Small investments with big returns: environmental genomic bioprospecting of microbial life

Vuong, Paton; Wise, Michael J.; Whiteley, Andrew S.; Kaur, Parwinder

doi:10.1080/1040841x.2021.2011833

Cited by 7 publications

(6 citation statements)

References 131 publications

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“…The microbial world are well-known for the vast diversity of functionalities they present ( Dunlap, 2001 ; Shu and Huang, 2022 ). These functionalities have been exploited by humans to produce novel products ( Stahl et al, 2013 ; Vuong et al, 2022 ), but also to degrade human produced waste ( Raziyafathima et al, 2016 ; Chiang et al, 2020 ; Gupta et al, 2022 ). Miraculously microbes have always been discovered that could degrade most of the novel products that humans synthesized and that become waste.…”

Section: Introduction: History and Benefits Of Using Filamentous Fung...mentioning

confidence: 99%

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

Ghosh

Rusyn

Dmytruk

et al. 2023

Front. Bioeng. Biotechnol.

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This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.

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Section: Introduction: History and Benefits Of Using Filamentous Fung...mentioning

confidence: 99%

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

Ghosh

Rusyn

Dmytruk

et al. 2023

Front. Bioeng. Biotechnol.

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“…Different approaches for microbial in silico bioprospecting are being already applied using bioinformatic resources. The two main approaches for the identification of microbial diversity are mining data from publicly available databases, or using raw data from different sampling sites following metagenomic pipelines (Vuong et al, 2022b). Within the available datasets, online trustworthy repositories are associated with the International Nucleotide Sequence Database: the DNA Databank of Japan (DDBJ; http:// www.ddbj.nig.ac.jp/), the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.…”

Section: Exploring Biodiversitymentioning

confidence: 99%

Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans

Rojo

Pillow

Kaur

2023

Front. Bioeng. Biotechnol.

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The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.

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“…More generally, NEON shotgun metagenomes can be used to investigate how variation in bioinformatic pipeline decisions affect ecological inferences. They may also act as a valuable resource for soil bioprospecting efforts, which use bioinformatic approaches to identify bioactive compounds with potential medical or industrial value ( Vuong et al , 2022 ).…”

Section: Applicationsmentioning

confidence: 99%

The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis

et al. 2022

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The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON’s shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.

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Small investments with big returns: environmental genomic bioprospecting of microbial life

Cited by 7 publications

References 131 publications

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans

The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis

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