Dataset for decipering the responses of Oenococcus oeni to acid stress

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This dataset contains all file used in the paper 'Altered metabolic strategies- Elaborate mechanisms of Oenococcus oeni in response to acid stress' conducted by Yiman Qi†, Hao Wang†, Xiangdan Chen, Gehong Wei*, Shiheng Tao*, and Mingtao Fan*

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I. Tables:

Table S1 Pan-genome statistics (Core, accessory, and unique genes) and pseudogenes of five O.oeni strains: SD-2a, PSU-1, UBOCC-A-315001, CRBO_1381, and 19. (A) Core genes; (B) Accessory genes; (C) Unique genes; (D) Pseudogenes. Pseudogenes with known function were marked with light blue shadow; (E) Statistics of all pseudogenes of five O.oeni strains; (F) Gene annotations of O.oeni SD-2a. Genes included in the genome-scale metabolic model (iQY500) are in green shadow, and (G) Gap metabolites in the genome-scale metabolic model of O.oeni SD-2a (iQY500).

Table S2 (A) Comparison between nutrition utilization assays and in silico predictions for validating genome-scale metabolic model of O.oeni SD-2a (iQY500); (B) Amino acid autotrophic phenotypes among O.oeni strains in literature. (C) Nutrition compositions of three media: FMATB, ATB, and MATB, which was used as constraints for validation of iQY500 by comparing relative growth between experimental measurements and in silico predictions.

Table S3 (A) Basic information and (B, C) relative abundances of metabolites identified by metabolome. (D, E) Enrichment analysis by Fisher’s exact test with Benjamini-Hochberg correction of metabolites identified by metabolome; (F) Metabolites detected by MS/MS but not included in iQY500

Table S4 (A) Function enrichment of differential expressed genes with different response patterns; (B) Five tightly connected clusters detected from the gene-metabolite bipartite network by the MCODE method; (C) Low expressed genes of O.oeni SD-2a in all samples; (D) Predicted fluxes of all reactions at 1h (consensus); (E) Predicted fluxes of all reactions at 3h (consensus); (F) Predicted fluxes of all reactions at 1h (50 samples); (G) Predicted fluxes of all reactions at 3h (50 samples).

II. Supplemental Text

1. Text S1: This text contains the detail of manual modification process of GEM of O.oeni SD-2a.

III. Supplemental Files:

1. transcriptome.zip: Raw counts of transcriptome data in all samples in the study.

2. REMI_input_file.zip: Transcirptome and metabolome data used in REMI analysis.

3. REMI_results_50_replicates.zip: Predicted flux distribution using REMI method (50 replicates).

4. Supplemental_File_1.zip: It contains all pseudogenes which be splited into several fragments.

5. Supplemental_File_2-GEMs.zip: five GEMs of O.oeni strains (.xml format)

6. Supplemental_File_3-mRNA-metabolite_bipartite_network.zip: Correlation matrix and Cytoscape format file of gene-metabolite bipartite network (correlation > 0.80).

7. Supplemental_File 4-query sequences.fasta: Query sequences for searching “missing” enzymes in O.oeni SD-2a.