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Molecules (Basel, Switzerland)2022; 27(6); doi: 10.3390/molecules27061867

Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase.

Abstract: Ligilactobacillus equi is common in the horse intestine, alleviates the infection of Salmonella, and regulates intestinal flora. Despite this, there have been no genomic studies on this species. Here, we provide the genomic basis for adaptation to the intestinal habitat of this species. We sequenced the genome of L. equi IMAU81196, compared this with published genome information from three strains in NCBI, and analyzed genome characteristics, phylogenetic relationships, and functional genes. The mean genome size of L. equi strains was 2.08 ± 0.09 Mbp, and the mean GC content was 39.17% ± 0.19%. The genome size of L. equi IMAU81196 was 1.95 Mbp, and the GC content was 39.48%. The phylogenetic tree for L. equi based on 1454 core genes showed that the independent branch of strain IMAU81196 was far from the other three strains. In terms of genomic characteristics, single-nucleotide polymorphism (SNP) sites, rapid annotation using subsystem technology (RAST), carbohydrate activity enzymes (CAZy), and predictions of prophage, we showed that strain L. equi JCM 10991T and strain DSM 15833T are not equivalent strains.It is worth mentioning thatthestrain of L. equi has numerous enzymes related to cellulose degradation, and each L. equi strain investigated contained at least one protophage. We speculate that this is the reason why these strains are adapted to the intestinal environment of horses. These results provide new research directions for the future.
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Publication Date: 2022-03-14 PubMed ID: 35335231PubMed Central: PMC8952416DOI: 10.3390/molecules27061867Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article presents a genomic-based analysis on how the Ligilactobacillus equi bacterium adapts to the horse intestine environment. The researchers conducted a comparative genomic study to understand the functionality and diversification of this bacterium, including its role in alleviating Salmonella infections and regulating intestinal flora in horses.

Methods and Materials

  • The research team sequenced the genome of a particular strain of Ligilactobacillus equi, known as IMAU81196.
  • They used comparative genomic analysis techniques to compare this genomic information with already-published genome information from three other strains available in the National Center for Biotechnology Information (NCBI) database.
  • The researchers examined multiple parameters, including genome characteristics, phylogenetic relationships, and functional genes.

Key Findings

  • On average, the genome size of Ligilactobacillus equi strains was approximately 2.08 +/- 0.09 Mbp, and the mean GC (Guanine-Cytosine) content was 39.17% +/- 0.19%.
  • The genome size for the particular strain L. equi IMAU81196 studied was 1.95 Mbp, with a GC content of 39.48%.
  • Through a phylogenetic tree constructed based on 1454 core genes, it was discovered that the independent branch of strain IMAU81196 was significantly distant from the other three strains. This suggests a level of genetic diversification.
  • Using genomic characteristics, single-nucleotide polymorphism (SNP) sites, rapid annotation using subsystem technology (RAST), carbohydrate activity enzymes (CAZy), and predictions of prophage, the team revealed that strains L. equi JCM 10991T and strain DSM 15833T are not equivalent strains.
  • A major discovery was that the strains of L. equi are rich in enzymes related to cellulose degradation. Each L. equi strain studied contained at least one protophages.
  • The presence of numerous cellulose-degradation enzymes and protophages suggests an adaption mechanism to the horse’s intestinal environment, which is consistent with the known biological roles of L. equi.

Conclusion and Future Directions

The findings reveal new insights into the genetic makeup and metabolic adaptations of the Ligilactobacillus equi strains in a horse’s intestine. With an understanding of how this bacterium adapts to its environment, further research can explore new methods of disease prevention and health management in horses.

Cite This Article

APA
Li Y, Liu C, Liu Q, Liu W. (2022). Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase. Molecules, 27(6). https://doi.org/10.3390/molecules27061867

Publication

Molecules (Basel, Switzerland)
ISSN: 1420-3049
NlmUniqueID: 100964009
Country: Switzerland
Language: English
Volume: 27
Issue: 6

Researcher Affiliations

Li, Yu
  • Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot 010018, China.
Liu, Chen
  • Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot 010018, China.
Liu, Qing
  • Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot 010018, China.
Liu, Wenjun
  • Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot 010018, China.

MeSH Terms

  • Animals
  • Cellulase / genetics
  • Ecosystem
  • Genome, Bacterial
  • Genomics
  • Horses
  • Intestines
  • Phylogeny
  • Prophages / genetics

Grant Funding

  • No. 31972095 / National Natural Science Foundation of China
  • 2019ZD06 / Major projects of Natural Science Foundation of Inner Mongolia Autonomous Region
  • 2021GG0080 / Inner Mongolia Autonomous Region Science and Technology Project

Conflict of Interest Statement

The authors declare that there are no conflict of interest.

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