New papers on Microbes & viruses
151 new papers on microbes & viruses in the last 7 days, within Biology. These are the 50 Pipette rates most worth reading, with the main result in the authors' own words.
The best of the week
A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity
Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories.
Peer-reviewed journalClaims a big stepA bacterial-killing type IV secretion system as a hidden antifungal device
This study reveals a paradigm-shifting role for bacterial type IV secretion system (T4SS) by demonstrating that a specialized bacterial-killing T4SS (T4SS BK ) in Lysobacter enzymogenes serves as a universal cross-kingdom antifungal weapon.
Peer-reviewed journalBold claims, read criticallyClaims a big stepReal-world useA glyoxal sensing Pseudomonas aeruginosa transcription factor enables lung infection
Here we describe the function, atomic structure and mechanism of the first bacterial transcription factor able to directly sense the dicarbonyl glyoxal (GO), which we aptly named the Glyoxal Regulator (GloR, from Pseudomonas aeruginosa PAO1), We show that GloR directly senses GO through a reversible cysteine modification that results in its binding to a conserved DNA regulatory motif (a glo box), which then triggers a transcriptional activation of a defined set of genes to help counter GO toxicity and enable acute lung infection.
PreprintBold claims, read criticallyClaims a big stepA Temporal Interactome Atlas across RNA Viruses reveals Convergent Vulnerabilities for Antiviral Repurposing
Together, InterVir and PROTEA establish an open-access resource for comparative virology, facilitating the identification of conserved host vulnerabilities and drug repurposing.
PreprintReal-world useTrimethoprim suppress phage activity and reduces toxin production in a clinical STEC strain, even in the presence of DNA-damaging antibiotics
Here, we describe how acid exposure and trimethoprim both potently suppress phage production ~100-fold, even in the presence of antibiotics that increase phage activity.
PreprintReal-world useThe Spatial Architecture of Human Subgingival Biofilms
We show that subgingival plaque is organized into recurrent multicellular assemblages of microbial consortia rather than unstructured layers of biomass, including assemblages defined as test-tube-brushes, corncobs and additional polymicrobial architectures with distinct taxonomic patterning.
PreprintThe biogeography of giant viruses and interactions with Eukaryotes across European lakes
Our results highlight that Nucleocytoviricota are ecologically relevant in lakes and that understanding their roles will be essential for predicting aquatic food webs under environmental change.
Peer-reviewed journalMicrofluidic Capture-Enrichment of individualized microbes from urban wastewater reveals a hidden reservoir of potential pre-emergent pathogens
These findings demonstrate that targeting PEPs can fundamentally expand the scope and quality of biosurveillance by providing a scalable strategy to identify, characterize, and close important gaps in our understanding of emerging microbial pathogens.
PreprintBold claims, read criticallyReal-world useGenetic diversity and phylogeography of swine influenza A virus in 2013-2022 in Europe using a harmonized genotyping nomenclature
Application of this tool to European sequence data revealed unprecedented genetic diversity, successfully identifying 150 swIAV genotypes mixing segments of both swine and human origin.
PreprintReal-world useExtensive horizontal gene transfer drives microbial adaptation and diversification in Kermadec Trench hadal microbiomes
In hadal sediment metagenomes analyzed here, we detect distant horizontal gene transfer (DHGT) across phyla/domains and estimate that it contributes on average ~13% of each genome and accounting for >46.7% of multi-copy gene expansions, with four phyla acquiring more than 30% of their genes via DHGT.
Peer-reviewed journalBold claims, read criticallyLoss of restriction-modification methyltransferases drives persistence to fluoroquinolones in Pseudomonas aeruginosa
Deletion of HsdM selectively increases the levels of persisters that survive treatment with fluoroquinolones by displaying enhanced SOS response but without acquiring resistance.
PreprintFatty acid synthesis restricts HIV-1 infection through regulation of the nuclear envelope in CD4+ T cells
Using a metabolically targeted small molecule screen, we identify de novo fatty acid synthesis as an unexpected determinant of resistance to HIV-1 infection in activated CD4+ T cells.
PreprintLive-cell imaging and ultrastructure expansion microscopy reveal the dynamic intracellular life cycle of Encephalitozoon intestinalis
Here we develop a live-cell imaging technique, "silhouette microscopy", that does not rely on genetic manipulation of microsporidia, and enables us to study the live cell dynamics of E. intestinalis replication in host cells, from entry to exit.
PreprintSpatiotemporal dynamics and stability of multi-kingdom microbial communities in hospital sinks acting as persistent pathogen reservoirs
Together, these findings identify hospital sink drains as persistent and structured multi-kingdom microbial reservoirs that harbor clinically relevant multidrug-resistant organisms (MDROs).
PreprintReal-world useSystematic mapping of bacteriophage gene essentiality with HIDEN-SEQ
Here we present HIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing), a transposon-insertion sequencing method for phages that systematically links viral genes to selectable phenotypes.
Peer-reviewed journalBold claims, read criticallyReal-world useMatrix-controlled emergence of biofilm architecture shapes antimicrobial survival
Rather than acting as a passive barrier, EPS therefore shapes antimicrobial susceptibility by reorganizing biofilm architecture and its transport properties.
PreprintHuman iPSC-derived neurons identify West Nile virus neuropathogenesis signatures and reveal strain-dependent neuroattenuation
Together, these findings uncover neuron-specific signatures of WNV pathogenesis and demonstrate that neuronal replication phenotypes can reveal strain-dependent virulence differences not captured by conventional cell lines.
PreprintFive-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation
Together, these results show that while core microbial responses to healthy eating exist, the structure and function of the human gut microbiome varies strongly with culture, geography, and long-term dietary practices.
Peer-reviewed journalResilience of blue carbon microbiomes in response to ecological and anthropogenic filtering
Collectively, our study quantifies the vulnerability of BCEs to future species loss while providing a scientific basis for confidence that blue carbon ecosystems, supported by phylogenetic redundancy, may sustain functional stability despite environmental change.
Peer-reviewed journalPolyketide synthase 12 is an in vivo essential source of novel mycolyl lipids in Mycobacterium tuberculosis
Thus, we used a new host-facing genomic-metabolomic-phenotypic approach to discover the functions of an in vivo essential Mtb gene, which controls the physical structure of the Mtb-host interface.
PreprintComprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry
Here we present a simple, optimized method based on liquid chromatography and high-resolution mass spectrometry, with an accompanying analysis pipeline, for the accurate quantification of more than 30 of these compounds, including ammonia.
PreprintA widespread bacterial toxin reveals a deeply divergent DNase family neutralized by diverse immunity proteins.
Here we identify Rehh as a widespread antibacterial toxin associated with multiple bacterial secretion systems and show that it is used in interbacterial competition.
PreprintMicrobiota-derived pantothenic acid rapidly restores colonic mucus barrier after antibiotic-induced dysbiosis
Here, we identify pantothenic acid (vitamin B5) as a microbial metabolite that rapidly restores colonic mucus integrity following antibiotic administration.
PreprintDivision of labor during bacterial warfare
The division of labor during bacterial warfare, therefore, enables powerful localized killing while safeguarding the population from self-destruction.
PreprintRapid Phenotypic Antibiotic Susceptibility Determination Direct From Spiked Urine Samples Shows Strong Correlation with Gold Standard for Urinary Tract Infection
Exposure to the drugs for only 90 minutes gave a Categorical Agreement of 98% to gold standard culture results across the resulting 247 bacteria/antibiotic pairs.
PreprintBold claims, read criticallyReal-world useInherited flagellar structures coordinate the onset of swimming among related E. coli cells
Together, our results show how the accumulation of a molecular machine integrates fluctuations, and how a checkpoint on its assembly sharpens them into a decision, setting both the speed and heritability of a behavioral trait.
PreprintBloom-forming bacteria heavily invest in anti-phage defense
This suggests that GSB-TRL01 invests heavily in anti-phage defense, leading to reduced lysis at high cell densities and allowing blooms to persist for weeks to months.
PreprintMycobacterium tuberculosis requires riboflavin biosynthesis for survival in the host
Our results demonstrate that M. tuberculosis requires RibA2 for viability at all stages of infection and support further characterization of the riboflavin biosynthesis pathway as a potential target for development of new anti-tubercular drugs.
PreprintReal-world useA Wolbachia pipientis protein confers resistance to virus infection in Drosophila melanogaster
In summary, we identified a Wolbachia-derived ankyrin domain containing protein that modulates host immunity through the IMD pathway.
PreprintActive layer microbial inocula restore missing functions across thawed permafrost soils
By restoring functions with a multifunctional microbial community, we demonstrate widespread functional limitations, as increased CO 2 emissions across four permafrost types, and onset N 2 O emissions in two of those.
Peer-reviewed journalReal-world useDual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system
Using phage infection and plasmid transformation assays in Pseudomonas aeruginosa, biochemical reconstitution, and structural biology, we show that MANTIS establishes self-identity through adenine hemimethylation of short asymmetric DNA sequences.
PreprintCutibacterium acnes-derived short-chain fatty acids drive lipogenesis and induce holocrine secretion in human sebocytes
Together, these findings redefine the relationship between microbiome and sebaceous glands, and identify C. canes as an active regulator promoting both sebogenesis and holocrine secretion for the release of lipids in the pilosebaceous unit.
PreprintBold claims, read criticallyConvergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
Most significantly, the phylodynamic signal that a dominant lineage had emerged within the infection, more so than any particular set of mutations, was associated with a more rapid decline in patient lung function.
PreprintReal-world useGenome-wide CRISPRi maps pneumococcal attachment and intracellular survival during single infection and Influenza co-infection
Taken together, our study provides a genome-scale resource of pneumococcal fitness determinants during infection and demonstrates that influenza co-infection selectively reshapes bacterial genetic dependencies rather than globally altering pathogenicity programs.
PreprintPotency of nucleoside analogs against Powassan virus replication and identification of 4'-fluorouridine as a therapeutic candidate for tick-borne orthoflavivirus encephalitis
These data identify 4'-fluorouridine as a promising therapeutic candidate for neurotropic flavivirus disease.
PreprintReal-world useA heterologous expression system allows rapid testing and discovery of resistance-conferring mutations from multiple pathogenic fungi
The heterologous expression system allows rapid construction of mutants, by taking advantage of the abundant genetic tools available for S. cerevisiae.
PreprintReal-world useMicroorganisms consume trace gases present throughout the Mariana Trench water column
Together, our results suggest H2 and CO are readily available to pelagic microbial populations and are biologically oxidised in the dark zone, supporting microbial energy acquisition and oceanic biogeochemical cycling.
PreprintNiche specialization and prevalence of comammox Nitrospira in the alkaline sediments of thermokarst lakes on the Tibetan Plateau
Researchers reveal that comammox Nitrospira become dominant nitrifiers in alkaline thermokarst lakes on the Tibetan Plateau and uncover their ecological adaptations to extreme saline-alkaline environments.
Peer-reviewed journalAxonal entry and retrograde transport define HSV-1 latency establishment and reactivation potential in neurons
Together, these findings identify axonal entry and transport as critical regulatory checkpoints in HSV-1 latency establishment and suggest that interference with retrograde trafficking may represent a strategy to limit neuroinvasion and life-long reactivations.
PreprintThe gut-liver axis and the role of bacteria in severe dengue virus infection in mice
Consistent with this, here we demonstrated that DENV2 infection of AG129 mice compromised the gut epithelial barrier, promoted bacterial translocation, and induced microbial changes indicative of dysbiosis, including a reduced abundance of putatively beneficial microbial taxa and disrupted microbial circadian oscillations.
PreprintA microbiome-derived metabolite from Staphylococcus epidermidis inhibits Staphylococcus aureus biofilm formation and virulence
Together, these findings uncover a previously unrecognized mechanism by which S. epidermidis suppresses S. aureus virulence and highlight the potential of microbiome-derived metabolites as therapeutics for the prevention and treatment of S. aureus skin infections.
PreprintReal-world useRelative humidity differentially modulates decay of structurally distinct respiratory viruses in deposited human saliva particles
These findings emphasize virus-specific environmental persistence and highlight limitations of relying on a single virus and particle matrix for defining public health strategies.
PreprintReal-world useGut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk
Notably, the Early Plateaued pattern is associated with a threefold elevated risk of T1D, whereas other patterns are not associated with T1D risk.
Peer-reviewed journalSelf-organized division of labor and selection for long-term antiviral defense in CRISPR arrays.
Spontaneous division of labor emerges in the dual memory regime, with spacers near the leader and distal ends specialized in short-term and long-term memory, respectively.
PreprintMapping the Functional Landscape and Viral Diversity of 2A Peptides
These findings define the sequence and functional landscape of viral 2A peptides and provide mechanistic and evolutionary insights into how nascent peptide ribosome exit tunnel interactions mediate StopGo translation.
PreprintAnoxygenic phototrophic Chlorobi use broad metabolic and resource acquisition strategies to support stable near-clonal blooms
Collectively, these findings identify physiological and metabolic strategies that may enable near-clonal Prosthecochloris populations to attain extraordinary biomass while coupling the sulfur, carbon, and nitrogen cycles in coastal euxinic environments.
PreprintProteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state
Here, we demonstrate that this phenotype has evolved through two temporally distinct tissue-specific proteolytic controls at the Spike (S) furin cleavage site (FCS).
PreprintHighly Pathogenic Avian Influenza Viruses H5N1 and H5N5 in Red Foxes (Vulpes vulpes) in Norway during 2022-2024
We investigated six cases of HPAI in red foxes (Vulpes vulpes) in Norway during 2022-2024 and identified infections with H5N1 and H5N5 viruses.
PreprintReal-world useSingle-cell analysis identifies TOP2α as a critical regulator of G2/M entry and differentiation-dependent productive HPV replication
These studies identify TOP2 as a critical regulator of HPV genome amplification upon differentiation.
PreprintMucD regulates alginate biosynthesis through the proteolytic control of AlgX and AlgK in Pseudomonas aeruginosa
Crucially, we demonstrate that MucD represses alginate biosynthesis post-translationally, in addition to its previously implicated role in transcriptional regulation.
Peer-reviewed journal