Skip to main content Skip to main navigation menu Skip to site footer

Gut microbiome analysis in human living close to livestock at Mlati district, Sleman, Yogyakarta

  • Yulia Sari ,
  • Betty Suryawati ,
  • Ari Natalia Probandari ,
  • Hartono ,
  • Wayan Tunas Artama ,
  • Bambang Purwanto ,
  • Soetrisno ,


Abstract

Background: Transmission of pathogenic and non-pathogenic microorganisms from animals to humans can affect the composition of gut bacteria (gut microbiome) in humans and can also be a potential source of transmission of zoonotic diseases. Therefore, this study aimed to analyze the gut microbiome interactions between the human and the livestock.

Method: This study was a cross-sectional study conducted in Mlati District, Slemanm Yogyakarta. The fecal sample was used to identify parasites by using trichrome staining. Then NGS selected samples were used to analyze the gut microbiome using Illumina high throughput 16S rRNA region V3-V4 sequencing.

Result: The analysis showed that Bacteroidetes was prevalent in the HCA group (57%), while Firmicutes (70%) were commonly found in HNC. Regarding the potential parasitic infection, direct microscopic examination and trichrome staining showed that Blastocystis sp and Entamoeba coli cyst was found in several subjects in HCA groups, with prevalence rate at 7.69% and 2.5%. Meanwhile, no parasite was found in HNC feces.

Conclusion: There was a significant difference in the gut microbiome and parasitic infections between the HCA and HNC groups, with Blastocystis sp and Entamoeba coli as the most prevalent parasites.

Keywords: livestock gut microbiome 16S rRNA gene high throughput sequencing

References

  1. Hale CR, Scallan E, Cronquist AB, et al. Estimates of enteric illness attributable to contact with animals and their environments in the United States. Clin Infect Dis. 2012;54(SUPPL.5). doi:10.1093/cid/cis051
  2. CDC. Zoonotic Diseases. Natl Cent Emerg Zoonotic Infect Dis. Published online 2017.
  3. Grace D, Lindahl J, Wanyoike F, Bett B, Randolph T, Rich KM. Poor livestock keepers: Ecosystem – poverty – health interactions. Philos Trans R Soc B Biol Sci. 2017;372(1725). doi:10.1098/rstb.2016.0166
  4. Song Se Jin, Lauber C, Gordon JI, Clemente JC, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013;2. doi:10.7554/elife.00458
  5. Misic A.M, Davis ME, Tyldsley AS, Hodkinson BP, Tolomeo P, Hu B, Nachamkin I, Lautenbach E MD and GE, Misic AM, Hodkinson BP, Tolomeo P, Hu B. The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites. Microbiome. 2015;3(1):2. doi:10.1186/s40168-014-0052-7
  6. Dietert RR, Dietert JM. The Microbiome and Sustainable Healthcare. 2015;(March). doi:10.3390/healthcare3010100
  7. Scher,JU and Abramson S. The microbiome and rheumatoid arthritis. Nat Rev Rheumatol. 2012;7(10):569-578. doi:10.1038/nrrheum.2011.121.The
  8. Huang, YJ and Boushey H. The Microbiome in Asthma. 2015;135(1):25-30. doi:10.1016/j.jaci.2014.11.011.The
  9. Tanja Magoc∗ and Steven L. Salzberg. FLASH: fast length adjustment of short reads to improve genome assemblies. Published online 2011:2957-2963.
  10. Caporaso JG, Lauber CL, Walters WA, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621-1624. doi:10.1038/ismej.2012.8
  11. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. 2011;27(16):2194-2200. doi:10.1093/bioinformatics/btr381
  12. Segata N. Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity. Curr Biol. 2015;25(14):R611-R613. doi:10.1016/j.cub.2015.05.040
  13. Buffie CG, Bucci V, Stein RR, et al. HHS Public Access. 2015;517(7533):205-208. doi:10.1038/nature13828.Precision
  14. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8(1):1-11. doi:10.1186/s13073-016-0307-y
  15. Weiss S, Xu ZZ, Peddada S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):1-18. doi:10.1186/s40168-017-0237-y
  16. Hao W, Lee Y. Microflora of the Gastrointestinal Tract A Review. 268(3):491-502.
  17. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. 2007;(May 2014):1027-1031. doi:10.1038/nature05414
  18. Zoetendal EG, Raes J, Van Den Bogert B, et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 2012;6(7):1415-1426. doi:10.1038/ismej.2011.212
  19. Leimena MM, Ramiro-Garcia J, Davids M, et al. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics. 2013;14(1):530. doi:10.1186/1471-2164-14-530
  20. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:36-44. doi:10.1136/bmj.k2179
  21. Karl PJ, Hatch AM, Arcidiacono SM, et al. Effects of psychological, environmental and physical stressors on the gut microbiota. Front Microbiol. 2018;9(SEP):1-32. doi:10.3389/fmicb.2018.02013

How to Cite

Sari, Y. ., Suryawati, B. ., Probandari, A. N. ., Hartono, Wayan Tunas Artama, Purwanto, B. ., & Soetrisno. (2022). Gut microbiome analysis in human living close to livestock at Mlati district, Sleman, Yogyakarta . Bali Medical Journal, 11(3), 1390–1396. https://doi.org/10.15562/bmj.v11i3.3774
ACM ACS APA ABNT Chicago Harvard IEEE MLA Turabian Vancouver
Download Citation
Endnote/Zotero/Mendeley (RIS) BibTeX

HTML
3

Total
1

Share