This ready-to-use gene catalog with 268,696 F3M-inferred (version 1.1.1) functional annotations can directly be used for mapping of metatranscriptomic fastQ reads and gene expression data analysis. The catalogs has been constructed from the pangenome data of 91 bacterial species (=96 specI) among the most commonly found in fermented vegetables related microbiomes. The species are listed in the metadata file available with the catalog (fermented_vegetables_genes_catalog_F3M_genome_list_V1_1_1.tsv). The catalog is made of three files : (1) fermented_vegetables_microbiomes_genes_catalogs.fasta; (2) fermented_vegetables_microbiomes_f3m_genes_catalog_V1_1_1_funct_annotations.tsv (for the F3M annotations) and (3) fermented_vegetables_microbiomes_f3m_genes_catalog_V1_1_1_gtdb_classification.tsv (for the GTDB taxonomy).