Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels

Genomic diversity landscape of the honey bee gut microbiota

(2019) Kirsten M. Ellegaard et al.   Nature Communications

Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment

(2019) Julia Polzin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Using niche breadth theory to explain generalization in mutualisms

(2018) Rebecca T. Batstone et al.   ECOLOGY

In Nature, There Is Only Diversity

(2018) Michael R. McLaren et al.   mBio

The European Nucleotide Archive in 2018

(2018) Peter W Harrison et al.   NUCLEIC ACIDS RESEARCH

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

(2018) Cervin Guyomar et al.   Microbiome

Mixed transmission modes and dynamic genome evolution in an obligate animal–bacterial symbiosis

(2017) Shelbi L Russell et al.   ISME Journal

Intrahost Genetic Diversity of Bacterial Symbionts Exhibits Evidence of Mixed Infections and Recombinant Haplotypes

(2017) Shelbi L. Russell et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Is the trophosome of Ridgeia piscesae monoclonal?

(2017) Maëva Perez et al.   SYMBIOSIS

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria

(2017) M Sabrina Pankey et al.   eLife

Direct-geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms

(2016) Jimena Barrero-Canosa et al.   ENVIRONMENTAL MICROBIOLOGY

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

(2016) Clotilde Bongrand et al.   ISME Journal

Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium

(2016) Vega Shah et al.   ISME Journal

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis

(2016) Ruby Ponnudurai et al.   ISME Journal

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

The Ecology and Evolution of Microbial Competition

(2016) Melanie Ghoul et al.   TRENDS IN MICROBIOLOGY

Origins and Evolutionary Flexibility of Chemosynthetic Symbionts From Deep-Sea Animals

(2016) Jillian M. Petersen et al.   BIOLOGICAL BULLETIN

Phosphate Limitation Induces Drastic Physiological Changes, Virulence-Related Gene Expression, and Secondary Metabolite Production in Pseudovibrio sp. Strain FO-BEG1

(2015) Stefano Romano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

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

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

Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population

(2015) Tetsuro Ikuta et al.   ISME Journal

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

A single natural nucleotide mutation alters bacterial pathogen host tropism

(2015) David Viana et al.   NATURE GENETICS

Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

(2015) Lizbeth Sayavedra et al.   eLife

The Pho regulon: a huge regulatory network in bacteria

(2015) Fernando Santos-Beneit   Frontiers in Microbiology

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Biodiversity and Ecosystem Functioning

(2014) David Tilman et al.   Annual Review of Ecology Evolution and Systematics

ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

(2014) Duleepa Jayasundara et al.   BIOINFORMATICS

Forever competent: deep-sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime

(2014) Cecilia Wentrup et al.   ENVIRONMENTAL MICROBIOLOGY

Settled, symbiotic, then sexually mature: adaptive developmental anatomy in the deep-sea, chemosymbiotic mussel Idas modiolaeformis

(2014) Sven R. Laming et al.   MARINE BIOLOGY

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

EXPLAINING MUTUALISM VARIATION: A NEW EVOLUTIONARY PARADOX?

(2013) Katy D. Heath et al.   EVOLUTION

A Phylum-Level Bacterial Phylogenetic Marker Database

(2013) Zhang Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

(2012) Y. Peng et al.   BIOINFORMATICS

Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer

(2012) Manuel Kleiner et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial individuality in the natural environment

(2012) M Ackermann   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

In situ measurements of hydrogen sulfide, oxygen, and temperature in diffuse fluids of an ultramafic-hosted hydrothermal vent field (Logatchev, 14°45′N, Mid-Atlantic Ridge): Implications for chemosymbiotic bathymodiolin mussels

(2011) Frank U. Zielinski et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Microbial nitrate respiration – Genes, enzymes and environmental distribution

(2011) Beate Kraft et al.   JOURNAL OF BIOTECHNOLOGY

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Is the coral-algae symbiosis really ‘mutually beneficial’ for the partners?

(2010) Scott A. Wooldridge   BIOESSAYS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Global regulation by the seven-component Pi signaling system

(2010) Yi-Ju Hsieh et al.   CURRENT OPINION IN MICROBIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Host control over infection and proliferation of a cheater symbiont

(2010) J. L. SACHS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Synergy of multiple partners, including freeloaders, increases host fitness in a multispecies mutualism

(2010) T. M. Palmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concepts and software for a rational design of polynucleotide probes

(2010) Cristina Moraru et al.   Environmental Microbiology Reports

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Occurrence of phosphate acquisition genes inProchlorococcuscells from different ocean regions

(2009) Adam C. Martiny et al.   ENVIRONMENTAL MICROBIOLOGY

Methanotrophic symbioses in marine invertebrates

(2009) Jillian M. Petersen et al.   Environmental Microbiology Reports

Assembly of Viral Metagenomes from Yellowstone Hot Springs

(2008) T. Schoenfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

(2008) Julie C. Robidart et al.   ENVIRONMENTAL MICROBIOLOGY

Absence of Cospeciation Between Deep-Sea Mytilids and Their Thiotrophic Endosymbionts

(2008) Yong-Jin Won et al.   JOURNAL OF SHELLFISH RESEARCH

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY

Conflict, cheats and the persistence of symbioses

(2008) Angela E. Douglas   NEW PHYTOLOGIST

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

(2008) Sheri L Simmons et al.   PLOS BIOLOGY

A bacterial metapopulation adapts locally to phage predation despite global dispersal

(2007) V. Kunin et al.   GENOME RESEARCH