Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Beneficial bile acid metabolism from Lactobacillus plantarum of food origin

(2020) Roberta Prete et al.   Scientific Reports

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

(2020) Ainsley C. Nicholson et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers

(2019) Nielson T. Baxter et al.   mBio

Clostridium scindens ATCC 35704: Integration of Nutritional Requirements, the Complete Genome Sequence, and Global Transcriptional Responses to Bile Acids

(2019) Saravanan Devendran et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet

(2019) Torben Sølbeck Rasmussen et al.   Viruses-Basel

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

(2019) Jan P. Meier-Kolthoff et al.   Nature Communications

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov.

(2018) Amadou Hamidou Togo et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

(2018) Łukasz Krych et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

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

Positions 299 and 302 of the GerAA subunit are important for function of the GerA spore germination receptor in Bacillus subtilis

(2018) Anna Grela et al.   PLoS One

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

(2018) Melhem Bilen et al.   Microbiome

The Role of Succinate in the Regulation of Intestinal Inflammation

(2018) Jessica Connors et al.   Nutrients

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Merdimonas faecis gen. nov., sp. nov., isolated from human faeces

(2017) Boram Seo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Introducing the sporobiota and sporobiome

(2017) George Tetz et al.   Gut Pathogens

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Genus delineation ofChlamydialesby analysis of the percentage of conserved proteins justifies the reunifying of the generaChlamydiaandChlamydophilainto one single genusChlamydia

(2016) Yvonne Pannekoek et al.   Pathogens and Disease

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

(2016) Ilias Lagkouvardos et al.   Scientific Reports

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

(2015) John W. Peters et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

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

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

(2015) Jan P Meier-Kolthoff et al.   Standards in Genomic Sciences

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age

(2014) Jan P. Meier-Kolthoff et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Commensal Clostridia: leading players in the maintenance of gut homeostasis

(2013) Loris R Lopetuso et al.   Gut Pathogens

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Gut microbiota, host health, and polysaccharides

(2012) Xiaofei Xu et al.   BIOTECHNOLOGY ADVANCES

Host Genetics and Environmental Factors Regulate Ecological Succession of the Mouse Colon Tissue-Associated Microbiota

(2012) Philip Smith et al.   PLoS One

Non-heme manganese catalase – The ‘other’ catalase

(2011) James W. Whittaker   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE