Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

Genome analysis of probiotic bacteria for antibiotic resistance genes

(2022) Mehdi Fatahi-Bafghi et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

The Probiotic Identity Card: A Novel “Probiogenomics” Approach to Investigate Probiotic Supplements

(2022) Gabriele Andrea Lugli et al.   Frontiers in Microbiology

The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella

(2022) Yuqiao Zhou et al.   Frontiers in Microbiology

In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health

(2022) Anna-Ursula Happel et al.   Microorganisms

Genome Characterization and Probiotic Potential of Corynebacterium amycolatum Human Vaginal Isolates

(2022) Irina V. Gladysheva et al.   Microorganisms

The genomic basis of the Streptococcus thermophilus health-promoting properties

(2022) Emeline Roux et al.   BMC GENOMICS

Analysis of the probiotic characteristics and adaptability of Lactiplantibacillus plantarum DMDL 9010 to gastrointestinal environment by complete genome sequencing and corresponding phenotypes

(2022) Dong-Mei Liu et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

(2022) Sijia Liu et al.   Microbiome

Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria

(2022) Xianqi Peng et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

(2022) Devin B. Holman et al.   Microbiology Spectrum

Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles

(2021) Jessica Esther Agius et al.   Frontiers in Microbiology

Exploiting heterologous and endogenous CRISPR‐Cas systems for genome editing in the probiotic Clostridium butyricum

(2021) Xiuqing Zhou et al.   BIOTECHNOLOGY AND BIOENGINEERING

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks

(2021) Ying Wang et al.   BMC GENOMICS

Authenticity of probiotic foods and dietary supplements: A pivotal issue to address

(2021) Vincenzina Fusco et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

antiSMASH 6.0: improving cluster detection and comparison capabilities

(2021) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Decreased expression of HADH is related to poor prognosis and immune infiltration in kidney renal clear cell carcinoma

(2021) Huiming Jiang et al.   GENOMICS

Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity

(2021) Özge Kahraman Ilıkkan   INDIAN JOURNAL OF MICROBIOLOGY

Comprehensive pan‐genome analysis of Lactiplantibacillus plantarum complete genomes

(2021) Francesco M. Carpi et al.   JOURNAL OF APPLIED MICROBIOLOGY

Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci

(2021) Janira Prichula et al.   Marine Drugs

Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture

(2021) Warapond Wanna et al.   Scientific Reports

Spotlight on the Compositional Quality of Probiotic Formulations Marketed Worldwide

(2021) Diletta Mazzantini et al.   Frontiers in Microbiology

Editorial: Bacteriocins and Other Ribosomally Synthesised and Post-translationally Modified Peptides (RiPPs) as Alternatives to Antibiotics

(2021) Harsh Mathur et al.   Frontiers in Microbiology

Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

(2021) Zhangming Pei et al.   mSystems

Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut

(2021) Jicheng Wang et al.   npj Biofilms and Microbiomes

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021

(2021) et al.   EFSA Journal

Characterization of antimicrobial peptides produced by Lactobacillus acidophilus LA-5 and Bifidobacterium lactis BB-12 and their inhibitory effect against foodborne pathogens

(2021) Saber Amiri et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Probiotics: Should All Patients Take Them?

(2021) Marta Katkowska et al.   Microorganisms

In Vitro Probiotic Characteristics and Whole Genome Sequence Analysis of Lactobacillus Strains Isolated from Cattle-Yak Milk

(2021) Juanshan Zheng et al.   Biology-Basel

The size of the immune repertoire of bacteria

(2020) Serena Bradde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk

(2020) Enriqueta Garcia-Gutierrez et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Applications of CRISPR-Cas systems in Lactic Acid Bacteria

(2020) Avery Roberts et al.   FEMS MICROBIOLOGY REVIEWS

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

(2020) Francesca De Filippis et al.   FEMS MICROBIOLOGY REVIEWS

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1

(2020) Kazeem Adekunle Alayande et al.   PLoS One

Streptococcus thermophilus: To Survive, or Not to Survive the Gastrointestinal Tract, That Is the Question!

(2020) Anđela Martinović et al.   Nutrients

Criteria to Qualify Microorganisms as “Probiotic” in Foods and Dietary Supplements

(2020) Sylvie Binda et al.   Frontiers in Microbiology

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

(2020) Markus H K Johansson et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A class Ⅲ bacteriocin with broad-spectrum antibacterial activity from Lactobacillus acidophilus NX2-6 and its preservation in milk and cheese

(2020) Fanqiang Meng et al.   FOOD CONTROL

Homologous expression and characterization of gassericin T and gassericin S, a novel class IIb bacteriocin produced by Lactobacillus gasseri LA327

(2019) Genki Kasuga et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Compositional assessment of bacterial communities in probiotic supplements by means of metagenomic techniques

(2019) Gabriele Andrea Lugli et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

An Overview on Streptococcus bovis/Streptococcus equinus Complex Isolates: Identification to the Species/Subspecies Level and Antibiotic Resistance

(2019) Arianna Pompilio et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genomic analysis of Lactobacillus reuteri WHH1689 reveals its probiotic properties and stress resistance

(2019) Lin Chen et al.   Food Science & Nutrition

Prophage Hunter: an integrative hunting tool for active prophages

(2019) Wenchen Song et al.   NUCLEIC ACIDS RESEARCH

Improving End-User Trust in the Quality of Commercial Probiotic Products

(2019) Scott A. Jackson et al.   Frontiers in Microbiology

Viability and Composition Validation of Commercial Probiotic Products by Selective Culturing Combined with Next-Generation Sequencing

(2019) Mati Ullah et al.   Microorganisms

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2019) Donghyeok Seol et al.   Frontiers in Microbiology

Development of omics‐based protocols for the microbiological characterization of multi‐strain formulations marketed as probiotics: the case of VSL#3

(2019) Diego Mora et al.   Microbial Biotechnology

Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem

(2019) Jee-Hwan Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

(2019) Enrique Doster et al.   NUCLEIC ACIDS RESEARCH

Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen

(2019) Piotr Jarocki et al.   Viruses-Basel

Lactobacillus acidophilus JCM 1132 Strain and Its Mutant with Different Bacteriocin-Producing Behaviour Have Various In Situ Effects on the Gut Microbiota of Healthy Mice

(2019) Gang Wang et al.   Microorganisms

Functional annotation of the genome unravels probiotic potential of Bacillus coagulans HS243

(2018) N.G. Kapse et al.   GENOMICS

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Role of Lactobacillus reuteri in Human Health and Diseases

(2018) Qinghui Mu et al.   Frontiers in Microbiology

The Road to Infection: Host-Microbe Interactions Defining the Pathogenicity of Streptococcus bovis/Streptococcus equinus Complex Members

(2018) Christoph Jans et al.   Frontiers in Microbiology

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update

(2018) Hasna Hanchi et al.   Frontiers in Microbiology

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Commercial Probiotic Products

(2017) Sanja Kolaček et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds

(2017) Lynn M. Naughton et al.   Frontiers in Microbiology

In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases

(2017) Komwit Surachat et al.   PLoS One

Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme

(2016) Christoph Jans et al.   BMC MICROBIOLOGY

Clostridium butyricum : from beneficial to a new emerging pathogen

(2016) N. Cassir et al.   CLINICAL MICROBIOLOGY AND INFECTION

A genomic view of food-related and probiotic Enterococcus strains

(2016) Julieta Bonacina et al.   DNA RESEARCH

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases

(2016) Wesley Morovic et al.   Frontiers in Microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing

(2016) Jennifer N. Patro et al.   mSphere

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

(2015) Analice C. Azevedo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

(2015) Yanhua Cui et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genome Instability in Lactobacillus rhamnosus GG

(2013) Wilbert Sybesma et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability

(2013) Masanori Fukao et al.   PLoS One

PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data

(2013) Salvatore Cosentino et al.   PLoS One

Characterization of putative class II bacteriocins identified from a non-bacteriocin-producing strain Lactobacillus casei ATCC 334

(2012) Yang-Cheng Kuo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

World Gastroenterology Organisation Global Guidelines

(2012) Francisco Guarner et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Lactobacillus acidophilus La-5 increases lactacin B production when it senses live target bacteria

(2009) Raquel Tabasco et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genes and Molecules of Lactobacilli Supporting Probiotic Action

(2008) S. Lebeer et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS