Meta‐omics assisted microbial gene and strain resources mining in contaminant environment

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

(2022) Karen Viacava et al.   ISME Journal

Approaches to Unmask Functioning of the Uncultured Microbial Majority From Extreme Habitats on the Seafloor

(2022) Stefanie Böhnke et al.   Frontiers in Microbiology

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

(2022) Sijia Liu et al.   Microbiome

Biphenyl-degrading Bacteria Isolation with Laser Induced Visualized Ejection Separation Technology and Traditional Colony Sorting

(2022) Aili Li et al.   BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY

KEGG for taxonomy-based analysis of pathways and genomes

(2022) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

(2022) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae

(2022) Zhe Zhang et al.   Nature Communications

UniProt: the Universal Protein Knowledgebase in 2023

(2022) et al.   NUCLEIC ACIDS RESEARCH

Community-integrated multi-omics facilitates the isolation of an organohalide dehalogenation microorganism

(2022) Yiqun Huang et al.   Innovation(United States)

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

(2021) Sandhya Mishra et al.   Frontiers in Bioengineering and Biotechnology

Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology

(2021) Shuanghong Yang et al.   Frontiers in Microbiology

Microbial degradation of multiple PAHs by a microbial consortium and its application on contaminated wastewater

(2021) Lige Zhang et al.   JOURNAL OF HAZARDOUS MATERIALS

Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges—A Review

(2021) Ton That Huu Dat et al.   Frontiers in Microbiology

Omics Approaches to Pesticide Biodegradation

(2020) Alexis Rodríguez et al.   CURRENT MICROBIOLOGY

(Micro)plastic crisis: Un-ignorable contribution to global greenhouse gas emissions and climate change

(2020) Maocai Shen et al.   JOURNAL OF CLEANER PRODUCTION

Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics

(2020) Hang T. Dam et al.   Frontiers in Microbiology

Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere

(2020) Olga V. Karnachuk et al.   ENVIRONMENTAL MICROBIOLOGY

A network approach to elucidate and prioritize microbial dark matter in microbial communities

(2020) Tatyana Zamkovaya et al.   ISME Journal

Innovations to culturing the uncultured microbial majority

(2020) William H. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Estimate of the sequenced proportion of the global prokaryotic genome

(2020) Zheng Zhang et al.   Microbiome

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

Heavy metal hypertolerant eukaryotic aldehyde dehydrogenase isolated from metal contaminated soil by metatranscriptomics approach

(2019) Arkadeep Mukherjee et al.   BIOCHIMIE

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis

(2019) Henning Schiebenhoefer et al.   Expert Review of Proteomics

Multi-metal tolerance of von Willebrand factor type D domain isolated from metal contaminated site by metatranscriptomics approach

(2019) Bharti Thakur et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus

(2019) Yifan Wang et al.   BIOCHEMISTRY

Detoxification of toxic heavy metals by serine protease inhibitor isolated from polluted soil

(2019) Arkadeep Mukherjee et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Culturing the human microbiota and culturomics

(2018) Jean-Christophe Lagier et al.   NATURE REVIEWS MICROBIOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

(2018) Dominik Danso et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

(2018) Qichao Tu et al.   BIOINFORMATICS

Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach

(2018) Bharti Thakur et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Recent Advances in Function-based Metagenomic Screening

(2018) Tanyaradzwa Rodgers Ngara et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

In situ cultivation of previously uncultivable microorganisms using the ichip

(2017) Brittany Berdy et al.   Nature Protocols

Polycyclic aromatic hydrocarbons contamination in surface soil of China: A review

(2017) Pei Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

(2016) Emna Bouhajja et al.   BIOTECHNOLOGY ADVANCES

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Metagenomics for the discovery of pollutant degrading enzymes

(2015) Lisa Ufarté et al.   BIOTECHNOLOGY ADVANCES

Microbial dehalogenation of organohalides in marine and estuarine environments

(2015) Giulio Zanaroli et al.   CURRENT OPINION IN BIOTECHNOLOGY

A decade of metaproteomics: Where we stand and what the future holds

(2015) Paul Wilmes et al.   PROTEOMICS

The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes

(2014) Anatoli Tchigvintsev et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomic analysis of oxygenases from activated sludge

(2014) Niti B. Jadeja et al.   BIORESOURCE TECHNOLOGY

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

(2014) Liang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals

(2013) Sarah J. Edwards et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

(2013) Cynthia C. Silva et al.   PLoS One

Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment

(2012) María-Eugenia Guazzaroni et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil

(2012) Alexandre de Menezes et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of a stable trichloroethene-degrading microbial community

(2012) Vanessa L Brisson et al.   ISME Journal

Application of metatranscriptomics to soil environments

(2012) Lilia C. Carvalhais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Identification and characterization of a novel thermostable pyrethroid-hydrolyzing enzyme isolated through metagenomic approach

(2012) Xinjiong Fan et al.   Microbial Cell Factories

A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community

(2012) Yun Wang et al.   PLoS One

Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach

(2011) Sintawee Sulaiman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cloning and characterisation of a novel 2,4-dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil

(2011) Yang Lu et al.   BIOTECHNOLOGY LETTERS

A novel family VII esterase with industrial potential from compost metagenomic library

(2011) Chul-Hyung Kang et al.   Microbial Cell Factories

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Directed Culturing of Microorganisms Using Metatranscriptomics

(2011) L. Bomar et al.   mBio

Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria

(2010) J. W. Craig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium

(2010) Nikki Kenters et al.   JOURNAL OF MICROBIOLOGICAL METHODS

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking

(2009) Sho Morimoto et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

(2009) Shoko Iwai et al.   ISME Journal

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

(2009) Christopher P Belnap et al.   ISME Journal

Biodegradation aspects of Polycyclic Aromatic Hydrocarbons (PAHs): A review

(2009) A.K. Haritash et al.   JOURNAL OF HAZARDOUS MATERIALS

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

Expression of esterase gene in yeast for organophosphates biodegradation

(2009) Devaiah M. Kambiranda et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Identification and characterization of novel poly(dl-lactic acid) depolymerases from metagenome

(2008) Daisuke Mayumi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Molecular cloning and characterization of a novel pyrethroid-hydrolyzing esterase originating from the Metagenome

(2008) Gang Li et al.   Microbial Cell Factories

SAR11 marine bacteria require exogenous reduced sulphur for growth

(2008) H. James Tripp et al.   NATURE

Enzymes go big: surface hydrolysis and functionalisation of synthetic polymers

(2007) Georg M. Guebitz et al.   TRENDS IN BIOTECHNOLOGY