Web Resources for Microbial Data

Sun, Qinglan; Liu, Li; Wu, Linhuan; Li, Wei; Liu, Quanhe; Zhang, Jianyuan; Liu, Di; Ma, Juncai

doi:10.1016/j.gpb.2015.01.008

Cited by 12 publications

(7 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…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

View full text Add to dashboard Cite

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.

show abstract

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

View full text Add to dashboard Cite

show abstract

“…In these ways, MG-RAST offers great flexibility in analysis, privacy, and sharing of data. Therefore, it is the most reviewed and explored tool in use today [8] , [13] , [19] . So far, more than 2000 metagenome projects and over 13,000 metagenomic datasets have been uploaded to the MG-RAST servers each month of 2015, indicating the great popularity of the tool.…”

Section: Mg-rastmentioning

confidence: 99%

Web Resources for Metagenomics Studies

Dudhagara

Bhavsar

Bhagat

et al. 2015

Genomics, Proteomics &Amp; Bioinformatics

View full text Add to dashboard Cite

The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.

show abstract

“…Bacteria were very small and harmful organism, some bacteria could cause various types of infectious diseases such as typhoid [1], common cold [2], influenza [3], pneumonia [4], malaria [5], amebiasis [6], syphilis and AIDS [7]. Bacteria may be innate resistant or acquire resistance to one or few classes of antimicrobial agents.…”

Section: Introductionmentioning

confidence: 99%

In Vitro and in Silico Antibacterial Activity of 1.5-BIS (3’-Ethoxy-4’-Hydroxyphenyl)-1-4-Pentadiene-3-One

Purwanggana

Mumpuni

Mulatsari

2018

Int J Pharm Pharm Sci

View full text Add to dashboard Cite

Objective: The main objective of this research were screened in vitro and in silico of 1,5-bis (3'-ethoxy-4'-hydroxyphenyl)-1,4-pentadiene-3-one as potential antibacterial agents. Methods:The in vitro antibacterial study was carried against Staphylococcus aureus, Staphylococcus epidermidis (gram positive) and Escherichia coli, Salmonella thypi (gram negative) using broth dilution method to determine Minimum Inhibitory Concentration (MIC), disc diffusion method to determine the diameter of inhibition zone. In silico antibacterial study was carried using computational software Protein-Ligand ANT System (PLANTS), computational docking was carried using receptor with Protein Data Bank (PDB) file 3MZD. The structures were optimized prior docking using YASARA, and MarvinSketch. The results of antibacterial testing were compared to two positive control drugs i. e amoxicillin and cefadroxil. Results:In vitro evaluation showed that 1,5-bis (3'-ethoxy-4'-hydroxyphenyl)-1,4-pentadiene-3-one has a better antibacterial activity than amoxicillin and cefadroxil with a Minimum Inhibitory Concentration (MIC) of 0.15 ppm and diameter of inhibition zone of 11.27±0.31, 11.35±0.39, 11.25±0.33, and 11.05±0.45 mm in Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, and Salmonella thypi, respectively. These results in line with in silico evaluation that showed 1,5-bis (3'-ethoxy-4'-hydroxyphenyl)-1,4-pentadiene-3-one has more negative docking score than amoxicillin, cefadroxil, and cloxacillin acyl as a native ligand on the 3MZD receptor. Conclusion:This results obtained in this research work were 1,5-bis (3'-ethoxy-4'-hydroxyphenyl)-1,4-pentadiene-3-one compound potential as an antibacterial agent.

show abstract

Web Resources for Microbial Data

Abstract: There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.

Cited by 12 publications

References 10 publications

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

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

Web Resources for Metagenomics Studies

In Vitro and in Silico Antibacterial Activity of 1.5-BIS (3’-Ethoxy-4’-Hydroxyphenyl)-1-4-Pentadiene-3-One

Contact Info

Product

Resources

About

Web Resources for Microbial Data

Abstract: There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.

Cited by 12 publications

References 10 publications

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

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

Web Resources for Metagenomics Studies

In Vitro and in Silico Antibacterial Activity of 1.5-BIS (3’-Ethoxy-4’-Hydroxyphenyl)-1-4-Pentadiene-3-One

Contact Info

Product

Resources

About

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

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