We isolated two lactobacillus murinus strains from WT and Tg (5XFAD) Alzheimer's disease (AD) mouse model feces. These two strains have different phenotypes and may have differential role in relation to AD progression. To identify potential novel strains and also offer as a reference genome used in further bacteria RNA sequencing experiment, we performed do novo genome assembly of these two strains. Here is the De novo assembly genome of Lactobacillus murinus strain from feces of 41-week-age WT mice (WT_L.m.).