Research graph
References from Bacterial immune systems as causes and consequences of microbiome structure. Local targets link to admitted publications; unresolved targets remain external evidence.
Ecological rules for the assembly of microbiome communities
10.1371/journal.pbio.3001116 · 2021 · External reference
The evolution of the host microbiome as an ecosystem on a leash
10.1038/nature23292 · 2017 · External reference
Scientists’ warning to humanity: microorganisms and climate change
10.1038/s41579-019-0222-5 · 2019 · External reference
Conceptual synthesis in community ecology
10.1086/652373 · 2010 · External reference
Structure, function and diversity of the healthy human microbiome
10.1038/nature11234 · 2012 · External reference
Microbial community structure and its functional implications
10.1038/nature08058 · 2009 · External reference
A cross-systems primer for synthetic microbial communities
10.1038/s41564-024-01827-2 · 2024 · External reference
How do interactions between mobile genetic elements affect horizontal gene transfer?
10.1016/j.mib.2023.102282 · 2023 · External reference
The impact of phage and phage resistance on microbial community dynamics
10.1371/journal.pbio.3002346 · 2024 · External reference
Interactions between bacterial and phage communities in natural environments
10.1038/s41579-021-00602-y · 2022 · External reference
Trophic interactions and the drivers of microbial community assembly
10.1016/j.cub.2020.08.007 · 2020 · External reference
The ecology and evolution of pangenomes
10.1016/j.cub.2019.08.012 · 2019 · External reference
Fitness costs of plasmids: a limit to plasmid transmission
10.1128/microbiolspec.mtbp-0016-2017 · 2017 · External reference
The highly diverse antiphage defence systems of bacteria
10.1038/s41579-023-00934-x · 2023 · External reference
A host of armor: prokaryotic immune strategies against mobile genetic elements
10.1016/j.celrep.2023.112672 · 2023 · External reference
Community context matters for bacteria-phage ecology and evolution
10.1038/s41396-021-01012-x · 2021 · External reference
Multi-layered genome defences in bacteria
10.1016/j.mib.2024.102436 · 2024 · External reference
The arms race between bacteria and their phage foes
10.1038/s41586-019-1894-8 · 2020 · External reference
The defensome of complex bacterial communities
10.1038/s41467-024-46489-0 · 2024 · External reference
Unresolved reference
2024 · External reference
High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems
10.1016/j.cub.2021.10.038 · 2022 · External reference
Unresolved reference
2025 · External reference
Systematic and quantitative view of the antiviral arsenal of prokaryotes
10.1038/s41467-022-30269-9 · 2022 · External reference
Prokaryotic innate immunity through pattern recognition of conserved viral proteins
2022 · External reference
Systematic discovery of antiphage defense systems in the microbial pangenome
10.1126/science.aar4120 · 2018 · External reference
Evolutionary ecology and interplay of prokaryotic innate and adaptive immune systems
10.1016/j.cub.2020.08.028 · 2020 · External reference
Persistence of plasmids targeted by CRISPR interference in bacterial populations
10.1073/pnas.2114905119 · 2022 · External reference
Inhibitors of bacterial immune systems: discovery, mechanisms and applications
10.1038/s41576-023-00676-9 · 2024 · External reference
Evolution and ecology of anti-defence systems in phages and plasmids
10.1016/j.cub.2024.11.033 · 2025 · External reference
Ecology and evolution of phages encoding anti-CRISPR proteins
10.1016/j.jmb.2023.167974 · 2023 · External reference
Diverse anti-defence systems are encoded in the leading region of plasmids
10.1038/s41586-024-07994-w · 2024 · External reference
Various plasmid strategies limit the effect of bacterial restriction-modification systems against conjugation
10.1093/nar/gkae896 · 2024 · External reference
Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response
10.1016/j.molcel.2022.01.012 · 2022 · External reference
The bacterial defense system MADS interacts with CRISPR-Cas to limit phage infection and escape
10.1016/j.chom.2024.07.005 · 2024 · External reference
CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance
10.1038/ncomms3087 · 2013 · External reference
Bacterial defense systems exhibit synergistic anti-phage activity
2024 · External reference
Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
10.1038/s41396-020-0635-1 · 2020 · External reference
Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition
10.1016/j.chom.2021.11.014 · 2022 · External reference
Antibiotics that affect translation can antagonize phage infectivity by interfering with the deployment of counter-defenses
2023 · External reference
Critically evaluating the relative importance of phage in shaping microbial community composition
10.1016/j.tim.2024.02.014 · 2024 · External reference
Long-term stability and Red Queen-like strain dynamics in marine viruses
10.1038/s41564-019-0628-x · 2020 · External reference
The pan-immune system of bacteria: antiviral defence as a community resource
10.1038/s41579-019-0278-2 · 2020 · External reference
Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages
10.1128/aem.00296-25 · 2025 · External reference
Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection
10.1038/s41467-021-22814-9 · 2021 · External reference
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa
10.1038/s41396-020-00860-3 · 2021 · External reference
CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens
10.1098/rstb.2020.0464 · 2022 · External reference
Microbial defenses against mobile genetic elements and viruses: who defends whom from what?
2022 · External reference
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
10.1093/nar/gku734 · 2014 · External reference
Defence systems and horizontal gene transfer in bacteria
10.1111/1462-2920.16630 · 2024 · External reference
Regulation of genetic flux between bacteria by restriction-modification systems
10.1073/pnas.1603257113 · 2016 · External reference
CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction
2018 · External reference
Beyond horizontal gene transfer: the role of plasmids in bacterial evolution
10.1038/s41579-020-00497-1 · 2021 · External reference
Evolutionary “Crowdsourcing”: alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene
10.1093/molbev/msad237 · 2023 · External reference
CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection
10.1016/j.chom.2012.06.003 · 2012 · External reference
The evolution of resistance against good and bad infections
10.1111/jeb.12291 · 2014 · External reference
Multidrug-resistant enterococci lack CRISPR-cas
10.1128/mbio.00227-10 · 2010 · External reference
Bacterial biodiversity drives the evolution of CRISPR-based phage resistance
10.1038/s41586-019-1662-9 · 2019 · External reference
The impact of bacteriophages on phyllosphere bacterial abundance and composition
10.1111/mec.14542 · 2018 · External reference
Why infectious disease research needs community ecology
10.1126/science.1259504 · 2015 · External reference
Impacts of biodiversity and biodiversity loss on zoonotic diseases
10.1073/pnas.2023540118 · 2021 · External reference
Effect of antibiotics on bacterial populations: a multi-hierachical selection process
10.12688/f1000research.9685.1 · 2017 · External reference
Invading with biological weapons: the importance of disease‐mediated invasions
10.1111/1365-2435.12011 · 2012 · External reference
Predation, apparent competition, and the structure of prey communities
10.1016/0040-5809(77)90042-9 · 1977 · External reference
Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare
10.1016/j.cub.2006.08.089 · 2006 · External reference
Bacteriophage-mediated competition in Bordetella bacteria
2006 · External reference
What makes a temperate phage an effective bacterial weapon?
2024 · External reference
Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence
10.1111/j.1752-4571.2008.00059.x · 2009 · External reference
Effects of host diversity on infectious disease
10.1146/annurev-ecolsys-102710-145022 · 2012 · External reference
The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities
10.1099/mic.0.001086 · 2021 · External reference
Evolution of suicide as a defence strategy against pathogens in a spatially structured environment
10.1111/ele.12064 · 2013 · External reference
Success of a suicidal defense strategy against infection in a structured habitat
10.1038/srep00238 · 2012 · External reference
Interspecific competition can drive plasmid loss from a focal species in a microbial community
10.1038/s41396-023-01487-w · 2023 · External reference
Unresolved reference
2023 · External reference
Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations
10.1098/rstb.2021.0234 · 2022 · External reference
What traits are carried on mobile genetic elements, and why?
10.1038/hdy.2010.24 · 2011 · External reference
CRISPR-Cas in mobile genetic elements: counter-defence and beyond
10.1038/s41579-019-0204-7 · 2019 · External reference
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting
10.1038/nature13637 · 2014 · External reference
Enterococcus faecalis strains with compromised CRISPR-Cas defense emerge under antibiotic selection for a CRISPR-targeted plasmid
2023 · External reference
Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system
10.1073/pnas.1617415113 · 2017 · External reference
The diversity-generating benefits of a prokaryotic adaptive immune system
10.1038/nature17436 · 2016 · External reference
CRISPR-induced distributed immunity in microbial populations
10.1371/journal.pone.0101710 · 2014 · External reference
Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire
10.1038/s41576-019-0172-9 · 2020 · External reference
A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome
10.1371/journal.pgen.1006838 · 2017 · External reference
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
10.1073/pnas.1600974113 · 2016 · External reference
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
10.1186/s40168-022-01328-6 · 2022 · External reference
Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts
10.1126/science.abg2166 · 2021 · External reference
Going viral: the role of mobile genetic elements in bacterial immunity
10.1016/j.chom.2024.05.017 · 2024 · External reference
Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors
10.1016/j.cell.2022.07.014 · 2022 · External reference
Diverse antiphage defenses are widespread among prophages and mobile genetic elements
10.1146/annurev-virology-100422-125123 · 2024 · External reference
Phages and their satellites encode hotspots of antiviral systems
10.1016/j.chom.2022.02.018 · 2022 · External reference
Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements
10.1371/journal.pbio.3002796 · 2024 · External reference
Requirements for mobilization of plasmids RSF1010 and ColE1 by the IncW plasmid R388: trwB and RP4 traG are interchangeable
10.1128/jb.176.14.4455-4458.1994 · 1994 · External reference
The phage-inducible chromosomal islands: a family of highly evolved molecular parasites
10.1146/annurev-virology-031413-085446 · 2015 · External reference
Anti-phage islands force their target phage to directly mediate island excision and spread
10.1038/s41467-018-04786-5 · 2018 · External reference
A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity
10.1038/nature11927 · 2013 · External reference
A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence-specific immunity against subviral parasites
10.7554/elife.68339 · 2021 · External reference
Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms race
10.1098/rstb.2018.0089 · 2019 · External reference
Phage predation, disease severity, and pathogen genetic diversity in cholera patients
10.1126/science.adj3166 · 2024 · External reference
Capturing dynamic phage-pathogen coevolution by clinical surveillance
2025 · External reference
Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era
10.1038/s41579-023-00926-x · 2024 · External reference
Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria
2008 · External reference
Examining horizontal gene transfer in microbial communities
10.1038/s41579-021-00534-7 · 2021 · External reference
Detecting horizontal gene transfer with metagenomics co-barcoding sequencing
2024 · External reference
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
10.1038/nbt.4037 · 2018 · External reference
Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry
10.1080/19490976.2022.2029673 · 2022 · External reference
Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements
10.7717/peerj.16695 · 2024 · External reference
Defining the human gut host-phage network through single-cell viral tagging
10.1038/s41564-019-0526-2 · 2019 · External reference
Mathematical models of plasmid population dynamics
10.3389/fmicb.2021.606396 · 2021 · External reference
Indirect fitness benefits enable the spread of host genes promoting costly transfer of beneficial plasmids
10.1371/journal.pbio.1002478 · 2016 · External reference
Not just a theory—the utility of mathematical models in evolutionary biology
10.1371/journal.pbio.1002017 · 2014 · External reference
Microbial community structure is affected by phage-resistance associated increases in host density
10.1093/femsec/fiaf027 · 2025 · External reference
The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time
10.1098/rstb.2014.0297 · 2015 · External reference
Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes
10.1038/s41564-024-01735-5 · 2024 · External reference
Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles
10.1038/s41467-017-00128-z · 2017 · External reference
Structure-guided discovery of viral proteins that inhibit host immunity
10.1016/j.cell.2024.12.035 · 2025 · External reference
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · 2024 · External reference
Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media
10.1038/s41467-023-44267-y · 2024 · External reference
CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus
10.1128/mbio.00262-15 · 2015 · External reference
Increasing productivity accelerates host-parasite coevolution
10.1111/j.1420-9101.2008.01501.x · 2008 · External reference
Identification of natural CRISPR systems and targets in the human microbiome
10.1016/j.chom.2020.10.010 · 2021 · External reference
The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity
10.1371/journal.pgen.1003312 · 2013 · External reference
Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants
10.1186/s40168-025-02139-1 · 2025 · External reference
Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model
2019 · External reference
Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community
10.1038/s41396-019-0511-z · 2020 · External reference
