An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

Satyabrata Bag; Bipasa Saha; Ojasvi Mehta; D Anbumani; Naveen Kumar; Mayanka Dayal; Archana Pant; Pawan Kumar; Shruti Saxena; Kristine H Allin; Torben Hansen; Manimozhiyan Arumugam; Henrik Vestergaard; Oluf Pedersen; Verima Pereira; Philip Abraham; Reva Tripathi; Nitya Wadhwa; Shinjini Bhatnagar; Visvanathan Gnana Prakash; Venkatesan Radha; R M Anjana; V Mohan; Kiyoshi Takeda; Takashi Kurakawa; G Balakrish Nair; Bhabatosh Das

doi:10.1038/srep26775

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

Satyabrata Bag, Bipasa Saha, Ojasvi Mehta, D Anbumani, Naveen Kumar, Mayanka Dayal, Archana Pant, Pawan Kumar, Shruti Saxena, Kristine H Allin, Torben Hansen, Manimozhiyan Arumugam, Henrik Vestergaard, Oluf Pedersen, Verima Pereira, Philip Abraham, Reva Tripathi, Nitya Wadhwa, Shinjini Bhatnagar, Visvanathan Gnana PrakashVenkatesan Radha, R M Anjana, V Mohan, Kiyoshi Takeda, Takashi Kurakawa, G Balakrish Nair, Bhabatosh Das

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Abstract

To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.

Originalsprog	Engelsk
Artikelnummer	26775
Tidsskrift	Scientific Reports
Vol/bind	6
Antal sider	9
ISSN	2045-2322
DOI	https://doi.org/10.1038/srep26775
Status	Udgivet - 31 maj 2016

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10.1038/srep26775Licens: CC BY

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental SamplesForlagets udgivne version, 2,4 MBLicens: CC BY

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Bag, S., Saha, B., Mehta, O., Anbumani, D., Kumar, N., Dayal, M., Pant, A., Kumar, P., Saxena, S., Allin, K. H., Hansen, T., Arumugam, M., Vestergaard, H., Pedersen, O., Pereira, V., Abraham, P., Tripathi, R., Wadhwa, N., Bhatnagar, S., ... Das, B. (2016). An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples. Scientific Reports, 6, Artikel 26775. https://doi.org/10.1038/srep26775

Bag, S, Saha, B, Mehta, O, Anbumani, D, Kumar, N, Dayal, M, Pant, A, Kumar, P, Saxena, S, Allin, KH , Hansen, T , Arumugam, M , Vestergaard, H , Pedersen, O, Pereira, V, Abraham, P, Tripathi, R, Wadhwa, N, Bhatnagar, S, Prakash, VG, Radha, V, Anjana, RM, Mohan, V, Takeda, K, Kurakawa, T, Nair, GB & Das, B 2016, 'An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples', Scientific Reports, bind 6, 26775. https://doi.org/10.1038/srep26775

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title = "An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples",

abstract = "To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.",

author = "Satyabrata Bag and Bipasa Saha and Ojasvi Mehta and D Anbumani and Naveen Kumar and Mayanka Dayal and Archana Pant and Pawan Kumar and Shruti Saxena and Allin, {Kristine H} and Torben Hansen and Manimozhiyan Arumugam and Henrik Vestergaard and Oluf Pedersen and Verima Pereira and Philip Abraham and Reva Tripathi and Nitya Wadhwa and Shinjini Bhatnagar and Prakash, {Visvanathan Gnana} and Venkatesan Radha and Anjana, {R M} and V Mohan and Kiyoshi Takeda and Takashi Kurakawa and Nair, {G Balakrish} and Bhabatosh Das",

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T1 - An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

AU - Bag, Satyabrata

AU - Saha, Bipasa

AU - Mehta, Ojasvi

AU - Anbumani, D

AU - Kumar, Naveen

AU - Dayal, Mayanka

AU - Pant, Archana

AU - Kumar, Pawan

AU - Saxena, Shruti

AU - Allin, Kristine H

AU - Hansen, Torben

AU - Arumugam, Manimozhiyan

AU - Vestergaard, Henrik

AU - Pedersen, Oluf

AU - Pereira, Verima

AU - Abraham, Philip

AU - Tripathi, Reva

AU - Wadhwa, Nitya

AU - Bhatnagar, Shinjini

AU - Prakash, Visvanathan Gnana

AU - Radha, Venkatesan

AU - Anjana, R M

AU - Mohan, V

AU - Takeda, Kiyoshi

AU - Kurakawa, Takashi

AU - Nair, G Balakrish

AU - Das, Bhabatosh

PY - 2016/5/31

Y1 - 2016/5/31

N2 - To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.

AB - To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.

U2 - 10.1038/srep26775

DO - 10.1038/srep26775

M3 - Journal article

C2 - 27240745

SN - 2045-2322

VL - 6

JO - Scientific Reports

JF - Scientific Reports

M1 - 26775

ER -

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

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