1. ABOUT THE DATASET -------------------- Title: Designing Structures to Support Biofilm Growth in a Colonic In Vitro Model - collated data Creator(s): Emily Dewhurst, William Davis Birch, Anthony Buckley, Peter Culmer, Nikil Kapur, Ines Moura Organisation(s): University of Leeds Rights-holder(s):Unless otherwise stated, Copyright 2026 University of Leeds Publication Year: 2026 Description: Scaffolds were designed to support biofilm growth within an in vitro gastrointestinal model. This dataset contains the data used during a study to compare two different scaffold designs. The data includes both qPCR and taxonomic data which were used in the associated publication. Cite as: Dewhurst, Emily, Davis Birch, William, Buckley, Anthony, Culmer, Peter R, Kapur, Nikil,and Moura, Ines B. (2026). University of Leeds. [Dataset]. https://doi.org/10.5518/1829 Related publication: Dewhurst, Emily, Davis Birch, William, Buckley, Anthony, Culmer, Peter R, Kapur, Nikil, and Moura, Ines B. Designing Structures to Support Biofilm Growth in a Colonic In Vitro Model. Microbial Biotechnology. In preparation. Contact: Ines Moura (I.B.Moura@leeds.ac.uk) 2. TERMS OF USE --------------- Copyright [2026] [University of Leeds]. This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.] 3. PROJECT AND FUNDING INFORMATION ---------------------------------- Title: Building microbial cities: engineering mucosal biofilm nurseries for Antimicrobial Resistant (AMR) research Dates: 2022 - 2026 Funding organisation: EPSRC Grant no.:95545289 4. CONTENTS ----------- FILE: qPCR_data.xlsx DESCRIPTION: This file contains data from real-time quantitative PCR of samples for 10 different populations, separated by experiment. All values reported are in log10copies/uL. STRUCTURE: Data is divided according to the experiment (1 or 2), which is indicated by the sheet name. Each sheet contains rows of sample data (1 row per sample), with sample information and bacterial abundance in the corresponding columns. EXAMPLE: For Experiment 2, the concentration of Bifidobacterium for a planktonic sample from vessel 1, collected from reactor 4 on day 14, is 8.58807531 log10copies/uL. FILE: 16S_rRNA_data.xlsx DESCRIPTION: This file contains taxonomic data from both experiments. Data is reported at a family level; only families with registered reads are included. Taxonomic data is reported as the relative abundance (%). STRUCTURE: Data is divided according to the experiment (1 or 2), which is indicated by the sheet name. Each sheet contains rows of sample data (1 row per sample), with sample information and the relative abundance of each family in the corresponding columns. EXAMPLE: For experiment 1, the planktonic sample collected from reactor 4 on day 14 has a relative abundance of 42.01% for Bifidobacteriaceae. 5. METHODS ---------- Two MiGut experiments were performed involving 2 different donors. Over the course of both experiments, planktonic and biofilm samples were collected. Biofilm coupons were sampled in duplicate. For the planktonic populations, 1 mL of gut model fluid was collected. Planktonic samples were centrifuged (15,000 rpm, 20 minutes) and the supernatant was discarded; the cell pellets and biofilm coupons were stored at -80°C until processing. DNA extraction was performed in a QIAcube HT (Qiagen) using the DNeasy 96 PowerSoil Pro kit (Qiagen). Samples were analysed using qPCR, targeting 10 bacterial populations (Eubacteria, Akkermansia muciniphila, Bacteroides, Bifidobacterium, C. coccoides group, C. leptum group, Enterobacteriaceae, Enterococcus, Lactobacillus, and Prevotella), as previously described (Moura et al., 2020;Zhang et al., 2020). Values from qPCR were converted to bacterial abundance using a concentration curve and Excel (v. 2508). Following DNA extraction, 16S rRNA V4 libraries were prepared as previously described (Buckley, et al., 2021). Libraries were analysed on a MiSeq sequencer (Illumina) using a 2 x 250 bp paired end reads cycle. Taxonomic analysis was performed used CLC Genomics Workbench (v. 25.0.2), with the CLC Microbial Genomics Module (v.25.1). Demultiplexed FASTQ files of 16S rRNA sequences were trimmed of adapter sequences and samples were filtered based on the number of reads across all samples to provide similar coverage. Operational taxonomic units (OTUs) were picked using the Greengenes (v.2022.10) reference database at a level of 97% similarity. Referenced articles for methods: Buckley, A.M., I.B. Moura, N. Arai, W. Spittal, E. Clark, Y. Nishida, et al. (2021) Trehalose-induced remodelling of the human microbiota affects clostridioides difficile infection outcome in an in vitro colonic model: A pilot study. Front Cell Infect Microbiol 11: 670935. Moura, I.B., C. Normington, D. Ewin, E. Clark, M.H. Wilcox, A.M. Buckley and C.H. Chilton (2020) Method comparison for the direct enumeration of bacterial species using a chemostat model of the human colon. BMC Microbiol 20: 2. Zhang, L., M. Shi, M. Tian, X. Wang, J. Ji, X. Liao, et al. (2020) Guidelines for absolute quantitative real‐time pcr for microbial determination in in vitro gastrointestinal digestion. Food Frontiers 1: 200-204.