Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates

(2018) Madhan R. Tirumalai et al.   BMC MICROBIOLOGY

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification

(2018) Elisa Salvetti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

(2018) Samanta Michelini et al.   Microbiome

Genetic Signatures of Dairy Lactobacillus casei Group

(2018) Alessandra Fontana et al.   Frontiers in Microbiology

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis

(2017) Jisu Kang et al.   Frontiers in Immunology

Next-generation probiotics: the spectrum from probiotics to live biotherapeutics

(2017) Paul W. O’Toole et al.   Nature Microbiology

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

(2017) Wirulda Pootakham et al.   Scientific Reports

Higher classification sensitivity of short metagenomic reads with CLARK- S

(2016) Rachid Ounit et al.   BIOINFORMATICS

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

(2016) Josef Wagner et al.   BMC MICROBIOLOGY

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

(2016) Satoshi Hiraoka et al.   MICROBES AND ENVIRONMENTS

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets

(2016) David Ainsworth et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

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

Identification of Lactic Acid Bacteria in Fruit Pulp Processing Byproducts and Potential Probiotic Properties of Selected Lactobacillus Strains

(2016) Estefânia F. Garcia et al.   Frontiers in Microbiology

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Validating bifidobacterial species and subspecies identity in commercial probiotic products

(2015) Zachery T. Lewis et al.   PEDIATRIC RESEARCH

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

(2015) Neelja Singhal et al.   Frontiers in Microbiology

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

(2015) Brendan P. Hodkinson et al.   Advances in Wound Care

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Use of MALDI-TOF for Diagnosis of Microbial Infections

(2013) D. Bailey et al.   CLINICAL CHEMISTRY

Peptidoglycan Hydrolases as Species-Specific Markers to Differentiate Lactobacillus helveticus from Lactobacillus gallinarum and Other Closely Related Homofermentative Lactobacilli

(2013) Iva Jebava et al.   CURRENT MICROBIOLOGY

Timely approaches to identify probiotic species of the genus Lactobacillus

(2013) Stefan R Herbel et al.   Gut Pathogens

Identification of lactobacilli isolated from food by genotypic methods and MALDI-TOF MS

(2012) Marta Dušková et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

MALDI-TOF MS in microbiological diagnostics—identification of microorganisms and beyond (mini review)

(2011) Andreas Wieser et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Rapid and Accurate Bacterial Identification in Probiotics and Yoghurts by MALDI-TOF Mass Spectrometry

(2011) Emmanouil Angelakis et al.   JOURNAL OF FOOD SCIENCE

Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons

(2010) R. Borriss et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov.

(2008) P. Mattarelli et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY