Biology subjects

Chakraborty, B.

Publications and source records attributed to Chakraborty, B..

18 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of the YsaN ATPase reveal dodecameric and tetradecameric assemblies in the Yersinia enterocolitica T3SS

Bacterial pathogens deploy sophisticated nanomachines such as the Type III Secretion System (T3SS) to inject effector proteins directly into host cells, thereby subverting cellular defenses and promoting infection. Central to this machinery is a conserved homo-oligomeric ATPase that fuels substrate unfolding and translocation. Despite extensive structural and biochemical studies, the precise mechanism of T3SS ATPase oligomer assembly and regulation remains incompletely understood, events crucial for the overall functionality of the T3SS. Here, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the Yersinia enterocolitica T3SS ATPase YsaN, captured in two previously uncharacterized oligomeric states, a dodecamer (12-mer) at 3.51 [A] and a tetradecamer (14-mer) at 3.80 [A] resolution. Both assemblies exhibit helical-like symmetry and conformational heterogeneity. A conserved longitudinal fissure interrupts the helical lattice and appears to mediate interconversion between the two states, while an N-terminal interface stabilized by inter-tier disulfide bonds and an extensive non-covalent network locks the assembly together. Molecular dynamics simulations reveal that ATP hydrolysis drives a global, correlated compaction upon transition to the ADP-bound state. Together, these structural, biochemical, and MD simulation data establish T3SS ATPases as dynamic, oligomerically plastic molecular motors and provide a mechanistic framework for chaperone-effector dissociation and substrate translocation.

biophysics↗

bioRxiv2026

Exploring the impact of intraspecific interaction between sibling colonies of Bacillus cereus MSM-S1 in the absence and presence of antibiotics

Bacillus cereus is a spore-forming pathogen and food contaminant that can survive in hostile environments through different survival strategies. As part of survival, B. cereus may also engage in intra- or interspecific interactions that shape its community structure and stress responses, enabling its persistence under unfavourable conditions. The present study explored intraspecific interactions, at the cell and molecular levels, between two sibling colonies of Bacillus cereus MSM-S1 grown through swarming adjacently on nutrient agar in the absence and presence of gentamicin. While growing alone, gentamicin altered the symmetrical colony morphology of B. cereus MSM-S1, which was associated with cell elongation, decreased flagellation and increased expression of the toxin gene nheA. During interaction, both in the absence and presence of gentamicin, the motility of sibling colonies towards each other was restricted, forming a distinct line/zone of demarcation between the colonies. Microscopic analysis at different time points (day 3, 5 and 7) revealed progressive changes in the swirling arrangement of cells at the interaction zone. In the absence of gentamicin, cells became jammed at the interacting front by day 7, whereas this effect was not observed in the presence of gentamicin on day 7. Cells at the interacting zone underwent gradual sporulation; notably, sporulation was less in the presence of gentamicin. Further analysis suggested that nutrient limitation was the major contributory factor for the formation of the zone of no growth between the interacting colonies. Moreover, the expression of quorum-sensing genes was down-regulated in cells at the interacting zone without gentamicin, but notably, upregulated in the presence of gentamicin. The expression of chemotaxis regulator gene, cheY, was also upregulated in interacting zone cells both in the absence and presence of gentamicin. In addition, increased expression of the global transcriptional regulator codY in the interacting zone under both conditions suggested its involvement in metabolic regulation during sibling colony interaction. The findings highlight modulated quorum sensing and sporulation as adaptive mechanisms in Bacillus cereus MSM-S1 to cope with external stress imposed by nutrient limitations caused by the growth of sibling colonies, whereas, cell elongation and toxin production together is a preferred survival strategy for a growing MSM-S1 colony when stress is imposed by gentamicin as antibiotic but sufficient nutrient is available.

microbiology↗

bioRxiv2026

Shear Strain Stiffening in Cartilage is Governed by a Mechanical Phase Transition

Large shear deformation in cartilage can lead to tissue failure and injury, which are often precursors to diseases such as post-traumatic osteoarthritis. Under shear, cartilage strain-stiffens prior to failure, which makes stiffening an important indicator of changes to the loading of the extracellular matrix that gives rise to this tissue's properties. While a variety of stiffening mechanisms ranging from uncrimping to fiber-alignment have been explored, whether such mechanisms apply to the depth dependent shear strain stiffening in articular cartilage remains poorly understood. Here, we present experiments and theory that support the idea that the strain-stiffening behavior is caused by a mechanical phase transition from a random isotropic network whose mechanics arise primarily from bending-dominated modes to one where the mechanics arise from stretching-dominated modes. Indeed, consistent with network model predictions, we find that stress-strain data for all depths can be collapsed onto a single universal curve that diverges at a depth-dependent critical strain. These results show that increasing the local concentration of collagen, which constitutes the primary load-bearing network in cartilage, decreases the critical strain at which the strain-stiffening transition occurs, while increasing the low-strain elastic modulus. Furthermore, we demonstrate that bulk compression leads to a higher critical strain and decreased low-strain elastic modulus. Network simulations capture this rich behavior, and indicate that under compression the network collapses, which allows for larger strains before the transition from bending-dominated to stretching-dominated mechanics occurs. Collectively, these findings shed light on the roles that tissue composition and axial strain play in the mechanisms that organize how articular cartilage stiffens during the lead-up to injury.

biophysics↗

bioRxiv2025

Dietary methionine restriction primes T cell metabolism for activation and tumor inhibition and enhances the efficacy of immune checkpoint blockade

The proliferation of many cancer cells is methionine dependent and dietary methionine restriction (MR) has shown anti-tumor effects in a wide variety of immunodeficiency preclinical models. Yet, whether MR exerts an anti-tumor effect in the presence of an immune-competent background remains inconclusive. Accumulating evidence has shown an essential role of methionine in immune cell differentiation and function. Thus, competition for methionine between tumor cells and immune cells in the tumor microenvironment may drive tumor growth and tumor response to therapy. Here, we aim to define the impact of MR on tumor growth and associated immunity. We first assessed the effect of MR in a series of immunocompetent mouse models of melanoma, colorectal cancer, breast cancer, and lung. MR led to a broad tumor inhibition effect across these models and such tumor inhibition was not sex-or genetic background-dependent but appears to be fully or partially immune-dependent. Through flow cytometry analysis, we found a consistent increase in intratumoral activated CD8+ T cells across different tumor models and depletion of CD8+ T cells partially or completely reversed MR-induced tumor inhibition in a model dependent manner. Interestingly in young healthy non-tumor-bearing mice, MR increased spleen CD3+ and CD8+ T cell populations. Metabolomics and RNAseq analysis of spleen-derived CD8+ T cells revealed significant increase in purine metabolism and amino acid metabolism and that are in line with the metabolic feature of activated T cells. Furthermore, MR improved the efficacy of anti-PD1 immune checkpoint blockade. Together, MR primes T cell metabolism for its anti-tumor effect and improves the efficacy of anti-PD1 checkpoint blockade.

cell biology↗

bioRxiv2025

FeSBCP Analogue from Cyanobacteria: Insights from in vitro and in silico Studies

The blue light responsive Cryptochrome/Photolyase Family harbours two important photoactivatable proteins - cryptochromes and photolyases. While cryptochromes are essentially photoreceptors with diverse biological activities including circadian rhythm, photolyases repair UV damaged cyclobutane pyrimidine dimers (CPD) or (6-4) pyrimidine-pyrimidone photoadducts. Both cryptochromes and photolyases share a common Photolyase Homology Region (PHR) where they harbour a light harvesting antenna chromophore and redox-active flavin di-nucleotide (FAD). Even though photolyases do not possess an extension in the C-terminal region unlike cryptochromes, a recent discovery of FeS cluster containing bacterial cryptochrome-photolyase proteins (FeSBCPs) present an interesting retreat from the conventional photolyase architecture. They possess an additional modular redox center, [4Fe4S] iron-sulfur cluster connected by conserved cysteine residues. Herein, we characterize a cyanobacterial FeSBCP from Cyanobium sp. using tools from bioinformatics, biochemistry and biophysics. Sequence analysis reveals substitution in the well-conserved aromatic residues, meant for electron transfer. In silico modeling and docking supported by electrophoretic mobility shift assay as well as spectroscopic measurements do suggest efficient binding and repair of CyPhrB to damaged single/double-stranded substrates containing 6-4 photolesion. Considering FeS clusters established roles in DNA binding/repair activities, we speculate the role of FeS clusters in FeSBCPs and existence of FeS-FAD-DNA triangle towards efficient electron transfer.

biochemistry↗

bioRxiv2024

Estrogens increase cancer cell efferocytosis to establish an immunosuppressive tumor microenvironment

Phagocytic clearance of apoptotic cancer cells (efferocytosis) by tumor-associated macrophages (TAMs) contributes in a substantial manner to the establishment of an immunosuppressive tumor microenvironment. This puts in context our observation that the female steroid hormone 17{beta}- estradiol (E2) facilitates tumor immune resistance through cancer cell extrinsic Estrogen Receptor (ER) signaling in TAMs. Notable was the finding that E2 induces the expression of CX3CR1 in TAMs to enable efferocytosis of apoptotic cancer cells which results in the suppression of type I interferon (IFN) signaling. Mechanistically, E2 facilitates calcium-dependent activation of the transcription factor NFATC1, which in turn induces CX3CR1 expression. This drives macrophage polarization towards an immune-suppressive state, increasing the ability of TAMs to engulf pro- inflammatory apoptotic cancer cells. Genetic or pharmacological inhibition of the E2/ER/CX3CR1 axis reversed the efferocytic activity of TAMs, rescued E2-dependent suppression of type I IFN signaling, and potentiated intratumoral adaptive immune cell function. Efferocytosis following radiation-induced cancer cell apoptosis limits the efficacy of radiation therapy. Importantly, we determined that preconditioning with either ER-directed endocrine therapies or CX3CR1 inhibition enhanced the antitumor efficacy of radiation therapy by reversing macrophage suppression and reviving intratumoral T cell activation. Our work defines the mechanisms by which E2 increases the efferocytotic activity of TAMs to establish an immunosuppressive tumor microenvironment and demonstrates how this process can be reversed with endocrine therapies which target ER.

cancer biology↗

bioRxiv2024

Loss of KDM6A-mediated genomic instability and metabolic reprogramming differentially regulates responses to immune checkpoint therapy and chemotherapy in bladder cancer.

Mutations in genes encoding critical epigenetic regulators are frequently noted in bladder cancer, however, the impact of these mutations on therapeutic efficacy is unclear. One of the most common driver mutations in bladder cancer occurs in the KDM6A gene, which encodes a histone demethylase that promotes gene transcription. Retrospective analyses of patients with bladder cancer demonstrated that KDM6A mutations correlate with improved overall survival (OS) with immune checkpoint therapy (ICT), while they are associated with lower OS in patients undergoing cisplatin-based chemotherapy. Mechanistic studies utilizing CRISPR-Cas9 mediated deletion of Kdm6a showed reduced expression of DNA mismatch repair (MMR) and DNA double-stranded base repair (DSBR) genes in tumor cells with improved response to anti-PD-1 therapy and attenuated sensitivity to cisplatin-based chemotherapy in preclinical models of bladder cancer. Additionally, the loss of Kdm6a-mediated reduction in glycolysis and intratumoral lactate accumulation impaired histone 3 lysine 9 lactylation (H3K9la) and histone 3 lysine 18 lactylation (H3K18la) in Tregs with concurrent decrease in the expression of key genes including Foxp3, Tgfb and Pdcd1 and their immune-suppressive function. Further, reduced expansion of PD-1hi Tregs improved the ratio of cytotoxic T cells to Tregs and response to anti-PD-1 therapy in Kdm6a deficient tumor-bearing mice. Collectively, this study provided key insights into the role of KDM6A-mediated epigenetic regulation of DNA repair and metabolic reprogramming which potentially govern response to chemotherapy and ICT thus highlighting the utility of KDM6A mutation status for patient stratification and development of personalized treatment algorithms.

immunology↗

bioRxiv2023

Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity, or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remains an open question. Here we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic and in vitro citrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping and denovo assembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups. IMPORTANCETooth decay is the most common preventable chronic disease, globally affecting more than two billion people. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of ADS activity among oral bacteria in a community context remains an open question. In the current study, we use a multi-omics approach to document the pervasiveness of expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.

microbiology↗

bioRxiv2023

Intragroup sociality drives individual participation in intergroup competition in an urban-dwelling nonhuman primate

There is significant variability in the extent to which individuals from group-living species participate in intergroup competition (IGC) over resources. Such variability may be particularly robust in human-impacted environments, wherein anthropogenic resources may strongly impact intergroup overlap and competition. Examining the socio-ecological causal factors driving these differences can shed new lights on animals costs-benefits trade-offs driving engagement in such interactions. Here we use (peri)urban-dwelling rhesus macaques (Macaca mulatta) as model-systems to examine how individual differences in socio-ecological characteristics (i.e., animals sex, rank, and affiliative connections) may influence propensities to participate in IGC in anthropogenic environments. We found that participation was strongly influenced by individuals affiliative connections. Interestingly, monkeys with more coalitionary support partners had higher IGC participation, but this was more pronounced for individuals that are more peripheral in their proximity and multilayer affiliative networks, compared to more socially central individuals. Moreover, males and low-ranking individuals were more likely to participate in IGC. Our findings suggest that differential access to socio-ecological resources likely drives IGC participation. The evaluation of such inter-individual differences in socio-ecological flexibility and decision-making in dynamic environments is critical for future research related to the links between behavioural ecology, health outcomes, and human-wildlife co-existence in anthropogenic landscapes.

animal behavior and cognition↗

bioRxiv2023

Histone Lactylation Drives CD8 T Cell Metabolism and Function

The activation and functional differentiation of CD8 T cells are linked to metabolic pathways that result in the production of lactate. Lactylation is a lactate-derived histone post-translational modification (hPTM); however, the relevance of histone lactylation in the context of CD8 T cell activation and function is not known. Here, we show the enrichment of H3K18-lactylation (H3K18la) and H3K9-lactylation (H3K9la) in human and murine CD8 T cells which act as transcription initiators of key genes regulating CD8 T cell phenotype and function. Further, we note distinct impacts of H3K18la and H3K9la on CD8 T cell subsets linked to their specific metabolic profiles. Importantly, we demonstrate that modulation of H3K18la and H3K9la by targeting metabolic and epigenetic pathways regulates CD8 T cell effector function including anti-tumor immunity in preclinical models. Overall, our study uncovers the unique contributions of H3K18la and H3K9la in modulating CD8 T cell phenotype and function intricately associated with metabolic state.

immunology↗

bioRxiv2023

Case report on lethal dog attacks on adult rhesus macaques (Macaca mulatta) in an anthropogenic landscape

For nonhuman primates living in anthropogenic areas, predation by larger predators is relatively rare. However, smaller predators such as free-ranging as well as domesticated dogs can shape the socioecology of urban nonhuman primates, directly by attacking and predating upon them, or indirectly by modifying their activity patterns. Here, we describe 3 (2 potentially lethal) cases of dog attacks on adult rhesus macaques inhabiting an anthropogenic landscape in Northern India, and the circumstances surrounding these incidents. We discuss the importance of considering the presence of dogs while studying nonhuman primate populations across the anthropogenic gradient and its implications for understanding how human presence can directly and indirectly affect predator-prey relationship in these areas, as well as its potential role in modifying group social dynamics as well as in transmission of zoonotic agents.

animal behavior and cognition↗

bioRxiv2023

Ca2+/Calmodulin Dependent Protein Kinase Kinase-2 (CaMKK2) promotes Protein Kinase G (PKG)-dependent actin cytoskeletal assembly to increase tumor metastasis

Triple-negative breast cancers (TNBCs) tend to become highly invasive early during cancer development. Despite some successes in the initial treatment of patients diagnosed with early-stage localized TNBC, the rate of metastatic recurrence remains high with poor long-term survival outcomes. Here we show that elevated expression of the serine/threonine-kinase, Calcium/Calmodulin (CaM)-dependent protein kinase kinase-2 (CaMKK2), is highly correlated with tumor invasiveness. We determined that genetic disruption of CaMKK2 expression, or inhibition of its activity, disrupted spontaneous metastatic outgrowth from primary tumors in murine xenograft models of TNBC. High-grade serous ovarian cancer (HGSOC), a high-risk, poor-prognosis ovarian cancer subtype, shares many genetic features with TNBC, and importantly, CaMKK2 inhibition effectively blocked metastatic progression in a validated xenograft model of this disease. Probing the mechanistic links between CaMKK2 and metastasis we defined the elements of a new signaling pathway that impacts actin cytoskeletal dynamics in a manner which increases cell migration/invasion and metastasis. Notably, CaMKK2 increases the expression of the phosphodiesterase PDE1A which decreases the cGMP-dependent activity of protein kinase G1 (PKG1). This inhibition of PKG1 results in decreased phosphorylation of Vasodilator-Stimulated Phosphoprotein (VASP), which in its hypophosphorylated state binds to and regulates F-actin assembly to facilitate contraction/cell movement. Together, these data establish a targetable CaMKK2-PDE1A-PKG1-VASP signaling pathway that controls cancer cell motility and metastasis. Further, it credentials CaMKK2 as a therapeutic target that can be exploited in the discovery of agents for use in the neoadjuvant/adjuvant setting to restrict tumor invasiveness in patients diagnosed with early-stage TNBC or localized HGSOC.

cancer biology↗

bioRxiv2019

Heart Rate n-Variability (HRnV) and Its Application to Risk Stratification of Chest Pain Patients in the Emergency Department

BackgroundChest pain is one of the most common complaints among patients presenting to the emergency department (ED). Causes of chest pain can be benign or life threatening, making accurate risk stratification a critical issue in the ED. In addition to the use of established clinical scores, prior studies have attempted to create predictive models with heart rate variability (HRV). In this study, we proposed heart rate n-variability (HRnV), an alternative representation of beat-to-beat variation in electrocardiogram (ECG) and investigated its association with major adverse cardiac events (MACE) for ED patients with chest pain. MethodsWe conducted a retrospective analysis of data collected from the ED of a tertiary hospital in Singapore between September 2010 and July 2015. Patients >20 years old who presented to the ED with chief complaint of chest pain were conveniently recruited. Five to six-minute single-lead ECGs, demographics, medical history, troponin, and other required variables were collected. We developed the HRnV-Calc software to calculate HRnV parameters. The primary outcome was 30-day MACE, which included all-cause death, acute myocardial infarction, and revascularization. Univariable and multivariable logistic regression analyses were conducted to investigate the association between individual risk factors and the outcome. Receiver operating characteristic (ROC) analysis was performed to compare the HRnV model (based on leave-one-out cross-validation) against other clinical scores in predicting 30-day MACE. ResultsA total of 795 patients were included in the analysis, of which 247 (31%) had MACE within 30 days. The MACE group was older and had a higher proportion of male patients. Twenty-one conventional HRV and 115 HRnV parameters were calculated. In univariable analysis, eleven HRV parameters and 48 HRnV parameters were significantly associated with 30-day MACE. The multivariable stepwise logistic regression identified 16 predictors that were strongly associated with the MACE outcome; these predictors consisted of one HRV, seven HRnV parameters, troponin, ST segment changes, and several other factors. The HRnV model outperformed several clinical scores in the ROC analysis. ConclusionsThe novel HRnV representation demonstrated its value of augmenting HRV and traditional risk factors in designing a robust risk stratification tool for patients with chest pain at the ED.

bioengineering↗

bioRxiv2019

Exploring novel probiotic mechanisms of Streptococcus A12 with functional genomics

Health-associated biofilms in the oral cavity are composed of a diverse group of microbial species that can foster an environment that is less favorable for the outgrowth of dental caries pathogens, like Streptococcus mutans. A novel oral bacterium, designated Streptococcus A12, was previously isolated from supragingival dental plaque of a caries-free individual, and was shown to interfere potently with the growth and virulence properties of S. mutans. Here, we apply functional genomics to begin to identify molecular mechanisms used by A12 to antagonize, and to resist the antagonistic factors of, S. mutans. Using bioinformatics, genes that could encode factors that enhance the ability of A12 to compete with S. mutans were identified. Selected genes, designated as potential competitive factors (pcf), were deleted. Certain mutant derivatives showed a reduced capacity to compete with S. mutans compared to the parental strain. The A12 pcfO mutant lost the ability to inhibit comX-inducing peptide (XIP) signaling by S. mutans, while mutants in the pcfFEG locus were impaired in sensing of, and were more sensitive to, the lantibiotic nisin. Loss of PcfV, annotated as a colicin V biosynthetic protein, resulted in diminished antagonism of S. mutans. Collectively, the data provide new insights into the complexities and variety of factors that affect biofilm ecology and virulence. Continued exploration of the genomic and physiologic factors that distinguish commensals from truly beneficial members of the oral microbiota will lead to a better understanding of the microbiome and new approaches to promote oral health.\n\nImportanceAdvances in defining the composition of health-associated biofilms have highlighted the important role for beneficial species in maintaining health. Comparatively little, however, has been done to address the genomic and physiological basis underlying the probiotic mechanisms of beneficial commensals. In this study, we explored the ability of a novel oral bacterial isolate, Streptococcus A12, to compete with the dental pathogen Streptococcus mutans, using various gene products with diverse functions. A12 displayed enhanced competitiveness by: i) disrupting intercellular communication pathways of S. mutans, ii) sensing and resisting antimicrobial peptides, and iii) producing factors involved in the production of a putative antimicrobial compound. Research on the probiotic mechanisms employed by Streptococcus A12 is providing essential insights into how beneficial bacteria may help maintain oral health, which will aid in the development of biomarkers and therapeutics that can improve the practice of clinical dentistry.

microbiology↗

bioRxiv2019

Amino Sugars Modify Antagonistic Interactions between Commensal Oral Streptococci and Streptococcus mutans

N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 of Streptococcus gordonii against the caries pathogen Streptococcus mutans. Here we examine how amino sugars affect the interaction of five low-passage clinical isolates of abundant commensal streptococci with S. mutans utilizing a dual-species biofilm model. Compared to glucose, growth on GlcN or GlcNAc significantly reduced the viability of S. mutans in co-cultures with most commensals, shifting the proportions of species. Consistent with these results, production of H2O2 was increased in most commensals when growing on amino sugars, and inhibition of S. mutans by Streptococcus cristatus, Streptococcus oralis, or S. gordonii was enhanced by amino sugars on agar plates. All commensals except S. oralis had higher arginine deiminase activities when grown on GlcN, and in some cases GlcNAc. In ex vivo biofilms formed using pooled cell-containing saliva (CCS), the proportions of S. mutans were drastically diminished when GlcNAc was the primary carbohydrate. Increased production of H2O2 could account in large part for the inhibitory effects of CCS biofilms. Surprisingly, amino sugars appeared to improve mutacin production by S. mutans on agar plates, suggesting that the commensals have mechanisms to actively subvert antagonism by S. mutans in co-cultures. Collectively, these findings demonstrate that amino sugars can enhance the beneficial properties of low-passage commensal oral streptococci and highlight their potential for moderating the cariogenicity of oral biofilms. SIGNIFICANCEDental caries is driven by dysbiosis of oral biofilms in which dominance by acid-producing and acid-tolerant bacteria results in loss of tooth mineral. Our previous work demonstrated the beneficial effects of amino sugars, GlcNAc and GlcN, in promoting the antagonistic properties of a health-associated oral bacterium, Streptococcus gordonii, in competition with the major caries pathogen Streptococcus mutans. Here we investigated 5 low-passage clinical isolates of the most common streptococcal species to establish how amino sugars may influence the ecology and virulence of oral biofilms. Using multiple in vitro models, including a human saliva-derived microcosm biofilm, experiments showed significant enhancement by at least one amino sugar in the ability of most of these bacteria to suppress the caries pathogen. Therefore, our findings demonstrated the mechanism of action by which amino sugars may affect human oral biofilms to promote health.

microbiology↗

bioRxiv2018

Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci

Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oral Streptococcus isolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented ten species: S. australis, A12-like, S. cristatus, S. gordonii, S. intermedius, S. mitis, S. oralis including S. oralis subsp. dentisani, S. parasanguinis, S. salivarius, and S. sanguinis. Mean ADS activity and antagonism on Streptococcus mutans UA159 were measured for each isolate, and each isolate was whole genome-shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species but not by phenotype. GWAS identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species-specific. Probiotic strains must be carefully selected based on characterization of each strain, and not based on inclusion within a certain species.\n\nImportanceRepresentative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics share those characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anti-caries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotype and anti-caries phenotypes of strains from ten species of oral Streptococci and demonstrate poor correlation between genotype and phenotype across all species.

microbiology↗

bioRxiv2017

Systemic Inflammation Mediates the Relationship between Obesity and Health Related Quality of Life

BackgroundAt the population level, obesity has been reported to be positively associated with low-level chronic inflammation, and negatively associated with several indices of health-related quality of life (HRQOL). It is however not clear if obesity-associated inflammation is partly responsible for the observed negative associations between obesity and HRQOL. The present study investigates this question by testing the hypothesis that systemic inflammation is a mediator of the observed association between obesity and a specific HRQOL index called \"healthy days\", as measured via a subset of the CDC HRQOL-4 questionnaire.\n\nMethodsDemographic, body mass index (BMI), C-reactive protein (CRP), inflammatory disease status, medication use, smoking, and HRQOL data were obtained from NHANES (2005-2008) and analyzed using sampling-weighted generalized linear models. Both main effects and interaction effects were analyzed to evaluate possible mediator-outcome confounding. Model robustness was tested via sensitivity analysis. Prior to model development, data was subjected to multiple imputation in order to mitigate information loss from survey non-response. Averaged results from the imputed datasets were reported in the form of odds ratios (OR) and confidence intervals (CI).\n\nResultsObesity (BMI >30kg/m2) was positively associated with poor physical healthy days (OR: 1.59, 95% CI: 1.15-2.21) in unadjusted models. Elevated and clinically raised levels of the inflammation marker CRP were also positively associated with poor physical healthy days (OR= 1.61, 95% CI: 1.23-2.12, and OR= 2.45, 95% CI: 1.84-3.26, respectively); additionally clinically raised CRP was positively associated with mental unhealthy days (OR= 1.66, 95% CI: 1.26-2.19). The association between obesity and physical HRQOL was rendered non-significant in models including CRP. Association between elevated and clinically raised CRP and physical unhealthy days remained significant even after adjustment for obesity or inflammation-modulating covariates (OR= 1.36, 95% CI :1.02-1.82, and OR= 1.75, 95% CI: 1.21-2.54, respectively).\n\nConclusionsSystemic inflammation is a significant mediator of the association between obesity and physical unhealthy days. and is also an independent determinant of physical and mental unhealthy days. Importantly, elevated inflammation below the clinical threshold is also negatively associated with physical healthy days and may warrant more attention from a population health perspective than currently appreciated.

epidemiology↗

bioRxiv2017

Electron microscopy reveals unique nano forms of bacterial spores

Endospore formation under environmental stress conditions is a well-established phenomenon for members of bacterial phylum Firmicutes, among which the most well studied ones belong to genus Bacillus and Clostridium. So far, known sizes of the spores are all larger than 500 nm. Nano-forms of bacteria have been reported but the notion still remains controversial. In this study, we provide visual evidences of living nano-entities (named here as nano-spores) formed by a bacterial species Bacillus cereus under prolonged stress, which are capable of escaping though standard sterile filtration procedure. The existence of nano-forms of bacteria was initially identified in a yeast ribosome preparation. We further demonstrate the transformation of the nano-spores into mature cells upon nutrient supply. Our study not only demonstrates the ability of bacteria to get transformed into yet-unknown form in order to survive under harsh environment, but also brings to light the existence of the smallest possible form of life.

microbiology↗