Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Aug 10;12(8):1636.
doi: 10.3390/microorganisms12081636.

Comparative Genomics of Limosilactobacillus reuteri YLR001 Reveals Genetic Diversity and Probiotic Properties

Lihong Zhang  1 , Md F Kulyar  2 , Tian Niu  1 , Shuai Yang  1 , Wenjing Chen  1
Affiliations

Comparative Genomics of Limosilactobacillus reuteri YLR001 Reveals Genetic Diversity and Probiotic Properties

Lihong Zhang et al. Microorganisms. .

Abstract

To gain deeper insights into the genomic characteristics of Limosilactobacillus reuteri (L. reuteri) YLR001 and uncover its probiotic properties, in the current study, a comprehensive analysis of its whole genome was conducted, explicitly exploring the genetic variations associated with different host organisms. The genome of YLR001 consisted of a circular 2,242,943 bp chromosome with a GC content of 38.84%, along with three circular plasmids (24,864, 38, 926, and 132,625 bp). Among the 2183 protein-coding sequences (CDSs), the specific genes associated with genetic adaptation and stress resistance were identified. We predicted the function of COG protein genes and analyzed the KEGG pathways. Comparative genome analysis revealed that the pan-genome contained 5207 gene families, including 475 core gene families and 941 strain-specific genes. Phylogenetic analysis revealed distinct host specificity among 20 strains of L. reuteri, highlighting substantial genetic diversity across different hosts. This study enhanced our comprehension of the genetic diversity of L. reuteri YLR001, demonstrated its potential probiotic characteristics, and established more solid groundwork for future applications.

Keywords: Limosilactobacillus reuteri; complete genome sequencing; probiotic properties; yak.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Circular genome map of L. reuteri YLR001.
Figure 2
Figure 2
KEGG classification statistics of the L. reuteri YLR001 genome annotation.
Figure 3
Figure 3
COG function classification of the L. reuteri YLR001 genome annotation.
Figure 4
Figure 4
Phylogenetic tree of L. reuteri YLR001. The tree was constructed using MEGA 6.0 by the Neighbor-Joining method based on 16S rRNA gene sequences with 1000 replications in a bootstrap test.
Figure 5
Figure 5
Phylogenetic tree of twenty L. reuteri strains. The phylogenetic tree was constructed based on the core gene families. The bootstrap support value before each node represents the confidence degree of each branch. The red dotted line in the figure highlights the bacterial strain under observation.
Figure 6
Figure 6
Numbers of orthologous gene families and unique genes among 20 L. reuteri strains. The different colors in the figure show different bacterial strains that were observed.
See this image and copyright information in PMC

References

    1. Zheng J., Wittouck S., Salvetti E., Franz C.M.A.P., Harris H.M.B., Mattarelli P., O’toole P.W., Pot B., Vandamme P., Walter J., et al. A Taxonomic Note on the Genus Lactobacillus: Description of 23 Novel Genera, Emended Description of the Genus Lactobacillus Beijerinck 1901, and Union of Lactobacillaceae and Leuconostocaceae. Int. J. Syst. Evol. Microbiol. 2020;70:2782–2858. doi: 10.1099/ijsem.0.004107. - DOI - PubMed
    1. Mu Q., Tavella V.J., Luo X.M. Role of Lactobacillus reuteri in Human Health and Diseases. Front. Microbiol. 2018;9:757. doi: 10.3389/fmicb.2018.00757. - DOI - PMC - PubMed
    1. Singh T.P., Tehri N., Kaur G., Malik R.K. Cell Surface and Extracellular Proteins of Potentially Probiotic Lactobacillus reuteri as an Effective Mediator to Regulate Intestinal Epithelial Barrier Function. Arch. Microbiol. 2021;203:3219–3228. doi: 10.1007/s00203-021-02318-2. - DOI - PubMed
    1. Liu H., Hou C., Wang G., Jia H., Yu H., Zeng X., Thacker P.A., Zhang G., Qiao S. Lactobacillus reuteri I5007 Modulates Intestinal Host Defense Peptide Expression in the Model of IPEC-J2 Cells and Neonatal Piglets. Nutrients. 2017;9:559. doi: 10.3390/nu9060559. - DOI - PMC - PubMed
    1. Ortiz-Rivera Y., Sánchez-Vega R., Gutiérrez-Méndez N., León-Félix J., Acosta-Muñiz C., Sepulveda D.R. Production of Reuterin in a Fermented Milk Product by Lactobacillus reuteri: Inhibition of Pathogens, Spoilage Microorganisms, and Lactic Acid Bacteria. J. Dairy Sci. 2017;100:4258–4268. doi: 10.3168/jds.2016-11534. - DOI - PubMed

LinkOut - more resources