Biology subjects

Avraham, R.

Publications and source records attributed to Avraham, R..

14 recordsLinked to original sources

bioRxiv2026

Antibiotics drive immunometabolic rewiring of human immune responses

Antibiotics are routinely evaluated for their antimicrobial activity, potential host toxicity, and disruption of the microbiome. Certain antibiotics can also impact cell-intrinsic host processes, including evolutionarily conserved processes in the mitochondria. These raise the possibility that antibiotics can directly impact host immunity, which relies on mitochondrial function for their immunometabolic activation. However, the immunological consequences of most antibiotics in current use have not been systematically examined. Here, we performed a comprehensive analysis of the effects of clinically used antibiotics on activation of primary human immune cells. We uncovered an underappreciated antibiotic-specific modulation of immune function in healthy individuals and infectious disease patients. Focusing on the immunomodulatory antibiotic ciprofloxacin, we found altered mitochondrial gene expression across multiple immune populations, driving distinct, lineage-specific responses and heightened sensitivity of T-cells. Ciprofloxacin impaired primary human T-cell expansion and activation and altered mitochondrial function and metabolism. We further demonstrated immunomodulatory effects of selected antibiotics in response to inactivated bacteria and during live viral infection. Finally, to test the implications of our findings in vivo, we showed that immune activation is altered shortly after a single dose of antibiotic administration in mice. This work established a widespread impact of antibiotics on immune-cell function, and identified mitochondrial perturbation as one underlying mechanism, with implications for host-pathogen interactions and antimicrobial therapy.

immunology↗

bioRxiv2026

Image-based transposon screening reveals a flavin reductase that restrains intracellular Salmonella replication in macrophages

Intracellular bacterial pathogens can survive and replicate within host cells, yet an isogenic population follows divergent fates: some bacteria are killed, some arrest growth, and others replicate to high numbers. Identifying the bacterial functions behind each fate requires recovering mutants from within the host cells displaying it. But systematic approaches, such as transposon insertion analysis, can only estimate fitness of mutants from the whole infected population. Here, we developed an approach that couples a genome-wide mutagenesis library to image-enabled cell sorting (ICS), sorting infected cells by the number of bacteria they contain and assigning mutants to defined replication outcomes. We applied this approach to Salmonella enterica serovar Typhimurium (S.Tm) in macrophages, and revealed genes required for replication from genes that restrain it, whose disruption increased replication. Among the latter we identified the cytosolic flavin reductase Fre, which supplies reduced flavins to a broad range of bacterial processes. We uncovered a mechanism whereby loss of fre protected S.Tm from oxidative and nitrosative damage and increased bacterial numbers. Inside macrophages this advantage was mediated by the upregulation of the iron-sulfur-independent cytochrome bd-I oxidase. By resolving a mutant library into phenotypically defined subpopulations, this framework can be applied to characterize bacterial or host genes that drive infection phenotypes in any infection model.

microbiology↗

bioRxiv2026

Epithelial innate immune sensing of pneumococci is inherently restricted to a small cellular minority across species and infection niches

Streptococcus pneumoniae colonises the nasopharynx asymptomatically yet causes life-threatening invasive disease. How it navigates early epithelial immune surveillance to cause disease remains unclear. Conventional innate immune models predict coordinated, population-wide epithelial responses to bacterial infection. Using single-cell RNA sequencing, RNA fluorescence in situ hybridization and in vivo mouse and zebrafish models, pneumococcal infection is instead shown to activate innate immune genes including chemokine, NF-{kappa}B regulatory, and prostaglandin pathway genes, in only 1-4% of lung epithelial cells. This restriction is seemingly pneumococcal-specific as Escherichia coli triggers responses in over 40% of the same cells. Strikingly, nasopharyngeal epithelial cells show complete immune silence to pneumococci while responding robustly to E. coli and Staphylococcus aureus, suggesting niche-specific immune evasion. Additionally, pharmacological inhibition of COX-2 significantly increased mortality in a zebrafish meningitis model, identifying prostaglandin signalling as a protective host response during invasive disease. Competence-associated surface remodelling contributes modestly and incrementally to immune restriction, while the predominant dampening is competence-independent. These findings challenge canonical epithelial immunity models against bacterial infection and provide a cellular framework for understanding pneumococcal commensalism and pathogenesis. Significance statementClassical innate immune models predict that bacterial infection triggers coordinated, population-wide transcriptional responses across the epithelium. Using single-cell RNA sequencing, RNA fluorescence in situ hybridization, and in vivo zebrafish and mouse models, we show that Streptococcus pneumoniae, responsible for over one million deaths annually, activates innate immune genes in only 1-4% of lung epithelial cells. Escherichia coli triggers responses in over 40% of the same cells, demonstrating this restriction is pneumococcal-specific. Nasopharyngeal epithelial cells, the bacteriums primary colonization niche, show complete immune silence to pneumococci, suggesting niche-specific evolutionary adaptation. The prostaglandin pathway is identified as a protective host response during invasive disease. These findings challenge canonical models of epithelial immunity and provide a cellular framework for pneumococcal commensalism and pathogenesis.

microbiology↗

bioRxiv2026

Single-cell transcriptome imaging reveals conserved and virulence-linked phenotypic states in bacteria

Single-cell phenotypic diversity underlies fundamental bacterial behaviors. Resolving this heterogeneity at scale while maintaining sensitive detection remains a central challenge. Here, we address this gap by combining the strengths of single-molecule fluorescence in situ hybridization (smFISH) and transcriptome-wide sequencing. We present par2FISH, a framework for discovering transcriptionally defined subpopulations across conditions by multiplexing tens of thousands of smFISH reactions. Through comparative single-cell transcriptomics in Escherichia coli and Salmonella, we uncover conserved and species-specific patterns of heterogeneity, including mutually exclusive states, coordinated metabolic specialization, and differential activation of virulence programs. We further obtain complete transcriptomes for selected subpopulations using marker-based cell sorting and RNA-sequencing (FACS-RNA-seq). This integrated strategy paves the way for exposing bacterial phenotypic landscapes and the environmental, physiological, and evolutionary factors that shape them.

microbiology↗

bioRxiv2025

Learning the DNA syntax of human microbiomes to infer health and disease

The human microbiome is a key factor in human health and alterations in community structure are associated with diverse pathological conditions. However, defining universal criteria to distinguish healthy from altered microbiome configurations remains challenging due to inter- and intra-individual variability, database-dependent approaches, and the complexity of analyzing numerous microbial features simultaneously. Here, we developed an approach that learns the syntax of the entire DNA of human microbial communities, using Sequence-Informed GC-normalized 4-mers (SIG-mers) that feed into statistical and machine learning frameworks. We identified distinct SIG-mer signatures that differentiate microbiomes of body sites across diverse healthy human populations. These signatures reveal both global microbiome shifts and individual-specific dynamics in response to antibiotic treatments and in chronic inflammatory disease. Leveraging machine learning models, we inferred health- and disease-associated microbiome states from SIG-mer profiles, capturing the degree of perturbation and disease severity. Our findings highlight SIG-mer profiling as a robust, unbiased and broadly applicable approach for personalized microbiome diagnostics and guiding therapeutic interventions.

microbiology↗

bioRxiv2025

Hypoxia-related immune subsets induced by Salmonella Typhi infection link early bacterial gut invasion to human infection outcomes

Salmonella Typhi (S. Typhi), the causative agent of typhoid disease, remains a major public health concern. Owing to the human-restricted nature of S. Typhi, current studies of typhoid pathogenesis in animal models are limited to a murine non-typhoidal pathogen. Furthermore, human studies are limited to analyses of peripheral immune responses which are blind to tissue-specific immunity and do not allow perturbations. What is now needed is an integrative approach that will provide mechanistic insights into S. Typhi pathogenesis and immune correlates of infection outcome. Here, we performed an integrated single-cell analysis of immune responses from the human S. Typhi challenge model and mouse model of typhoid disease, to associate biological mechanism with human infection outcome. Most prominent, we revealed immune subsets with a hypoxia-related signature in circulating immune cells from individuals that develop disease in the human challenge model. This signature was also evident in the mouse model in activated macrophages infiltrating into the Peyers patches, but not during infection with a mutant strain impaired for gut invasion. We further identified hypoxia-related signature as a general immune correlate of disease outcome in other infection- and inflammatory-related diseases. Collectively, using integrated analysis of mouse and human infection models, we revealed a hypoxia-related signature that link immune responses during bacterial invasion to increased risk of developing typhoid disease in humans, suggesting a possible causative role during the development of typhoid disease.

immunology↗

bioRxiv2024

Early and Delayed STAT1-Dependent Responses Drive Local Trained Immunity of Macrophages in the Spleen

Trained immunity (TI) is the process wherein innate immune cells gain functional memory upon exposure to specific ligands or pathogens, leading to augmented inflammatory responses and pathogen clearance upon secondary exposure. While the differentiation of hematopoietic stem cells (HSCs) and reprogramming of bone marrow (BM) progenitors are well-established mechanisms underpinning durable TI protection, remodeling of the cellular architecture within the tissue during TI remains underexplored. Here, we study the effects of peritoneal Bacillus Calmette-Guerin (BCG) administration to find TI-mediated protection in the spleen against a subsequent heterologous infection by the Gram-negative pathogen Salmonella Typhimurium (S.Tm). Utilizing single cell RNA-sequencing and flow cytometry, we discerned STAT1-regulated genes in TI-associated resident and recruited splenic myeloid populations. The temporal dynamics of TI were further elucidated, revealing both early and delayed myeloid subsets with time-dependent, cell type-specific STAT1 signatures. Using lineage tracing, we find that tissue-resident red pulp macrophages (RPM), initially depleted by BCG exposure, are restored from both tissue-trained, self-renewing macrophages and from bone marrow-derived progenitors, fostering long lasting local defense. Early inhibition of STAT1 activation, using specific JAK-STAT inhibitors, reduces both RPM loss and recruitment of trained monocytes. Our study suggests a temporal window soon after BCG vaccination, in which STAT1-dependent activation of long-lived resident cells in the tissue mediates localized protection.

immunology↗

bioRxiv2023

Monocyte-derived microglia with Dnmt3a mutation cause motor pathology in aging mice

Microglia are established in embryogenesis forming a self-containing cellular compartment resisting seeding with cells derived from adult definitive hematopoiesis. We report that monocyte-derived macrophages (MoM{Phi}) accumulate in the brain of aging mice with distinct topology, including the nigrostriatum and medulla, but not the frontal cortex. Parenchymal MoM{Phi} adopt bona fide microglia expression profiles. Unlike microglia, these monocyte-derived microglia (MoMg) are due to their hematopoietic origin targets of clonal hematopoiesis (CH). Using a chimeric transfer model, we show that hematopoietic expression of DNMT3AR822H, a prominent mutation in human CH, renders MoMg pathogenic promoting motor deficits resembling atypical Parkinsonian disorders. Collectively, these data establish in a mouse model that MoMg progressively seed the brains of aging healthy mice, accumulate in selected areas, and, when carrying a somatic mutation associated with CH, can contribute to brain pathology.

immunology↗

bioRxiv2023

Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation

Bacteria undergo cycles of growth and starvation, to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. While high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individual Salmonella cells using Fluorescence In-Situ Hybridization (rRNA-FISH). During the transition from exponential to stationary phase we measured a dramatic decrease in rRNA numbers only in a subpopulation, resulting in a bimodal distribution of cells with high and low rRNA content. We showed that the two subpopulations are phenotypically distinct when subjected to nutritional upshifts. Using a transposon screen coupled with rRNA-FISH, we identified two mutants acting on rRNA transcription shutdown and degradation, that abolished the formation of the subpopulation with low rRNA content. Our work suggests that Salmonella employs a bet-hedging strategy in regulating ribosomal levels that may be beneficial for survival.

microbiology↗

bioRxiv2022

Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks

Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA-sequencing (scRNA-seq) are increasingly used to study the host factors underlying diverse cellular phenotypes. But current approaches do not permit the simultaneous unbiased study of both host and bacterial factors during infection. Here, we developed scPAIR-seq, an approach to analyze both host and pathogen factors during infection by combining multiplex-tagged mutant bacterial library with scRNA-seq to identify mutant-specific changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We developed a pipeline to independently analyze redundancy between effectors and mutant-specific unique fingerprints, and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.

microbiology↗

bioRxiv2022

Bacterial lifestyle switch in response to algal metabolites

Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we profiled bacterial transcriptomes in response to infochemicals derived from algae in exponential and stationary growth, which induced the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. We found that algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. In the pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and many transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7, and negated the DMSP-inducing lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological status of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during the interactions. Significance StatementMicroorganisms in the marine environment play crucial roles in the regulation of Earths climate and elemental cycling. Understanding microbial interactions and the metabolic exchange that drives them is necessary for disentangling the complexity of the marine ecosystem. Here we demonstrate how the opportunistic pathogen Sulfitobacter D7 switches its lifestyle from coexistence to pathogenicity in response to metabolites released by Emiliania huxleyi, a bloom-forming unicellular alga. By mapping bacterial transcriptional profiles, we show that the algal metabolite dimethylsulfoniopropionate (DMSP), an important signaling molecule in the marine environment, is essential for the bacterial lifestyle switch. However, the activity of DMSP depended on additional algal signals. This work emphasizes how metabolic crosstalk can influence the nature and fate of microbial interactions, which have cascading effects on large-scale oceanic processes.

microbiology↗

bioRxiv2021

scRNA-seq Reveals A Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella

Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population defined by unique molecular features, but the implications to their function during infection is unknown. Here, we applied high resolution kinetic analysis using microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe an eclipse like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue resident red pulp macrophages. A second phase involved bacterial growth mediated by intracellular replication within a macrophage population we termed CD9 macrophages, that originate from non-classical monocytes. Nr4a1e2-/- mice, specifically depleted of non-classical monocytes but not other mononuclear cells, are more resistant to S.Tm infection. Our study underscores a cell-type specific host-pathogen interaction that determines early infection growth dynamics and has implications to the infection outcome of the entire organism.

immunology↗

bioRxiv2020

A single dose of recombinant VSV-{triangleup}G-spike vaccine provides protection against SARS-CoV-2 challenge

The COVID-19 pandemic caused by SARS-CoV-2 that emerged in December 2019 in China resulted in over 7.8 million infections and over 430,000 deaths worldwide, imposing an urgent need for rapid development of an efficient and cost-effective vaccine, suitable for mass immunization. Here, we generated a replication competent recombinant VSV-{Delta}G-spike vaccine, in which the glycoprotein of VSV was replaced by the spike protein of the SARS-CoV-2. In vitro characterization of the recombinant VSV-{Delta}G-spike indicated expression and presentation of the spike protein on the viral membrane with antigenic similarity to SARS-CoV-2. A golden Syrian hamster in vivo model for COVID-19 was implemented. We show that vaccination of hamsters with recombinant VSV-{Delta}G-spike results in rapid and potent induction of neutralizing antibodies against SARS-CoV-2. Importantly, single-dose vaccination was able to protect hamsters against SARS-CoV-2 challenge, as demonstrated by the abrogation of body weight loss of the immunized hamsters compared to unvaccinated hamsters. Furthermore, whereas lungs of infected hamsters displayed extensive tissue damage and high viral titers, immunized hamsters lungs showed only minor lung pathology, and no viral load. Taken together, we suggest recombinant VSV-{Delta}G-spike as a safe, efficacious and protective vaccine against SARS-CoV-2 infection.

microbiology↗

bioRxiv2020

Antiviral activity of Glucosylceramide synthase inhibitors against SARS-CoV-2 and other RNA virus infections

The need for antiviral drugs is real and relevant. Broad spectrum antiviral drugs have a particular advantage when dealing with rapid disease outbreaks, such as the current COVID-19 pandemic. Since viruses are completely dependent on internal cell mechanisms, they must cross cell membranes during their lifecycle, creating a dependence on processes involving membrane dynamics. Thus, in this study we examined whether the synthesis of glycosphingolipids, biologically active components of cell membranes, can serve as an antiviral therapeutic target. We examined the antiviral effect of two specific inhibitors of GlucosylCeramide synthase (GCS); (i) Genz-123346, an analogue of the FDA-approved drug Cerdelga(R), (ii) GENZ-667161, an analogue of venglustat which is currently under phase III clinical trials. We found that both GCS inhibitors inhibit the replication of four different enveloped RNA viruses of different genus, organ-target and transmission route: (i) Neuroinvasive Sindbis virus (SVNI), (ii) West Nile virus (WNV), (iii) Influenza A virus, and (iv) SARS-CoV-2. Moreover, GCS inhibitors significantly increase the survival rate of SVNI-infected mice. Our data suggest that GCS inhibitors can potentially serve as a broad-spectrum antiviral therapy and should be further examined in preclinical and clinical trial. Analogues of the specific compounds tested have already been studied clinically, implying they can be fast-tracked for public use. With the current COVID-19 pandemic, this may be particularly relevant to SARS-CoV-2 infection. One Sentence SummaryAn analogue of Cerdelga(R), an FDA-approved drug, is effective against a broad range of RNA-viruses including the newly emerging SARS-CoV-2.

microbiology↗