Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria ) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

(2020) Oleksandr M. Maistrenko et al.   ISME Journal

Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili

(2020) Kate Ligthart et al.   TRENDS IN MICROBIOLOGY

Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation

(2020) Zhichao Zhou et al.   ISME Journal

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

(2020) Jacob P. Beam et al.   Frontiers in Microbiology

The Wood‐Ljungdahl pathway as a key component of metabolic versatility in Candidate phylum Bipolaricaulota (Acetothermia, OP1)

(2019) Noha H. Youssef et al.   Environmental Microbiology Reports

The Type VI secretion system: a versatile bacterial weapon

(2019) Sarah Coulthurst   MICROBIOLOGY-SGM

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

(2019) Kerrin Mendler et al.   NUCLEIC ACIDS RESEARCH

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

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

(2019) Dongwan D. Kang et al.   PeerJ

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

(2019) Devin F. R. Doud et al.   ISME Journal

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

(2018) Stephanie A. Eichorst et al.   ENVIRONMENTAL MICROBIOLOGY

Peatland Acidobacteria with a dissimilatory sulfur metabolism

(2018) Bela Hausmann et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Refining the taxonomic structure of the phylum Acidobacteria

(2018) Svetlana N. Dedysh et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

(2018) Christian Rinke et al.   ISME Journal

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies

(2017) Ryan M Ziels et al.   ISME Journal

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

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

(2017) Le Huang et al.   NUCLEIC ACIDS RESEARCH

Simulation ofDeepwater Horizonoil plume reveals substrate specialization within a complex community of hydrocarbon degraders

(2017) Ping Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags

(2017) Carl-Eric Wegner et al.   Frontiers in Microbiology

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

(2017) Eric D. Becraft et al.   Frontiers in Microbiology

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

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

Energetics and Application of Heterotrophy in Acetogenic Bacteria

(2016) Kai Schuchmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

(2016) Anna M. Kielak et al.   Frontiers in Microbiology

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Formaldehyde Concentration in Discharge from Land Based Aquaculture Facilities in Atlantic Canada

(2015) Benoit A. Lalonde et al.   BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY

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

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

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

(2015) Anne M. Spain et al.   PeerJ

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

(2014) Albert Leopold Müller et al.   ISME Journal

Community structure and elevational diversity patterns of soil Acidobacteria

(2014) Yuguang Zhang et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

(2014) Ibrahim F. Farag et al.   PLoS One

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Comparative genomic and physiological analysis provides insights into the role ofAcidobacteriain organic carbon utilization in Arctic tundra soils

(2012) Suman R. Rawat et al.   FEMS MICROBIOLOGY ECOLOGY

Sialic acid utilization by the soil bacteriumCorynebacterium glutamicum

(2012) Nadine Gruteser et al.   FEMS MICROBIOLOGY LETTERS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)

(2012) Iain Anderson et al.   Standards in Genomic Sciences

First insights into the syntrophic acetate-oxidizing bacteria - a genetic study

(2012) Bettina Müller et al.   MicrobiologyOpen

The inositol phosphates in soils and manures: Abundance, cycling, and measurement

(2011) Courtney Giles et al.   CANADIAN JOURNAL OF SOIL SCIENCE

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria

(2011) Amaya M. Garcia Costas et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into chemotaxonomic composition and carbon cycling of phototrophic communities in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analog for ancient microbial mat systems

(2011) S. I. BÜHRING et al.   Geobiology

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

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

(2011) Jean F. Challacombe et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

(2009) N. L. Ward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aerobic methanol-oxidizingBacteria in soil

(2009) Steffen Kolb   FEMS MICROBIOLOGY LETTERS

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Phylogenetic diversity of Acidobacteria in a former agricultural soil

(2008) Anna Kielak et al.   ISME Journal

Characterization of a Novel Methanol Dehydrogenase in Representatives of Burkholderiales: Implications for Environmental Detection of Methylotrophy and Evidence for Convergent Evolution

(2008) M. G. Kalyuzhnaya et al.   JOURNAL OF BACTERIOLOGY