Abstract
Lactobacillus acidophilus is a common kind of lactic acid bacteria usually found in the human gastrointestinal tract, oral cavity, vagina, and various fermented foods. At present, many studies have focused on the probiotic function and industrial application of L. acidophilus. Additionally, dozens of L. acidophilus strains have been genome sequenced, but there has been no research to compare them at the genomic level. In this study, 46 strains of L. acidophilus were performed comparative analyses to explore their genetic diversity. The results showed that all the L. acidophilus strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition of bacteriocin operon, CRISPR-Cas systems and prophages mainly. Additionally, L. acidophilus was a pan-genome open species with a difference in carbohydrates utilization, antibiotic resistance, EPS operon, surface layer protein operon and other functional gene composition. This work provides a better understanding of L. acidophilus from a genetic perspective, and offers a frame for the biotechnological potentiality of this species.
Highlights
Eleven strains of L. acidophilus were isolated from healthy human feces from different regions of China (Table 1), 16S rRNA genes were sequenced for species identification
11 strains of L. acidophilus were isolated from human feces in different areas in China (Table 2), and in total 46 genomes were compared in this study (Table 1)
After Clusters of Orthologous Groups (COG) comparison and analysis of the difference in the number of functional genes, the results showed that there was a significant difference in some functional genes, such as amino acid transport genes, carbohydrate transport and metabolism genes, cell wall/membrane/envelope biogenesis genes, coenzyme transport genes, defense mechanisms genes, energy production genes, mobilome genes and transcription genes in L. acidophilus (Figure 8a–i)
Summary
NCFM (a typical L. acidophilus strain) is one of the most well commercially and clinically well-researched probiotics. Since it was isolated, it has been studied and found to have a variety of beneficial properties for gastrointestinal and general health. Alleviating inflammatory bowel disease through reducing cytokines is the most well-known benefit of L. acidophilus [1,2,3]. Other health-associated functions of L. acidophilus have attracted much attention, such as in alleviating cancer [4,5], regulating immunity [6,7], reducing cholesterol [8], and relieving diarrhea [9]. It had been found that L. acidophilus could directly or indirectly interfere with the intestinal microbiota or host metabolism by some active substances, such as extracellular polysaccharides (EPS), surface layer protein (SLP) and bacteriocin
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