To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites DOI Creative Commons
Jorge A. Moura de Sousa, Eduardo P. C. Rocha

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 377(1842)

Published: Nov. 29, 2021

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used satellites to hijack phages sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements poorly known. Here, we show P4-like present more than 30% genomes Enterobacterales, almost half those Escherichia coli , multiple distinct copies. We identified over 1000 with very conserved genetic organization core genome a few hotspots highly variable genes. These never found plasmids have little homology known phages, suggesting an independent evolutionary origin. Instead, they scattered across chromosomes, possibly because their integrases often exchanged other elements. rooted phylogenies hijacking functions correlated suggest longstanding coevolution. They also reveal broad host ranges elements, as identical genera. Our results constitute distinct, widespread ancient family mobile pave way for studying evolution antagonistic interactions between This article is part theme issue ‘The secret lives microbial elements’.

Language: Английский

Systematic and quantitative view of the antiviral arsenal of prokaryotes DOI Creative Commons
Florian Tesson, Hervé Alexandre, Ernest Mordret

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 10, 2022

Bacteria and archaea have developed multiple antiviral mechanisms, genomic evidence indicates that several of these systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool automatically detects known prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced genomes, find strategies vary drastically between phyla, species strains. Variations composition correlate with genome size, viral threat, lifestyle traits. will facilitate large-scale analysis defense study host-virus interactions prokaryotes.

Language: Английский

Citations

437
Interactions between bacterial and phage communities in natural environments DOI
Anne Chevallereau, Benoît J. Pons, Stineke van Houte

et al.

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(1), P. 49 - 62

Published: Aug. 9, 2021

Language: Английский

Citations

412
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains DOI Creative Commons
Adam J. Hockenberry, Claus O. Wilke

PeerJ, Journal Year: 2021, Volume and Issue: 9, P. e11396 - e11396

Published: May 6, 2021

Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages capable of a latent phase infection within host cell (lysogenic cycle), whereas virulent directly replicate lyse cells upon (lytic cycle). Accurate lifestyle identification is critical for determining the role individual phage species ecosystems their effect on evolution. Here, we present BACPHLIP, BACterioPHage LIfestyle Predictor. BACPHLIP detects presence set conserved protein domains an input genome uses this data to predict via Random Forest classifier that was trained dataset 634 genomes. On independent test 423 phages, has accuracy 98% greatly exceeding previously existing tools (79%). freely available GitHub ( https://github.com/adamhockenberry/bacphlip ) code used build provided in separate repository https://github.com/adamhockenberry/bacphlip-model-dev users wishing interrogate re-train underlying classification model.

Language: Английский

Citations

192
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts DOI Creative Commons
Xiaoqing Luo, Pandeng Wang, Jia‐Ling Li

et al.

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Nov. 5, 2022

Abstract Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although functions of AMGs have been extensively reported in numerous environments, we still know little about drivers that shape viral community-wide AMG compositions natural ecosystems. Exploring is critical a deeper understanding complex interplays among viruses, hosts, environments. Results Here, investigated impact lifestyles (i.e., lytic lysogenic), habitats water, particle, sediment), prokaryotic hosts on profiles by utilizing metagenomic metatranscriptomic techniques. We found were most drivers, followed host identities. Specifically, irrespective what viruses came from, exhibited greater diversity tended to encode chaperone biosynthesis, signaling proteins, lipid metabolism, which could boost progeny reproduction, whereas temperate apt survivability. Moreover, communities mediate cycles, especially nitrogen different manners via AMGs. When focusing each lifestyle, further clear dissimilarity between water sediment, as well divergent encoded infecting orders. Conclusions Overall, our study provides first systematic characterization expands knowledge distinct interactions with from an perspective, virus-host-environment conditions.

Language: Английский

Citations

118
Phage–host coevolution in natural populations DOI

Damien Piel,

Maxime Bruto, Yannick Labreuche

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 1075 - 1086

Published: June 27, 2022

Language: Английский

Citations

115
Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion DOI Creative Commons
Eugen Pfeifer, Rémy A. Bonnin, Eduardo P. C. Rocha

et al.

mBio, Journal Year: 2022, Volume and Issue: 13(5)

Published: Sept. 26, 2022

Antibiotic resistance is rapidly spreading via the horizontal transfer of genes in mobile genetic elements. While plasmids are key drivers this process, few integrative phages encode antibiotic genes. Here, we find that phage-plasmids, elements both and plasmids, often carry We found 60 phage-plasmids with 184 genes, providing for broad-spectrum-cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, colistin. These a hot spots, seem to have been cotranslocated transposable elements, class I integrons, which had not previously phages. tried induce six (including four integrons) succeeded five cases. Other prophages were coinduced these experiments. As proof concept, focused on P1-like element encoding an extended spectrum β-lactamase,

Language: Английский

Citations

95
Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations DOI Creative Commons
Matthieu Haudiquet, Jorge A. Moura de Sousa, Marie Touchon

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1861)

Published: Aug. 22, 2022

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those their hosts. In general, costly to donor cell while potentially beneficial recipients. The diversity and plasticity cell-MGEs interactions, among MGEs, result in complex evolutionary processes where source, or even existence selection for maintaining a function genome, unclear. For example, MGE-driven HGT depends on envelope structures defense systems, many these transferred by MGEs themselves. can spur periods intense increasing own rates horizontal transmission upon communicating, eavesdropping, sensing environment host physiology. This may high-frequency genes unrelated MGE. Here, we review how drive mechanisms, selective pressures genomic traits affect flow, therefore adaptation, populations. encoding adaptive niche-defining means that intragenomic conflicts alliances between cells key functional diversification. article part discussion meeting issue 'Genomic population pathogens'.

Language: Английский

Citations

88
Genetic determinants of host tropism in Klebsiella phages DOI Creative Commons
Beatriz Beamud, Neris García‐González,

Mar Gómez-Ortega

et al.

Cell Reports, Journal Year: 2023, Volume and Issue: 42(2), P. 112048 - 112048

Published: Feb. 1, 2023

Bacteriophages play key roles in bacterial ecology and evolution are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show narrow host range for most phages, with <2% 6,319 combinations tested yielding detectable interactions. Bacterial capsule diversity is main factor restricting phage range. Consequently, phage-encoded depolymerases tropism, depolymerase sequence types associated ability infect specific capsular across families. all broader found do not encode canonical depolymerases, suggesting alternative modes entry. These findings expand our knowledge complex interactions between bacteria their viruses point out feasibility predicting first steps infection using genome sequences.

Language: Английский

Citations

50
Phage-plasmids promote recombination and emergence of phages and plasmids DOI Creative Commons
Eugen Pfeifer, Eduardo P. C. Rocha

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 20, 2024

Abstract Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both is blurred existence known prophage-plasmids or phage-plasmids, which transfer horizontally cells viruses vertically within cellular lineages plasmids. Here, we study flow three elements. We show repertoire phage-plasmids overlaps with those phages By tracking recent recombination events, find exchange genes more frequently than phages, direct less frequent in comparison. The results suggest can mediate including element core functions, defense systems, antibiotic resistance. Moreover, a combination inactivation may result conversion For example, loss turns P1-like into integrative prophages (that no longer phages). Remarkably, some latter have acquired conjugation-related functions to became mobilisable conjugation. Thus, our work indicates play key role across their hosts, act intermediates one type another.

Language: Английский

Citations

42
Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens DOI Creative Commons

Amany M. Al-Anany,

Rabia Fatima, Alexander P. Hynes

et al.

Cell Reports, Journal Year: 2021, Volume and Issue: 35(8), P. 109172 - 109172

Published: May 1, 2021

There is renewed interest in bacterial viruses (phages) as alternatives to antibiotics. All phage treatments date have used virulent phages rather than temperate ones, these can integrate into the genome of host and lie dormant. However, are abundant easier isolate. To make use entities, we leverage stressors known awaken dormant, integrated phages. Co-administration HK97 with sub-inhibitory concentrations antibiotic ciprofloxacin results eradication (≥8 log reduction) vitro. This synergy mechanistically distinct from phage-antibiotic-synergy described for Instead, specifically selects against bacteria which has integrated. As interaction between such be widespread, this approach may broadly applicable enable combat infections.

Language: Английский

Citations

75