River ecosystems are very important parts of the water cycle and an excellent habitat, food, and drinking water source for many organisms, including humans. Antibiotics are emerging contaminants which can enter rivers from various sources. Several antibiotics and their related antibiotic resistance genes (ARGs) have been detected in these ecosystems by various research programs and could constitute a substantial problem. The presence of antibiotics and other resistance cofactors can boost the development of ARGs in the chromosomes or mobile genetic elements of natural bacteria in rivers. The ARGs in environmental bacteria can also be transferred to clinically important pathogens. However, antibiotics and their resistance genes are both not currently monitored by national or international authorities responsible for controlling the quality of water bodies. For example, they are not included in the contaminant list in the European Water Framework Directive or in the US list of Water‐Quality Benchmarks for Contaminants. Although ARGs are naturally present in the environment, very few studies have focused on non‐impacted rivers to assess the background ARG levels in rivers, which could provide some useful indications for future environmental regulation and legislation. The present study reviews the antibiotics and associated ARGs most commonly measured and detected in rivers, including the primary analysis tools used for their assessment. In addition, other factors that could enhance antibiotic resistance, such as the effects of chemical mixtures, the effects of climate change, and the potential effects of the coronavirus disease 2019 pandemic, are discussed. Environ Toxicol Chem 2022;41:687–714. © 2022 SETAC

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/etc.5289

Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges

Web Resources for Metagenomics Studies

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.

In vitro and in silico antibacterial activity of 1.5-bis (3'-ethoxy-4'-hydroxyphenyl)-1-4-pentadiene-3-one

The tremendous progress in next-generation sequencing (NGS) technology has brought an avalanche of sequence-based data. This huge volume of data has resulted in novel challenges for existing bioinformatics tools in terms of data handling and subsequent analyses. Additionally, complexity of such data makes the task of analysis of metagenomic datasets more complicated for available bioinformatics pipelines. Here we are dealing with various bioinformatics tools, available online for analysis of WGS-based metagenome datasets, and simultaneously comparing their analysis pipelines. In the last one decade, over a dozen of such online tools/servers have been developed which are accessible via public domain. IMG/M and MG-RAST are two of the most popular tools as per the number of citations they received in peer-reviewed scientific journals till December 2016. This chapter discusses and compares 11 online bioinformatics tools detailing their sequence data handling, pipelines for annotation, sequence clustering methods, user-friendly attributes, and feasibility of data repository.

Bioinformatics Tools for Shotgun Metagenomic Data Analysis

The number of studies aimed at proving the prebiotic properties of certain substances or compositions has been actively increasing, which has led to a large accumulation of scientific information that is fragmented and not systematized. Moreover, a number of criteria have been applied in these studies. The lack of an accessible and convenient information space to compare the obtained results seems to hold back not only scientific development, but also practical development in this field. A database called the «On-line Database of Researches on Activity of Prebiotics» (ODRAP) is presented in this article, which contains information about both prebiotics and some probiotics, that were used in these researches. Currently, ODRAP collects 25 bacteria genera or their combinations, 59 bacteria species, 140 prebiotic substances, 61 prebiotic production companies, 2 methods of fermentation, and 271 analyzed articles from 2001 till 2019. To facilitate access to the database, a special Web-interface was created, which allows any user who opens the Web-page to obtain information about the features and activities of prebiotics, as well as to sort the data by species and genus of bacteria applied in tests, the chemical nature or source of prebiotics, and other parameters. The convenience of the Web-interface is that it allows access to the database, regardless of the user platform and from anywhere, via the Internet.

/pdf/online-database-for-retrieval-information-about-prebiotics-3cbxbu4nmi.pdf

Online Database for Retrieval Information about Prebiotics and Their Activity

/pdf/web-resources-for-microbial-data-1kenmlj1kd.pdf

Web Resources for Microbial Data

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