates that SF samples can be used to reliably study the microbiome in acutely sick patient populations, thus creating and enabling further outcomes-based metagenomic studies on similarly valuable cohorts.

Original languageEnglish
Article number13351
JournalScientific Reports
Volume9
Issue number1
ISSN2045-2322
DOIs
Publication statusPublished - 16 Sep 2019

ID: 58076245