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Microbiome and Metagenomics Researches in Nigeria
Published in Nwadiuto (Diuto) Esiobu, James Chukwuma Ogbonna, Charles Oluwaseun Adetunji, Olawole O. Obembe, Ifeoma Maureen Ezeonu, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Microbiomes and Emerging Applications, 2022
Francisca O. Nwaokorie, Ime R. Udotong, Nwadiuto (Diuto) Esiobu, Ifeoma Enweani-Nwokelo
The most widely employed sequencing technology is the amplicon metagenomics where sub-genomes or genes (partial or entire) are studied using universal primers. Whole genome metagenomics reveals the entire microbial makeup of a niche and is often used in public health risk assessment food safety and in discovering and mining bioresources (Mercer et al., 2020). The tools for metagenomic analysis are the DNA processed through workflow of library preparation, sequencing and bioinformatics analysis (Figure 1.1).
Current Use and Future Promise of Genetic Engineering
Published in Michael Hehenberger, Zhi Xia, Huanming Yang, Our Animal Connection, 2020
Michael Hehenberger, Zhi Xia, Huanming Yang
Metagenomics (also named environmental genomics, ecogenomics, or community genomics) is the study of genetic material recovered directly from environmental samples. Recent studies use “shotgun” Sanger sequencing or second generation pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Metagenomics offers a powerful lens for viewing the microbial world. However, a challenge that is present in human microbiome studies is to avoid including the host DNA in the study.
Current Use and Future Promise of Genetic Engineering
Published in Michael Hehenberger, Zhi Xia, Our Animal Connection, 2019
Metagenomics (also named environmental genomics, ecogenomics, or community genomics) is the study of genetic material recovered directly from environmental samples. Recent studies use “shotgun” Sanger sequencing or second generation pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Metagenomics offers a powerful lens for viewing the microbial world. However, a challenge that is present in human microbiome studies is to avoid including the host DNA in the study.
Aerosol partitioning potential of bacteria presenting antimicrobial resistance from different stages of a small decentralized septic treatment system
Published in Aerosol Science and Technology, 2023
Gabriela E. Ramos, Hyoungmook Pak, Ryan Gerlich, Anish Jantrania, Brooke L. Smith, Maria D. King
Previous studies have focused on the presence, dissemination, and removal efficiencies of ARB and ARGs in municipal WWTPs, however, there is limited understanding of ARB/ARG behavior in decentralized wastewater treatment facilities (Chen and Zhang 2013; H. Li et al. 2020; Sharma et al. 2019). Metagenomic approaches are currently being used to efficiently monitor antimicrobial resistance among various environmental sources (de Abreu, Perdigão, and Almeida 2020; Garrido-Cardenas, Polo-López, and Oller-Alberola 2017; Guo et al. 2017; Han and Yoo 2020; The Global Sewage Surveillance project consortium, Hendriksen et al. 2019; Yadav and Kapley 2021). Metagenomic analysis is a relatively new technique that has made it possible to study the microbial diversity of a sample without having to isolate and cultivate each microorganism (Garrido-Cardenas, Polo-López, and Oller-Alberola 2017). The use of metagenomics in AMR studies can provide more insight into the development of microbial pathogenicity by analyzing ARGs transfer from pathogenic and nonpathogenic bacteria (Beceiro, Tomás, and Bou 2013; de Abreu, Perdigão, and Almeida 2020; Roberts 2017). Although atmospheric ARB/ARG has received scientific attention, only a limited number of metagenomic studies has been conducted in this field.
Microbiology in Water-Miscible Metalworking Fluids
Published in Tribology Transactions, 2020
Frederick J. Passman, Peter Küenzi
Metagenomics, also known as next-generation sequencing, is the study of genetic material from environmental samples and enables population analysis of microbial DNA of both culturable and unculturable microbes. This newer technique allows examination of thousands of organisms in parallel and has been widely applied in recent microbiological studies (197). Di Maiuta et al. (34) used this technique to analyze in-use MWFs. However, this technique also has drawbacks, because contamination in the laboratory and of DNA extraction kits is widespread and does impact microbiome studies, especially analysis of low microbial biomass samples (198, 199).
Omics to address the opportunities and challenges of nanotechnology in agriculture
Published in Critical Reviews in Environmental Science and Technology, 2021
Sanghamitra Majumdar, Arturo A. Keller
Recent advances in tools for genomics and transcriptomics in conjunction with metabolomics and proteomics have the potential to accelerate agricultural development (Gómez-Merino et al., 2015). An area that can benefit substantially from these approaches is the plant-microbe interaction. Microbial communities play an important role in plant growth and productivity by directly controlling soil processes like stabilizing soil structure, nutrient bioavailability, degradation of organic pollutants, CO2 fixation and C degradation. They are however highly sensitive and susceptible to toxicity from stressors. Next generation sequencing technologies such as pyrosequencing and Illumina-based sequencing has resolved complexities in the microbial community with higher accuracy than conventional methods (Xu & Wang, 2019). Metagenomics allows to collectively characterize genome sequences of known and unknown members of the entire microbial community in an environmental sample, without having to isolate each into pure cultures. ENMs present in the agricultural soil from intentional use of nano-enabled agrochemicals or unintentional incorporation in the biosolids or irrigation water have the potential to impact the soil microbial community thereby affecting the agricultural productivity (Judy et al., 2015). Metagenomic analysis of the soil microbial community provide potential means to design sustainable ENMs with potential to bolster plant protection against pests and enhance productivity and nutritional quality (Judy et al., 2015; Metch et al., 2018). However, although the metagenomic analysis provide important information on the functional capacity of the soil microbial community, it does not reflect the metabolic activities of individual species or the community.