Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

Microbial consortium OEM1 cultivation for higher lignocellulose degradation and chlorophenol removal

(2017) Jiajin Liang et al.   RSC Advances

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

(2017) Olga E. Petrova et al.   Scientific Reports

Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities

(2017) Anna M. Alessi et al.   Scientific Reports

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

(2016) Diego Javier Jiménez et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity

(2016) Larisa Cortes-Tolalpa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

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

(2016) Luciana Principal Antunes et al.   Scientific Reports

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

(2016) Gina R. Lewin et al.   PLoS One

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

(2016) Senta Heiss-Blanquet et al.   PLoS One

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

(2016) Bruno L. Mello et al.   Scientific Reports

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities

(2015) Wuttichai Mhuantong et al.   Biotechnology for Biofuels

Metasecretome analysis of a lignocellulolytic microbial consortium grown on wheat straw, xylan and xylose

(2015) Diego Javier Jiménez et al.   Biotechnology for Biofuels

Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock

(2015) Ajaya K Biswal et al.   Biotechnology for Biofuels

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw

(2015) Diego Javier Jiménez et al.   Scientific Reports

The Role of Ciliate Protozoa in the Rumen

(2015) Charles J. Newbold et al.   Frontiers in Microbiology

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass

(2014) Stephanie A. Eichorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation

(2014) Hailan Piao et al.   BIOTECHNOLOGY AND BIOENGINEERING

Impacts of environmental stress on growth, secondary metabolite biosynthetic gene clusters and metabolite production of xerotolerant/xerophilic fungi

(2014) Angel Medina et al.   CURRENT GENETICS

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage

(2014) Lin-xing Chen et al.   ISME Journal

Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics

(2014) Ashley S Johnson-Rollings et al.   ISME Journal

Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions

(2014) C.W. Simmons et al.   JOURNAL OF APPLIED MICROBIOLOGY

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis

(2014) Yu Xia et al.   Scientific Reports

Tracking organic matter and microbiota dynamics during the stages of lignocellulosic waste composting

(2013) Juan A. López-González et al.   BIORESOURCE TECHNOLOGY

Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing

(2013) Vidya de Gannes et al.   BIORESOURCE TECHNOLOGY

Lignocellulose-degrading enzymes from termites and their symbiotic microbiota

(2013) Jinfeng Ni et al.   BIOTECHNOLOGY ADVANCES

Analysis of pectin mutants and natural accessions of Arabidopsis highlights the impact of de-methyl-esterified homogalacturonan on tissue saccharification

(2013) Fedra Francocci et al.   Biotechnology for Biofuels

Diversity of protists and bacteria determines predation performance and stability

(2013) Muhammad Saleem et al.   ISME Journal

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

Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

(2013) Deborah A. Neher et al.   PLoS One

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

(2013) Vidya De Gannes et al.   Frontiers in Microbiology

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

(2012) Hui Wei et al.   Biotechnology for Biofuels

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

(2012) Thomas Schneider et al.   ISME Journal

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Chemical and morphological characterization of sugarcane bagasse submitted to a delignification process for enhanced enzymatic digestibility

(2011) Camila Rezende et al.   Biotechnology for Biofuels

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Complete genome sequence of Truepera radiovictrix type strain (RQ-24T)

(2011) Natalia Ivanova et al.   Standards in Genomic Sciences

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Lessons from the Terra Preta de Índios of the Amazon region for the utilisation of charcoal for soil amendment

(2009) Etelvino H. Novotny et al.   JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY

Engineering the cell wall by reducing de-methyl-esterified homogalacturonan improves saccharification of plant tissues for bioconversion

(2009) V. Lionetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA