Acta Scientific Nutritional Health (ASNH)(ISSN: 2582-1423)

Review Article Volume 4 Issue 7

Whole-Genome Sequencing of Lactobacillus fermentum and its Application as Probiotic in Poultry Feed

Rafia Sameen1 and Shakira Ghazanfar2*

1Department of Animal Genomics and Biotechnology, PIASA National Agriculture Research Centre, Islamabad, Pakistan
2National Institute of Genomics and Agriculture Biotechnology (NIGAB), National Agriculture Research Centre, Islamabad, Pakistan

*Corresponding Author: Shakira Ghazanfar, National Institute of Genomics and Agriculture Biotechnology (NIGAB), National Agriculture Research Centre, Islamabad, Pakistan.

Received: May 22, 2020; Published: June 19, 2020



 Aviculture is the efficient animal production system and good source of animal protein worldwide. Poultry gastrointestinal tract houses certain microbial communities with bacteria being dominant above all. These bacteria produce beneficial products and result in non-pathogenic immune response providing nutrition and protection for animals. Antibiotic treatment causes reduction of beneficial bacterial population in intestine which can be controlled by probiotic supplements. Probiotics play their role to control intestinal pathogens by competing for adhesion sites and nutrients, producing anti-bacterial substances. Lactic acid bacteria could be a good probiotic for animal use among which Lactobacillus fermentum is major heterofermentative specie found to have probiotic potential and can be used in supplements for animal feed. Its probiotic potential was well studied by its tolerance to inhibitory substances like bile and salt, its antimicrobial activity and evaluation by supplementing it in poultry feed. To identify probiotic properties of Lactobacillus fermentum, its whole-genome was sequenced and analysed. Whole genome sequencing is a DNA sequencing technology that has revolutionized genomic research. Whole genome is sequenced, assembled and annotated using bioinformatics tool and then analyzed. Galaxy is one of most commonly used genome analysis tool that provides data analysis support through framework, to give simple interfaces to certain powerful tools and automatically manage computational details. Following to evaluation of probiotic potential through certain parameters and whole genome sequencing, antimicrobial resistance can also be evaluated to make a decision about safety of L. fermentum use as probiotic in poultry feed. Administration of L. fermentum to poultry showed beneficial effects on their growth. Introduction

Keywords: Probiotics; Lactobacillus fermentum; Whole Genome Sequencing (WGS); Galaxy



  1. Clavijo Viviana and Martha Josefina Vives Flórez. "The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: a review”. Poultry Science3 (2018): 1006-1021.
  2. Wei S., et al. “Bacterial census of poultry intestinal microbiome”. Poultry Science3 (2013): 671-683.
  3. Yegani M and DR Korver. "Factors affecting intestinal health in poultry”. Poultry Science10 (2008): 2052-2063.
  4. Kumar Sanjay., et al. “Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens”. PLoS One 2 (2018).
  5. Mancabelli Leonardo., et al. “Insights into the biodiversity of the gut microbiota of broiler chickens”. Environmental Microbiology12 (2016): 4727-4738.
  6. Shang Yue., et al. “Chicken gut microbiota: Importance and detection technology”. Frontiers in Veterinary Science 5 (2018): 254.
  7. Han Geon Goo., et al. “Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens”. Springerplus1 (2016): 911.
  8. Oakley Brian B., et al. “The chicken gastrointestinal microbiome”. FEMS Microbiology Letters2 (2014): 100-112.
  9. Idoui Tayeb. "Probiotic properties of Lactobacillus strains isolated from gizzard of local poultry”. Iranian Journal of Microbiology2 (2014): 120.
  10. Reque Elizete de F., et al. “Isolation, identification and physiological study of Lactobacillus fermentum LPB for use as probiotic in chickens”. Brazilian Journal of Microbiology4 (2000): 303-307.
  11. Lin Wen-Hsin., et al. “Different probiotic properties for Lactobacillus fermentum strains isolated from swine and poultry”. Anaerobe3-4 (2007): 107-113.
  12. Dickson EM., et al. “A novel species-specific PCR assay for identifying Lactobacillus fermentum”. Journal of Medical Microbiology3 (2005): 299-303.
  13. Raja M Mohamed Mahroop., et al. “Lactobacillus as a probiotic feed for chickens”. International Journal of Poultry Science 8 (2009): 763-767.
  14. Ibrahim Salam A. “Lactic Acid Bacteria: Lactobacillus: Other Species” (2016).
  15. Torshizi MA., et al. “Screening of indigenous strains of lactic acid bacteria for development of a probiotic for poultry”. Asian-Australasian Journal of Animal Sciences10 (2008): 1495-1500.
  16. Behjati Sam and Patrick S Tarpey. "What is next generation sequencing?”. Archives of Disease in Childhood-Education and Practice 6 (2013): 236-238.
  17. Pightling, Arthur W., et al. “Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations”. Frontiers in Microbiology 9 (2018): 1482.
  18. Khan M., et al. “Growth-promoting effects of single-dose intragastrically administered probiotics in chickens”. British Poultry Science6 (2007): 732-735.
  19. Sun Zhihong., et al. “Complete genome sequence of the probiotic Lactobacillus fermentum F-6 isolated from raw milk”. Journal of Biotechnology 194 (2015): 110-111.
  20. Ekblom, Robert and Jochen BW Wolf. "A field guide to whole‐genome sequencing, assembly and annotation”. Evolutionary Applications9 (2014): 1026-1042.
  21. Gautam Sanjay S., et al. “A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens”. Journal of Biological Methods1 (2019).
  22. Dunn Paul., et al. “Next generation sequencing methods for diagnosis of epilepsy syndromes”. Frontiers in Genetics 9 (2018): 20.
  23. Lampa Samuel., et al. “Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data”. Gigascience1 (2013): 2047-217X.
  24. Yandell Mark and Daniel Ence. "A beginner's guide to eukaryotic genome annotation”. Nature Reviews Genetics5 (2012): 329-342.
  25. Blankenberg Daniel., et al. “Galaxy: a web‐based genome analysis tool for experimentalists”. Current Protocols in Molecular Biology1 (2010): 19-10.
  26. Blankenberg Daniel and Jennifer Hillman-Jackson. "Analysis of next-generation sequencing data using Galaxy”. Stem cell transcriptional networks. Humana Press, New York, NY (2014): 21-43.
  27. Zankari Ea., et al. “Identification of acquired antimicrobial resistance genes”. Journal of Antimicrobial Chemotherapy11 (2012): 2640-2644.


Citation: Rafia Sameen and Shakira Ghazanfar. “Whole-Genome Sequencing of Lactobacillus fermentum and its Application as Probiotic in Poultry Feed". Acta Scientific Nutritional Health 4.7 (2020): 49-54.


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