Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

Dynamic change of bacterial community during dairy manure composting process revealed by high-throughput sequencing and advanced bioinformatics tools

(2020) Xiao-Zhong Zhong et al.   BIORESOURCE TECHNOLOGY

Isolation of Thermostable Lignocellulosic Bacteria From Chicken Manure Compost and a M42 Family Endocellulase Cloning From Geobacillus thermodenitrificans Y7

(2020) Lingling Ma et al.   Frontiers in Microbiology

Integral approach using bacterial microbiome to stabilize municipal solid waste

(2020) Macarena M. Jurado et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

(2020) Stefanie Lutz et al.   Frontiers in Microbiology

Food Waste Composting and Microbial Community Structure Profiling

(2020) Kishneth Palaniveloo et al.   Processes

Genome-centric metagenomic insights into the impact of alkaline/acid and thermal sludge pre-treatment on digestion sludge microbiome

(2020) Zhiwei Liang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Denitrification during composting: Biochemistry, implication and perspective

(2020) Mingzi Shi et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Assembling Reads Improves Taxonomic Classification of Species

(2020) Quang Tran et al.   Genes

910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens

(2020) Aditya Bandla et al.   Scientific Data

Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats

(2019) Simona Iacob et al.   Frontiers in Microbiology

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

(2019) Paula B. Matheus Carnevali et al.   Nature Communications

Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting

(2019) Natalia Maria Silva et al.   PLoS One

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation

(2018) Pilar Eliana Puentes-Téllez et al.   MICROBIAL ECOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Genomics and Ecology of Novel N 2 O-Reducing Microorganisms

(2018) Sara Hallin et al.   TRENDS IN MICROBIOLOGY

Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C

(2018) Ana B. Flórez et al.   Frontiers in Microbiology

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

(2018) Gherman V. Uritskiy et al.   Microbiome

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Metabolic defence against oxidative stress: the road less travelled so far

(2017) J. Lemire et al.   JOURNAL OF APPLIED MICROBIOLOGY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia

(2017) Diego Javier Jiménez et al.   TRENDS IN MICROBIOLOGY

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

(2017) Leandro N. Lemos et al.   Frontiers in Microbiology

A bacterial pioneer produces cellulase complexes that persist through community succession

(2017) Sebastian Kolinko et al.   Nature Microbiology

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses

(2017) Salvatore Montella et al.   Scientific Reports

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition

(2016) Cheng Wang et al.   Biotechnology for Biofuels

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

(2016) Jiwoong Kim et al.   BMC BIOINFORMATICS

Anionically Stabilized Cellulose Nanofibrils through Succinylation Pretreatment in Urea-Lithium Chloride Deep Eutectic Solvent

(2016) Tuula Selkälä et al.   ChemSusChem

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis

(2016) Jennifer Hiras et al.   mBio

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Communications

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

(2016) Luciana Principal Antunes et al.   Scientific Reports

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Correction for Zelezniak et al., Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synergism of Glycoside Hydrolase Secretomes from Two Thermophilic Bacteria Cocultivated on Lignocellulose

(2014) Kundi Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria

(2014) Joseph Nesme et al.   ENVIRONMENTAL MICROBIOLOGY

Resistance to rifampicin: a review

(2014) Beth P Goldstein   JOURNAL OF ANTIBIOTICS

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

The cellulolytic system ofThermobifida fusca

(2013) Eva Maria Gomez del Pulgar et al.   CRITICAL REVIEWS IN MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

(2013) Layla Farage Martins et al.   PLoS One

Bacterial oxygen production in the dark

(2012) K.F. Ettwig et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Lignocellulosic ethanol: From science to industry

(2012) L. Viikari et al.   BIOMASS & BIOENERGY

Dueling Regulatory Properties of a Transcriptional Activator (MtrA) and Repressor (MtrR) That Control Efflux Pump Gene Expression in Neisseria gonorrhoeae

(2012) Y. M. Zalucki et al.   mBio

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Complete genome sequence of Thermobispora bispora type strain (R51T)

(2010) Konstantinos Liolios et al.   Standards in Genomic Sciences

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov.

(2009) H. Yokoyama et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY