eLife: latest articles by subject

Obtaining maximum information from colony counts with REPOP

spresse@asu.edu (Carol Yunxiao Slayton) — Fri, 09 Oct 2026 00:00:00 +0000

Bacterial counts from native environments, such as soil or the animal gut, often show substantial variability across replicate samples. This heterogeneity is typically attributed to genetic or environmental factors. A common approach to estimating bacterial populations involves successive dilution and plating, followed by multiplying colony counts by dilution factors. This method, however, overestimates the heterogeneity in bacterial population because it conflates the inherent uncertainty in drawing a subsample from the total population with the uncertainty in the sample arising from biological origins. In other words, this approach may obscure features that may otherwise be present in the data, hinting at the presence of genuine subpopulations. For example, in plate counting applied to Caenorhabditis elegans gut microbiota, observed multimodality is often interpreted as large host-to-host variance, while the randomness introduced by measurement is frequently ignored. To explicitly account for the uncertainty introduced by dilution and plating randomness, we introduce REPOP, a PyTorch-based library to REconstruct POpulations from Plates within a Bayesian framework. Beyond simple cases, REPOP addresses more complex scenarios, including multimodal populations and correcting the mathematically subtle, but experimentally relevant, bias introduced by excluding plates deemed too crowded to distinguish individual colonies. We demonstrate REPOP’s ability to resolve distinct population peaks otherwise obscured by standard multiplication methods. Applications to both simulated and experimental datasets, including bacterial samples of different concentrations and ones from the gut microbiota of C. elegans, show that REPOP accurately recovers the underlying multimodality by properly accounting for error propagation, where naive multiplication fails. REPOP is available on GitHub: https://github.com/LabPresse/REPOP.

The structural context of mutations in proteins predicts their effect on antibiotic resistance

annagreen@umass.edu (Anna G Green) — Fri, 09 Oct 2026 00:00:00 +0000

In Mycobacterium tuberculosis, a prevalent and deadly pathogen, resistance to antibiotics evolves primarily through non-synonymous mutations in proteins. Sequence-based analyses can uncover the genetic basis of antibiotic resistance, but these methods focus on primary sequence and often neglect other biological signals, such as protein structural information. We hypothesize that integrating the structural context of mutations improves the prediction of effects on function and phenotype. We curate high-confidence structural annotations for the M. tuberculosis proteome from 1350 crystallography and 2337 AlphaFold predictions, and mutations from over 31,000 M. tuberculosis isolates. We demonstrate that mutations in proteins known to cause resistance are clustered in 3D space, even in proteins where inactivating mutations at any position are thought to cause resistance. We find over 450 proteins in the M. tuberculosis proteome that display signals of clustered mutations, many of which have a known relationship with antibiotic resistance. We show that a supervised classifier trained on 3D distance to known resistance sites alone has an F1 score of 96.5% at classifying mutations as resistance-conferring on a held-out test set. This work demonstrates that protein structure provides useful information for categorizing which variants may cause antibiotic resistance, even when the majority of structures are AI-predicted.

Human CD1c-autoreactive T-cells recognise Mycobacterium tuberculosis-infected antigen-presenting cells and display cytotoxic effector programmes

s.mansour@soton.ac.uk (Alasdair Leslie) — Mon, 05 Oct 2026 00:00:00 +0000

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death from infection globally yet the contribution of non-classical T-cell pathways to human immunity remains poorly defined. CD1c-autoreactive T-cells, which recognise self-lipids presented by the antigen-presenting molecule CD1c, are frequent in human blood but their role during infection remains unclear. Here, we investigate how CD1c-expressing antigen-presenting cells (APCs) and Mtb infection shape CD1c-autoreactive T-cell responses using engineered human APC systems, complemented by single-cell transcriptomic profiling to define the ex vivo phenotypic landscape of these T-cells. CD1c is present within human TB granulomas, whereas Mtb down-modulates CD1c expression on infected APCs, consistent with an immune evasion strategy. CD1c-autoreactive T-cells respond more strongly to Mtb-infected CD1c⁺ APCs than to uninfected cells, exhibiting enhanced activation, cytotoxicity, and diverse cytokine secretion via CD1c-dependent recognition. Under in vitro conditions, these T-cells reduce relative Mtb burden in infected phagocytes. Single-cell RNA sequencing reveals cytotoxic effector-memory programmes and expression of antimicrobial molecules, providing a mechanistic basis for these responses. Together, these findings define a human CD1c-restricted T-cell response to Mtb-infected APCs and identify autoreactive CD1c-restricted T-cells as a candidate cellular axis for lipid-directed immunity in TB.

The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome

joseph.mougous@yale.edu (Andrew L Goodman) — Fri, 02 Oct 2026 00:00:00 +0000

Bacteria inhabiting the mammalian gut coexist in dense communities where contact-dependent antagonism mechanisms are widespread. The type VI secretion system (T6SS) is an interbacterial toxin delivery pathway prevalent among gut Bacteroidales, yet its function in naturally evolved microbiomes remains poorly defined. Here, we examine the role of the T6SS in Bacteroides within a physiologically relevant gut community derived from wild mice (the WildR microbiome). Using newly developed genetic tools and a strategy for functional replacement of strains within the WildR community, we demonstrate that the WildR isolate B. acidifaciens employs a T6SS to antagonize co-resident Bacteroidales. We also show that loss of T6SS function compromises the long-term maintenance of B. acidifaciens in the community but not its initial colonization, establishing the system as a determinant of strain persistence. The T6SS we identified resides on an integrative and conjugative element (ICE). ICE-seq, a targeted sequencing approach, reveals that the T6SS-ICE is distributed among select Bacteroidales and Muribaculaceae species in the WildR microbiome, between which it appears to be recently exchanged. We also show that transfer of the T6SS-ICE to WildR isolate Phocaeicola vulgatus confers transient colonization benefits in mice, but is linked to eventual population decline. Our findings demonstrate that the T6SS can stabilize the presence of specific strains within a complex, co-evolved gut microbiome, yet its value is context dependent and constrained by the ecological and physiological landscape of the host community.

Distinct allosteric remodeling of HIV-1 Env dynamics on virions by gp41-directed antibodies reveals two modes of neutralization

maolin.lu@uthct.edu (Baoshan Zhang) — Fri, 02 Oct 2026 00:00:00 +0000

HIV-1 envelope glycoprotein (Env), a gp120–gp41 trimer, undergoes coordinated conformational changes that drive membrane fusion and allow immune evasion by transiently concealing neutralization-sensitive epitopes. Most broadly neutralizing antibodies (bNAbs) target gp120, whereas a distinct subset recognizes conserved gp41 regions, such as the fusion peptide and the membrane-proximal external region; however, their impact on Env dynamics and associated neutralization mechanisms remains unclear. By using bioorthogonal tagging for single-molecule FRET, we monitored real-time bNAb-induced conformational sampling of Env on intact virions. Most gp41-directed bNAbs allosterically stabilized the prefusion-closed (PC) state, whereas the bivalent 10E8.4/iMab favored both PC and CD4-bound open (predominant) states. Antibodies redistributed the conformational populations of Env with modest kinetic effects, preserving a sequential transition pathway. These findings reveal two modes of neutralization for gp41-directed antibodies, fixing the PC conformation and opening it up – in both cases, with neutralization occurring via long-range allosteric control of Env dynamics.

A novel rapid host cell entry pathway determines the intracellular fate of Staphylococcus aureus

martin.fraunholz@uni-wuerzburg.de (Adriana Moldovan) — Wed, 23 Sep 2026 00:00:00 +0000

Staphylococcus aureus is an opportunistic pathogen causing severe diseases. Recently, S. aureus was recognized as an intracellular pathogen, whereby the intracellular niche promotes immune evasion and antibiotic resistance. Interaction of S. aureus with versatile host cell receptors was described previously, suggesting that internalization of the pathogen can occur via several pathways. It remains elusive whether the pathway of internalization can affect the intracellular fate of the bacteria. Here, we identified a mechanism governing cellular uptake of S. aureus which relies on lysosomal Ca²⁺, lysosomal exocytosis, and occurs concurrently to other well-known entry pathways within the same host cell population. This internalization pathway is rapid and active within only a few minutes after bacterial contact with host cells. Compared to slow bacterial internalization, the rapid pathway demonstrates altered phagosomal maturation as well as translocation of the pathogen to the host cytosol and ultimately results in different rates of intracellular bacterial replication and host cell death. We show that these alternative infection outcomes are caused by the mode of bacterial uptake.

Identifying a novel mechanism of L-leucine uptake in Mycobacterium tuberculosis using a chemical genomic approach

nisheeth@thsti.res.in (Bappaditya Dey) — Wed, 23 Sep 2026 00:00:00 +0000

Amino acid biosynthesis is vital for Mycobacterium tuberculosis (Mtb) proliferation and tuberculosis (TB) pathogenesis. However, it is not clear how amino acids are transported in Mtb, particularly the branched-chain amino acids (BCAAs) that contribute to the production of the cell-wall lipid component precursors, such as acetyl-CoA and propionyl-CoA. While performing the screening of an FDA-approved repurposed library of small molecule inhibitors against the auxotrophic strain Mtb mc² 6206, which lacks leuC-leuD and panC-panD genes, we identified a molecule, namely semapimod, which exclusively inhibits the growth of the auxotrophic strain, whereas no effect is observed against the wild-type Mtb H₃₇Rv. Interestingly, 24 hr of exposure of Mtb mc² 6206 to semapimod causes massive transcriptional reprogramming with differential expression of >450 genes associated with a myriad of metabolic activities. By performing a series of experiments, we affirm that semapimod indeed inhibits the L-leucine uptake in Mtb mc² 6206 by targeting a protein involved in the cell-wall lipid biosynthesis pathway. Remarkably, semapimod treatment of mice infected with Mtb H₃₇Rv causes a significant reduction of bacterial load in lungs and spleen, despite showing no efficacy against the pathogenic strain in vitro. Overall findings of our study reveal that together with an endogenous pathway for L-leucine biosynthesis, a well-orchestrated machinery for its uptake is functional in Mtb, which is important for intracellular survival of the TB pathogen.

Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome

schlotc@gmail.com (Christian Schlötterer) — Fri, 18 Sep 2026 00:00:00 +0000

Most microbiome research focuses on the taxonomic composition at the species level to understand the impact of environmental factors, but intraspecific diversity has largely been ignored. To address this significant knowledge gap, we took advantage of the simple, culturable microbiome of Drosophila. First, we documented that natural populations of D. simulans harbor three diverged clades of Lactiplantibacillus plantarum, a key nutritional symbiont. We studied the distinct ecological roles of these three clades by exposing flies with their native microbiome to two temperature regimes in the laboratory. Tracking the three clades within the complete Drosophila microbiome over a period of more than 10 years at two temperatures, we identified strikingly distinct dynamics in response to the selection regime. We confirmed the functional differentiation of the three clades using in vitro growth measurements and in vivo mono-association assays. Our results highlight that environmental selection operates at the subspecies level. Therefore, we conclude that the functional diversification of the microbiome can only be understood when intra- and interspecific diversity is considered.

Screening the MMV Pathogen Box reveals the mitochondrial bc₁-complex as a drug target in mature Toxoplasma gondii bradyzoites

blumem@rki.de (Deborah Maus) — Thu, 17 Sep 2026 00:00:00 +0000

The apicomplexan parasite Toxoplasma gondii infects 25–30% of the global human population and can cause life-threatening diseases in immunocompromised patients. The chronically infectious forms of the parasite, bradyzoites, persist within cysts in brain and muscle tissue, and are responsible for its transmission and remission of the disease. Currently available treatment options are very limited and are only effective against the fast-replicating tachyzoites, but fail to eradicate the chronic stages of T. gondii. The cause of these treatment failures remains unclear. Here, we utilized our recently developed human myotube-based culture model to screen compounds from the MMV Pathogen Box against pan-resistant in vitro bradyzoites, and identified multiple compounds with simultaneous activity against tachyzoites and bradyzoites. Stable isotope-resolved metabolic profiling on tachyzoites and bradyzoites identified the mitochondrial bc₁-complex as a target of bradyzocidal compounds and defined their metabolic impacts on both parasite forms. Our data suggest that mature bradyzoites rely on mitochondrial ATP production.

Acyl carrier protein is essential for apicoplast biogenesis in malaria parasites independent of fatty acid synthesis

sprigge2@jhu.edu (James A Wohlschlegel) — Mon, 14 Sep 2026 00:00:00 +0000

Acyl carrier protein (ACP) and its 4-phosphopantetheine prosthetic group canonically function as the soluble scaffold for acyl chain assembly and elongation during type II fatty acid biosynthesis (FASII). Plasmodium malaria parasites retain a FASII pathway in the apicoplast organelle that has been the subject of considerable scrutiny and confusion. Although apicoplast FASII is essential for Plasmodium falciparum growth within mosquitoes and the human liver, this pathway is dispensable and largely inactive in blood-stage parasites that can scavenge host fatty acids. In contrast to FASII enzymes that can be disrupted without fitness defect, we report that knockout or ligand-dependent knockdown of apicoplast ACP is lethal to blood-stage P. falciparum, indicating an essential FASII-independent function. Loss of ACP impairs the biosynthesis of essential isoprenoid precursors and blocks apicoplast biogenesis. Using proximity biotinylation and biochemical interaction studies, we identified a key role for ACP in binding and stabilizing apicoplast pyruvate kinase II (PKII). This critical enzyme is the only known source of nucleoside triphosphates (NTPs) in this organelle and is required for isoprenoid synthesis and apicoplast biogenesis. Our work reveals that ACP knockdown results in destabilization and loss of PKII, which is sufficient to explain ACP essentiality in this stage. This work unveils essential ACP function at a key biochemical hub controlling broad apicoplast metabolism in malaria parasites that is independent of the canonical ACP role in FASII.

Intracellular growth of Chlamydia trachomatis leads to global histone hypermethylation by impairing demethylation

asubtil@pasteur.fr (Adrian Gabriel Torres) — Mon, 14 Sep 2026 00:00:00 +0000

Chlamydia trachomatis, an intracellular bacterium, highjacks metabolites from the host cell for its own proliferation. We provide evidence of global hypermethylation of the host proteome, including histones, during the late stages of infection. Single cell analyses revealed co-occurrence of several methylated residues on histones, while infection did not alter S-adenosyl methionine levels. Histone hypermethylation correlated positively with bacterial load and was prevented by antibiotic treatment. Mapping of trimethylation of histone 3 at residues K4 and K9 revealed a broad distribution throughout chromatin. Nuclear fractions of infected cells exhibited a fourfold decrease of demethylase activity against H3K4me3 and a twofold increase in succinate concentration, a competitive inhibitor for the demethylase co-factor a-ketoglutarate. Supplementation of the culture medium with dimethyl-ketoglutarate (DMKG) or with iron, a second co-factor of histone lysine demethylases, reduced histone hypermethylation. DMKG supplementation modified the transcription of about one third of the infection-responsive genes, indicating that histone hypermethylation contributes to modulating the transcriptional response of the host to infection. Finally, chemical inhibition of histone demethylases in a mouse model of infection showed a moderate benefit regarding the outcome of infection. Overall, our data show that the metabolic pressure exerted by a pathogen with an intracellular lifestyle drives epigenetic changes in infected cells.

The C3–C3aR axis modulates trained immunity in alveolar macrophages

alexander.earhart@wustl.edu (Aasritha Nallapu) — Thu, 10 Sep 2026 00:00:00 +0000

Complement protein C3 is crucial for immune responses in mucosal sites such as the lung, where it aids in microbe elimination, and enhances inflammation. While trained immunity – enhanced secondary responses of innate immune cells after prior exposure – is well-studied, the role of the complement system in trained immune responses remains unclear. We investigated the role of C3 in trained immunity and found that alveolar macrophage (AM) C3 and C3aR1 expression increased in humans after an intranasal exposure to a training stimulus. In vivo, trained wild-type mice showed significantly elevated proinflammatory cytokines and increased C3a levels upon a second stimulus. Ex vivo, trained C3-deficient AMs displayed reduced chemokine and cytokine output as well as impaired phagocytosis and reactive oxygen species production compared to wild-type AMs. Real-time confocal microscopy of live, intact mouse alveoli revealed that AMs internalize C3 rapidly after alveolar microinstillation, as compared to C3a. Correspondingly, the blunted cytokine output was restored by exogenous C3 but not by C3a. Inhibiting C3aR, both pharmacologically and with a genetic C3aR knockout, prevented this restoration, indicating the necessity of C3aR engagement. Mechanistically, trained WT AMs demonstrated enhanced glycolytic activity compared to C3-deficient AMs – a defect corrected by exogenous C3 in a C3aR-dependent manner. These findings reveal that C3 modulates trained immunity in AMs through C3aR signaling and highlight a novel role for C3 in trained immunity.

In vitro sexual dimorphism establishment in schistosomes

Matt.Berriman@glasgow.ac.uk (Benjamin J Hulme) — Thu, 10 Sep 2026 00:00:00 +0000

Schistosomes are parasitic flatworms that cause Schistosomiasis, a major neglected tropical disease that affects more than 250 million people worldwide. With two distinct sexes, a heterogametic female (ZW) and a homogametic male (ZZ), schistosomes are an exception among flatworms, which are largely hermaphroditic. Sexual dimorphism in schistosomes only becomes apparent by adulthood within the mammalian host. However, the cellular and molecular mechanisms underlying the sexual differentiation of are poorly understood, partly due to intrinsic challenges in assessing parasite development in vivo. Therefore, robust and reproducible approaches for maintaining and developing parasites in vitro are needed to overcome these difficulties. To date, few studies have focused on protocols that allow cultured parasites to reach sexual dimorphic stages, and none have been reproduced, limiting the ability to understand the sexual biology of this major human parasite. Here, we refine a protocol for long-term culture of newly transformed cercariae that developed in vitro into sexually dimorphic forms. We assessed the effect of adding two different sera, foetal bovine serium (FBS) and human serum (HS), to culture medium supplemented with red blood cells. In contrast to FBS-culture parasites, those grown in HS digested red blood cells, a crucial step for long term parasite development. Furthermore, sexual dimorphism was clearly established in the HS-cultured parasites, albeit delayed, in contrast to most FBS-cultured parasites that did not progress beyond an early liver stage. Moreover, in EdU-pulse experiments, cells within HS-cultured parasites continuously proliferated, but markedly fewer proliferated in FBS-culture. By enabling reproducible parasite develoment in vitro, this protocol creates new opportunities for dissecting mechanisms that underly sexual dimorphim, as well as for screening in vitro for new interventions across the life cycle of these major human parasites.

Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA

jfraser@fraserlab.com (Babak Javid) — Fri, 04 Sep 2026 00:00:00 +0000

Despite redundant cellular pathways to minimize translational errors, errors in protein synthesis are common. Pathways and mechanisms to minimize errors are classified as pre-ribosomal or ribosomal. Pre-ribosomal pathways are primarily concerned with the appropriate charging of tRNAs with their cognate amino acids. By contrast, the ribosomal decoding center is considered ‘blind’ to mischarged tRNAs since these have cognate codon•anti-codon pairing. Here, we identified that in mycobacteria, deletion of the 16S ribosomal RNA methyltransferase gidB led to increased ribosomal discrimination of mischarged tRNAs. Discrimination only occurred in mycobacteria enriched from environments or genetic backgrounds with high rates of mistranslation. GidB deletion was necessary, but not sufficient for reducing mistranslation due to misacylation. Analysis of new cryo-EM structures of the M. smegmatis ribosomes derived from wild-type and gidB-deleted strains point to the interaction between the base methylated by GidB on the 16S RNA and an asparagine on the ribosomal S12 protein that, when mistranslated to aspartate, may be involved in altering translational fidelity. Our data suggest a mechanism by which mycobacterial ribosomes can discriminate mischarged tRNAs and that 16S rRNA differential methylation by GidB may act to prevent catastrophic translational error.

Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis

h.strahl@ncl.ac.uk (Davide Marenduzzo) — Wed, 02 Sep 2026 00:00:00 +0000

Proteins can diffuse micrometers in seconds, yet bacterial cells are able to maintain stable protein gradients. The best-studied bacterial protein gradient is the Min system of Escherichia coli. In rod-shaped bacteria, the MinCD proteins prevent formation of minicells by inhibiting FtsZ polymerization close to the cell poles. In E. coli, these proteins oscillate between cell poles within a minute, resulting in an increased MinCD concentration at the poles. This oscillation is caused by the interaction between MinD and the protein MinE, which form an ATP-driven reaction-diffusion system, whereby the ATPase MinD cycles between a monomeric cytosolic and a dimeric membrane-attached state. Bacillus subtilis also has MinCD, but lacks MinE. In this case, MinCD forms a static gradient that requires the transmembrane protein MinJ, located at cell poles and cell division sites. A recent reaction-diffusion model was successful in recreating the MinD gradient in B. subtilis, assuming that MinD cycles between cytosol and membrane, like in E. coli. Here, we show that the monomeric and dimeric states of B. subtilis MinD have comparable membrane affinities, that MinD interacts with MinJ as a dimer, and that MinJ is not required for membrane localization of MinD. Based on these new findings, we tested different models, using kinetic Monte Carlo simulations, and found that a difference in diffusion rate between the monomer and dimer, rather than a difference in membrane affinity, is important for B. subtilis MinCD gradient formation.

Three metabolic pathways replenishing the one-carbon pool collectively support growth and virulence of Listeria monocytogenes

sascha.kahlfuss@med.ovgu.de (Dunja Bruder) — Wed, 19 Aug 2026 00:00:00 +0000

The bacterium Listeria monocytogenes can grow in the cytoplasm of infected human cells, but there it relies on specific biosynthetic pathways for intracellular nutrient supply. We previously found that the glycine cleavage system (GCS) is needed for intracellular growth. The GCS decarboxylates glycine for generation of 1C-tetrahydrofolates (1C-THF), folate-dependent one-carbon donors needed for biosynthesis of other metabolites. We continued our studies on the GCS and showed that a L. monocytogenes ΔgcvPAB mutant, lacking the GCS glycine dehydrogenase, is attenuated without resembling the phenotype of classical virulence factor mutants. The ΔgcvPAB mutant also grew poorly in synthetic medium, explained by the presence of glycine that was toxic for this strain. Selection of glycine-resistant suppressors yielded a survivor, in which the N- and C-terminal parts of the formate-tetrahydrofolate ligase (fhs) gene, which is naturally separated into two parts by a premature stop codon in the L. monocytogenes reference strain EGD-e were reassembled into a full-length open-reading frame. Like the GCS, Fhs also feeds the 1C-THF pool, and its restoration cured the virulence defects of the ΔgcvPAB mutant. Another suppressor had a mutated glyA gene, encoding serine hydroxymethyltransferase, and combinatorial deletions of gcvPAB and glyA in fhs⁻ and fhs⁺ backgrounds demonstrated a role of GlyA in 1C-THF metabolism. Our results show that three pathways feed the 1C-THF pool to support growth and virulence of L. monocytogenes and represent the first example of the spontaneous reactivation of an L. monocytogenes gene that is inactivated by a premature stop codon.

Replicative slender bloodstream forms complete transmission of Trypanosoma brucei without prior differentiation into stumpy forms

markus.engstler@biozentrum.uni-wuerzburg.de (Anna Sophie Kreis) — Wed, 19 Aug 2026 00:00:00 +0000

We have previously shown that the slender form of Trypanosoma (T.) brucei is able to infect teneral tsetse flies, develop to the first fly form, which is the procyclic form, and complete the life cycle in the insect vector (Schuster et al., 2021). Further, analysis of the transmission index (TI; defined as the number of salivary gland infections relative to the number of midgut infections) revealed a higher TI for slender as compared to stumpy forms under laboratory conditions, which included the addition of N-acetylglucosamine (NAG) to the infective bloodmeal. Here, we show that slender trypanosomes can establish infections in both male and female tsetse flies and in both teneral and non-teneral flies without requiring supplements in the bloodmeal. Additionally, an RNA sequencing time course was performed on both slender and stumpy cells during their transition into procyclic forms. This analysis revealed that slender- and stumpy-form trypanosomes remain transcriptionally distinct throughout differentiation into the procyclic form. Furthermore, while the protein associated with differentiation 1 (PAD1) remains essential for the transition, slender cells do not require expression of other hallmark stumpy-form traits, such as cell-cycle arrest or the shortening of their flagella or microtubule corset. Instead, slender trypanosomes are able to transition directly into procyclic forms. Taken together, these findings demonstrate that slender cells of T. brucei can follow a distinct transcriptional trajectory towards the procyclic form and can establish infections in teneral and non-teneral tsetse flies, thereby contributing to the transmission and spread of these African parasites.

Five-layer systems analysis of Leishmania stage differentiation reveals an essential role for protein degradation in parasite development

pascale.pescher@pasteur.fr (Anne Boland) — Wed, 12 Aug 2026 00:00:00 +0000

Vector-borne, protist parasites have evolved complex developmental programs to adapt to very distinct host environments. How these important pathogens transition between insect and mammalian stages is only poorly understood. Here, we investigated stage differentiation in Leishmania donovani, a trypanosomatid parasite with constitutive gene transcription, offering a model to study post-transcriptional regulation. Using a five-layer integrative systems analysis (genome to metabolome), we compared hamster-derived amastigotes and culture-derived promastigotes. Genomic adaptation was excluded as a major driver of differentiation, while differential mRNA turnover emerged as a key mechanism of stage-specific gene expression. Transcriptomic and proteomic comparisons revealed a broad dynamic range of protein abundance changes that correlated poorly with mRNA levels. This discrepancy was linked to (i) altered snoRNA expression and rRNA modifications, indicating stage-specific tuning of translation, and (ii) differential protein degradation, supported by proteomics following proteasome inhibition with lactacystin. Lactacystin impaired amastigote-to-promastigote differentiation, highlighting the importance of proteasomal activity. Overall, our analysis links Leishmania development to coordinated post-transcriptional regulatory networks. Our findings provide a powerful new resource for research programs that aim to dissect the emergent properties of regulatory networks and feedback loops underlying Leishmania stage differentiation, serving as a blueprint for other vector-borne pathogens that rely on disease-associated developmental transitions.

A dual role for PGLYRP1 in host defense and immune regulation during B. pertussis infection

cskerry@som.umaryland.edu (Ciaran Skerry) — Tue, 11 Aug 2026 00:00:00 +0000

Bordetella pertussis, the etiologic agent of whooping cough, remains a serious public health concern despite widespread vaccination. Improved therapeutics and vaccines are urgently needed. Host recognition of bacterial peptidoglycan (PGN), including B. pertussis extracellular PGN fragment tracheal cytotoxin (TCT) shapes the immune response to infection. Peptidoglycan recognition proteins (PGLYRPs) are a conserved innate immune family that bind bacterial PGN and are primarily known for bactericidal activity in mammals; however, their immune modulatory roles are beginning to gain appreciation. The role of PGLYRPs in mammalian host defenses to Gram-negative pathogens, such as B. pertussis, remains largely unknown. Here, using knockout mice, single-cell and bulk transcriptomics, and functional assays, we identify a dual role for PGLYRP1 in modulating host immune responses to B. pertussis. PGLYRP1 contributes to antibacterial responses and paradoxically dampens inflammatory responses and inhibits bacterial killing later in infection. Mechanistically, PGLYRP1 enhances NOD1 signaling in response to TCT while suppressing NOD2− and triggering receptor expressed on myeloid cells-1 (TREM-1)-mediated inflammatory pathways. TCT-bound PGLYRP1 selectively impairs TREM-1 activation compared to PGNs from other bacteria. These findings demonstrate that B. pertussis co-opts PGLYRP1 to alter immune signaling, revealing a novel immune evasion mechanism with implications for vaccine design and host-directed therapeutics.

Nanoscopy reveals heparan sulfate clusters as docking sites for SARS-CoV-2 attachment and entry

jyewdell@nih.gov (Albert J Jin) — Thu, 06 Aug 2026 00:00:00 +0000

Virus entry is thought to involve binding a unique receptor for cell attachment and cytosolic entry. For SARS-CoV-2 underlying the COVID-19 pandemic, angiotensin-converting enzyme 2 (ACE2) is widely considered the receptor for cell-surface attachment and subsequent cell entry. Using advanced light microscopy to resolve individual virions and receptors, we found instead that heparan sulfate (HS), not ACE2, mediates SARS-CoV-2 cell-surface attachment, and subsequent endocytosis. ACE2 functions only downstream of HS to enable viral genome expression. Instead of binding single HS molecules that electrostatically interact with viral surface proteins weakly, SARS-CoV-2 binds clusters of ~6–137 HS molecules projecting 60–410 nm above the plasma membrane. These tall, HS-rich clusters, present at about one per 6 μm², act as docking sites for viral attachment. Blocking HS binding with the clinically used HS-binding agent pixantrone strongly inhibited an authentic pathogen, the SARS-CoV-2 Omicron JN.1 subvariant, from attaching to and infecting human airway cells. This work establishes a revised entry paradigm in which HS clusters mediate SARS-CoV-2 attachment and endocytosis, with ACE2 acting downstream, thereby identifying HS interactions as a key anti-COVID-19 strategy. This paradigm and its therapeutic implications may apply broadly beyond COVID-19 because, analogous to SARS-CoV-2, HS binds many other viruses but is only considered an attachment regulator.

Pathogen-phage geomapping to overcome resistance

camilla.do@bcm.edu (Anthony W Maresso) — Thu, 06 Aug 2026 00:00:00 +0000

The rise of antibiotic resistance has renewed interest in bacteriophages as therapeutic alternatives. However, coevolution of phage and bacteria will naturally give rise to phage-resistant pathogens, complicating phage therapy efforts. A critical bottleneck in the production of phage therapeutics is the discovery of virulent phages against resistant pathogens. Conventional methods for discovery are time-consuming, biased, and laborious, limiting the potential for identifying suitable phage candidates. To overcome these limitations, we combined small-volume environmental sampling with 16 S rRNA sequencing to identify reservoirs where bacterial hosts co-exist with their phage predators. This strategy, which we term geographical phage mapping (geΦmapping), pinpoints ecological ‘hotspots’ for targeted phage hunting. We further developed a portable phage hunting device (ΦHD) that generates highly enriched phage concentrates directly from these reservoirs. By integrating geΦmapping with high-throughput enrichment, we constructed the RΦ library, a diverse collection of novel phages. We captured and isolated 36 new phages targeting extremely resistant organisms across various ESKAPE pathogens when conventional phage hunting and experimental evolution approaches failed.

High-throughput quantification of population dynamics using luminescence

science@maltemuetter.ch (Daniel C Angst) — Wed, 05 Aug 2026 00:00:00 +0000

Bacterial population decline at antibiotic concentrations above the minimum inhibitory concentration (MIC) remains poorly characterized. This is because colony-forming units (CFU), the standard method to quantify inhibition, are slow, labor-intensive, and costly. Luminescence assays are widely used to quantify population dynamics at subinhibitory concentrations, yet their limitations and reliability at high concentrations remain underexplored. Here, we compared luminescence- and CFU-based rates in Escherichia coli across 20 antimicrobials. In our experiments, luminescence- and CFU-based rates did not differ significantly for half of them. For the other half, CFU-based decline rates were consistently higher. The estimates differed for two main reasons: First, because light intensity tracks biomass more closely than population size, luminescence declined more slowly than the population when bacteria filamented. Second, CFU-based estimates indicated a steeper decline when treatment reduced the number of colonies formed per plated bacterium. This can result from changes in clustering behavior, physiological changes that impair culturability, or antimicrobial carryover. Thus, the suitability of luminescence to quantify bacterial decline depends on the physiological effects of the antimicrobial and whether the quantity of interest is cell number or biomass. Within these limitations, luminescence can serve as an efficient, high-throughput alternative for quantifying bacterial dynamics at super-MIC concentrations.

Apparent cooperativity between human CMV virions introduces errors in conventional methods of calculating multiplicity of infection

brent.ryckman@mso.umt.edu (Brent Ryckman) — Wed, 05 Aug 2026 00:00:00 +0000

Whether infection of cells by individual virions occurs randomly, or if there is some form(s) of competition or cooperativity between individual virions, remains largely unknown for most virus–cell associations. Here, we studied cooperativity/competition for three different strains of human cytomegalovirus (HCMV) on two different cell types (fibroblasts and epithelial cells). By titrating viral inocula concentrations in small steps over several orders of magnitude, and by using flow cytometry to precisely measure the frequency of infected cells, we found that for most virus–cell associations, the frequency of cell infection increases faster than linear with an increasing inoculum concentration, indicating cooperativity between individual infecting virions. Mathematical modeling suggests that this apparent cooperativity cannot be explained by heterogeneity in either the infectivity of the individual virions or the resistance of individual cells to infection, or by simple aggregation/clumping of viral particles. Stochastic simulations of two additional alternative models that allow for (1) reduction in cell resistance to infection when exposed to multiple virions, or (2) compensation in infectivity of poorly infectious virions when coinfecting cells with more infectious virions, resulted in apparent viral cooperativity. Analysis of other published datasets suggests the presence of apparent viral cooperativity for HIV and vaccinia virus, infecting CRFK or HeLa cells, respectively, but not for tobacco mosaic virus forming plaques on plant leaves. We thus (1) propose a methodology to rigorously evaluate apparent cooperativity of viruses infecting target cells, and (2) demonstrate that knowing the degree of virus cooperativity for any given virus–cell combination is important for an accurate quantification of multiplicity of infection.

Niche exclusion of a lung pathogen in mice with designed probiotic communities

collette2@llnl.gov (Adam P Arkin) — Tue, 04 Aug 2026 00:00:00 +0000

For years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by Burkholderia thailandensis in mice. We demonstrate that understanding of antagonistic interactions between a pathogen and airway microbiota in vitro can guide identification of probiotics with protective capabilities in vivo. Specifically, we show that niche overlap between the probiotic and pathogen is indicative of probiotic performance in vivo. This work serves as a foundation for the rational design of probiotic communities for protection against and treatment of respiratory infections.

Reprogramming of host energy metabolism mediated by the TNF-iNOS-HIF-1α axis plays a key role in host resistance to Plasmodium infection

kelycatarine@gmail.com (Diego Luis Costa) — Mon, 27 Jul 2026 00:00:00 +0000

TNF has a dual effect in Plasmodium infection, bolstering the host's immune defense while also inducing sickness behavior. Here, we confirm that TNF signaling hampers physical activity, food intake, and energy expenditure while enhancing glucose uptake by the liver and spleen, as well as controlling parasitemia in Plasmodium chabaudi (Pc)-infected mice. We also report that TNF is required for expression of inducible nitric oxide synthase (iNOS), stabilization of hypoxia-inducible factor 1α (HIF-1α), expression of glucose transporter GLUT1, and enhanced glycolysis in monocytic cells from Pc-infected mice. Importantly, Pc-infected Nos2^-/-, TNFR1 cKO, and HIF-1a cKO mice show impaired release of TNF and glycolysis in monocytes, along with increased parasitemia and disease tolerance. Altogether, our results indicate that TNF-iNOS-HIF-1α-induced glycolysis in monocytes plays a critical role in host defense and sickness behavior in Pc-infected mice.

An abundant merozoite surface protein of Plasmodium falciparum modulates susceptibility to inhibitory antibodies

danny.wilson@adelaide.edu.au (Danny W Wilson) — Mon, 27 Jul 2026 00:00:00 +0000

Malaria merozoite surface proteins (MSPs) are thought to have important roles in red blood cell (RBC) invasion and their exposure on the parasite surface makes them attractive vaccine candidates. However, their role in invasion has not been directly demonstrated and their biological functions remain unknown. One of the most abundant merozoite surface proteins is PfMSP2, a likely ancestral protein that has been maintained in the Plasmodium falciparum lineage and is a focus of vaccine development. Using CRISPR-Cas9 gene editing, we removed PfMSP2 from two different P. falciparum lines with no impact on parasite replication or phenotype in vitro, demonstrating that it is not essential for RBC invasion. Interestingly, loss of PfMSP2 led to increased inhibitory potency of antibodies targeting other merozoite proteins involved in invasion, particularly PfAMA1. In a solid-phase model, increasing concentrations of PfMSP2 protein reduced binding of different antibodies against PfAMA1 in a dose-dependent manner. These data suggest that PfMSP2 can modulate the susceptibility of merozoites to protective inhibitory antibodies. The results of this study change our understanding of the potential functions of PfMSP2 and establish a new concept in malaria where a surface protein can reduce the protective efficacy of antibodies targeting a different antigen. These findings have important implications for understanding malaria immunity and informing vaccine development.

Enteropathogenic Escherichia coli-mediated fast and coordinated Ca^²+ responses regulate NF-κB activation

guy.tranvannhieu@i2bc.paris-saclay.fr (Fangrui Guo) — Wed, 22 Jul 2026 00:00:00 +0000

Enteropathogenic Escherichia coli (EPEC) is a major bacterial enteropathogen causing infectious diarrhea among children in developing countries. Here, we found that EPEC induced isolated Ca²⁺ responses in epithelial cells, triggered by extracellular ATP (eATP). These responses were dependent on type III secretion (T3S) and down-regulated by the bacterial secreted protease EspC, consistent with eATP released by the T3S translocon pore-forming activity in host membranes. By performing high-speed Ca²⁺ imaging, we uncovered that at the onset of infection, low eATP levels triggered Ca²⁺-responses involving the whole cell but showing small amplitude and fast kinetics usually associated with local Ca²⁺ responses. The findings, supported by theoretical modeling, evoke a conceptual shift whereby low amounts of inositol 1, 4, 5-trisphosphate (IP₃) induced by low eATP levels and subsequent moderate Ca²⁺ release enable the fast coordination of IP₃ receptor cluster activation throughout the cell. Importantly, these yet undescribed coordinated fast responses occurred over prolonged time periods and defined a cell state with dampened activation of the pro-inflammatory transcriptional activator NF-kB associated with a decrease in its Ca²⁺-dependent O-linked β-N-acetylglucosamine modification.

The adaptive landscapes of three global Escherichia coli transcriptional regulators

caua.westmann@ieu.uzh.ch (Andreas Wagner) — Tue, 21 Jul 2026 00:00:00 +0000

The evolution of gene regulation is a major source of evolutionary adaptation and innovation, particularly when organisms encounter new or changing environments. Central to this process is the emergence of new transcription factor binding sites (TFBSs). Adaptive landscapes provide a powerful framework to study such emergence by linking regulatory DNA sequences to their transcriptional outputs. Although several landscapes have been characterized for DNA, RNA, and proteins, large-scale in vivo adaptive landscapes for bacterial TFBSs remain scarce. Here, we address this gap by experimentally mapping the first comprehensive in vivo regulatory landscapes for three global transcription factors in Escherichia coli: cAMP receptor protein, Fis, and IHF. Using a massively parallel reporter assay, we quantify the regulation strength of more than 30,000 TFBS variants for each factor, and reconstruct their adaptive landscapes. All three landscapes are highly rugged and exhibit pervasive epistasis, with thousands of local peaks distributed broadly across sequence space. This ruggedness contrasts sharply with the much smoother TFBS landscapes of eukaryotes. It suggests greater constraints on the evolution of prokaryotic gene regulation. Nonetheless, evolutionary simulations show that ~10% of evolving populations can reach a peak of strong regulation, a proportion that is significantly greater than in comparable random landscapes. Adaptive evolution starting from the same DNA sequence can attain different high peaks, and some peaks are reached more frequently than others. Together, our results show that de novo adaptive evolution of new gene regulation in bacteria is feasible, but subject to a blend of chance, historical contingency, and evolutionary biases.