Indian Journal of Microbiology

, Volume 59, Issue 4, pp 482–489 | Cite as

Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples

  • Mohita Gaur
  • Aarushi Vasudeva
  • Anoop Singh
  • Vishal Sharma
  • Himani Khurana
  • Ram Krishan Negi
  • Jung-Kul Lee
  • Vipin Chandra Kalia
  • Richa MisraEmail author
  • Yogendra SinghEmail author
Original Research Article


Metagenomics is the study of gene pool of an entire community in a particular niche. This provides valuable information about the functionality of host-microbe interaction in a biological ecosystem. Efficient metagenomic DNA extraction is a critical pre-requisite for a successful sequencing run in a metagenomic study. Although isolation of human stool metagenomic DNA is fairly standardized, the same protocol does not work as efficiently in fecal DNA from other organisms. In this study, we report a comparison of manual and commercial DNA extraction methods for diverse samples such as human stool, fish gut and soil. Fishes are known to have variable microbial diversity based on their food habits, so the study included two different varieties of fishes. A modified protocol for effective isolation of metagenomic DNA from human milk samples is also reported, highlighting critical precautions. Recent studies have emphasized the importance of studying functionality of human milk metagenome to understand its influence on infants’ health. While manual method works well with most samples and therefore can be a method of choice for testing new samples, broad-range commercial kit offers advantage of high purity and quality. DNA extraction of different samples would go a long way in unraveling the unexplored association between microbes and host in a biological system.


Metagenomic DNA Stool Fecal Milk Fish gut Soil 



We thank the volunteers who provided samples and the staff at Maulana Azad Medical College and Associated Hospital. This work was funded by SERB (JC Bose research fellowship to YS). This work was supported by Brain Pool grant (NRF-2019H1D3A2A01060226) by National Research Foundation (NRF), South Korea to work at Konkuk University (VCK). This research was supported by Basic Science Research Program (2013M3A6A8073184) through the NRF funded by the Ministry of Education, Science and Technology, South Korea (JKL). The work was also supported by Science and Engineering Research Board (GIA/3186/2019-20). The funding organization had no role in the study design or manuscript preparation.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interests.

Ethical Standard

All procedures performed in the study involving human samples were in accordance with the ethical standards of the institute.


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Copyright information

© Association of Microbiologists of India 2019

Authors and Affiliations

  1. 1.Department of ZoologyUniversity of DelhiDelhiIndia
  2. 2.Department of Chemical EngineeringKonkuk UniversitySeoulRepublic of Korea
  3. 3.Department of Zoology, Sri Venkateswara CollegeUniversity of DelhiDelhiIndia

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