Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

(2018) Daniel H. Huson et al.   Biology Direct

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening

(2018) Ilhan Cem Duru et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The human skin microbiome

(2018) Allyson L. Byrd et al.   NATURE REVIEWS MICROBIOLOGY

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Population Dynamics of Lactobacillus helveticus in Swiss Gruyère-Type Cheese Manufactured With Natural Whey Cultures

(2018) Aline Moser et al.   Frontiers in Microbiology

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

(2018) Michael Schmid et al.   Frontiers in Microbiology

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

(2018) Aaron M. Walsh et al.   Microbiome

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

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

Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable

(2018) Oscar van Mastrigt et al.   BMC GENOMICS

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

(2018) Michael Schmid et al.   NUCLEIC ACIDS RESEARCH

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations

(2018) Katherine Lavelle et al.   Viruses-Basel

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Detection and enumeration of Lactobacillus helveticus in dairy products

(2017) Aline Moser et al.   INTERNATIONAL DAIRY JOURNAL

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

Dense and accurate whole-chromosome haplotyping of individual genomes

(2017) David Porubsky et al.   Nature Communications

Extensive horizontal gene transfer in cheese-associated bacteria

(2017) Kevin S Bonham et al.   eLife

Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products

(2017) Aline Moser et al.   Frontiers in Microbiology

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling

(2017) Vitor C. Piro et al.   Microbiome

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

bcgTree: automatized phylogenetic tree building from bacterial core genomes

(2016) Markus J. Ankenbrand et al.   GENOME

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

(2016) Yu-Chih Tsai et al.   mBio

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Developing a kinetic model for co-culture of yogurt starter bacteria growth in pH controlled batch fermentation

(2015) Marzieh Aghababaie et al.   JOURNAL OF FOOD ENGINEERING

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

(2015) Zhihong Sun et al.   Nature Communications

The human gut virome: a multifaceted majority

(2015) Lesley A. Ogilvie et al.   Frontiers in Microbiology

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

(2014) Mathieu Almeida et al.   BMC GENOMICS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures

(2014) Francesca De Filippis et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Lactobacillus helveticus: importance in food and health

(2014) Giorgio Giraffa   Frontiers in Microbiology

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei

(2014) Michael T. Leonard et al.   Frontiers in Microbiology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Invited review: Microbial evolution in raw-milk, long-ripened cheeses produced using undefined natural whey starters

(2013) Monica Gatti et al.   JOURNAL OF DAIRY SCIENCE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Lactobacillus helveticus: the proteolytic system

(2013) M. W. Griffiths et al.   Frontiers in Microbiology

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters

(2012) Benedetta Bottari et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

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

Bacteriophages of lactic acid bacteria and their impact on milk fermentations

(2011) Josiane E Garneau et al.   Microbial Cell Factories

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

(2010) Terry Disz et al.   BMC BIOINFORMATICS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Split defect and secondary fermentation in Swiss-type cheeses – A review

(2009) David F.M. Daly et al.   Dairy Science & Technology

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Variation in caseinolytic properties of six cheese related Lactobacillus helveticus strains

(2009) Marie P. Jensen et al.   INTERNATIONAL DAIRY JOURNAL

Variation in aminopeptidase and aminotransferase activities of six cheese related Lactobacillus helveticus strains

(2009) Marie P. Jensen et al.   INTERNATIONAL DAIRY JOURNAL

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Microbial diversity in Natural Whey Cultures used for the production of Caciocavallo Silano PDO cheese

(2008) D ERCOLINI et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

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