Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Jan. 31, 2025

The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence significance of systems, their responses to abiotic stress ecological consequences remain poorly understood in soil ecosystems. We established microcosm with varying concentrations hexavalent chromium (Cr(VI)) investigate adaptive modifications under stress. Utilizing hybrid metagenomic assembly long-read short-read sequencing, we discovered were more diverse prevalent heavily polluted soils, which was corroborated by meta-analyses public datasets from various heavy metal-contaminated sites. As Cr(VI) concentration increased, prokaryotes favoring mutualism gradually supplanted those incurring high costs. Additionally, as enriched exhibited synchronization microbial metal resistance genes. Furthermore, proportion carried mobile genetic elements (MGEs), including plasmids viruses, increased approximately 43% 39%, respectively, rising Cr concentrations. This trend is conducive strengthening dissemination sharing resources within communities. Overall, our study reveals modification ecosystems stress, well positive contributions establishing evolution resistance. These findings advance understanding adaptation stressful environments may inspire novel approaches manipulation bioremediation. Video Abstract.

Language: Английский

---

Going viral: The role of mobile genetic elements in bacterial immunity

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(6), P. 804 - 819

Published: June 1, 2024

Language: Английский

---

Antiviral defense systems in the rumen microbiome

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

ABSTRACT The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, diversity prevalence antiviral defense systems complex communities are still unknown. We therefore investigated abundance viral 3,038 high-quality archaeal genomes from rumen. In total, 14,241 31,948 antiviral-related genes were identified. Those represented 114 unique system types grouped into 49 families. observed a high genomes. number systems, families, density varied widely genome to genome. Additionally, per correlated positively with families size. Restriction modification, Abi, cas most common, but many rare present only 1% Antiviral prevalent diverse rumen, few dominant, indicating that rarely present. collection throughout rumen may represent pool mechanisms can be shared by different members community modulate phage–host interaction. IMPORTANCE Phages act antagonistically at cell level have mutualistic microbiome level. This shapes structure microbial is mainly driven mechanism. such mechanism larger than previously thought. Because that, we described genomes, metagenome-assembled (MAGs) isolates, While seem among bacteria archaea, common. suggests these not microbes could community. consistent “pan-immune system” model, which appears common across environments.

Language: Английский

---

Gut phages and their interactions with bacterial and mammalian hosts

Journal of Bacteriology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

ABSTRACT The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, bacterial members have been subject intense research. Less well studied large bacteriophages gut, which number billions viral particles per gram feces, consist considerable unknown “dark matter.” This gut-residing bacteriophages, called “phageome,” plays central role through predation transformation native bacteria, interactions with their hosts. this review, we will summarize what known about composition origins phageome, as its homeostasis host health. Furthermore, outline phages hosts, plot course for mechanistic study these systems.

Language: Английский

---

Natural Products and Microbiomes

Published: Jan. 1, 2025

Language: Английский

---

Invasive bacteriophages between a bell and a hammer: a comprehensive review of pharmacokinetics and bacterial defense systems

Discover Life, Journal Year: 2025, Volume and Issue: 55(1)

Published: April 3, 2025

Language: Английский

---

Advancing RNA phage biology through meta-omics

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(8)

Published: April 22, 2025

Abstract Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in 1960s, they have been used as important models to understand principal processes of life, including translation and genetic code. While phages were generally thought rare oddities nature, meta-omics methods rapidly changing this simplistic view by studying diverse biomes unprecedented resolution. Metatranscriptomics dramatically expanded number known from tens thousands, revealed widespread abundance, discovered several new families potential largely unknown hosts, biology, environmental impact. At same time, (meta)genomic analyses bacterial hosts discovering an arsenal defense systems bacteria employ protect themselves predation, whose functions immunity against we only beginning understand. Here, I review how approaches advancing field phage biology a focus might fight them.

Language: Английский

---

Heterogeneity in recombination rates and accessory gene co-occurrence distinguish Pseudomonas aeruginosa phylogroups

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

ABSTRACT Pseudomonas aeruginosa (class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It also an opportunistic pathogen that causes variety of chronic acute infections in humans. Its ability to thrive diverse environments exhibit wide range phenotypes lies part on its large gene pool, but the processes govern inter-strain genomic variation remain unclear. Here, we aim characterize recombination features accessory genome structure P. using 840 globally distributed sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding known phylogroups), two which are most prominent. Notable epidemic clones found phylogroups: ST17, ST111, ST146, ST274, ST395 phylogroup 1, ST235 ST253 2. phylogroups differ frequency characteristics homologous their core genomes, including specific genes frequently recombine impact diversity. Each phylogroup’s characterized by unique co-occurrence networks shared genes, anti-phage defense systems. Different pools antimicrobial resistance virulence exist display dissimilar patterns co-occurrence. Altogether, our results indicate each displays distinct histories acquiring exogenous DNA, may contribute predominance global population. Our study has important implications for understanding dynamics, within-species heterogeneity, clinically relevant traits . IMPORTANCE consummate opportunist inhabits many nosocomial non-clinical environments, posing major health burden worldwide. reveals phylogroup-specific differences within This partly explains remarkable ecological phenotypic traits, thus circumventing clinical public intervention strategies contain it. help inform efforts control prevent diseases, managing transmission, therapeutic efforts, circulation environmental reservoirs.

Language: Английский

---

Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(3)

Published: July 2, 2024

Prokaryotes encode an arsenal of highly diverse immune systems to protect themselves against invading nucleic acids such as viruses, plasmids and transposons. This includes invader-interfering that neutralize invaders their host, abortive-infection systems, which trigger dormancy or cell death in host offer population-level immunity. Most prokaryotic are found across different environments phyla, but distribution appears biased the factors influence largely unknown. Here, we compared combined system identification tools DefenseFinder PADLOC obtain expanded view arsenal. Our results show number encoded is positively correlated with genome size specific linked phylogeny. Furthermore, reveal certain more frequently by hosts a relatively high optimum growth temperature, while generally low temperature. Combined, our study reveals several correlate differences extends understanding how prokaryotes from environments.

Language: Английский

---

Synthesis of Mesoporous Catechin Nanoparticles as Biocompatible Drug-Free Antibacterial Mesoformulation

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(39), P. 26983 - 26993

Published: Sept. 18, 2024

While polyphenolic substances stand as excellent antibacterial agents, their antimicrobial properties rely on the auxiliary support of micro-/nanostructures. Despite offering a novel avenue for enhancing polymer performance, controllable fabrication mesoporous polymeric nanomaterials encounters significant challenges due to intricate intermolecular forces. In this article, catechin nanoparticles have been successfully fabricated using balanced multivariate interaction approach. The harmonization water-ethanol ratio and ionic strength effectively balances forces hydrogen bonding π-π stacking, facilitating controlled assembly mesostructures. exhibit uniform spherical structure (∼100 nm), open mesopores with diameter ∼15 nm, high surface area ∼106 m

Language: Английский

---