Faecalibacterium is a bacterial genus in which F. prausnitizii is considered a next-generation probiotic for human gut health. Since 2021, six other species from the genus have been described, and genomic data suggests dozens of undescribed species have associations with different hosts, diets, and geographical locations. As the probiotic effect is strain-dependent, this diversity represents an unexplored potential for strain screening and the development of new probiotic products.
Recently, Faecalibacterium has been associated with a healthy gut of the Pacific white shrimp (Penaeus vannamei), and F. praunitzii was shown to protect it from the pathogen Vibrio parahemolyticus, a major seafood-borne zoonotic pathogen that causes gastroenteritis in humans and acute hepatopancreatic necrosis disease (AHPND) in shrimp. P. vannamei is the most cultivated shrimp species, with a global production value of U$ 29 billion in 2022. Its production has faced economic losses due to outbreaks of devastating bacterial diseases, such as white feces syndrome, related to dysbiosis in the shrimp gut microbiota. In this context, probiotic Faecalibacterium strains could be incorporated into the shrimp diet. Genomic analyses can help identify new species and variants that can be used for diagnosis methods, probiotics development, and culture media design for previously unculturable bacteria. This study aimed to identify marker genes for Faecalibacterium species in the shrimp gut and to develop selective culture media to isolate strains of undescribed species, with applications for shrimp aquaculture.
The reference genomes of 70 Faecalibacterium species identified by the Genome Taxonomy Database (r220) were retrieved and annotated using Prokka v. 1.14.6. Orthologous genes were identified using OrthoFinder v. 2.5.5, and the exclusive genes of each genome were identified using an R script, with their functional annotation predicted using eggNOG-mapper v. 2.1.12. The 70 reference genomes had between 8 and 183 candidate marker genes. Among the 63 genomes from undescribed species, 34 had between 1 and 12 of these genes annotated as enzymes and from 1 to 17 as proteins that participate in metabolic pathways. The marker genes will be validated through a co-abundance analysis of those genes in DNA sequencing reads from public P. vannamei gut microbiomes. The validated genes will be investigated for their potential application in developing selective culture media. Additionally, metagenome-assembled genomes will be obtained from the public DNA sequencing reads to evaluate the functional diversity of Faecalibacterium strains from the P. vannamei gut.