4.6 Article

Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity

Related references

Note: Only part of the references are listed.
Article Microbiology

Antimicrobial susceptibility testing of Eggerthella lenta blood culture isolates at a university hospital in Belgium from 2004 to 2018

Baptist Declerck et al.

Summary: This study evaluated the susceptibility of Eggerthella lenta blood culture isolates to antibiotics commonly used for anaerobic infections. The results showed susceptibility to certain antibiotics, such as amoxicillin-clavulanate, metronidazole, and meropenem, while caution is advised for the use of piperacillin-tazobactam and clindamycin.

ANAEROBE (2021)

Article Biochemistry & Molecular Biology

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y. Galperin et al.

Summary: The COG database, created in 1997 and most recently updated in 2014, includes extensive information on bacterial and archaeal genomes. The current version introduces new features and plans for future expansion and refinement of annotations.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria

Jordan E. Bisanz et al.

CELL HOST & MICROBE (2020)

Review Microbiology

Bacteriophages of the Human Gut: The Known Unknown'' of the Microbiome

Andrey N. Shkoporov et al.

CELL HOST & MICROBE (2019)

Article Biotechnology & Applied Microbiology

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Ho Bin Jang et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Cytoscape Automation: empowering workflow-based network analysis

David Otasek et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

MUMmer4: A fast and versatile genome alignment system

Guillaume Marcais et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Review Genetics & Heredity

Phage-Encoded Anti-CRISPR Defenses

Sabrina Y. Stanley et al.

ANNUAL REVIEW OF GENETICS, VOL 52 (2018)

Article Multidisciplinary Sciences

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts

Travis N. Mavrich et al.

SCIENTIFIC REPORTS (2018)

Article Biochemistry & Molecular Biology

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

Ana Laura Grazziotin et al.

NUCLEIC ACIDS RESEARCH (2017)

Review Ecology

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

Cristina Howard-Varona et al.

ISME JOURNAL (2017)

Review Multidisciplinary Sciences

Chemical transformation of xenobiotics by the human gut microbiota

Nitzan Koppel et al.

SCIENCE (2017)

Article Virology

How to Name and Classify Your Phage: An Informal Guide

Evelien M. Adriaenssens et al.

VIRUSES-BASEL (2017)

Article Biochemical Research Methods

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

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Jan P. Meier-Kolthoff et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

ViPTree: the viral proteomic tree server

Yosuke Nishimura et al.

BIOINFORMATICS (2017)

Review Chemistry, Analytical

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Leighton Pritchard et al.

ANALYTICAL METHODS (2016)

Article Microbiology

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota

Gabriele Andrea Lugli et al.

ENVIRONMENTAL MICROBIOLOGY (2016)

Review Microbiology

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

Peter Spanogiannopoulos et al.

NATURE REVIEWS MICROBIOLOGY (2016)

Article Biochemistry & Molecular Biology

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

David Arndt et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Revised Estimates for the Number of Human and Bacteria Cells in the Body

Ron Sender et al.

PLOS BIOLOGY (2016)

Article Biochemical Research Methods

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

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

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Microbiology

Clinical and Microbiological Characteristics of Eggerthella lenta Bacteremia

B. J. Gardiner et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2015)

Article Biochemical Research Methods

PanGP: A tool for quickly analyzing bacterial pan-genome profile

Yongbing Zhao et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Automated classification of tailed bacteriophages according to their neck organization

Anne Lopes et al.

BMC GENOMICS (2014)

Review Microbiology

When a Virus is not a Parasite: The Beneficial Effects of Prophages on Bacterial Fitness

Joseph Bondy-Denomy et al.

JOURNAL OF MICROBIOLOGY (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

Joe Bondy-Denomy et al.

NATURE (2013)

Review Pharmacology & Pharmacy

Developing a metagenomic view of xenobiotic metabolism

Henry J. Haiser et al.

PHARMACOLOGICAL RESEARCH (2013)

Article Multidisciplinary Sciences

Bacteriophage adhering to mucus provide a non-host-derived immunity

Jeremy J. Barr et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Virology

Headful DNA packaging: Bacteriophage SPP1 as a model system

Leonor Oliveira et al.

VIRUS RESEARCH (2013)

Article Biochemical Research Methods

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

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Medicine, General & Internal

Multiple Pyogenic Liver Abscesses Caused by Eggerthella lenta Treated with Ertapenem: A Case Report

Richard M. Elias et al.

CASE REPORTS IN MEDICINE (2012)

Article Virology

The genomes and comparative genomics of Lactobacillus delbrueckii phages

Katja-Anneli Riipinen et al.

ARCHIVES OF VIROLOGY (2011)

Article Biochemical Research Methods

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

Marcus Lechner et al.

BMC BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

WebMGA: a customizable web server for fast metagenomic sequence analysis

Sitao Wu et al.

BMC GENOMICS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Microbiology

Polymicrobial Bloodstream Infection with Eggerthella lenta and Desulfovibrio desulfuricans

Karin Liderot et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Aaron E. Darling et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Three-dimensional structure of tropism-switching Bordetella bacteriophage

Wei Dai et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Microbiology

Interaction of dietary resveratrol with animal-associated bacteria

Carina M. Jung et al.

FEMS MICROBIOLOGY LETTERS (2009)

Review Microbiology

Comparative genomics: the bacterial pan-genome

Herve Tettelin et al.

CURRENT OPINION IN MICROBIOLOGY (2008)

Review Pharmacology & Pharmacy

The gastrointestinal microbiota as a site for the biotransformation of drugs

Tiago Sousa et al.

INTERNATIONAL JOURNAL OF PHARMACEUTICS (2008)

Article Biotechnology & Applied Microbiology

Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans

T Clavel et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)

Article Biochemistry & Molecular Biology

The HHpred interactive server for protein homology detection and structure prediction

J Söding et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Mauve: Multiple alignment of conserved genomic sequence with rearrangements

ACE Darling et al.

GENOME RESEARCH (2004)

Review Microbiology

Phage as agents of lateral gene transfer

C Canchaya et al.

CURRENT OPINION IN MICROBIOLOGY (2003)

Article Multidisciplinary Sciences

Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage

MS Liu et al.

SCIENCE (2002)