Metagenomics: Retrospect and Prospects in High Throughput Age

Kumar, Satish; Krishnani, Kishore Kumar; Bhushan, Bharat; Brahmane, M. P.

doi:10.1155/2015/121735

Cited by 46 publications

(27 citation statements)

References 111 publications

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“…In recent years, metagenomics has emerged as a powerful tool to study microbial diversity in a culture independent manner [22], an approach that is helping define the microbiome of mosquitoes [23][24][25][26]. Part of the uncovered microbiome is the insect-specific viruses (ISVs), viruses restricted to arthropods that are unable to replicate in vertebrate cells [27].…”

Section: Introductionmentioning

confidence: 99%

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis

et al. 2020

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Arboviruses cause diseases of significant global health concerns. Interactions between mosquitoes and their microbiota as well as the important role of this interaction in the mosquito's capacity to harbor and transmit pathogens have emerged as important fields of research. Aedes aegypti is one of the most abundant mosquitoes in many geographic locations, a vector capable of transmitting a number of arboviruses such as dengue and Zika. Currently, there are few studies on the metavirome of this mosquito particularly in the Americas. This study analyzes the metavirome of A. aegypti from Grenada, a Caribbean nation with tropical weather, abundant A. aegypti, and both endemic and arboviral pathogens transmitted by this mosquito. Between January and December 2018, 1152 mosquitoes were collected from six semi-rural locations near houses in St. George Parish, Grenada, by weekly trapping using BG-Sentinel traps. From these, 300 A. aegypti were selected for analysis. The metavirome was analyzed using the Illumina HiSeq 1500 for deep sequencing. The generation sequencing library construction protocol used was NuGEN Universal RNA with an average read length of 125 bp. Reads were mapped to the A. aegypti assembly. Non-mosquito reads were analyzed using the tools FastViromeExplorer. The NCBI total virus, RNA virus, and eukaryotic virus databases were used as references. The metagenomic comparison analysis showed that the most abundant virus-related reads among all databases and assemblies was Phasi Charoen-like virus. The Phasi Charoen-like virus results are in agreement to other studies in America, Asia and Australia. Further studies using wild-caught mosquitoes is needed to assess the impact of this insect-specific virus on the A. aegypti lifecycle and vector capacity.

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Section: Introductionmentioning

confidence: 99%

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis

et al. 2020

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“…Size of library was 644 bp and the library was sequenced using the Illumina sequencing chemistry to generate ~150 Mb of data per sample. The next generation sequencing (NGS) for the sample was performed on the Illumina platform, HiSeq 2500 (Kumar et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

“…In this paper, we present the fi ndings of metagenomic analysis leveraging next-generation sequencing (NGS) performed using Hiseq 2500 system (Kumar et al, 2015). The Metagenomics was carried on the defi ned microbial consortium identifi ed from water ecosystems, Yamuna River (North India) and Godavari River (South India) capable of simultaneous degradation of organochlorine pesticides (Bidlan, 2003).…”

Section: Introductionmentioning

confidence: 99%

16S metagenomic analysis and taxonomic distribution of enriched microbial consortia capable of simultaneous biodegradation of organochlorines by illumina platform

Raju¹,

Bidlan²

2017

Biosci. Biotech. Res. Comm

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Organochlorine pesticides are ubiquitous group of recalcitrant molecules that accumulate in food chains and have inherent toxic effects and adverse health effects. To circumvent the problem, microbial communities are found to be promising candidates for degrading the organochlorine pesticide's and removal of residues. In this study, a novel microbial consortium isolated from Yamuna and Godavari rivers capable of simultaneous biodegradation of organochlorine pesticides (DDT and Lindane) was subjected to metagenomic sequencing. This consortia used was enriched by progressively increasing concentrations of Lindane and DDT (organochlorine pesticides) for months till a stable Lindane and DDT tolerant population was established, and found to be degrading mixture of organochlorine pesticides with concentrations up to 30 ppm of DDT and Lindane. Currently, in the realm of our knowledge very few metagenomic analysis were carried out to characterize the consortia and understand the biodiversity of microbial communities in the riverine ecosystems, that was found to be unique and highly effi cient in bio-degradation of organochlorine pesticides. The study concluded biodiversity with a shannon alpha-diversity index of 3.0317 and identifi ed 871 species with Brevundimonas diminuta (previously assigned to the genus Pseudomanas) having abundance ratio of 17.57 % followed by Stenotrophomonas acidaminiphila in the mixed consortium and deciphered the systematic and functional contexts within riverine metagenome.

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“…They provide Metagenomics sequence data derived from a range of platforms which includes Roche 454, Ion Torrent and Illumina Sequence [14]. EBI Metagenomics divides their sequence data in different biomes from which they have isolated.…”

Section: Input Datamentioning

confidence: 99%

Determination of Uncultured Microorganisms Based on Metagenomics Signature or Biomarkers at Fresh Water Reservoirs

Panchal¹,

Bhairavkar²,

Patil³

2018

OAJS

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Metagenomics is the branch of science which does the direct analysis of genetic material of environmental samples. Maximum microorganisms present in the ecosystem are unculturable. Metagenomics with the expansion in the field of Next Generation Sequencing (NGS) has generated large amount of raw sequence reads of uncultured microbes from different ecosystem. This combination opens door for new metabolites, drug targets, new species and unknown world of new genes could be utilized for the therapeutics. Biomarkers could be utilized as an indicator for the identification of any biological processes, disease genes, metabolites, enzymes, and antibiotics while biosensor is an analytical devise for the detection of analyte with the help of biological component (biomarkers) and physicochemical detector. Current study tried to find probable biomarkers which could be utilized for biosensor development especially for uncultured microorganisms from fresh water ecosystems. We collected all fresh water raw reads from publically available different repositories. After preliminary screening on huge data sets, we performed quality analysis on raw read sequences, generated 10 different conserve domains by multiple sequence alignment. These CDs could be promising biomarkers for the identification of uncultured microbes from fresh water ecosystems which may be pathogenic for humans. DNA hybridization based Biosensor could be synthesized by using by using this biomarker sequences for detecting the presence of uncultured microorganisms (pathogenic/non-pathogenic) in fresh water ecosystem.

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Metagenomics: Retrospect and Prospects in High Throughput Age

Cited by 46 publications

References 111 publications

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis

16S metagenomic analysis and taxonomic distribution of enriched microbial consortia capable of simultaneous biodegradation of organochlorines by illumina platform

Determination of Uncultured Microorganisms Based on Metagenomics Signature or Biomarkers at Fresh Water Reservoirs

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