Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities

Circuitry Rewiring Directly Couples Competence to Predation in the Gut Dweller Streptococcus salivarius

(2018) Johann Mignolet et al.   Cell Reports

Global Prevalence of Helicobacter pylori Infection: Systematic Review and Meta-Analysis

(2017) James K.Y. Hooi et al.   GASTROENTEROLOGY

Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania

(2017) Iulia Lupan et al.   MICROBES AND ENVIRONMENTS

Mechanisms of gene flow in archaea

(2017) Alexander Wagner et al.   NATURE REVIEWS MICROBIOLOGY

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

(2017) Jianhua Guo et al.   WATER RESEARCH

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome

(2017) Pia S. Pannaraj et al.   JAMA Pediatrics

Potential Effects of Horizontal Gene Exchange in the Human Gut

(2017) Aaron Lerner et al.   Frontiers in Immunology

Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity

(2017) Angela M. Patterson et al.   Frontiers in Immunology

Proteobacteria explain significant functional variability in the human gut microbiome

(2017) Patrick H. Bradley et al.   Microbiome

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

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

It’s the song, not the singer: an exploration of holobiosis and evolutionary theory

(2016) W. Ford Doolittle et al.   BIOLOGY & PHILOSOPHY

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

(2016) Michael J. Coyne et al.   BMC GENOMICS

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

Mechanisms and consequences of bacterial resistance to antimicrobial peptides

(2016) D.I. Andersson et al.   DRUG RESISTANCE UPDATES

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers

(2016) Lorenzo Proia et al.   ENVIRONMENTAL POLLUTION

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Speciation by Symbiosis: the Microbiome and Behavior

(2016) J. Dylan Shropshire et al.   mBio

Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts

(2016) Gili Aviv et al.   mBio

Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

(2016) Angela E. Douglas et al.   mBio

Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori

(2016) Sebastian Bubendorfer et al.   Nature Communications

Horizontal Transfer of a Novel Soil Agarase Gene from Marine Bacteria to Soil Bacteria via Human Microbiota

(2016) Tao Song et al.   Scientific Reports

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

(2016) Ron Sender et al.   PLOS BIOLOGY

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

The structure and diversity of human, animal and environmental resistomes

(2016) Chandan Pal et al.   Microbiome

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

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

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

Microbiota in Breast Milk of Chinese Lactating Mothers

(2016) Olga Sakwinska et al.   PLoS One

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents

(2015) Johan Bengtsson-Palme et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Understanding bacterial resistance to antimicrobial peptides: From the surface to deep inside

(2015) Simone Maria-Neto et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance

(2015) Kenji K. Kojima et al.   BMC GENOMICS

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

(2015) Calum J. Walsh et al.   BMC MICROBIOLOGY

The culturome of the human nose habitats reveals individual bacterial fingerprint patterns

(2015) Ursula Kaspar et al.   ENVIRONMENTAL MICROBIOLOGY

Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA

(2015) Cedric A. Brimacombe et al.   JOURNAL OF BACTERIOLOGY

The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer

(2015) S. Borgeaud et al.   SCIENCE

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

(2015) T. W. Cullen et al.   SCIENCE

Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

(2015) Michiel Vos et al.   TRENDS IN MICROBIOLOGY

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Are Human Intestinal Eukaryotes Beneficial or Commensals?

(2015) Julius Lukeš et al.   PLoS Pathogens

Allergies, Helicobacter pylori and the continental enigmas

(2015) Ramakrishnan Sitaraman   Frontiers in Microbiology

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Diversity and dynamics of bacteriocins from human microbiome

(2014) Jinshui Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

Minor Fitness Costs in an Experimental Model of Horizontal Gene Transfer in Bacteria

(2014) Anna Knöppel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

(2014) Aurélien Trompette et al.   NATURE MEDICINE

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Human Intestinal Cells Modulate Conjugational Transfer of Multidrug Resistance Plasmids between Clinical Escherichia coli Isolates

