Biology subjects

Palmer, K.

Publications and source records attributed to Palmer, K..

At least 19 recordsLinked to original sources

bioRxiv2026

DISRUPTION OF A DNA REPAIR PROTEIN PROMOTES ANTIBIOTIC RESISTANCE IN ACINETOBACTER BAUMANNII

Acinetobacter baumannii is a high priority Gram negative opportunistic pathogen known for its high rates of multidrug resistance (MDR). Minocycline (MIN), a tetracycline class antibiotic, is one of the most effective antibiotics for treating A. baumannii infections in patients. Unfortunately, MIN resistance is spreading internationally and has begun to emerge in the United States. While efflux pumps are correlated with MIN resistant A. baumannii, clinical data suggests alternative mechanisms of MIN resistance. To explore the genetic basis for MIN resistance in A. baumannii we employed a machine learning model to predict genetic resistance correlates from clinical isolates. Mutations in ruvB, a DNA repair protein, were strongly correlated with MIN resistant clinical strains of A. baumannii .Consistent with the prediction, tn26 insertion in ruvB in A. baumannii strain AB5075, and deletion of ruvB in strain ATCC 19606, increased MIN minimum inhibitory concentrations to a level that exceeds the MIN resistance breakpoint. RuvB complexes with RuvA and RuvC to resolve Holliday junctions during recombination. However, only ruvB mutants showed the resistance phenotype; neither ruvA nor ruvC mutants were MIN resistant, suggesting loss of the activity of the complex was not the basis for resistance. We observed ruvB mutants produced increased biomass during planktonic growth relative to the other two ruv mutants. Upon examination, the ruvB::tn26 mutant had a 451% increase in biomass and 360% thicker biofilms relative to wildtype. We determined the disruption of ruvB lead to thicker biofilms and enriched in extracellular DNA (eDNA), and DNase I treatment collapsed the enhanced biofilm phenotype and markedly reduced tetracycline class MICs. FLAG-RuvA accumulated within the biofilm matrix in the absence of RuvB, supporting a model in which RuvA contributes to stabilization of eDNA-rich structures. In a murine pneumonia model, ruvB disruption did not significantly alter survival or pulmonary burden in untreated infection but reduced bacterial dissemination and increased minocycline resistance. Together, these findings reveal an unexpected connection between Holliday junction processing, eDNA-rich biofilm architecture, and antibiotic resistance in A. baumannii.

microbiology↗

bioRxiv2026

The DUF998 family protein DrmA modulates cationic glycolipid levels and the emergence of high-level daptomycin resistance in Enterococcus faecalis

Daptomycin resistance (DAP-R) in enterococci is associated with alterations in the membrane lipid composition. The membrane-bound protein MprF is responsible for the synthesis of amino acid-modified lipids in bacteria, and these modified lipids contribute to DAP-R in some Gram-positive pathogens. In enterococci, MprF synthesizes three lysine-modified lipids: the phospholipid lysyl-phosphatidylglycerol (Lys-PG), and the newly identified cationic glycolipids lysyl-diglucosyl-diacylglycerol (Lys-Glc2-DAG) and lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG). Given the recent discovery of cationic glycolipids in enterococci, we re-examined a collection of laboratory-evolved DAP-R E. faecalis to investigate whether these lipids contribute to DAP-R. We found that levels of Lys-Glc2-DAG were strikingly reduced in DAP-R variants with high-level resistance. The dramatic alterations in Lys-Glc2-DAG levels were temporally coupled with the emergence of loss-of-function mutations in the gene drmA, which encodes a DUF998 family protein of unknown function. DrmA is a membrane protein with six predicted transmembrane helices and is widely distributed among Gram-positive and Gram-negative bacteria, including plant and animal pathogens. Complementation of the DAP-R strains with wild-type E. faecalis drmA significantly lowered their DAP MIC, reversing their trajectory to high-level DAP-R. Using genetic and lipidomic approaches in the natively DAP-sensitive strain OG1RF, we conclusively linked drmA loss-of-function with significantly reduced Lys-Glc2-DAG levels as well as a small but significant increase in Lys-PG levels. Yet, drmA inactivation in OG1RF did not alter its DAP MIC. We conclude that drmA loss-of-function confers elevated DAP MIC on the background of preceding mutations in the DAP-R evolutionary trajectory, most likely mutations in cls1. The recurrence of drmA mutations in multiple studies underscores its importance in DAP-R evolution. Overall, our work identifies a role for the DUF998 family in cellular lipid homeostasis and confirms its significant role in the evolution of DAP-R.

microbiology↗

bioRxiv2026

Isolation of bioconcrete-producing bacteria for urea-free marine applications

Concrete repair and replacement have significant environmental and economic costs. Bacteria can form bioconcrete via microbially-induced carbonate precipitation (MICP). Bioconcrete-forming bacteria can be incorporated into concrete at mixing and heal cracks where and when they occur. Bioconcrete formation is a byproduct of alterations to the local environment occurring during normal metabolic activities of bacteria. Bacteria thus "make" bioconcrete by different metabolic mechanisms, and the environment plays a substantial role in the yield and physical properties of bioconcrete produced by a given bacterium. The ureolytic bacterium Sporosarcina pasteurii is a commonly used organism for MICP, but it requires urea supplementation and generates nitrogenous waste. The marine environment is understudied for bioconcrete applications, yet self-healing structures are needed in this environment, wherein urea and nitrogenous waste would be detrimental to native biota. Here, we assessed S. pasteurii bioconcrete production under marine-like media conditions with urea and calcium supplementation. S. pasteurii generated higher bioconcrete yields in these media compared to standard medium. We then designed an enrichment protocol to isolate and characterize non-urea-requiring bioconcrete-forming bacteria from Atlantic seawater. We identified isolates from the Sulflitobacter, Marinobacter, and Bacillus genera, two of which yielded higher bioconcrete in seawater-mimicking media compared to model non-ureolytic bacteria. Scanning electron microscopy/energy dispersive spectroscopy and Fourier transform infrared spectroscopy revealed distinct chemical and structural features of bioconcrete produced by bacteria in seawater-mimicking medium. Overall, our work establishes a pipeline for the isolation and characterization of novel bioconcrete-forming bacteria from marine samples, with application to marine self-healing materials. ImportanceBacteria can stimulate the formation of calcium carbonate, referred to as bioconcrete, around their cells. Bioconcrete can be applied towards the sustainable healing of cracks in concrete structures. However, the specific chemical composition of the concrete and the environment the concrete is placed in limit the usefulness and applicability of individual bacterial species towards bioconcrete formation. Here, we focused on the marine environment, which has been less studied in the bioconcrete field relative to the terrestrial environment. We used marine-mimicking growth media to evaluate bioconcrete formation by model bacteria previously used by bioconcrete researchers as well as to isolate novel bioconcrete-forming bacteria from Atlantic seawater. Further, we used analytical chemistry and microscopy techniques to characterize the similarities and differences among the bioconcrete produced by the bacteria. Overall, we provide a framework for the isolation and characterization of bioconcrete-forming bacteria for application to sustainable infrastructure in the marine environment.

microbiology↗

bioRxiv2026

Modeling patient variants of Cnot1 and Cdc42bpb results in distinct forms of congenital diaphragmatic hernia in mice

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly characterized by impairment of both diaphragm and lung development in utero. CDH presents as a spectrum of forms and severities, with diaphragm defects arising in the dorsal/posterior region typically correlating with more severe pulmonary disease and higher risk of mortality than those appearing in ventral/anterior regions. The genetic etiology underlying CDH is complex, with many genes implicated showing variable expressivity and incomplete penetrance in both human patients and mouse models. Here we present in vivo validation of two genes previously unassociated with CDH: the CDC42-interacting kinase CDC42BPB; and CNOT1, a scaffolding protein of the CCR4-NOT protein complex, critical for mRNA regulation through modifications such as deadenylation. Each gene was found to have a damaging, de novo missense variant in a recent large-scale CDH patient sequencing screen. Loss of Cdc42bpb leads to ventral diaphragmatic hernias, heart septal defects and minor lung epithelial differentiation defects in mouse embryos. Installation of the orthologous patient-specific missense variant through CRISPR/Cas9 editing leads to less severe ventral diaphragm defects. Mouse embryos with either one or two copies of the orthologous Cnot1 variant, c.1867C>T (p.R623W), develop dorsal diaphragmatic hernias with low (<50%) penetrance, and mutants showed alterations in mRNA isoform expression consistent with the molecular role of Cnot1 in RNA splicing. These results underscore the power of in vivo functional modeling to validate genes and patient-specific variants uncovered by patient sequencing, reveal two previously unrecognized genetic causes of CDH, and highlight the heterogeneity of different patient anatomic presentations.

genetics↗

bioRxiv2025

Synthesis of perfluorooctanoic acid-containing membrane lipids by human pathobionts

Per- and polyfluoroalkyl substances (PFAS) are synthetic fluorinated compounds used widely in industrial and consumer products. They are unusually stable due to carbon-fluorine bonds and resistant to degradation, making them persistent contaminants in water, soil, and biota. PFAS are associated with adverse health effects in humans including cancer and liver disease. The effects of PFAS on human-associated bacteria are largely unexplored, a significant gap in knowledge because these bacteria are exposed to PFAS in vivo at sites including the colon and bladder. One of the best studied PFAS compounds is perfluorooctanoic acid (PFOA), an eight-carbon perfluorinated carboxylic acid whose structure is analogous to a fatty acid. Here, we cultured Enterococcus faecalis, a Gram-positive bacterium, and Pseudomonas aeruginosa, a Gram-negative bacterium, in growth medium supplemented with PFOA and corresponding control conditions and performed lipidomic analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to elucidate lipid remodeling in response to PFOA exposure. Strikingly, novel fluoroalkyl-containing membrane lipids are synthesized by both of these bacteria, with each species synthesizing unique fluoroalkyl-lipids. Moreover, a high-level daptomycin-resistant strain of E. faecalis produces strikingly high levels of fluoroalkyl-lipids, demonstrating that prior antibiotic exposure and concomitant effects on bacterial evolution can alter bacterial interactions with PFAS. Because bacterial lipids are important immunomodulators in vivo, we propose that PFAS-containing bacterial lipids may be novel mediators of host-microbe-pollutant interactions. Our results also establish a novel mechanism for the bioaccumulation of PFOA and, potentially, for bioremediation of PFOA in biological systems such as the human gastrointestinal tract.

microbiology↗

bioRxiv2025

From Chewing to Chirping: The Misophonia Audiovisual Trigger Archive (MATA)

Misophonia is an emerging condition in which everyday sounds, such as chewing, sniffing, or tapping, evoke disproportionately intense emotional and physiological responses. Despite growing recognition of its clinical significance, progress in understanding misophonia has been hindered by the limited availability of standardized and ecologically valid stimulus sets. Here, we present a large, open-access archive of 1,300 five-second audiovisual clips spanning 12 empirically validated categories of misophonic triggers. This resource extends beyond orofacial movement-related sounds to include a diverse array of real-world triggers, and its audiovisual format enables systematic investigation of how visual context shapes responses to misophonic sounds. The archive lowers the barrier for laboratories to study misophonia, promotes reproducibility across sites, and offers applications ranging from crowdsourced assessments of population-level sensitivities to machine learning approaches for automated trigger detection. By providing the largest and most diverse audiovisual misophonia stimulus repository to date, this resource is designed to accelerate mechanistic, clinical, and translational research on misophonia and related sensory-emotional phenomena.

neuroscience↗

bioRxiv2025

A compendium of adipocyte morphologies across different breast pathologies

Adipocytes are abundant in the breast tissue microenvironment. In breast cancer, they can change morphologically according to their proximity to tumour cells, with the closest becoming cancer-associated adipocytes (CAAs). It remains unclear whether breast cancer risk factors, including menopausal status, body mass index (BMI), and mammographic density (MD), influence CAAs morphology in breast carcinogenesis. This study aimed to quantify morphological differences in adipocytes across breast cancer pathologies and associated risk factors. Whole slide images of hematoxylin and eosin stained cancer (n = 149) and normal (n = 182) breast tissue samples were analysed. Parameters representative of adipocyte morphology: perimeter, area, concavity, and aspect ratio, were measured using ImageJ. Adipocytes were considered close ([≤] 2 mm) or distant (>2 mm) to cancer cells in cancer samples or breast epithelial cells in normal samples. Close adipocytes in cancer samples were designated CAAs. CAAs decreased in size compared to distant adipocytes (p [≤] 0.0001). A similar trend was observed between close and distant adipocytes in normal (p [≤] 0.0001). CAAs size increased post menopause (p [≤] 0.0001). CAAs size positively correlated with BMI (p [≤] 0.0001). In cancer cases, distant adipocyte size increased and concavity decreased with increasing MD (p [≤] 0.01). Smaller CAAs were associated with poorer survival (p [≤] 0.05). Morphological differences were identified in adipocytes dependent on location within the breast, tissue, pathology and risk factors. Understanding what drives these morphological differences could provide mechanistic insight into whether risk factor-induced alterations in adipocytes influence their role in breast carcinogenesis.

cancer biology↗

bioRxiv2025

Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harbored by Enterococcus faecalis laboratory model strains and clinical isolates

Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor; and laboratory model strains as donor versus recent human isolates as donor during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both wild-type and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared to 4-log for pCF10). Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defense, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens, and highlighting pTEF2 as a plasmid for additional mechanistic study. IMPORTANCEThe emergence of MDR bacteria, including MDR E. faecalis, limits treatment options and necessitates development of alternative therapeutics. In these circumstances, bacterial CRISPR-Cas systems are being explored by the field to develop CRISPR-based antimicrobials. However, in many cases CRISPR-Cas efficacy has only been assessed using laboratory model strains. More studies are required that investigate clinical isolates, as those are the intended targets for CRISPR antimicrobials. Here, we demonstrated how the number of plasmids harbored by an E. faecalis donor strain can affect the apparent efficacy of CRISPR-Cas anti-plasmid defense in a recipient strain. Overall, our research is important to develop improved CRISPR-based antimicrobials to combat the spread and accumulation of antibiotic resistance determinants.

microbiology↗

bioRxiv2025

Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites

SF3B1 is a core component of the spliceosome involved in branch point recognition and 3 splice site selection. SF3B1 mutation is common in myelodysplastic syndrome and other blood disorders. The most common mutation in SF3B1 is K700E, a lysine to glutamic acid change within the pre-mRNA interacting heat repeat domain. A hallmark of SF3B1 mutation is an increased use of cryptic 3 splice sites; however, the properties distinguishing SF3B1-sensitive splice junctions from other alternatively spliced junctions are unknown. We identify a subset of 192 core splice junctions that are mis-spliced with SF3B1 K700E mutation. We use our core set to test whether SF3B1-sensitive splice sites are different from control cryptic 3 splice sites via RNA structural accessibility. As a comparison, we define a set of SF3B1-resistant splice junctions with cryptic splice site use that does not change with SF3B1 K700E mutation. We find sequence differences between SF3B1-sensitive and SF3B1-resistant junctions, particularly at the cryptic sites. SF3B1-sensitive cryptic 3 splice sites are within an extended polypyrimidine tract and have lower splice site strength scores. We develop experimental RNA structure data for 83 SF3B1-sensitive junctions and 39 SF3B1-resistant junctions. We find that the pattern of structural accessibility at the NAG splicing motif in cryptic and canonical 3 splice sites is similar. In addition, this pattern can be found in both SF3B1-resistant and SF3B1-sensitive junctions. However, SF3B1-sensitive junctions have cryptic splice sites that are less structurally distinct from the canonical splice sites. In addition, SF3B1-sensitive splice junctions are overall more flexible than SF3B1-resistant junctions. Our results suggest that the SF3B1-sensitive splice junctions have unique structure and sequence properties, containing poorly differentiated, weak splice sites that lead to altered 3 splice site recognition in the presence of SF3B1 mutation.

molecular biology↗

bioRxiv2024

Biosynthesis of glucosaminyl phosphatidylglycerol in Pseudomonas aeruginosa

Glucosaminyl phosphatidylglycerol (GlcN-PG) was first identified in bacteria in the 1960s and was recently reported in Pseudomonas aeruginosa. Despite the important implications in altering membrane charge (by the modification of anionic PG with cationic glucosamine), the biosynthesis and functions of GlcN-PG have remained uncharacterized. Using bioinformatic and lipidomic analysis, we identified a 3-gene predicted operon, renamed as gpgSDF, that is responsible for the biosynthesis and potential transport of GlcN-PG in P. aeruginosa: gpgS encodes a novel glycotransferase that is responsible for the modification of phosphatidylglycerol (PG) with N-acetylglucosamine (GlcNAc) to produce GlcNAc-PG, and gpgD encodes a novel deacetylase that removes the acetyl group from GlcNAc-PG to produce GlcN-PG. The third gene, gpgF, is predicted to encode a flippase whose activity remains to be experimentally verified. A P. aeruginosa gpgD transposon mutant accumulates GlcNAc-PG and lacks GlcN-PG, and as expected, the complementation of gpgD restores the production of GlcN-PG. Moreover, the heterologous expression of gpgSDF in Escherichia coli resulted in production of both GlcNAc-PG and GlcN-PG. The identification of the biosynthetic genes of GlcN-PG paves the way for the investigation of its biological and pathological functions, which has significant implications in our understanding of the unique membrane physiology, pathogenesis and antimicrobial resistance of P. aeruginosa. ImportanceThe identification of the biosynthetic genes of GlcN-PG paves the way for the investigation of its biological and pathological functions, which has significant implications in our understanding of the unique membrane physiology, pathogenesis and antimicrobial resistance of P. aeruginosa.

microbiology↗

bioRxiv2024

A frameshift mutation in the murine Prkra gene causes dystonia and exhibits abnormal cerebellar development and reduced eIF2α phosphorylation.

Mutations in Prkra gene, which encodes PACT/RAX cause early onset primary dystonia DYT-PRKRA, a movement disorder that disrupts coordinated muscle movements. PACT/RAX activates protein kinase R (PKR, aka EIF2AK2) by a direct interaction in response to cellular stressors to mediate phosphorylation of the subunit of the eukaryotic translation initiation factor 2 (eIF2). Mice homozygous for a naturally arisen, recessively inherited frameshift mutation, Prkralear-5J exhibit progressive dystonia. In the present study, we investigate the biochemical and developmental consequences of the Prkralear-5J mutation. Our results indicate that the truncated PACT/RAX protein retains its ability to interact with PKR, however, it inhibits PKR activation. Furthermore, mice homozygous for the mutation have abnormalities in the cerebellar development as well as a severe lack of dendritic arborization of Purkinje neurons. Additionally, reduced eIF2 phosphorylation is noted in the cerebellums and Purkinje neurons of the homozygous Prkralear-5J mice. These results indicate that PACT/RAX mediated regulation of PKR activity and eIF2 phosphorylation plays a role in cerebellar development and contributes to the dystonia phenotype resulting from this mutation. Summary StatementThis study shows, for the first time, a role of reduced eIF2 phosphorylation in DYT-PRKRA and the cerebellum development in a mouse model.

molecular biology↗

bioRxiv2023

Lipid discovery enabled by sequence statistics and machine learning

Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that Streptococcus agalactiae MprF synthesizes lysyl-phosphatidylglycerol (Lys-PG) from anionic PG, and a novel cationic lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), from neutral glycolipid Glc-DAG. This unexpected result prompted us to investigate whether Lys-Glc-DAG occurs in other MprF-containing bacteria, and whether other novel MprF products exist. Here, we studied protein sequence features determining MprF substrate specificity. First, pairwise analyses identified several streptococ-cal MprFs synthesizing Lys-Glc-DAG. Second, a restricted Boltzmann machine-guided approach led us to discover an entirely new substrate for MprF in Enterococcus, diglucosyl-diacylglycerol (Glc2-DAG), and an expanded set of organisms that modify glycolipid substrates using MprF. Overall, we combined the wealth of available sequence data with machine learning to model evolutionary constraints on MprF sequences across the bacterial domain, thereby identifying a novel cationic lipid.

microbiology↗

bioRxiv2023

CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure

The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system CRISPR-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its anti-plasmid efficacy in an agricultural niche - manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach. ImportanceAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas - a bacterial defense system - to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium - Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure, and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas based strategies for control of antibiotic resistance in agricultural settings.

microbiology↗

bioRxiv2023

Characterization of the Oral Bacteriome of the Healthy Lewis Rat

Rodents are the most frequently utilized animals for in vivo research, and rats are the most abundant rodent used to study peri-implantitis disease and progression. However, there are very few studies available that elucidate the healthy oral microbiome of rats. The aim of this study was to characterize the healthy oral bacteriome of the male Lewis rat at two unique niches, the gums and first molar, by sequencing the 16S rDNA v1-v3 region. We collected the microbiota of 12 male Lewis rats at the toothless alveolar crest and the first molar, on both sides of the mouth. We identified an average of 20,820 sequences per sample. There were no significant differences between the rat groups or sample sites in the diversity ( or {beta}) of the bacteriome. A total of 359 amplicon sequence variants (ASVs) were identified in the bacteriome, correlating to the phyla Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Parallels exist at the genus level between human and rat oral bacteriomes, however, the overall diversity between comparable sites is lower in rats than humans. Similar findings were reached when using pooled or individual swab samples of rat mouths. This study characterizes two unique ecological niches within the healthy rat oral bacteriome and provides a baseline for comparison with future studies. IMPORTANCERats are frequently used for dental research, but little is known about their normal oral microbiota. Here, we use DNA sequence analysis to identify bacterial groups colonizing the rat mouth at the tooth surface and at the gums. This work contributes to our knowledge of bacterial diversity in the rat mouth.

microbiology↗

bioRxiv2022

VanRS and CroRS cross-talk revealed by coevolutionary modeling regulates antibiotic resistance in VanA-type vancomycin-resistant Enterococcus faecalis

Enterococcus faecalis is an opportunistic pathogen that can cause bacteremia and endocarditis. Previous studies have shown that concurrent treatment with cephalosporin and vancomycin antibiotics exhibit synergy in vancomycin-resistant E. faecalis to render the bacterium susceptible to antibiotic treatment whereas treatment with each antibiotic separately was not successful. Proteins responsible for mediating vancomycin and cephalosporin resistance are classified as two-component systems (TCS). TCS consist of a histidine kinase that phosphorylates a response regulator after environmental activation. These signaling networks have been shown to exhibit cross-talk interactions, and through direct coupling analysis, we identify encoded specificity between vancomycin resistance TCS, which are horizontally acquired, and cephalosporin resistance TCS, which are endogenous to E. faecalis. To verify cross-talk between these pathways is responsible for vancomycin and cephalosporin synergy, we use RNA-Seq to identify differentially expressed genes in VanA- and VanB-type vancomycin resistant enterococci after treatment with the cephalosporin antibiotic, ceftriaxone, and also with vancomycin. We find that cross-talk between VanSA and CroR in strain HIP11704 may be responsible for synergy, demonstrating that horizontally acquired TCS can have large impacts on pre-existing signaling networks. The presence of encoded specificity between exogenous TCS and endogenous TCS show that the systems co-evolve, and cross-talk between these systems may be exploited to engineer genetic elements that disrupt antibiotic resistance TCS pathways. Author SummaryBacteria may transmit genetic elements to other bacteria through the process known as horizontal gene transfer. In some enterococci, vancomycin resistance genes are acquired this way. Proteins encoded within the bacterial genome can interact with proteins acquired through horizontal gene transfer. The interaction that occurs between proteins VanSA and VanRA is known to mediate vancomycin antibiotic resistance in VanA-type vancomycin resistant enterococci (VRE), and the interaction between proteins CroS and CroR is an important pathway in cephalosporin antibiotic resistance. We show that the VanSA, which is obtained through horizontal gene transfer, inhibits CroR under treatment with antibiotics vancomycin and ceftriaxone. This interaction is responsible for the observed synergy between vancomycin and ceftriaxone in VanA-type VREs. These findings demonstrate how horizontally acquired genes may produce proteins that interrupt known protein interactions, including antibiotic resistance signaling pathways in bacteria. Furthermore, the specific mechanism found for VanA-type VREs provides a basis for engineering of horizontally acquired proteins that disrupt antibiotic resistance pathways.

microbiology↗

bioRxiv2022

Efficacy of plasmid-encoded CRISPR-Cas antimicrobial is affected by competitive factors found in wild Enterococcus faecalis isolates

Enterococcus faecalis is a leading cause of hospital-acquired infections. These infections are becoming more difficult to treat due to the increasing emergence of E. faecalis strains resistant to last resort antibiotics. Over the past decade, multiple groups have engineered the naturally occurring bacterial defense system CRISPR-Cas as a sequence-specific antimicrobial to combat antibiotic-resistant bacteria. We have previously established that the type II CRISPR-Cas system of E. faecalis can be reprogrammed as a CRISPR-Cas antimicrobial and delivered to antibiotic-resistant recipients on a conjugative pheromone-responsive plasmid. Using a co-culture system, we showed sequence-specific depletion of antibiotic resistance from E. faecalis model strains, both in vitro and in vivo. Although this and other studies have demonstrated the potential use for CRISPR-Cas as an antimicrobial, most have deployed the system against model bacterial strains. Thus, there is limited knowledge on how effective these potential therapies are against recently isolated and uncharacterized strains with limited laboratory passage, which we refer to here as wild strains. Here, we compare the efficacy of our previously established CRISPR-Cas antimicrobials against both E. faecalis model strains and wild E. faecalis fecal isolates. We demonstrate that these wild isolates can antagonize the CRISPR-Cas antimicrobial donor strain via competitive factors like cytolysin. Furthermore, we show that the wild isolates can effectively prevent delivery of the CRISPR-Cas antimicrobial plasmids, consequently avoiding CRISPR-Cas targeting. Our results emphasize the requisite to study CRISPR-Cas antimicrobials against wild strains to understand limitations and develop delivery systems that can endure competitive interspecies interactions in the gut microenvironment and effectively deliver CRISPR-Cas antimicrobials to their intended targets. IMPORTANCEEnterococcus faecalis is a major nosocomial pathogen. Traditional antibiotics continue to lose potency against these opportunistic pathogens as they become increasingly resistant to more antibiotics. We previously showed that our CRISPR-Cas antimicrobials can deplete drug resistance in or kill E. faecalis model strains. Here, we examined the efficacy of CRISPR-Cas antimicrobials against a recent collection of E. faecalis fecal isolates. We found that CRISPR-Cas delivery and efficacy is affected by competitive factors produced by the wild isolates. Our study emphasizes the need to study CRISPR-Cas antimicrobials in the context of wild bacterial isolates, which are the intended target for this potential therapy, in order to understand limitations and develop CRISPR-enhanced antimicrobials with effective clinical applications.

microbiology↗

bioRxiv2021

The extracellular matrix gene, Svep1, orchestrates airway patterning and the transition from lung branching morphogenesis to alveolar maturation in the mouse

Disruptions in airway branching or alveolar differentiation during lung development can lead to severe respiratory deficiencies and neonatal death. The molecular mechanisms governing branching patterning and early alveolar formation remain elusive. Loss of Svep1 function in mice results in various developmental defects, including lung hypoplasia and perinatal lethality. Our examination of the lungs of Svep1 knockout (Svep1-/-) mouse embryos, both in vivo and in vitro, revealed that Svep1 mutants exhibit an increase in the number of disorganized distal airway tips and progressively greater disruption of lung lobe morphology over time and saccular development. Svep1 interacts with FGF signaling to regulate smooth muscle differentiation and, together with Fgf9, guides airway branching patterning. Transcriptomic data from the lungs of Svep1-/- embryos revealed dysregulated gene expression affecting saccular maturation. Our findings demonstrate that Svep1 is a key extracellular matrix player shaping airway morphology and influencing alveolar fate. These insights offer potential avenues for therapeutic interventions in congenital lung disorders.

developmental biology↗

bioRxiv2020

Streptococcus pneumoniae, S. mitis, and S. oralis produce a phosphatidylglycerol-dependent, ltaS-independent glycerophosphate-linked glycolipid

Lipoteichoic acid (LTA) is a cell surface polymer of Gram-positive bacteria. LTA participates in host-microbe interactions including modulation of host immune reactions. It was previously reported that the major human pathogen Streptococcus pneumoniae and the closely related oral commensals S. mitis and S. oralis produce Type IV LTAs. Herein, using liquid chromatography/mass spectrometry (LC/MS)-based lipidomic analysis, we found that in addition to Type IV LTA biosynthetic precursors, S. mitis, S. oralis, and S. pneumoniae also produce glycerophosphate (Gro-P)-linked dihexosyl-diacylglycerol (DAG), which is a biosynthetic precursor of Type I LTA. Mutants in cdsA and pgsA produce dihexosyl-DAG but lack (Gro-P)-dihexosyl-DAG, indicating that the Gro-P moiety is derived from phosphatidylglycerol (PG), whose biosynthesis requires these genes. S. mitis, but neither S. pneumoniae nor S. oralis, encodes an ortholog of the PG-dependent Type I LTA synthase, ltaS. By heterologous expression analyses, we confirmed that S. mitis ltaS confers poly-(Gro-P) synthesis in both Escherichia coli and Staphylococcus aureus, and that S. mitis ltaS can rescue the severe growth defect of a S. aureus ltaS mutant. However, despite these observations, we do not detect a poly-(Gro-P) polymer in S. mitis using an anti-Type I LTA antibody. Moreover, (Gro-P)-linked dihexosyl-DAG is still synthesized by a S. mitis ltaS mutant, demonstrating that S. mitis LtaS does not catalyze the transfer of Gro-P from PG to dihexosyl-DAG. Finally, a S. mitis ltaS mutant has increased sensitivity to human serum, demonstrating that ltaS confers a beneficial but currently undefined function in S. mitis. Overall, our results demonstrate that S. mitis, S. pneumoniae, and S. oralis produce a (Gro-P)-linked glycolipid via a PG-dependent, ltaS-independent mechanism. ImportanceLTA is an important cell wall component synthesized by Gram-positive bacteria. Disruption of LTA production can confer severe physiological defects and attenuation of virulence. We report here the detection of a biosynthetic precursor of Type I LTA, in addition to the previously characterized Type IV LTA, in the total lipid extracts of S. pneumoniae, S. oralis, and S. mitis. Our results indicate that a novel mechanism is responsible for producing the Type I LTA intermediate. Our results are significant because they identify a novel feature of S. pneumoniae, S. oralis, and S. mitis glycolipid biology.

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