Title : Genomic structure and probiotic potential of megasphaera elsdenii CH4: A promising candidate for cattle supplementation
Abstract:
Probiotics are widely used in the prevention and treatment of infectious diseases, primarily through the modulation of immune and physiological systems. This study analysed the genomic structure of Megasphaera elsdenii CH4, a probiotic strain isolated from the rumen of a Holstein dairy cow, with the aim of identifying putative probiotic genes. Genomic DNA was extracted and sequenced using the Illumina NextSeq 550 platform, generating 5,589,766 paired-end reads (2 × 150 bp). The reads were assembled using SPAdes v3.15.3, and genome completeness was assessed with CheckM v1.0.18. Taxonomic classification was performed based on both whole-genome and 16S rRNA sequences. Genome annotation was conducted using PGAP v6.7 and RAST with SEED viewer v2.0. Genome alignment and SNP confirmation were carried out using progressiveMauve and BWA-MEM, respectively. Comparative analysis revealed multiple genomic inversions in M. elsdenii CH4 relative to a reference strain. The genome harbours several loci containing gene clusters associated with different CRISPR array types and subtypes, along with Cas proteins such as Cas1, Cas2, Cas3, Cas7, Cas8, Cse1, and components of the Csm complex. The SNP analysis identified synonymous and missense variants, though none appeared to impact on any protein function. Six putative genes were linked to host adhesion and immunomodulation. Additional genes, including PerR, OhrR, dnaK, and groES, likely contribute to the strain's adaptation and resilience in the gut environment. Overall, Megasphaera elsdenii CH4 demonstrates strong potential as a probiotic candidate, possessing genomic features that support functional stability and effective host interaction.
