FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Molecules / Comparative Genomic Analysis Reveals Intestinal Habitat Adap...
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.
Get Full Text
Publication Date: 2022-03-14 PubMed ID: 35335231PubMed Central: PMC8952416DOI: 10.3390/molecules27061867Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

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.

References

This article includes 57 references
  1. Zheng J.S., Wittouck S., Salvetti E., Franz C., Harris H.M.B., Mattarelli P., O’Toole P.W., Pot B., Vandamme P., Walter J.. 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.0.004107pubmed: 32293557google scholar: lookup
  2. Krumbeck J.A., Marsteller N.L., Frese S.A., Peterson D.A., Ramer-Tait A.E., Hutkins R.W., Walter J.. Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract.. Environ. Microbiol. 2016;18:2172–2184.
    doi: 10.1111/1462-2920.13108pubmed: 26530032google scholar: lookup
  3. Sun Z.H., Harris H.M.B., McCann A., Guo C.Y., Argimon S., Zhang W.Y., Yang X.W., Jeffery I.B., Cooney J.C., Kagawa T.F.. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.. Nat. Commun. 2015;6:13.
    doi: 10.1038/ncomms9322pmc: PMC4667430pubmed: 26415554google scholar: lookup
  4. Zhai Q.X., Tian F.W., Wang G., Chen W.. Progress in Research on the Role of Intestinal Microbiota in Human Health.. Food Sci. 2013;79:106–108.
    doi: 10.1016/0003-9969(59)90009-3google scholar: lookup
  5. Dec M., Stępień-Pyśniak D., Puchalski A., Hauschild T., Pietras-Ożga D., Ignaciuk S., Urban-Chmiel R.. Biodiversity of Ligilactobacillus salivarius Strains from Poultry and Domestic Pigeons.. Animals 2021;11:972.
    doi: 10.3390/ani11040972pmc: PMC8065712pubmed: 33807321google scholar: lookup
  6. Yao M.F., Lu Y.M., Zhang T., Xie J.J., Han S.Y., Zhang S.B., Fei Y.Q., Ling Z.X., Wu J.J., Hu Y.. Improved functionality of Ligilactobacillus salivarius Li01 in alleviating colonic inflammation by layer-by-layer microencapsulation.. NPJ Biofilms Microbomes 2021;7:10.
    doi: 10.1038/s41522-021-00228-1pmc: PMC8270932pubmed: 34244520google scholar: lookup
  7. Jia D., Wang Y., Wang J.H., Liu J.L., Li H.H., Liu A.H., Wang J.M., Guan G.Q., Luo J.X., Yin H.. Lactobacillus animalis pZL8a: A potential probiotic isolated from pig feces for further research.. 3 Biotech 2021;11:1–11.
    doi: 10.1007/s13205-021-02681-3pmc: PMC7895895pubmed: 33680697google scholar: lookup
  8. Morotomi M., Yuki N., Kado Y., Kushiro A., Shimazaki T., Watanabe K., Yuyama T.. Lactobacillus equi sp nov., a predominant intestinal Lactobacillus species of the horse isolated from faeces of healthy horses.. Int. J. Syst. Evol. Microbiol. 2002;52:211–214.
    doi: 10.1099/00207713-52-1-211pubmed: 11837305google scholar: lookup
  9. Morita H., Nakano A., Shimazu M., Toh H., Nakajima F., Nagayama M., Hisamatsu S., Kato Y., Takagi M., Takami H.. Lactobacillus hayakitensis, L-equigenerosi and L-equi, predominant lactobacilli in the intestinal flora of healthy thoroughbreds.. Anim. Sci. J. 2009;80:339–346.
    doi: 10.1111/j.1740-0929.2009.00633.xpubmed: 20163646google scholar: lookup
  10. Yu J., Zhao J., Song Y.Q., Zhang J.C., Yu Z.J., Zhang H.P., Sun Z.H.. Comparative Genomics of the Herbivore Gut Symbiont Lactobacillus reuteri Reveals Genetic Diversity and Lifestyle Adaptation.. Front. Microbiol. 2018;9:12.
    doi: 10.3389/fmicb.2018.01151pmc: PMC5994480pubmed: 29915568google scholar: lookup
  11. Song Y., Sun Z., Zhang H.. Microevolution of lactic acid bacteria—A review.. Wei Sheng Wu Xue Bao Acta Microbiol. Sin. 2015;55:1371–1377.
    pubmed: 26915217
  12. Kazou M., Alexandraki V., Blom J., Pot B., Tsakalidou E., Papadimitriou K.. Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species within the Lactobacillus salivarius Clade.. Front. Microbiol. 2018;9:16.
    doi: 10.3389/fmicb.2018.01244pmc: PMC6004923pubmed: 29942291google scholar: lookup
  13. Jia Y., Yang B., Ross P., Stanton C., Zhang H., Zhao J.X., Chen W.. Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches.. Genes 2020;11:95.
    doi: 10.3390/genes11010095pmc: PMC7016874pubmed: 31947593google scholar: lookup
  14. O’Donnell M.M., Harris H.M.B., O’Toole P.W., Ross R.P.. The Genome of the Predominant Equine Lactobacillus Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host.. Genome Announc. 2014;2:e01155-13.
    doi: 10.1128/genomeA.01155-13pmc: PMC3894277pubmed: 24435863google scholar: lookup
  15. Amano Y., Kanda T.. New insights into cellulose degradation by cellulases and related enzymes.. Trends Glycosci. Glycotechnol. 2002;14:27–34.
    doi: 10.4052/tigg.14.27google scholar: lookup
  16. Makarova K., Slesarev A., Wolf Y., Sorokin A., Mirkin B., Koonin E., Pavlov A., Pavlova N., Karamychev V., Polouchine N.. Comparative genomics of the lactic acid bacteria.. Proc. Natl. Acad. Sci. USA. 2006;103:15611–15616.
    doi: 10.1073/pnas.0607117103pmc: PMC1622870pubmed: 17030793google scholar: lookup
  17. Chan J.Z.M., Halachev M.R., Loman N.J., Constantinidou C., Pallen M.J.. Defining bacterial species in the genomic era: Insights from the genus Acinetobacter.. BMC Microbiol. 2012;12:11.
    doi: 10.1186/1471-2180-12-302pmc: PMC3556118pubmed: 23259572google scholar: lookup
  18. Grim C.J., Kotewicz M.L., Power K.A., Gopinath G., Franco A.A., Jarvis K.G., Yan Q.Q., Jackson S.A., Sathyamoorthy V., Hu L.. Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation.. BMC Genom. 2013;14:16.
    doi: 10.1186/1471-2164-14-366pmc: PMC3680222pubmed: 23724777google scholar: lookup
  19. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M.. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.. Int. J. Syst. Evol. Microbiol. 2007;57:81–91.
    doi: 10.1099/ijs.0.64483-0pubmed: 17220447google scholar: lookup
  20. Richter M., Rossello-Mora R.. Shifting the genomic gold standard for the prokaryotic species definition.. Proc. Natl. Acad. Sci. USA. 2009;106:19126–19131.
    doi: 10.1073/pnas.0906412106pmc: PMC2776425pubmed: 19855009google scholar: lookup
  21. Feng S.L.. Research on method of the construction of phylogenetic trees.. Inf. Technol. 2009;6:38–44.
  22. Chen Y.S., Miyashita M., Suzuki K., Sato H., Hsu J.S., Yanagida F.. Lactobacillus pobuzihii sp nov., isolated from pobuzihi (fermented cummingcordia). Int. J. Syst. Evol. Microbiol. 2010;60:1914–1917.
    doi: 10.1099/ijs.0.016873-0pubmed: 19783610google scholar: lookup
  23. Ganzle M.G.. Lactic metabolism revisited: Metabolism of lactic acid bacteria in food fermentations and food spoilage.. Curr. Opin. Food Sci. 2015;2:106–117.
    doi: 10.1016/j.cofs.2015.03.001google scholar: lookup
  24. Shortt C., Hasselwander O., Meynier A., Nauta A., Fernandez E.N., Putz P., Rowland I., Swann J., Turk J., Vermeiren J.. Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrients.. Eur. J. Nutr. 2018;57:25–49.
    doi: 10.1007/s00394-017-1546-4pmc: PMC5847024pubmed: 29086061google scholar: lookup
  25. Yu J., Song Y.Q., Ren Y., Qing Y.T., Liu W.J., Sun Z.H.. Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus.. BMC Microbiol. 2017;17:213.
    doi: 10.1186/s12866-017-1120-5pmc: PMC5670709pubmed: 29100523google scholar: lookup
  26. Konstantinidis K.T., Tiedje J.M.. Trends between gene content and genome size in prokaryotic species with larger genomes.. Proc. Natl. Acad. Sci. USA. 2004;101:3160–3165.
    doi: 10.1073/pnas.0308653100pmc: PMC365760pubmed: 14973198google scholar: lookup
  27. Mahony J., Bottacini F., van Sinderen D., Fitzgerald G.F.. Progress in lactic acid bacterial phage research.. Microb. Cell Fact. 2014;13:12.
    doi: 10.1186/1475-2859-13-S1-S1pmc: PMC4155818pubmed: 25185514google scholar: lookup
  28. Kim S.H., Bae S., Song M.. Recent Development of Aminoacyl-tRNA Synthetase Inhibitors for Human Diseases: A Future Perspective.. Biomolecules 2020;10:1625.
    doi: 10.3390/biom10121625pmc: PMC7760260pubmed: 33271945google scholar: lookup
  29. Ibba M., Soll D.. Aminoacyl-tRNA synthesis.. Annu. Rev. Biochem. 2000;69:617–650.
    doi: 10.1146/annurev.biochem.69.1.617pubmed: 10966471google scholar: lookup
  30. Lombard V., Ramulu H.G., Drula E., Coutinho P.M., Henrissat B.. The carbohydrate-active enzymes database (CAZy) in 2013.. Nucleic Acids Res. 2014;42:D490–D495.
    doi: 10.1093/nar/gkt1178pmc: PMC3965031pubmed: 24270786google scholar: lookup
  31. Yin Q., Yue D.M., Peng Y.K., Liu Y., Xiao L.. Occurrence and Distribution of Antibiotic-resistant Bacteria and Transfer of Resistance Genes in Lake Taihu.. Microbes Environ. 2013;28:479–486.
    doi: 10.1264/jsme2.ME13098pmc: PMC4070710pubmed: 24240317google scholar: lookup
  32. Almeciga-Diaz C.J., Gutierrez A.M., Bahamon I., Rodriguez A., Rodriguez M.A., Sanchez O.F.. Computational analysis of the fructosyltransferase enzymes in plants, fungi and bacteria.. Gene. 2011;484:26–34.
    doi: 10.1016/j.gene.2011.05.024pubmed: 21679751google scholar: lookup
  33. Dwivedi S., Sahrawat K., Puppala N., Ortiz R.. Plant prebiotics and human health: Biotechnology to breed prebiotic-rich nutritious food crops.. Electron. J. Biotechnol. 2014;17:238–245.
    doi: 10.1016/j.ejbt.2014.07.004google scholar: lookup
  34. Sanchez C.. Lignocellulosic residues: Biodegradation and bioconversion by fungi.. Biotechnol. Adv. 2009;27:185–194.
    doi: 10.1016/j.biotechadv.2008.11.001pubmed: 19100826google scholar: lookup
  35. Sista Kameshwar A.K., Qin W.. Understanding the structural and functional properties of carbohydrate esterases with a special focus on hemicellulose deacetylating acetyl xylan esterases.. Mycology 2018;9:273–295.
    doi: 10.1080/21501203.2018.1492979pmc: PMC6282417pubmed: 30533253google scholar: lookup
  36. Chen X., Wei Y., Ji X.. Research progress of prophages.. Yi Chuan = Hered. 2021;43:240–248.
    doi: 10.16288/j.yczz.20-355pubmed: 33724208google scholar: lookup
  37. Canchaya C., Fournous G., Brussow H.. The impact of prophages on bacterial chromosomes.. Mol. Microbiol. 2004;53:9–18.
    doi: 10.1111/j.1365-2958.2004.04113.xpubmed: 15225299google scholar: lookup
  38. De Sordi L., Lourenco M., Debarbieux L.. The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract.. Cell Host Microbe. 2019;25:210–218.
    doi: 10.1016/j.chom.2019.01.018pubmed: 30763535google scholar: lookup
  39. Bakhshinejad B., Ghiasvand S.. Bacteriophages in the human gut: Our fellow travelers throughout life and potential biomarkers of heath or disease.. Virus Res. 2017;240:47–55.
    doi: 10.1016/j.virusres.2017.07.013pubmed: 28743462google scholar: lookup
  40. Dalmasso M., Hill C., Ross R.P.. Exploiting gut bacteriophages for human health.. Trends Microbiol. 2014;22:399–405.
    doi: 10.1016/j.tim.2014.02.010pubmed: 24656964google scholar: lookup
  41. Minot S., Sinha R., Chen J., Li H.Z., Keilbaugh S.A., Wu G.D., Lewis J.D., Bushman F.D.. The human gut virome: Inter-individual variation and dynamic response to diet.. Genome Res. 2011;21:1616–1625.
    doi: 10.1101/gr.122705.111pmc: PMC3202279pubmed: 21880779google scholar: lookup
  42. Ventura M., Canchaya C., Kleerebezem M., de Vos W.A., Siezen R.J., Brussow H.. The prophage sequences of Lactobacillus plantarum strain WCFS1.. Virology. 2003;316:245–255.
    doi: 10.1016/j.virol.2003.08.019pubmed: 14644607google scholar: lookup
  43. Wang S., Yang B., Ross R.P., Stanton C., Zhao J.X., Zhang H., Chen W.. Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches.. Genes 2020;11:17.
    doi: 10.3390/genes11010070pmc: PMC7016997pubmed: 31936280google scholar: lookup
  44. Tang H., Bowers J.E., Wang X., Ming R., Alam M., Paterson A.H.. Synteny and Collinearity in Plant Genomes.. Science. 2008;320:486–488.
    doi: 10.1126/science.1153917pubmed: 18436778google scholar: lookup
  45. Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I., de Montigny J., Marck C., Neuveglise C., Talla E.. Genome evolution in yeasts.. Nature. 2004;430:35–44.
    doi: 10.1038/nature02579pubmed: 15229592google scholar: lookup
  46. Nakatani Y., Takeda H., Kohara Y., Morishita S.. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.. Genome Res. 2007;17:1254–1265.
    doi: 10.1101/gr.6316407pmc: PMC1950894pubmed: 17652425google scholar: lookup
  47. Yu J., Wang W.H., Menghe B.L.G., Jiri M.T., Wang H.M., Liu W.J., Bao Q.H., Lu Q., Zhang J.C., Wang F.. Diversity of lactic acid bacteria associated with traditional fermented dairy products in Mongolia.. J. Dairy Sci. 2011;94:3229–3241.
    doi: 10.3168/jds.2010-3727pubmed: 21700007google scholar: lookup
  48. Jin H., Mo L.X., Pan L., Hou Q.C., Li C.J., Darima I., Yu J.. Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses.. J. Dairy Sci. 2018;101:6885–6896.
    doi: 10.3168/jds.2018-14403pubmed: 29753477google scholar: lookup
  49. Yu J., Gao W., Qing M.J., Sun Z.H., Wang W.H., Liu W.J., Pan L., Sun T., Wang H.M., Bai N.. Identification and characterization of lactic acid bacteria isolated from traditional pickles in Sichuan, China.. J. Gen. Appl. Microbiol. 2012;58:163–172.
    doi: 10.2323/jgam.58.163pubmed: 22878734google scholar: lookup
  50. Luo R.B., Liu B.H., Xie Y.L., Li Z.Y., Huang W.H., Yuan J.Y., He G.Z., Chen Y.X., Pan Q., Liu Y.J.. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler.. GigaScience. 2015;4:1.
    doi: 10.1186/s13742-015-0069-2pmc: PMC4496933pubmed: 26161257google scholar: lookup
  51. Chen J., Yang X., Chen J., Cen Z., Guo C., Jin T., Cui Y.. SISP: A Fast Species Identification System for Prokaryotes Based on Total Nucleotide Identity of Whole Genome Sequences.. Infect. Dis. Transl. Med. 2015;1:30–55.
  52. Chen C.J., Chen H., Zhang Y., Thomas H.R., Frank M.H., He Y.H., Xia R.. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.. Mol. Plant. 2020;13:1194–1202.
    doi: 10.1016/j.molp.2020.06.009pubmed: 32585190google scholar: lookup
  53. Seemann T.. Prokka: Rapid prokaryotic genome annotation.. Bioinformatics. 2014;30:2068–2069.
    doi: 10.1093/bioinformatics/btu153pubmed: 24642063google scholar: lookup
  54. Page A.J., Cummins C.A., Hunt M., Wong V.K., Reuter S., Holden M.T.G., Fookes M., Falush D., Keane J.A., Parkhill J.. Roary: Rapid large-scale prokaryote pan genome analysis.. Bioinformatics. 2015;31:3691–3693.
    doi: 10.1093/bioinformatics/btv421pmc: PMC4817141pubmed: 26198102google scholar: lookup
  55. Zhang H., Yohe T., Huang L., Entwistle S., Wu P.Z., Yang Z.L., Busk P.K., Xu Y., Yin Y.B.. dbCAN2: A meta server for automated carbohydrate-active enzyme annotation.. Nucleic Acids Res. 2018;46:W95–W101.
    doi: 10.1093/nar/gky418pmc: PMC6031026pubmed: 29771380google scholar: lookup
  56. Zhou Y., Liang Y.J., Lynch K.H., Dennis J.J., Wishart D.S.. PHAST: A Fast Phage Search Tool.. Nucleic Acids Res. 2011;39:W347–W352.
    doi: 10.1093/nar/gkr485pmc: PMC3125810pubmed: 21672955google scholar: lookup
  57. Darling A.C.E., Mau B., Blattner F.R., Perna N.T.. Mauve: Multiple alignment of conserved genomic sequence with rearrangements.. Genome Res. 2004;14:1394–1403.
    doi: 10.1101/gr.2289704pmc: PMC442156pubmed: 15231754google scholar: lookup

Citations

This article has been cited 4 times.
  1. Qin X, Xi L, Zhao L, Han J, Qu H, Xu Y, Weng W. Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics. Front Cell Infect Microbiol 2025;15:1590839.
    doi: 10.3389/fcimb.2025.1590839pubmed: 40692682google scholar: lookup
  2. Shi R, Tian X, Ji A, Zhang T, Xu H, Qi Z, Zhou L, Zhao C, Li D. A Mixture of Soybean Oil and Lard Alleviates Postpartum Cognitive Impairment via Regulating the Brain Fatty Acid Composition and SCFA/ERK(1/2)/CREB/BDNF Pathway. Nutrients 2024 Aug 10;16(16).
    doi: 10.3390/nu16162641pubmed: 39203778google scholar: lookup
  3. Rios Galicia B, Sáenz JS, Yergaliyev T, Camarinha-Silva A, Seifert J. Host specific adaptations of Ligilactobacillus aviarius to poultry. Curr Res Microb Sci 2023;5:100199.
    doi: 10.1016/j.crmicr.2023.100199pubmed: 37727231google scholar: lookup
  4. Li XB, Huang XX, Li Q, Li XY, Li JH, Li C, He LJ, Jing HX, Yang KL. Effects of different grains on bacterial diversity and enzyme activity associated with digestion of starch in the foal stomach. BMC Vet Res 2022 Nov 17;18(1):407.
    doi: 10.1186/s12917-022-03510-2pubmed: 36397114google scholar: lookup
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.