Biology subjects

Johnston, C. D.

Publications and source records attributed to Johnston, C. D..

12 recordsLinked to original sources

bioRxiv2026

PSMε controls skin commensal CD8+ T cell activation

Upon skin colonization, the prevalent human skin commensal S. epidermidis can elicit a CD8+ T cell response that protects against pathogens or clears tumors. The microbial features that drive this response are undefined, limiting our ability to understand and predict commensal-immune crosstalk and to engineer potent commensal-derived immunotherapies. To uncover these microbial features, we harnessed both the natural variation in CD8+ T cell induction across primary human isolates of Staphylococcus and our ability to genetically manipulate these strains. Stimulatory strains exhibit increased quorum sensing activation, which turns on a unique commensal-associated gene family, called phenol-soluble modulin {varepsilon} (PSM{varepsilon}), that is required for CD8+ T cell activation. PSM{varepsilon} not only acts as the immunodominant CD8+ T cell antigen but also enhances cross-presentation in an antigen-agnostic manner. Co-delivering PSM{varepsilon} promotes CD8+ T cell priming to an exogenous antigen via a mechanism that is independent of formyl peptide receptor and co-stimulatory receptor upregulation. Thus, we demonstrate that specific aspects of microbiome-immune crosstalk can be distilled to molecular components, which engage in previously undescribed mechanisms and can be harnessed for immunotherapy without requiring live bacterial colonization.

immunology↗

bioRxiv2026

Genetic engineering of Staphylococcus haemolyticus: Overcoming Restriction-Modification Barriers and Targeting Virulence Genes

Staphylococcus haemolyticus is an emerging multidrug-resistant nosocomial pathogen noted for robust biofilm formation and complex restriction-modification (RM) systems that hinder genetic manipulation. These barriers have severely limited mechanistic studies into its pathogenesis and immune evasion. Here, we report the development of a molecular toolbox that enables precise genomic engineering of clinical S. haemolyticus isolates. Using PacBio Single Molecule Real Time (SMRT) and bisulfite sequencing, we defined the complete genomes and methylomes of nine isolates, generating a functional readout of the active RM defences present in each strain. Among the RM systems identified, a Type II (PDLC03279) and a Type III (PDL3649/PDLC03643) system were significantly overrepresented in clinical isolates, suggesting a potential role in adaptation to host or hospital-associated environments. To bypass these RM barriers, we implemented a dual strategy: first, applying SyngenicDNA-based approaches to eliminate RM target motifs from genetic tools; and second, engineering a surrogate E. coli strain (JMC4) to mimic conserved S. haemolyticus methylation patterns. These tools significantly enhanced transformation efficiency and enabled targeted knockout of four putative virulence genes (sraP, secA2, capA, and capI), as well as allelic exchange of the native capsule operon with the corresponding region from a non-encapsulated isolate. To our knowledge, this is the first report of precise genomic modifications in S. haemolyticus. The establishment of robust molecular tools for transformation and genome editing lays a foundation for future functional studies of virulence and host adaptation in this resilient opportunistic pathogen. Data summaryAll genomic data were deposited in the European Nucleotide Archive and are available in NCBI under the project accession number PRJEB2705. Supporting data are provided in supplementary data files. Accession numbers are given in Table 1. O_TBL View this table: org.highwire.dtl.DTLVardef@1706c82org.highwire.dtl.DTLVardef@1e40917org.highwire.dtl.DTLVardef@10e7d3org.highwire.dtl.DTLVardef@1e3e64corg.highwire.dtl.DTLVardef@1249b03_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONS. haemolyticus isolates used in this study. C_TABLECAPTION C_TBL Impact statementStaphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen which causes disease in vulnerable patients. Previously, genetic modification of this pathogen was prevented due to the prevalence of strain-specific restriction modification systems, which use DNA methylation to identify and foreign DNA (including plasmids) when it enters the cells, and then destroy it using restriction enzymes. We analysed the methylomes of a selection of S. haemolyticus strains and used this data to tailor molecular tools to evade the RM systems. This enabled us to improve transformation efficiency and perform genome editing, including large-scale chromosomal modifications and targeted deletion of suspected virulence genes (a first for S. haemolyticus). Beyond its immediate relevance to researchers studying this pathogen, the tools and approaches developed here have broader utility for genetic engineering of other coagulase-negative staphylococci and bacteria with similar RM barriers. Additionally, we found that two RM systems were enriched in clinical strains, suggesting they may have a function in virulence, in addition to their roles as bacterial phage defence systems.

molecular biology↗

bioRxiv2025

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

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

microbiology↗

bioRxiv2025

Complete genome sequences of Fusobacterium watanabei sp. isolates

We report the complete genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database (GTDB) indicates that Fusobacterium watanabei genomes are part of the "Fusobacterium nucleatum_J" group, which also encompasses the previously published FNU strain and Fna C1 isolates.

microbiology↗

bioRxiv2025

A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species

Gardnerella species are central to bacterial vaginosis (BV), a condition affecting nearly one in three women of reproductive age and associated with preterm birth and increased susceptibility to sexually transmitted infections. Despite decades of study, progress in defining Gardnerella diversity has been hindered by inconsistent taxonomy and poor-quality genomic resources. Here, we sequenced 392 new Gardnerella isolates from asymptomatic and BV-associated microbiota and integrated this collection with all publicly available genomes. After stringent curation, we generated a high-quality reference set of 313 distinct genomes that underpins a comprehensive taxonomic framework. Using average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomics, we resolved 21 genomic lineages encompassing 11 species and 15 subspecies, each assigned a provisional formal name. Integration of complete long-read assemblies enabled construction of the first syntenic Gardnerella pangenome, revealing lineage-specific repertoires of virulence, metabolic, and defense systems - including variable sialidases (NanH), vaginolysin, and amino-acid biosynthetic pathways - and defining conserved genomic architecture across species. Comparative methylome profiling further highlighted restriction-modification system diversity that may influence genetic exchange. Finally, we identified the first native cryptic plasmids in Gardnerella, overturning the assumption that the genus lacks plasmids, and demonstrated their use in generating a replicative E. coli-Gardnerella shuttle vector. Together, these results establish a complete genomic and functional framework for Gardnerella, providing a reproducible foundation for mechanistic and translational studies of BV and a model for resolving taxonomy and functional stratification in other urogenital-associated bacteria.

microbiology↗

bioRxiv2023

Fusobacterium sphaericum sp. nov., isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

microbiology↗

bioRxiv2022

Helicobacter pylori chronic infection selects for effective colonizers of metaplastic glands

Chronic gastric infection with Helicobacter pylori can lead to progressive tissue changes that culminate in cancer, but how H. pylori adapts to the changing tissue environment during disease development is not fully understood. In a transgenic mouse gastric metaplasia model, we found that strains from unrelated individuals differed in their ability to infect the stomach, to colonize metaplastic glands, and to induce proliferation and alter the expression of metaplasia-associated proteins. H. pylori isolates from different stages of disease from a single individual had differential ability to colonize healthy and metaplastic gastric glands. Exposure to the metaplastic environment selected for high gastric colonization by one of these strains. Complete genome sequencing revealed a unique alteration in the frequency of a variant allele of the putative adhesin sabB, arising from a recombination event with the related sialic acid binding adhesin (SabA) gene. Mutation of sabB strongly reduced adherence to both normal and metaplastic gastric tissue in multiple strain backgrounds and highly attenuated stomach colonization. Thus, the changing gastric environment during disease development promotes bacterial adhesin gene variation associated with enhanced gastric colonization. ImportanceChronic infection with Helicobacter pylori is the primary risk factor for developing stomach cancer. As disease progresses H. pylori must adapt to a changing host tissue environment that includes induction of new cell fates in the cells that line the stomach. We tested representative H. pylori isolates collected from the same patient during early and later stages of disease in a mouse model where we can rapidly induce disease-associated tissue changes. Only the later-stage H. pylori strains could robustly colonize the diseased stomach environment. We also found that the ability to colonize the diseased stomach was associated with genetic variation in a putative cell surface adhesin gene called sabB. Additional experiments revealed that SabB promotes binding to stomach tissue and is critical for stomach colonization by the late-stage strains. Thus, H. pylori diversifies its genome during disease progression and these genomic changes highlight critical factors for bacterial persistence.

microbiology↗

bioRxiv2022

The cancer chemotherapeutic 5-fluorouracil is a potent inhibitor of Fusobacterium nucleatum and its activity is modified by the intratumoral microbiota

Fusobacterium nucleatum is among the most prevalent and dominant bacterial species in colorectal cancer (CRC) tumor tissue, and growing evidence supports its role in cancer progression and poorer patient prognosis. Here we perform a small molecule inhibitor screen of 1,846 bioactive compounds against a CRC isolate of F. nucleatum and find that 15% of inhibitors are antineoplastic agents including fluoropyrimidines. Validation of these findings reveal that 5-fluorouracil (5-FU), the first-line chemotherapeutic used to treat CRC worldwide, is a potent inhibitor of F. nucleatum CRC isolates at concentrations found in serum of CRC patients treated with 5-FU. We also identify members of the intratumoral microbiota that are resistant to 5-FU, including Escherichia coli. Further, CRC E. coli isolates can modify 5-FU and relieve 5-FU toxicity towards otherwise-sensitive F. nucleatum and human CRC epithelial cells. Lastly, we demonstrate that ex-vivo CRC tumor microbiota from patients undergo different levels of community disruption after 5-FU exposure and have the potential to deplete 5-FU levels, thereby reducing local drug efficacy. Together, these observations argue for further investigation into the role that the CRC intratumoral microbiota plays in patient response to chemotherapy.

microbiology↗

bioRxiv2022

A bacterial pan-genome makes gene essentiality strain-dependent and evolvable

Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality, and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Tn-Seq, whole-genome sequencing, and RNA-Seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species pan-genome, we identify a species-wide essentialome that can be subdivided into universal, strain-specific and accessory essential genes. By employing forced-evolution experiments we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms we show that gene-essentiality can be highly influenced and/or dependent on: 1) the composition of the accessory genome; 2) the accumulation of toxic intermediates; 3) functional redundancy; 4) efficient recycling of critical metabolites; and 5) pathway rewiring. While this functional characterization underscores the evolvability-potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.

microbiology↗

bioRxiv2021

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrums chromosomal structure, pangenome and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites including one RM system hotspot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCEDolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the U.S. across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.

microbiology↗

bioRxiv2020

Photochemical probe identification of the small-molecule binding site in a mammalian membrane-bound O-acyltransferase

The mammalian membrane-bound O-acyltransferase (MBOAT) superfamily is involved in biological processes including growth, development and appetite sensing. MBOATs are attractive drug targets in cancer and obesity; however, information on the binding site and molecular mechanisms underlying small-molecule inhibition is elusive. This study reports development of a photochemical probe to interrogate the small-molecule binding site in the human MBOAT Hedgehog acyltransferase (HHAT) based on HHAT inhibitor RUSKI-201. Structure-activity relationship investigation identified the improved enantiomeric inhibitor IMP-1575, which is the most potent HHAT inhibitor reported to-date, and guided rational design of a photocrosslinking probe that maintained HHAT-inhibitory potency. Photocrosslinking and proteomic sequencing of HHAT delivered identification of the first small-molecule binding site in a mammalian MBOAT. Topology and homology data suggested a potential mechanism for HHAT inhibition which was confirmed via kinetic analysis. Our results provide an optimal HHAT inhibitor IMP-1575 (Ki = 38 nM) and a strategy for mapping of interaction sites in MBOATs.

biochemistry↗

bioRxiv2018

SyngenicDNA: stealth-based evasion of restriction-modification barriers during bacterial genetic engineering

Restriction-modification (RM) systems hinder the use of genetic approaches in the vast majority of bacteria. Here, we describe a systematic approach to adapt genetic tools for use in bacteria that are genetically intractable or poorly tractable owing to active RM defenses. In this process, we determine the genome and methylome of a bacterial strain and use this information to define the bacteriums RM target motifs. We then synonymously eliminate RM targets from the nucleotide sequence of a genetic tool in silico, synthesize an RM-silent SyngenicDNA tool and propagate the tool as novel minicircle plasmids, termed SyMPL tools, before transformation. Using SyngenicDNA and SyMPL tools, we achieved a profound, >100,000- fold, improvement in the transformation of a clinically relevant USA300 strain of Staphylococcus aureus demonstrating the efficacy of these approaches for evading RM systems. The SyngenicDNA and SyMPL approaches are effective, flexible, and should be broadly applicable in microbial genetics. We expect these will facilitate a new era of microbial genetics free of the restraints of restriction-modification barriers.

microbiology↗