Web Resources for Metagenomics Studies

Dudhagara, Pravin; Bhavsar, Sunil; Bhagat, Chintan; Ghelani, Anjana; Bhatt, Shreyas; Patel, Rajesh

doi:10.1016/j.gpb.2015.10.003

Cited by 33 publications

(17 citation statements)

References 38 publications

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“…The advent of Next-Generation Sequencing (NGS) technologies has made it possible to perform sequencing based metagenomic analysis. NGS aids in complete decoding of the entire community [5]. Healthy population of microbes in CWS is essential for the optimized removal of pollutants in the system.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Usharani

2019

ILNS

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Constructed wetlands are ecofriendly, cost effective technology involved in treatment of wastewaters. The goal of this study is focused on characterization of microbial community existing in constructed wetland system planted withCyperusalternifoliustreating sewage contaminated with heavy metals. The characteristics of effluent met the standards of discharge for inland use and irrigation. Microbes in constructed wetland apparently play a pivotal role in the efficiency of system for removal of organics, nutrients, suspended solids and heavy metal. To expose the active players in the lime light, a representative soil sample from the reed bed was collected and characterized for microbial community analysis. Metagenomic studies of the bacterial and fungal flora were identified. Results revealed that the phylum Proteobacteria (38.27%) and Ascomycota (77.47%) dominated in the bacterial and fungal kingdom respectively. However, in the bacterial kingdom at species level major portion remain unclassified exceptPseudomonasalcaligenesbut in the fungal kingdom at species level only 3.1% remain unclassified. The role of bacteria in wastewater treatment is exemplified in previous reports but the role of fungi in wastewater system needs exploration. However, the findings reveal that the identified microbes might have definitely played a vital role in wastewater treatment. The database available for the identification of bacterial species remain undiscovered for a major portion and requires up gradation. Next generation sequence being a high end technology in microbial ecology decodes the entire community in environmental samples but lack of database limits the identification. Implementation of improvements in the paucity of data bases is essential.

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Section: Introductionmentioning

confidence: 99%

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Usharani

2019

ILNS

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“…The most important contribution of these two alignment-free methods (OPD and BLSOM) is to predict the functions of the increasingly large number of functionunknown proteins derived from poorly characterized organisms, such as those studied using metagenomic approaches (Dudhagara et al, 2015;Noecker et al, 2017), and thus to serve a new and powerful tool in the postgenome era.…”

Section: Discussionmentioning

confidence: 99%

A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance

et al. 2020

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As a result of the extensive decoding of a massive amount of genomic and metagenomic sequence data, a large number of genes whose functions cannot be predicted by sequence similarity searches are accumulating, and such genes are of little use to science or industry. Current genome and metagenome sequencing largely depend on high-throughput and low-cost methods. In the case of genome sequencing for a single species, high-density sequencing can reduce sequencing errors. For metagenome sequences, however, high-density sequencing does not necessarily increase the sequence quality because multiple and unknown genomes, including those of closely related species, are likely to exist in the sample. Therefore, a function prediction method that is robust against sequence errors becomes an increased need. Here, we present a method for predicting protein gene function that does not depend on sequence similarity searches. Using an unsupervised machine learning method called BLSOM (batch-learning self-organizing map) for short oligopeptide frequencies, we previously developed a sequence alignment-free method for clustering bacterial protein genes according to clusters of orthologous groups of proteins (COGs), without using information from COGs during machine learning. This allows function-unknown proteins to cluster with function-known proteins, based solely on similarity with respect to oligopeptide frequency, although the method required high-performance supercomputers (HPCs). Based on a wide range of knowledge obtained with HPCs, we have now developed a strategy to correlate function-unknown proteins with COG categories, using only oligopeptide frequency distances (OPDs), which can be conducted with PC-level computers. The OPD strategy is suitable for predicting the functions of proteins with low sequence similarity and is applied here to predict the functions of a large number of gene candidates discovered using metagenome sequencing.

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“…The GS De Novo Assembler (Roche) was used to trim and group the data (i.e., adapter, linker and primer sequences) based on MID as well as generate consensus sequences of the DNA libraries. The assembled contigs were used in a metagenomic analysis with the CAMERA database [27] [28].…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (<i>Gallus gallus domesticus</i>) during Downstream Poultry Processing

Guttala¹,

Medrano²,

Bray³

et al. 2017

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Antibiotic growth promoters that have been historically employed to control pathogens and increase the rate of animal development for human consumption are currently banned in many countries. Probiotics have been proposed as an alternative to control pathogenic bacteria. Traditional culture methods typically used to monitor probiotic effects on pathogens possess significant limitations such as a lack in sensitivity to detect fastidious and non-culturable bacteria, and are both time consuming and costly. Here, we tested next generation pyrosequencing technology as a streamline and economical method to monitor the effects of a probiotic on microbial communities in juvenile poultry (Gallus gallus domesticus) after exposure to several microbiological challenges and litter conditions. Seven days and repeated again at 39 days following hatching, chicks were challenged with either Salmonella enterica serovar Enteritidis, Campylobacter jejuni, or no bacteria in the presence of, or without a probiotic (i.e., Bacillus subtilis) added to the feed. Three days following each of two challenges (i.e., days 10 and 42, respectively) the microbiome distributions of the poultry caecum were characterized based on 16S rDNA analysis. Generated PCR products were analyzed by automated identification of the samples after pooling, multiplexing and sequencing. A bioinformatics pipeline was then employed to identify microbial distributions at the phylum and genus level for the treatments. In conclusion, our results demonstrated that pyrosequencing technology is a rapid, efficient and cost-effective method to monitor the effects of probiotics on the microbiome of poultry propagated in an agricultural setting.

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Web Resources for Metagenomics Studies

Cited by 33 publications

References 38 publications

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (<i>Gallus gallus domesticus</i>) during Downstream Poultry Processing

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Web Resources for Metagenomics Studies

Cited by 33 publications

References 38 publications

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (&lt;i&gt;Gallus gallus domesticus&lt;/i&gt;) during Downstream Poultry Processing

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Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (<i>Gallus gallus domesticus</i>) during Downstream Poultry Processing