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

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

doi:10.1038/srep26775

Cited by 172 publications

(120 citation statements)

References 17 publications

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“…Additionally, NGS methods have been refined to extract the microbial DNA of sufficient purity and quantity for such assays. 28 The increasing interest in NGS-based microbiome research has urged scientists to assess PTB as a polymicrobial disease, because the infectious agents could be bacteria, virus, or fungus such as yeast. the upper part of the myometrium.…”

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confidence: 99%

Provocative ideas on human placental biology: A prerequisite for prevention and treatment of neonatal health challenges

Sehgal

Bhatnagar

Pallavi

2017

American J Rep Immunol

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this meeting were the critical evaluation of placental physiology and its development.Special emphasis was placed on understanding the consequences and implications of placental development in sustenance of pregnancy and in pregnancy-associated complications such as preeclampsia, intrauterine growth restriction, and preterm birth.This meeting brought together experienced as well as novice clinicians and biologists who have a keen interest in the field of placental biology, including development of new technologies and methods for evaluating the role of placenta in predicting pregnancy outcomes. The meeting primarily focused on (i) high-throughput "-omics" approaches, (ii) maternal nutrition and placental function, (iii) placental infection and inflammation, (iv) real-time evaluation of placental development: tools for placental research, and (v) epidemiologic relevance of placental-based research. Unanimous consensus emerged among the participants to carry out additional work focused on these areas. In this article, we summarize the talks and review the published literature on the above-mentioned niches. As a direct outcome of this meeting, a request for applications has been announced by the Department of Biotechnology, Government of India, for pursuing research in this vital but understudied domain. K E Y W O R D Sclinical imaging, epidemiology, maternal nutrition, omics, placenta | LAYING THE BACKGROUNDProf. Renu Dhingra, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, introduced the basics of placental anatomy and development. Placenta is a noteworthy organ that has evolved to support fetus in utero and is likely to be the key determinant of fetal growth. Formation of placenta requires a developmental progression, which proceeds in a specific order over time, specified by the trophoblast but dependent on maternal environment for correct expression.The trophoblast of the embedded/implanted blastocyst differentiates into two cellular layers inner mononuclear cytotrophoblast and outer multinucleated syncytiotrophoblast. Development of this discoid, chorioallantoic, and haemochorial human placenta is then characterized by lacunar and villous stages thus giving rise to primary, secondary, and tertiary chorionic villi. The development of placenta is not autonomous but is affected by maternal, periconceptional, genetic, and immune factors, which further influence the process of implantation, spiral artery remodeling, uteroplacental blood flow, and thus placental supply of nutrients and oxygen to fetus. Placental structural and functional abnormalities may not only cause numerous adverse pregnancy outcomes but also affect the long-term health of both mother and offspring. Thus, increasing the understanding of its structure and

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confidence: 99%

Provocative ideas on human placental biology: A prerequisite for prevention and treatment of neonatal health challenges

Sehgal

Bhatnagar

Pallavi

2017

American J Rep Immunol

Self Cite

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“…Nevertheless, Henriques et al successfully purified freshwater samples on 5 µm membranes, then concentrated microorganisms on 0.2 µm pore-size filters, washed them in TE buffer, centrifuged (15 200 g, 10 min) and further processed by two commercial kits [42]. In a need for adequate DNA extraction from environmental samples, Bag et al proposed THSTI method using enzymes, buffers, glass and zirconia beads, among others [52].…”

Section: Extraction Of Dna From Arb and Tap Water Samplesmentioning

confidence: 99%

“…The applied procedures may affect all the subsequently obtained results. In the case of molecular biology investigations, the most essential stage is the extraction of DNA [52,53].…”

Section: Extraction Of Dna From Arb and Tap Water Samplesmentioning

confidence: 99%

The occurrence of antibiotic resistance genes in tap water – a review

Siedlecka

2018

E3S Web Conf.

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Abstract. The study presents a review of the occurrence of genetic determinants of antibiotic resistance in tap water. The aim of this study was also to compare the applied methods for antibiotic resistance genes (ARGs) investigations in tap water. As the concentration of ARGs in treated, drinking water is expected to be very low and may cause problems in a standard isolation procedure, the special emphasis is placed on the applied procedures of DNA extraction and their efficiency. The study presents the first attempts to obtain DNA directly from tap water. Further efforts must be put to determine the final amount of obtained DNA and the presence of chosen ARGs among the molecules.

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“…Nevertheless, DNA extraction continues to be a large source of experimental variability in 16S rRNA sequence analysis and the most time-consuming step in a high-throughput pipeline [6]. Although DNA extraction protocols have been published for low bacterial biomasses [10,11], they are hard to implement as part of a high-throughput pipeline. Further, those focused on low biomass can become saturated with high biomass samples leading to uneven sequence sampling bias.…”

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Improved Yield and Accuracy for DNA Extraction in Microbiome Studies with Variation in Microbial Biomass

et al. 2019

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A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.

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

Cited by 172 publications

References 17 publications

Provocative ideas on human placental biology: A prerequisite for prevention and treatment of neonatal health challenges

Provocative ideas on human placental biology: A prerequisite for prevention and treatment of neonatal health challenges

The occurrence of antibiotic resistance genes in tap water – a review

Improved Yield and Accuracy for DNA Extraction in Microbiome Studies with Variation in Microbial Biomass

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