Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere

Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle

(2019) Vitaly V. Kadnikov et al.   EXTREMOPHILES

Effects of Attenuated S. agalactiae Strain YM001 on Intestinal Microbiota of Tilapia Are Recoverable

(2019) Ming Li et al.   Frontiers in Microbiology

Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution

(2019) Olga V. Karnachuk et al.   ISME Journal

Metamorphoses of Lyme disease spirochetes: phenomenon of Borrelia persisters

(2019) Natalie Rudenko et al.   Parasites & Vectors

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

(2019) Karissa L. Cross et al.   NATURE BIOTECHNOLOGY

Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon

(2019) Shruti Gupta et al.   Frontiers in Microbiology

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Enhanced nitrogen removal using solid carbon source in constructed wetland with limited aeration

(2018) Zhongchen Yang et al.   BIORESOURCE TECHNOLOGY

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats

(2018) Xiyang Dong et al.   ISME Journal

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer

(2018) Vitaly V. Kadnikov et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Bacteria of the Genus Sphaerochaeta from Low-Temperature Heavy Oil Reservoirs (Russia)

(2018) S. Kh. Bidzhieva et al.   MICROBIOLOGY

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

(2018) Ryan M. Brown et al.   FISH & SHELLFISH IMMUNOLOGY

Rectinema cohabitans gen. nov., sp. nov., a rod-shaped spirochaete isolated from an anaerobic naphthalene-degrading enrichment culture

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer

(2017) V. V. Kadnikov et al.   MICROBIOLOGY

In situ cultivation of previously uncultivable microorganisms using the ichip

(2017) Brittany Berdy et al.   Nature Protocols

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

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

Description of ‘Candidatus Marispirochaeta associata’ and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov.

(2016)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface

(2016) Yulia A. Frank et al.   Frontiers in Microbiology

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

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

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

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Origin and Evolution of the Sodium -Pumping NADH: Ubiquinone Oxidoreductase

(2014) Adrian Reyes-Prieto et al.   PLoS One

Characterization of precipitates formed by H2S-producing, Cu-resistant Firmicute isolates of Tissierella from human gut and Desulfosporosinus from mine waste

(2013) Olga P. Ikkert et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema

(2013) Birte Abt et al.   Standards in Genomic Sciences

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

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring

(2010) G. Dubinina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Spirochete round bodies Syphilis, Lyme disease & AIDS: Resurgence of “the great imitator”?

(2010) Lynn Margulis et al.   SYMBIOSIS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Destruction of spirochete Borrelia burgdorferi round-body propagules (RBs) by the antibiotic Tigecycline

(2009) O. Brorson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney

(2008) H. Imachi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE