4.8 Article

The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses

Related references

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

Expanding known viral diversity in the healthy infant gut

Shiraz A. Shah et al.

Summary: Deep sequencing of faecal viromes from 647 healthy infants identified over 230 previously unknown gut virus families, expanding our understanding of the diversity in the human infant gut virome. The findings highlight the importance of the gut microbiome in infancy for the development of the immune system and long-term protection against chronic diseases. This study provides valuable insights into the viral diversity in the infant gut virome and expands phage taxonomy, serving as a resource for future research.

NATURE MICROBIOLOGY (2023)

Article Microbiology

Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants

Emily A. Kaelin et al.

Summary: This study found that changes in the viral and bacterial composition of the gut precede the onset of necrotizing enterocolitis (NEC) in preterm infants. The results suggest that the early life virome signatures in preterm infants may play a role in NEC.

NATURE MICROBIOLOGY (2022)

Article Biotechnology & Applied Microbiology

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Stephen Nayfach et al.

Summary: CheckV is an automated pipeline for identifying closed viral genomes, estimating completeness of genome fragments, and removing host-related regions. By comparing sequences with a large database of complete viral genomes, CheckV assesses the quality of viral genomes assembled from metagenome data. Removing host contamination improves the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

NATURE BIOTECHNOLOGY (2021)

Article Microbiology

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Jiarong Guo et al.

Summary: VirSorter2 is a virus identification tool that leverages genome-informed database advances and multiple classifiers to improve accuracy and range of virus sequence detection. It uniquely performs consistently with high accuracy across viral diversity and minimizes errors associated with atypical cellular sequences.

MICROBIOME (2021)

Article Gastroenterology & Hepatology

Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model

Torben Solbeck Rasmussen et al.

Review Microbiology

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

Andrey N. Shkoporov et al.

CELL HOST & MICROBE (2019)

Article Multidisciplinary Sciences

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Yi Duan et al.

NATURE (2019)

Review Virology

Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System

Jonas D. Van Belleghem et al.

VIRUSES-BASEL (2019)

Article Biotechnology & Applied Microbiology

Towards standards for human fecal sample processing in metagenomic studies

Paul I. Costea et al.

NATURE BIOTECHNOLOGY (2017)

Review Biochemistry & Molecular Biology

Bacteria-Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

Pauline D. Scanlan

TRENDS IN MICROBIOLOGY (2017)

Review Gastroenterology & Hepatology

Stable core virome despite variable microbiome after fecal transfer

Felix Broecker et al.

GUT MICROBES (2017)

Article Chemistry, Physical

Formulation, stabilisation and encapsulation of bacteriophage for phage therapy

Danish J. Malik et al.

ADVANCES IN COLLOID AND INTERFACE SCIENCE (2017)

Article Microbiology

Practical considerations for large-scale gut microbiome studies

Doris Vandeputte et al.

FEMS MICROBIOLOGY REVIEWS (2017)

Article Multidisciplinary Sciences

Sample storage conditions significantly influence faecal microbiome profiles

Jocelyn M. Choo et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Microbiology

Comparison of methods for fecal microbiome biospecimen collection

Christine Dominianni et al.

BMC MICROBIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Influence of environmental variables in the efficiency of phage therapy in aquaculture

Yolanda J. Silva et al.

MICROBIAL BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

Rapid evolution of the human gut virome

Samuel Minot et al.

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

Article Microbiology

Storage conditions of intestinal microbiota matter in metagenomic analysis

Silvia Cardona et al.

BMC MICROBIOLOGY (2012)

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 Multidisciplinary Sciences

Hypervariable loci in the human gut virome

Samuel Minot et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biotechnology & Applied Microbiology

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

Kyoung-Ho Kim et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biotechnology & Applied Microbiology

The influence of external factors on bacteriophages-review

E. Jonczyk et al.

FOLIA MICROBIOLOGICA (2011)

Article Biochemistry & Molecular Biology

The human gut virome: Inter-individual variation and dynamic response to diet

Samuel Minot et al.

GENOME RESEARCH (2011)

Article Multidisciplinary Sciences

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

Luke R. Thompson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Biotechnology & Applied Microbiology

Isoelectric points of viruses

B. Michen et al.

JOURNAL OF APPLIED MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

Viruses in the faecal microbiota of monozygotic twins and their mothers

Alejandro Reyes et al.

NATURE (2010)

Article Biochemical Research Methods

Effects of freezing and storage temperature on MS2 viability

MR Olson et al.

JOURNAL OF VIROLOGICAL METHODS (2004)