Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

High proportions of bacteria are culturable across major biomes

(2019) Adam C. Martiny   ISME Journal

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov

(2019) Despina Tsementzi et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA

(2019) Carlos A. Ruiz‐Perez et al.   Environmental Microbiology Reports

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

(2018) Michael W. Henson et al.   ISME Journal

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

(2018) Luis M. Rodriguez-R et al.   mSystems

How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

(2018) Luis M. Rodriguez-R et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia

(2018) Yunpeng Zhao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake

(2018) Keith Arora-Williams et al.   Microbiome

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics

(2018) Si-Yu Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

(2018) Alexandra Meziti et al.   ISME Journal

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

imGLAD: accurate detection and quantification of target organisms in metagenomes

(2018) Juan C. Castro et al.   PeerJ

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

(2018) Alexandra M. Linz et al.   PeerJ

Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

(2018) Maliheh Mehrshad et al.   Microbiome

Less effective selection leads to larger genomes

(2017) Tristan Lefébure et al.   GENOME RESEARCH

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

(2017) Stefan M Neuenschwander et al.   ISME Journal

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves 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

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

(2017) Shaomei He et al.   mSphere

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics

(2016) Alexandra Meziti et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

(2015) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Impacts of the Three Gorges Dam on microbial structure and potential function

(2015) Qingyun Yan et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Type material in the NCBI Taxonomy Database

(2014) Scott Federhen   NUCLEIC ACIDS RESEARCH

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

(2014) Despina Tsementzi et al.   Environmental Microbiology Reports

Cooperative secretions facilitate host range expansion in bacteria

(2014) Luke McNally et al.   Nature Communications

Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

(2014) Christopher Staley et al.   Frontiers in Microbiology

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

(2013) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) J. J. Morris et al.   mBio

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Statistical Inference on the Mechanisms of Genome Evolution

(2011) Michael Lynch   PLoS Genetics

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

(2009) C. Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS