New technologies for developing phage-based tools to manipulate the human microbiome

Bacteriophage uptake by mammalian cell layers represents a potential sink that may impact phage therapy

(2021) Marion C. Bichet et al.   iScience

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

(2020) Jens Walter et al.   CELL

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner

(2020) Mohammadali Khan Mirzaei et al.   Cell Host & Microbe

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

Interaction between microbiota and immunity in health and disease

(2020) Danping Zheng et al.   CELL RESEARCH

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

(2020) Torben Sølbeck Rasmussen et al.   GUT

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts

(2020) Kosuke Fujimoto et al.   Cell Host & Microbe

An ecological framework to understand the efficacy of fecal microbiota transplantation

(2020) Yandong Xiao et al.   Nature Communications

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

(2020) Nathan T. Porter et al.   Nature Microbiology

Adsorption sequencing (AdsorpSeq) as a rapid method to link environmental bacteriophages to hosts

(2020) Patrick A. de Jonge et al.   iScience

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

Phage Therapy in the Resistance Era: Where Do We Stand and Where Are We Going?

(2020) Tiffany Luong et al.   CLINICAL THERAPEUTICS

In situ reprogramming of gut bacteria by oral delivery

(2020) Bryan B. Hsu et al.   Nature Communications

Deciphering functional redundancy in the human microbiome

(2020) Liang Tian et al.   Nature Communications

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus

(2019) Rebekah M. Dedrick et al.   NATURE MEDICINE

Gastrointestinal diagnosis using non-white light imaging capsule endoscopy

(2019) Gerard Cummins et al.   Nature Reviews Gastroenterology & Hepatology

Bacteriophages engineered to display foreign peptides may become short‐circulating phages

(2019) Katarzyna Hodyra‐Stefaniak et al.   Microbial Biotechnology

Multiplex transcriptional characterizations across diverse bacterial species using cell‐free systems

(2019) Sung Sun Yim et al.   Molecular Systems Biology

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

(2019) Karissa L. Cross et al.   NATURE BIOTECHNOLOGY

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

(2019) Zheng Kuang et al.   SCIENCE

Defining the human gut host–phage network through single-cell viral tagging

(2019) Mária Džunková et al.   Nature Microbiology

Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis

(2019) Kevin Yehl et al.   CELL

Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies

(2019) Krystyna Dąbrowska et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

(2019) Yi Duan et al.   NATURE

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phage resistance at the cost of virulence: Listeria monocytogenes serovar 4b requires galactosylated teichoic acids for InlB-mediated invasion

(2019) Eric T. Sumrall et al.   PLoS Pathogens

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

An intravital window to image the colon in real time

(2019) Nikolai Rakhilin et al.   Nature Communications

Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity

(2018) Mariann Landsberger et al.   CELL

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

(2018) Takuro Nunoura et al.   SCIENCE

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections

(2018) Ruiyao Cai et al.   NATURE NEUROSCIENCE

Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice

(2017) Sunny H. Wong et al.   GASTROENTEROLOGY

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Extending the Host Range of Bacteriophage Particles for DNA Transduction

(2017) Ido Yosef et al.   MOLECULAR CELL

Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

(2017) Hao Wu et al.   NATURE MEDICINE

In situ cultivation of previously uncultivable microorganisms using the ichip

(2017) Brittany Berdy et al.   Nature Protocols

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Quantification of diverse virus populations in the environment using the polony method

(2017) Nava Baran et al.   Nature Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk

(2016) Weifei Zhu et al.   CELL

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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

(2016) Ron Sender et al.   PLOS BIOLOGY

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Bacteriophage Combinations Significantly Reduce Clostridium difficile GrowthIn Vitroand ProliferationIn Vivo

(2015) Janet Y. Nale et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Clostridium butyricumStrains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates

(2015) Nadim Cassir et al.   CLINICAL INFECTIOUS DISEASES

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

(2014) Liang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota

(2014) Y. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

(2014) Casey M. Theriot et al.   Nature Communications

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

(2013) Elke Allers et al.   ENVIRONMENTAL MICROBIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

(2012) Omry Koren et al.   CELL

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistantPseudomonas aeruginosa; a preliminary report of efficacy

(2009) A. Wright et al.   CLINICAL OTOLARYNGOLOGY