Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems

mBio, Journal Year: 2024, Volume and Issue: 15(3)

Published: Feb. 7, 2024

To verify whether members of the phylum

Language: Английский

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Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 28, 2025

Abstract Bacterial pathogens can undergo striking adaptive evolutionary change in the context of infection, driven by selection forces associated with host defenses and antibiotic treatment. In this work, we analyze transcriptional landscape adaptation an emerging zoonotic pathogen, Bordetella hinzii , as it evolved during a 45-month infection IL12Rβ1-deficient immunocompromised host. We find evidence multiple niche-specific modifications intravascular gastrointestinal compartments, involving superoxide dismutase system, glutamate ectoine metabolism, chaperone-mediated protein folding, pilus organization, peptide transport. Individual blood lineages displayed glutathione, phenylacetate, 3-phenylpropionate iron cluster assembly, electron transport, whereas individual demonstrated changes relating to gluconeogenesis, de novo pyrimidine synthesis, transport peptides phosphate ions. Down regulation flagellar operon corresponding loss structures occurred lineages, suggesting tradeoff between motility immune evasion. Finally, methylome analysis demonstrates alteration global genome methylation Type III methyltransferase. Our findings reveal plasticity how pathogen transcriptomes explore functional space they evolve demonstrate that such may uncover phenotypic adaptations not apparent from genomic alone.

Language: Английский

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Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 18, 2025

Abstract As an integral part of the global wellbeing, health wild animals should be regarded just as important that humans and livestock. The investigation wildlife health, however, is limited by availability samples. In attempt to implement a method with little invasiveness broad areas application, shotgun metagenomics were utilised investigate faecal microbiome its antimicrobial resistance genes (AMRG) in roe deer. These can facilitate resistances (AMR) bacteria are therefore increasing importance health. Accordingly, abundance potential vectors like needs assessed. samples additionally investigated for ESBL- E. coli , antibiotic resistant pathogen concern, via cultivation. Twenty-seven hunt-harvested Western Pomerania sampled. This study first our knowledge describe European deer ( Capreolus capreolus ), providing insights into bacterial archaeal composition. Among animals, was mostly similar showed comparable composition what has been reported related species, ratio 1.76 between Bacillota Bacteroidota . normalised AMR found 0.035 on average, which other investigations ruminants. Selective cultivation no animals. prevalence AMRG line previous results. use allowed simultaneous deer, suggests it promising monitoring wildlife. prokaryotic assemblage faeces differences microbiomes published cervids discussed.

Language: Английский

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Life on the dry side: a roadmap to understanding desiccation tolerance and accelerating translational applications

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 6, 2025

Abstract To thrive in extreme conditions, organisms have evolved a diverse arsenal of adaptations that confer resilience. These species, their traits, and the mechanisms underlying them comprise valuable resource can be mined for numerous conceptual insights applied objectives. One most dramatic to water limitation is desiccation tolerance. Understanding tolerance has important potential implications medicine, biotechnology, agriculture, conservation. However, progress been hindered by lack standardization across sub-disciplines, complicating integration data slowing translation basic discoveries into practical applications. Here, we synthesize current knowledge on evolutionary, ecological, physiological, cellular scales provide roadmap advancing research. We also address critical gaps technical roadblocks, highlighting need standardized experimental practices, improved taxonomic sampling, development new tools studying biology dry state. hope this perspective serve as accelerating research breakthroughs unlocking global challenges related climate change, food security, health.

Language: Английский

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Comparative genomics of Elusimicrobiaceae (phylum Elusimicrobiota) and description of the isolates Elusimicrobium simillimum sp. nov., Elusimicrobium posterum sp. nov., and Parelusimicrobium proximum gen. Nov. sp. nov.

Systematic and Applied Microbiology, Journal Year: 2025, Volume and Issue: 48(3), P. 126606 - 126606

Published: April 13, 2025

The tree of life comprises many deep-branching lineages with no or only very few cultured representatives. One such lineage is the phylum Elusimicrobiota, which contains two described species and whose biology has been poorly explored. We isolated three new from this intestinal tracts cockroaches. Like their closest relative, Elusimicrobium minutum, member family Elusimicrobiaceae to date, they are small, pleomorphic gram-negative rods characterized by a distinct cell cycle, like all ultramicrobacteria, pass through 0.22-μm filter membrane. Physiological characterization isolates revealed that obligately anaerobic fermenters lack catalase cytochrome c oxidase activities but can remove oxygen environment in non-respiratory manner. Their substrate range limited hexoses, as d-glucose, d-galactose, N-acetyl-d-glucosamine, fermented lactate, acetate, ethanol, hydrogen major products. Comparative genome analysis, included more than 100 MAGs uncultured Elusimicrobiaceae, underlying metabolic pathways outlined phylogenomic framework family. Based on phylogenomic, physiological, morphological evidence, we describe Parelusimicrobium proximum gen. nov., sp. posterum simillimum nov. under rules ICNP. high-quality genomes representatives, propose comprehensive taxonomy SeqCode, including genera Avelusimicrobium, Proelusimicrobium, candidate genus "Pseudelusimicrobium".

Language: Английский

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Macroevolutionary dynamics in micro-organisms: generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(5)

Published: May 1, 2024

Abstract Prokaryotes dominate the Tree of Life, but our understanding macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver prokaryote diversity. However, relatively little known about how prokaryotes successfully transition and persist across environments, these might vary between biomes lineages. Here, we investigate biome specialization in natural populations focal bacterial phylum, Myxococcota, sampled range replicated soils freshwater marine sediments Cornwall (UK). By targeted deep sequencing protein-coding gene rpoB, found >2,000 unique Myxococcota lineages, with majority (77%) classified as specialists only <5% lineages distributed salt barrier. Discrete character evolution models revealed that one rarely transitioned into another biome. Instead, evolved generalism mediated specialists. State-dependent diversification variation speciation rates tree, was independent association or specialization. Our findings were robust phylogenetic uncertainty, different levels species delineation, assumed amounts unsampled resulting an incomplete phylogeny. Overall, results consistent “jack-of-all-trades” tradeoff where generalists suffer cost any individual environment, rapid niche shed light on bacteria could biomes.

Language: Английский

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Adaptive radiations in natural populations of prokaryotes: innovation is key

FEMS Microbiology Ecology, Journal Year: 2023, Volume and Issue: 99(12)

Published: Nov. 13, 2023

Prokaryote diversity makes up most of the tree life and is crucial to functioning biosphere human health. However, patterns mechanisms prokaryote diversification have received relatively little attention compared animals plants. Adaptive radiation, rapid an ancestor species into multiple ecologically divergent species, a fundamental process by which macrobiological generated. Here, we discuss whether ecological opportunity could lead similar bursts in bacteria. We explore how adaptive radiations prokaryotes can be kickstarted horizontally acquired key innovations allowing lineages invade new niche space that subsequently partitioned among diversifying specialist descendants. novel zones are colonized exploited after evolution innovation certain types more prone radiation. Radiation specialists does not necessarily speciation bacteria when barriers recombination absent. propose this scenario, niche-specific genes accumulate within single lineage, leading open pangenome.

Language: Английский

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Evolutionary Transitions of DNA Replication Origins Between Archaea and Bacteria

Journal of Basic Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

ABSTRACT DNA replication origins play a crucial role in cellular division and are evolutionarily conserved across domains. This study investigated the evolutionary transitions of between archaea bacteria by analyzing 2733 bacterial 257 archaeal genomes. Our findings revealed that certain methanogens share phylogenetic proximity, suggesting interactions diverse ecological systems. Evolutionary may have occurred gut bacteria, haloarchaea ( Halogeometricum borinquense DSM 11551 Halovivax ruber XH‐70), halobacteria, sulfur‐reducing archaea. Methanosarcina barkeri M. ), Methanosaeta thermophila , Methanococcoides burtonii ) were closely related to respiratory tract humans. Methanohalobium evestigatum is strongly linked animal pathogen Mycoplasma putrefaciens ). Several thermophilic hydrogenotrophic clustered with oral fish pathogens. Pyrococcus furiosus P. was origin plant sheds light on drivers evolution their microbial speciation adaptation. highlight influence mutualistic parasitic relationships these transitions. It could significant implications biotechnology medicine, such as developing novel antimicrobial strategies understanding host‐pathogen dynamics.

Language: Английский

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Microscopic and metatranscriptomic analyses revealed unique cross-domain symbiosis betweenCandidatusPatescibacteria/candidate phyla radiation (CPR) and methanogenic archaea in anaerobic ecosystems

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 25, 2023

Abstract To verify the parasitic lifestyle of Candidatus Patescibacteria in enrichment cultures derived from a methanogenic bioreactor, we applied multifaceted approaches combining cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses. Cultivation experiments with addition exogenous archaea acetate, amino acids, nucleoside monophosphates 16S rRNA gene sequencing confirmed increase relative abundance Ca . methanogens. The predominant were Yanofskybacteria 32-520 lineages (to which belongs to class Paceibacteria) positive linear relationships ( r 2 ≥ 0.70) between Methanothrix , suggesting that tendency growth rate is similar host. By fluorescence situ hybridization (FISH) observations, FISH signals Methanospirillum cells lineages, respectively, significantly lower than those methanogens without Patescibacteria, their interaction. TEM SEM observations also support parasitism cell walls plugs these associated submicron often deformed. In particular, some -like filamentous dented where attached. Metatranscriptomic analyses identified highly expressed secreted genes genomes 32-520, contain adhesion-related domains host cells. Considering results through combination microscopic expression, computational modeling, propose interactions belonging Paceibacteria are parasitism.

Language: Английский

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Evolutionary Transitions of DNA Replication Origins between Archaea and Bacteria

Published: Jan. 1, 2024

DNA replication is a fundamental process in all cells, initiated at specific locations known as origins, and functionally conserved across three domains of life. In this study, we analyzed the phylogenetic proximity origins to infer evolutionary transitions among prokaryotic genomes. We used 2733 bacterial 257 archaeal genomes predict their origins. Evolutionary for might have occurred between gut methanogens bacteria, haloarchaea halobacteria, sulfur-reducing archaea bacteria. Methanosarcina barkeri, Methanosaeta thermophila, Methanococcoides burtonii were closely related respiratory tract bacteria humans. Methanohalobium evestigatum has linked animal pathogen, Mycoplasma putrefaciens. Several thermophilic hydrogenotrophic been clustered with oral fish pathogens. Pyrococcus furiosus evolutionarily plant Mutualism, parasitism, environmental lifestyles are factors that determine survival fitness new niches. The results our study demonstrated significant terms result ancestral ecosystems. This provides valuable insights into molecular evolution drive speciation through ecological or inheritance.

Language: Английский

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