{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kavana Bywater-Brenna"],"organism":["Clostridioides difficile"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15646"],"description":["This experiment was performed largely to capture the dynamic transcriptional changes occurring in C. difficile when cultured within a 9 species synthetic gut communal consortium over a 48 h time series when cultured as a biofilm in vitro."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - For the multispecies microbiota community, overnight cultures of each species were grown in  Schaedler anaerobe broth (SAB)supplemented with 2 g/L L-cysteine  and 0.005 g/L vitamin K. Overnight cultures  were mixed so that each species had a final concentration of 0.1 OD600 within the mixture. For C. difficile monoculture controls, overnight cultures were also diluted to a  final concentration of 0.1 OD600. 2 mL aliquots of these cultures were then pipetted into pre-reduced 12-well tissue culture treated polystyrene plates (Falcon®, Corning, USA). Biofilms were washed at the desired timepoints with 1 mL PBS, and disrupted with 750 µL LETS buffer (0.1M LiCl, 0.01M Na2EDTA, 0.01M Tris-HCl (pH 7.5), 0.2% SDS) for subsequent TRIzol-based extraction.","Nucleic Acid Extraction - Samples were homogenised in 2 mL Lysing Matrix B (MP Biomedicals, USA) tubes, by bead beating for 6 cycles at 6.5 m/s for 40 seconds in a FastPrep-24-5G (MP Biomedicals, USA). Samples were kept on ice for 3 min between each cycle. The samples were subsequently spun at 15,000 x g for 10 min, and the supernatants were transferred into 2 mL nuclease-free Biosphere screw-cap tubes (Sarstedt Ltd., Germany) prior to extraction.  A 1 mL aliquot of TRIzol Reagent (Invitrogen, USA) was added to each supernatant, followed by a 5 min incubation at RT. 200 µL chloroform (Sigma-Aldrich, USA) was added to each sample and briefly vortexed and incubated again at RT for 5 min. Following this incubation, the samples were centrifuged at 12,000 x g at 4°C for 15 min. The resulting up","Sequencing - The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification. This was performed by Genewiz (Azenta)","Library Construction - RNA sequencing library preparation was prepared using NEBNext rRNA Depletion Kit (Bacteria) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, rRNA was depleted with NEBNext rRNA Depletion Kit (Bacteria). rRNA depleted RNAs were fragmented. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library amplification. The dUTP incorporated into the cDNA of the second strand enabled its specific degradation to maintain strand specificity. This was performed by Genewiz ("],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were trimmed to remove adapter contaminants using Trimmomatic (Version 0.39)92, based on a list of common adapter sequences. Unpaired reads were ignored. FastQC was rerun to ensure satisfactory quality of output files. Following trimming, reads were aligned to the appropriate genomes (concatenated in the case of synthetic community samples) using HISAT-2 (Version 2.1.0). As reads came from strictly bacterial cultures, the in-built splice-awareness setting was turned off in HISAT-2. Unpaired reads were ignored during this step. Samtools were used to convert the resulting SAM files to BAM files, and were subsequently sorted and indexes. Unmapped reads were discarded during this step. Gene counts from the resulting BAM files were generated using Libinorm which was "],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Clostridioides difficile is a major cause of hospital-associated diarrhoea worldwide. The intricate interactions between  C. difficile and the resident gut microbiota play a crucial role in determining the outcome of  C. difficile infection (CDI), although the molecular mechanisms underlying many  C. difficile -commensal interactions are not understood. Here we show that selected  Bacteroides species can inhibit  C. difficile growth within mixed biofilms. A transcriptomic analysis of  C. difficile-Bacteroides biofilms showed significant metabolic shifts, with distinct changes in carbohydrate and amino acid metabolism and, interestingly, a downregulation of  C. difficile toxin gene expression. A significant reduction in  C. difficile toxin production was evident in  C. difficile -  Bacteroi"],"study_type":["RNA-seq of total RNA"],"species":["Clostridioides difficile"],"pubmed_title":["Bacteroides-driven metabolic remodelling suppresses Clostridioides difficile toxin expression in mixed biofilm communities"],"pubmed_authors":["Kavana Bywater-Brenna","Kavana Kalea Bywater-Brenna, Simran Kaur Aulakh, Kiran Raosaheb Patil,  Niranjan Nagarajan and Meera Unnikrishnan","Meera Unnikrishnan"],"additional_accession":[]},"is_claimable":false,"name":"Temporal RNASeq of C. difficile cultured within synthetic multispecies biofilm relative to C. difficile monoculture biofilms.","description":"This experiment was performed largely to capture the dynamic transcriptional changes occurring in C. difficile when cultured within a 9 species synthetic gut communal consortium over a 48 h time series when cultured as a biofilm in vitro.","dates":{"release":"2026-09-23T00:00:00Z","modification":"2026-09-23T01:00:45.88Z","creation":"2025-09-30T23:10:54.491Z"},"accession":"E-MTAB-15646","cross_references":{"ENA":["ERP180844"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.09.03.674004"]}}