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Background  Recent experimental evidence showed that lactobacilli could be used as potential therapeutic agents for hyperammonemia. However, lack of understanding on how lactobacilli reduce blood ammonia levels limits application of lactobacilli to treat hyperammonemia.    Results  We report the finished and annotated genome sequence of  L. amylovorus  JBD401 (GenBank accession no. CP012389).  L. amylovorus  JBD401 reducing blood ammonia levels dramatically was identified by high-throughput screening of several thousand probiotic strains both within and across  Lactobacillus  species  in vitro . Administration of  L. amylovorus  JBD401 to hyperammonemia-induced mice reduced the blood ammonia levels of the mice to the normal range. Genome sequencing showed that  L. amylovorus  JBD401 had a circular chromosome of 1,946,267 bp with an average GC content of 38.13%. Comparative analysis of the  L. amylovorus  JBD401 genome with  L. acidophilus  and  L. amylovorus  strains showed that  L. amylovorus  JBD401 possessed genes for ammonia assimilation into various amino acids and polyamines Interestingly, the genome of  L. amylovorus  JBD401 contained unusually large number of various pseudogenes suggesting an active stage of evolution.    Conclusions   L. amylovorus  JBD401 has genes for assimilation of free ammonia into various amino acids and polyamines which results in removal of free ammonia in intestinal lumen to reduce the blood ammonia levels in the host. This work explains the mechanism of how probiotics reduce blood ammonia levels.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4672-3) contains supplementary material, which is available to authorized users.

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis