SHIP gut microbiome dataset for glaucoma analysis

The Study of Health in Pomerania (SHIP) is a population-based study. SHIP consists of the two independent cohorts: SHIP-START and SHIP-TREND. The aim of the study is the investigation of common risk factors, subclinical disorders and manifest diseases in the population of Northeast Germany. 16S rRNA gene sequencing was performed as described elsewhere (1,2). In brief, fecal samples were collected at home, and then transported to the laboratory by the participants or courier. The DNA was isolated (PSP Spin Stool DNA Kit; Stratec Biomedical AG, Birkenfeld, Germany) and stored at −20°C until analysis. 16S rRNA gene sequencing of the V1–V2 region was performed on a MiSeq platform (Illumina, San Diego, California, USA). MiSeq FastQ files were created using CASAVA 1.8.2. For amplicon-data processing the open-source software package DADA2 (v.1.10) was used (3,4). Samples were normalized to 10,000 16S rRNA gene read counts. 16S rRNA gene sequencing data from SHIP was used for replication analysis to investigate the association between glaucoma prevalence and the gut microbiome (Vergroesen, JE et al.). A total of 2.546 SHIP participants were included in the replication analysis. [1] Frost, F., Kacprowski, T., Rühlemann, M., Bülow, R., Kühn, J.-P., Franke, A., Heinsen, F.-A., Pietzner, M., Nauck, M., Völker, U., Völzke, H., Aghdassi, A. A., Sendler, M., Mayerle, J., Weiss, F. U., Homuth, G., & Lerch, M. M. (2019). Impaired Exocrine Pancreatic Function Associates With Changes in Intestinal Microbiota Composition and Diversity. Gastroenterology, 156(4), 1010–1015. https://doi.org/10.1053/j.gastro.2018.10.047 [2] Frost, F., Kacprowski, T., Rühlemann, M. C., Franke, A., Heinsen, F.-A., Völker, U., Völzke, H., Aghdassi, A. A., Mayerle, J., Weiss, F. U., Homuth, G., & Lerch, M. M. (2019). Functional abdominal pain and discomfort (IBS) is not associated with faecal microbiota composition in the general population. Gut, 68(6), 1131–1133. https://doi.org/10.1136/gutjnl-2018-316502 [3] Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods, 13(7), 581-3. https://doi.org/10.1038/nmeth.3869 [4] Frost, F., Kacprowski, T., Rühlemann, M., Pietzner, M., Bang, C., Franke, A., Nauck, M., Völker, U., Völzke, H., Dörr, M., Baumbach, J., Sendler, M., Schulz, C., Mayerle, J., Weiss, F. U., Homuth, G., & Lerch, M. M. (2021). Long-term instability of the intestinal microbiome is associated with metabolic liver disease, low microbiota diversity, diabetes mellitus and impaired exocrine pancreatic function. Gut, 70(3), 522–530. https://doi.org/10.1136/gutjnl-2020-322753