(2014) Ana Manuel Dantas Machado et al.   PLoS One

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

(2014) M. J. Coyne et al.   mBio

The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome

(2014) Adam P. Roberts et al.   Frontiers in Cellular and Infection Microbiology

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

(2014) Jennifer R Huddleston   Infection and Drug Resistance

Antimicrobial peptides and gut microbiota in homeostasis and pathology

(2013) Maureen J. Ostaff et al.   EMBO Molecular Medicine

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

(2013) Sören Franzenburg et al.   ISME Journal

Persistence of the Oral Probiotic Streptococcus salivarius M18 Is Dose Dependent and Megaplasmid Transfer Can Augment Their Bacteriocin Production and Adhesion Characteristics

(2013) Jeremy P. Burton et al.   PLoS One

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery

(2012) Raul Cabrera-Rubio et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

The immune response to tuberculosis infection in the setting of Helicobacter pylori and helminth infections

(2012) S. PERRY et al.   EPIDEMIOLOGY AND INFECTION

The human microbiome: A hot spot of microbial horizontal gene transfer

(2012) Li Liu et al.   GENOMICS

SOS Response Activation and Competence Development Are Antagonistic Mechanisms in Streptococcus thermophilus

(2012) C. Boutry et al.   JOURNAL OF BACTERIOLOGY

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Multiple Pathways of Plasmid DNA Transfer in Helicobacter pylori

(2012) Stefanie Rohrer et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes

(2012) J.-H. Hehemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Symbiotic View of Life: We Have Never Been Individuals

(2012) Scott F. Gilbert et al.   QUARTERLY REVIEW OF BIOLOGY

An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

(2012) P. Jorth et al.   mBio

A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals

(2012) Rosanna A Alegado et al.   eLife

Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

(2011) Mikihiko Kawai et al.   BMC MICROBIOLOGY

Intercellular Nanotubes Mediate Bacterial Communication

(2011) Gyanendra P. Dubey et al.   CELL

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Catecholamines increase conjugative gene transfer between enteric bacteria

(2011) Greg Peterson et al.   MICROBIAL PATHOGENESIS

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

IS-Linked Movement of a Restriction-Modification System

(2011) Noriko Takahashi et al.   PLoS One

Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk

(2011) Katherine M. Hunt et al.   PLoS One

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

(2011) S. Budroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Describing the Mechanism of Antimicrobial Peptide Action with the Interfacial Activity Model

(2010) William C. Wimley   ACS Chemical Biology

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

(2010) Brian V Jones et al.   BMC GENOMICS

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

(2010) On On Lee et al.   ISME Journal

Extracellular DNA: A Major Proinflammatory Component of Pseudomonas aeruginosa Biofilms

(2010) J. I. Fuxman Bass et al.   JOURNAL OF IMMUNOLOGY

Long-term impacts of antibiotic exposure on the human intestinal microbiota

(2010) C. Jernberg et al.   MICROBIOLOGY-SGM

A new vision of immunity: homeostasis of the superorganism

(2010) G Eberl   Mucosal Immunology

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer

(2010) Wolfgang Fischer et al.   NUCLEIC ACIDS RESEARCH

Genome comparison and context analysis reveals putative mobile forms of restriction–modification systems and related rearrangements

(2010) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

Infection with Helicobacter pylori Is Associated with Protection against Tuberculosis

(2010) Sharon Perry et al.   PLoS One

A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

(2010) Patrick Olbermann et al.   PLoS Genetics

Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR

(2009) M.C. Collado et al.   LETTERS IN APPLIED MICROBIOLOGY

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

(2009) Dangeruta Kersulyte et al.   PLoS One

Estimating the extent of horizontal gene transfer in metagenomic sequences

(2008) Javier Tamames et al.   BMC GENOMICS

Polymyxin B: a new strategy for multidrug-resistant Gram-negative organisms

(2008) Zhe Yuan et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One

The convergence of carbohydrate active gene repertoires in human gut microbes

(2008) C. A. Lozupone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA