Size matters: Anaerobic granules exhibit distinct ecological and physico-chemical gradients across biofilm size

Anaerobic biological decomposition of organic matter is ubiquitous in Nature wherever anaerobic environments prevail, and is catalysed by hydrolytic, fermentative, acetogenic, methanogenic, and various other groups. It is also harnessed in innovative ways in engineered systems that may rely on small (0.1-4.0 mm), spherical, anaerobic granules. These biofilms are crucial to the operational success of a range of widely applied engineered-ecosystems designed for wastewater treatment. The structure and function of granule microbiomes underpin their utility. Here, granules were separated into ten size fractions (proxies for age), hypothesizing that small granules are 'young' and larger ones are 'old'. Gradients were observed across size in terms of volatile solids, density, settleability, biofilm morphology, methanogenic activity, and profiles of extracellular polymeric substances, suggesting ongoing development of physico-chemical characteristics as granules develop. Short-read amplicon sequencing indicated a negative relationship between granule size and community diversity. Furthermore, as size increased, the methanogenic archaea dominated the microbiome. Small granules were found to harbour a sub-group of highly specific taxa, and the identification of generalists and specialists may point to substantial resilience of the microbiome. The findings of this study indicate opportunities for precision management of wastewater treatment systems. They suggest that size is an important indicator for aggregate utility - size may, indeed, determine many of the characteristics of both the individual-granule microbiomes and the overall function of a wastewater treatment system.

Bacterial clustering biomaterials as anti-infective therapies

In Nature, bacterial clustering by host-released peptides or nucleic acids is an evolutionarily conserved immune defense strategy employed to prevent adhesion of pathogenic microbes, which is prerequisite for most infections. Synthetic anti-adhesion strategies present as non-lethal means of targeting bacteria and may potentially be used to avoid resistance against antimicrobial therapies. From bacteria-agglutinating biomolecules discovered in nature to synthetic designs involving peptides, cationic polymers and nanoparticles, the modes of actions appear broad and unconsolidated. Herein, we present a critical review and update of the state-of-the-art in synthetic bacteria-clustering designs with proposition of a more streamlined nomenclature and classification. Overall, this review aims to consolidate the conceptual framework in the field of bacterial clustering and highlight its potentials as an avenue for discovering novel antibacterial biomaterials.

Fusarium oxysporum NAD+ hydrolase FonNADase1 is essential for pathogenicity and inhibits plant immune responses

Plants use nicotinamide adenine dinucleotide (NAD+) as a key signaling molecule to activate immune responses. However, whether pathogens secrete specific NAD+ hydrolases (NADases) to affect plant NAD+ levels for infection remains unclear. Here, we report the function and possible mechanism of fungal NADases in watermelon Fusarium wilt fungus Fusarium oxysporum f. sp. niveum (Fon) pathogenicity. Fon secretes two NADases, FonNADase1 and FonNADase2, both of which harbor a secretory signal peptide and an NADase-active tuberculosis necrotizing toxin (TNT) domain. FonNADase1 and FonNADase2 are not involved in the growth, development, or stress responses of Fon. Moreover, only FonNADase1 is essential for Fon pathogenicity, and FonNADase1 deletion results in decreased invasive growth and spread within watermelon plants. FonNADase1 and FonNADase2 are functional NADases capable of decreasing plant NAD+ levels and FonNADase1 inhibits INF1- and BAX-induced cell death and chitin-triggered immune responses in Nicotiana benthamiana leaves in an NADase activity-dependent manner. Furthermore, FonNADase1 inhibited INF1- and BAX-induced expression of defense genes, such as NbPR1a, NbPR2, NbLOX, NbERF1, NbHIN1, and NbHSR203J, in N. benthamiana leaves and affected the expression of a set of immunity-associated genes in watermelon plants. These findings suggest that FonNADase1 plays a key role in Fon pathogenicity by affecting fungal invasive growth and spread within plants as well as modulating host immune responses, thus highlighting the critical role of fungal NADases in pathogenicity.

Pediatric blepharokeratoconjunctivitis: A challenging ocular surface disease

Pediatric blepharokeratoconjunctivitis (PBKC) is a chronic and recurrent ocular surface inflammatory disorder affecting children in early life. It is frequently under- or late- diagnosed, representing a potential cause of severe visual morbidity worldwide. An expert panel consensus recently agreed on its definition and proposed diagnostic criteria for suspected and definitive PBKC to reduce confusion and avoid varied terminology previously used in the literature, improving early and precise diagnosis. Previous evidence has pointed to the role of the adaptive immune system in recognizing and handling antigenic eyelid bacterial products, particularly from the cell wall, and the direct toxic and inflammatory effects of their cytolytic exotoxins on the ocular surface. PBKC is a frequent referral in pediatric and cornea clinics characterized by a history of recurrent chalazia, blepharitis, meibomian gland dysfunction, conjunctival hyperemia, phlyctenules formation, and corneal infiltrates with vascularization and scarring. The latter is a major cause of significant visual loss and amblyopia. Current treatment strategies aim to control inflammation on the ocular surface, halt disease progression, and avoid corneal involvement. Further research on pathogenic mechanisms will shed light on novel potential therapeutic strategies. Awareness of PBKC should enhance early diagnosis, prompt adequate treatment, and improve outcomes. We compile current evidence on epidemiology, pathophysiology, clinical spectrum of disease, diagnostic criteria, and management strategies for PBKC.

Participation of a cysteine tetrad in the recycling mechanism of methionine sulfoxide reductase A from radiation-tolerant Deinococcus bacteria

Methionine oxidation leads to the formation of methionine sulfoxide (MetO), which is reduced back to Met by methionine sulfoxide reductases (Msrs). The catalytic mechanism used by A-type Msr (MsrA) for MetO reduction requires a catalytic cysteine (Cys), which is converted to a sulfenic acid. In general, two resolving Cys are required for the regeneration of the catalytic Cys forming two consecutive disulfide bridges, the last one being efficiently reduced by thioredoxin (Trx). Here, we performed the biochemical characterization of MsrA from Deinococcus deserti. It possesses four Cys, two present in the active site motif (18 and 21) and two distal ones (53 and 163). We produced MsrA variants mutated for these cysteines and analyzed their capacity to reduce MetO in the presence of the NADPH-Trx reductase/Trx system, their ability to form heterodimers with Trxs, and their redox status after incubation with MetO. We show that all four Cys are involved in the regeneration process of enzyme activity by Trx. After MetO reduction by Cys18, a first disulfide bridge is formed with Cys21. A second disulfide involving Cys21 with either Cys53 or Cys163 is reduced by Trx, and a third Cys53-Cys163 disulfide can be formed and also reduced by Trx. These findings highlighting for the first time the involvement of a Cys tetrad in the catalytic and regeneration mechanisms for a MsrA are placed in a structural context by performing 3D modelling and discussed in relation to the known recycling mechanisms involving a Cys triad.

Broad-spectrum antiviral ferruginol analog affects the viral proteins translation and actin remodeling during dengue virus infection

Dengue virus infection is the most important arbovirosis around the world. To date, no antiviral drugs have been approved for its treatment. Host-targeted antivirals (HTA) have emerged as a promising strategy, because of their high barrier to resistance. Using plaque-forming unit assays, molecular docking, fluorescence microscopy, image analysis, and molecular/cellular assays, it was found that 18-(phthalimide-2-yl)-ferruginol, a semi-synthetic analog of the bioactive diterpenoid ferruginol, couples with high affinity to RhoA GTPase. In addition, this molecule dramatically reduced actin filament formation and induced cellular morphological changes, when added to cell cultures before or after infection, without effect on microtubules or intermediate filaments. RhoA activation in infected cells was affected when the compound was added after 6 h.p.i. Furthermore, this compound decreased dengue virus-2 (DENV-2) E protein, NS3 protein, and dsRNA as measured by fluorescence microscopy, and changes in the distribution pattern of these viral components. 18-(phthalimide-2-yl)-ferruginol treatment at 6 and 12 h.p.i. reduces the virus yield. Western blot and RT-qPCR assays reveal that this analog decreased viral protein translation. Flow cytometry and wound-healing experiments also hint that cellular effects prompted for this compound do not relate to early apoptotic events and they could be reversible. Overall, our findings strongly suggest that 18-(phthalimide-2-yl)-ferruginol has an HTA mechanism, possibly disrupting the polyprotein translation of DENV-2 via alteration of RhoA-mediated actin remodeling and other related cellular and viral processes.

Stabilizing Mutations Enhance Evolvability of BlaC β-lactamase by Widening the Mutational Landscape

Antimicrobial resistance is fueled by the rapid evolution of β-lactamases. However, a gain of new enzyme activity often comes at the expense of reduced protein stability. This evolutionary constraint is often overcome by the acquisition of stabilizing mutations that compensate for the loss of stability invoked by new function mutations. Here, we report three stabilizing mutations (I105F, H184R, and V263I) in BlaC, a serine β-lactamase from Mycobacterium tuberculosis. Using a severely destabilized variant as a template for random mutagenesis and selection, these three mutations emerged together and were able to fully restore resistance toward the antibiotic carbenicillin. In vitro characterization shows that all three mutations increase chemical and thermal stability, which leads to elevated protein levels in the periplasm of Escherichia coli. We demonstrate that the introduction of stabilizing mutations substantially enhances the evolvability of the enzyme. These findings illustrate the important role of stabilizing mutations in enzyme evolution by alleviating function-stability trade-offs and broadening the accessible evolutionary landscape.

Antibiofilm capacity of PMMA surfaces: A review of current knowledge

The emergence of microorganisms resistant to antimicrobial therapies, associated with the decline in the development of new drugs, including antibiotics, antifungals, and antivirals, highlights the need for alternative strategies to combat microorganisms that cause infections, especially multidrug-resistant bacteria. Polymethylmethacrylate (PMMA) is a material widely used in the biomedical field, with uses ranging from surgical implants, bone cements, and dental devices, to laboratory equipment and three-dimensional models for surgical planning. Despite its multiple applications, PMMA has the disadvantage of favoring microbial adhesion, due to the porous nature of the material, associated with poor bond strength, thermal instability and water sorption in the oral environment, which can contribute to infection development. To mitigate this problem, the scientific community is looking to modify PMMA to give it antimicrobial properties. This review presents possible approaches that include changes to the topography of PMMA, creating textured or nanostructured surfaces, and chemical modifications, such as incorporating antimicrobial agents into the PMMA matrix or surface treatments. Both strategies aim to hinder the adhesion and growth of microorganisms. In addition, combining these approaches seeks a synergistic effect and could become a promising mechanism for preventing infections.

Prevalence of Clostridium perfringens in sheep (Ovis aries) and goat (Capra hircus) populations across Asia: A systematic review and meta-analysis

South Asia, East Asia, and Southeast Asia have consistently been the regions with the highest prevalence of Clostridium perfringens in sheep and goats. Given the significant economic importance of sheep and goats in these regions and the potential threat posed by this pathogen, a thorough investigation of the prevalence of C. perfringens in sheep and goats throughout Asia is important to inform the development of robust and effective regulatory measures to prevent its spread among sheep and goats. In this study, we conducted a systematic review and meta-analysis in accordance with the PRISMA guidelines to quantitatively estimate the prevalence of C. perfringens in sheep and goats. Through extensive searches of eligible studies in electronic databases, 29 studies were identified. The pooled prevalence estimate was 38.8 % (95 %CI: 30.9-46.9), with type A showing the highest prevalence. Additionally, the results of the subgroup analysis indicated that the prevalence of C. perfringens in sheep and goats varied based on factors such as age, sample type, sample size, vaccination status, and sampling time. These findings emphasise the need for vaccination and ongoing surveillance to mitigate the risk of C. perfringens-associated outbreaks.

Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules

Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.

Engineering proteins with catechol chemistry for biotechnological applications

Developing proteins with increased chemical space by expanding the amino acids alphabet has been an emerging technique to compete for the obstacle encountered by their need in various applications. 3,4-Dihydroxyphenylalanine (L-DOPA) catecholic unnatural amino acid is abundantly present in mussels foot proteins through post-translational modification of tyrosine to give a strong adhesion toward wet rocks. L-DOPA forms: bidentate coordination, H-bonding, metal-ligand complexes, long-ranged electrostatic, and van der Waals interactions via a pair of donor hydroxyl groups. Incorporating catechol in proteins through genetic code expansion paved the way for developing: protein-based bio-sensor, implant coating, bio-conjugation, adhesive bio-materials, biocatalyst, metal interaction and nano-biotechnological applications. The increased chemical spaces boost the protein properties by offering a new chemically active interaction ability to the protein. Here, we review the technique employed to develop a genetically expanded organism with catechol to provide novel properties and functionalities; and we highlight the importance of L-DOPA incorporated proteins in biomedical and industrial fields.

Structural investigation of vitamin K epoxide reductase domain-containing protein in Leptospira species: a potential target for the development of new leptospirosis treatments as an alternative to antibiotics

Leptospirosis is a worldwide zoonosis caused by the motile bacterium Leptospira. This disease can cause hemorrhagic symptoms, multi-visceral and renal failures, resulting in one million cases and approximately 60,000 deaths each year. The motility of Leptospira is highly involved in its virulence and is ensured by the presence of two flagella in the periplasm. Several proteins that require the formation of disulfide bridges are essential for flagellar function. In Leptospira, these redox reactions are catalysed by the vitamin K epoxide reductase domain-containing protein (VKORdcp). The aim of the present work was to study the conservation of VKORdcp among Leptospira species and its interactions with putative substrates and inhibitor. Our results evidenced the presence of ten amino acids specific to either pathogenic or saprophytic species. Furthermore, structural studies revealed a higher affinity of the enzyme for vitamin K1 quinone, compared to ubiquinone. Finally, characterisation of the binding of a potential inhibitor revealed the involvement of some VKORdcp amino acids that have not been present in the human enzyme, in particular the polar residue D114. Our study thus paves the way for the future development of Leptospira VKORdcp inhibitors, capable of blocking bacterial motility. Such molecules could therefore offer a promising therapeutic alternative to antibiotics, especially in the event of the emergence of antibiotic-resistant strains.

Deciphering the distribution and types of Multicopper oxidases in Basidiomycota fungi

Multicopper oxidases (MCOs) comprise different types of enzymes widely distributed in nature with quite diverse functions. Laccases are the most interesting MCOs from a biotechnological point of view, particularly those secreted by ligninolytic Basidiomycota fungi due to their versatility to oxidize lignin and a variety of aromatic substrates. The term "laccase" has been broadly (but sometimes erroneously) applied due to their low sequence homology and some overlapping activities with other MCO groups. We examined the distribution and phylogenetic relationships of MCOs in Basidiomycota fungi aiming to provide a complete and precise picture of the different MCO types across the division, including fungal orders phylogenetically distant from those typically studied. The phylogenetic tree revealed eight clusters of MCOs, each sharing common sequence/structural features. With this information we classified the MCOs in eight groups and described their distinctive amino acid residues. These eight MCO types are: laccases (LAC), ferroxidases (FOX), laccase-ferroxidases (LAC-FOX), ascorbate oxidases (AO), fungal pigment MCOs, and three new groups of laccase-like enzymes or "atypical laccases" related to but different from laccases sensu stricto, namely novel laccases (NLAC), new MCO (NMCO) and new laccases with potential ferroxidase activity (NLF). Additionally, several MCOs already described in the literature were reclassified into the updated groups.

Comprehensive method for isolation and functional characterization of bacterial vesicles from human biological samples

Bacterial vesicles (BVs) are membrane-bound extracellular vesicles (EV) released from bacteria. They are known to play crucial role in bacterial communication, host-pathogen interactions, transfer of virulence factors, contribute to immune modulation and are the key players in microbial pathogenesis and survival in the host. Despite their significance, isolation and investigating BVs from human samples remains challenging, necessitating an easy, reliable and reproducible protocol. BVs have been limited due to methodological difficulties in isolating them from host-derived EVs, and the existing knowledge primarily relies on bacteria cultured under controlled laboratory conditions. This study presents a method, where we can identify the enriched BVs and characterizing them from plasma and stool samples of healthy individuals. Blood and fecal samples were collected, processed to density gradient ultracentrifugation to isolate and enrich BVs. Morphological characterization was performed using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA). Further, molecular markers OmpA (BV marker) was used to differentiate from host EVs (Alix as marker) using Western blot. Further the BV fraction was analyzed for LPS and LTA using ELISA. To understand functional relevance, BVs proteomics was performed from BV enriched plasma and stool using mass spectrometry from healthy individuals. The enriched BVs were also co-cultured with healthy peripheral blood mononuclear cells, labelled with Pkh26 dye and analysed at different time points for mRNA expression of candidate genes involved in immune regulation by qRT-PCR. Both TEM and NTA confirmed the presence of BVs, with sizes ranging from 25 nm to 250 nm. The western blot analysis revealed the fractions 6-9 are enriched with host EVs with the presence of Alix and fractions 10-13 contains BVs with the presence of OmpA. Interestingly, the proteomic analysis identified 439 proteins associated with plasma-derived BVs and 327 in stool-derived BVs, with 300 common to both. The Gene ontology and KEGG pathway analysis revealed the majority of proteins associated were immune regulation, cell activation, binding, and catalytic activity. Next, the functional assays indicated BVs were uptaken by PBMCs within 10 mins and it upregulated Toll-like receptor 2 (TLR-2) expression within 30 min. Hence, study establishes a reliable method to identify enriched BV population from human samples. Revealed the proteins associated with BVs in healthy individuals and their role in immune regulation. These findings may provide a platform to investigate BVs potential for diagnostic and therapeutic applications in various diseases.

Targeting motility of Listeria monocytogenes: Alternative strategies to control foodborne illness

Listeria monocytogenes, a gram-positive facultative anaerobic bacterium, demonstrates remarkable adaptability to various environmental stressors in food processing environments. It can survive and grow under extremely challenging environmental conditions such as low pH and temperatures, high salinity, and UV radiation. Its ability to generate biofilms at multiple stages of the food processing chain poses significant food safety issues. This bacterium is known for causing severe listeriosis, making it a major problem in microbiology and food safety. L. monocytogenes relies on motility to explore surfaces, attach, and build biofilms. It comprises actin-based motility, which is used for cell-to-cell propagation inside host tissues, and flagellar-driven motility, which assists in surface colonization and infection spread. Flagellar motility also plays an important function in increasing virulence throughout infection cycles. L. monocytogenes motility is regulated by a complex network of regulatory proteins that govern the expression of motility-associated genes. These proteins directly impact pathogenicity by influencing motility and biofilm formation, as well as an indirect impact via regulatory pathways. Efforts to control L. monocytogenes infections and decrease food safety impact include a variety of procedures. Natural compounds, synthetic agents, nanomaterials, and conjugates have emerged as intriguing options for inhibiting motility, disrupting biofilm formation, and reducing virulence. These strategies focus on vital elements of the L. monocytogenes life cycle and pathophysiology to improve food safety and public health. This review provides a comprehensive discussion of the regulatory mechanisms governing L. monocytogenes motility, emphasizing their role in pathogenicity, and explores potential strategies for attenuating the motility and virulence properties. Understanding these mechanisms is essential for developing targeted therapeutic approaches against L. monocytogenes infections and improving food safety practices.

Controlling the carbon flux between glycolysis and the pentose phosphate pathway via targeted protein degradation in Corynebacterium glutamicum

Controlling the carbon flux is important for efficient production of value-added chemicals using microbial cell factories. In this study, we developed a system to control the carbon flux in Corynebacterium glutamicum via targeted protein degradation. We employed an SspB-dependent protein degradation system targeting the SsrA tag and applied it to control the carbon flux. First, we selected a degradation tag efficiently recognized by the ClpXP protease in C. glutamicum using green fluorescent protein (GFP) as a model protein. Among the four tags examined in this study, a mutant SsrA tag with DAS residues from Escherichia coli resulted in specific GFP degradation only when the adaptor SspB was induced in C. glutamicum. Next, we applied this system to control the carbon flux. We selected phosphoglucoisomerase (PGI) encoded by pgi, as a target protein, to control the carbon flux between glycolysis and pentose phosphate pathway (PPP) and 1,5-diaminopentane as a model product to evaluate this control system. Compared with the parental strain, the specific growth rate of the engineered strain decreased by 36 %, whereas the yield and production rate of 1,5-diaminopentane increased by 193 % and 70 %, respectively. This is the first report on the application of a protein degradation system to control carbon flux in C. glutamicum. The system developed in this study can be widely applied for designing C. glutamicum cell factories for efficient production of varied value-added chemicals.

In Vitro Activity of Bacteriophages Against Ocular Methicillin-resistant S. aureus Isolates Collected in the US

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of sight-threatening infections in the US. These strains pose a significant challenge in managing ocular infections, as they frequently exhibit resistance to first-line empirical antibiotics. To assess the potential of bacteriophages as innovative topical therapies for treatment of recalcitrant ocular infections, we evaluated the in vitro antimicrobial activity of a set of anti-S. aureus phages against a collection of ocular MRSA clinical isolates collected in the US.

METHODS

The host range of six phages (V4SA2, V1SA9, V1SA12, V1SA19, V1SA20 and V1SA22) was assessed using the spot assay on a panel of 50 multidrug-resistant (MDR) ocular MRSA isolates selected to be representative of clones circulating in the US. Subsequently, liquid culture-based host range assay was performed for the three most active phages using different multiplicity of infection (MOI of 10-2, 1 or 100 phages/bacteria).

RESULTS

In total, 90.0% of bacterial isolates were susceptible to at least one of the six phages. The spot host range assay showed that phages V1SA19, V1SA20 and V1SA22 had the broadest spectrum, being active against 86%, 84% and 82% of the isolates, respectively, including the MDR-MRSA CC5 and the community-associated CC8 lineages. A phage dose effect was observed across the liquid culture-based host range assay.

CONCLUSION

Phages V1SA19, V1SA20 and V1SA22 exhibited high antimicrobial activity against ocular MRSA. Bacteriophages represent a promising anti-infective strategy in ophthalmology that could be explored for improved topical therapy of recalcitrant MRSA infections.

Phytopathogenic fungi and oomycetes causing diseases in Theobroma cacao: Chemical and genetic features

Phytopathogenic fungi (PF) and oomycetes (Oo) represent some of the most significant plant pathogens globally, causing extensive damage and economic losses in the chocolate tree, Theobroma cacao. This review aims to elucidate the molecular mechanisms behind cacao-PF/Oo interactions, with a particular emphasis on virulence factors. Despite their importance, the secondary metabolites (SMs) produced during controlled interactions between PF, Oo, and T. cacao remain underexplored. We have conducted a comprehensive review of the most critical PF and Oo species that infect T. cacao and highlighted the agricultural relevance of their SM chemistry. This investigation analyzes peer-reviewed papers from electronic databases PubMed, MDPI, ScienceDirect, Google Scholar, and SCOPUS. Through this analysis, we identify gaps in the current understanding and propose potential directions for future research. This includes a deeper investigation into the role of SMs in pathogen virulence, which could inform the development of more effective disease management strategies.

Advantages in orthopaedic implant infection diagnostics by additional analysis of explants

PURPOSE

Implant-associated infections are the most challenging complication in orthopaedics and trauma surgery as they often lead to long courses of illness and are a financial burden for the healthcare system. There is a need for fast, simple, and cheap identification of pathogens but the ideal detection method was not found yet. The work aims to test whether the detection of pathogens culturing the removed implant is more successful than from simultaneously taken tissue samples or punction fluid.

METHODS

Implants were removed due to infection, irritation, or loosening. Tissue samples and joint fluids were processed for bacterial growth in sterile conditions. Samples were incubated and checked for growth. Bacterial identification and antibiotic sensitivity testing were performed. Data were anonymized, and statistical analysis was done using Excel and SAS, employing tests like Shapiro-Wilk, Mann-Whitney-U, and Kruskal-Wallis. Ethical approval was obtained for this study.

RESULTS

Between February 2018 and April 2019, a total of 163 patients (175 cases) underwent orthopaedic implant removal for various reasons. 30 cases were not usable or analyzable due to missing or damaged reference material, so 145 cases could be evaluated due to study protocol. The range of detected bacteria was as expected and included low-virulent bacteria such as Micrococcus luteus and Corynebacteria. Pathogen detection by culture of the the explant´s was more sensitive (84.83%) than pathogen detection from tissue samples and punction fluid (64.14%, p<0.0001). Comorbidities did not play any role in the quality of detection but prior antibiotic treatment did influence the results of tissue diagnostics.

CONCLUSION

This study showed with a higher frequency of bacterial detection of orthopedic explant´s surface compared to tissue samples or punction fluid. This may reduce the number of samples and cost but enhances the quality of orthopaedic implant-related infection diagnostics.

Promoted sulfamethoxazole extracellular biodegradation in Citrobacter freundii JH@Pd by launching AcrB efflux pump

This study found that bio-Pd0 nanoparticles could launch proton motive force (PMF)-mediated antibiotics efflux pump (AEP) to confer the detoxification capability on Citrobacter freundii, as evidenced by the highest sulfamethoxazole (SMX) specific degradation rate (81.7 μg L-1 mg-1 protein d-1) at high PMF (pH 6). The batch experiment and RT-qPCR results indicated that bio-Pd0 activated the AcrB efflux pump through upregulating the AEP transcriptional regulation factor ramA (2.7-3.1 times), which benefited the intra/extracellular respiration and ATP production/utilization. Path analysis revealed that the prosperity of metabolic activity and extracellular electron output capacity enabled SMX biodegradation, mainly through the electron redistribution and energy optimization with the formate dehydrogenase/hydrogenase based Short-chain (FDH/Hase-S-chain). The upregulation of hypE (2.7-8.6 times) and atpD (1.9-2.3 times) genes encoding the Hase respiratory chain and the F-type ATP synthase, respectively, further supports this mechanism. These novel findings provided a new strategy to improve the biodegradation efficiency of antibiotics wastewater.

Cross-talk between signal transduction systems and metabolic networks in antibiotic resistance and tolerance

The comprehensive antibiotic resistance of pathogens signifies the oneset of the "post-antibiotic era", and the myriad treatment challenges posed by "superbugs" have emerged as the primary threat to human health. Recent studies indicate that bacterial resistance and tolerance development are mediated at the metabolic level by various signalling networks (e.g., quorum sensing systems, second messenger systems, and two-component systems), resulting in metabolic rearrangements and alterations in bacterial community behaviour. This review focuses on current research, highlighting the intrinsic link between signalling and metabolic networks in bacterial resistance and tolerance.

Post-translational assembly of multi-functional antibody

The advent of multi-specific antibodies has introduced a significant advantage over traditional monoclonal antibody therapeutics by engaging multiple targets and pathways. This review delves into the post-translational assembly techniques for multi-specific antibodies, highlighting the innovations and challenges associated with approaches of chemical conjugation, oligonucleotide-mediated assembly, and protein-protein interactions. Chemical conjugation methods have evolved to enhance the assembly process's specificity and flexibility, enabling transient engagement and versatile antibody formats. Meanwhile, oligonucleotide-mediated assembly leverages the precision of Watson-Crick base pairing, granting unmatched control over the antibody's structure and functional orientation. Additionally, protein-protein interaction strategies, notably through SpyTag/SpyCatcher systems, present a direct assembly approach without necessitating ancillary modifications, streamlining the production process. This review summarizes the significance of these methodologies in generating antibodies with diverse structures and multi-target engagement capabilities, underscoring their potential in improving therapeutic efficacy and reducing production complexity.

Role of non-exponential reversal times in aggregation models of bacterial populations

Individual bacteria typically follow somewhat simple rules of motion, but collective behavior can exhibit complex behavioral patterns. For instance, the formation and dispersal of aggregates of reversing bacteria in biofilms are primarily driven by coordinated motion among cells. Many mathematical models of aggregation assume that cells have no memory, e.g., the time between their behavior changes, such as direction reversals, is exponentially distributed. However, in practice, the distribution is quite distinct from exponential. Therefore, in this paper, we analyze numerically the importance of non-exponential reversal times in 1D agent-based and kinetic models of aggregation. In particular, we consider these models in a practical parameter regime by fitting a Gamma distribution to represent the run times of myxobacteria and study their collective behavior with exponential and non-exponential reversal times. We demonstrate that non-exponential reversal times aid aggregation and result in tighter aggregates. We compare and contrast the behavior of agent-based and kinetic models that consider aggregation driven by chemotaxis. Thus, incorporating non-exponential reversal times into models of aggregation can be particularly important for reproducing experimental data, such as aggregate persistence and dispersal. These results provide a simple example of how the existence of memory helps bacteria coordinate their behaviors.

Association of Chronic Periodontitis with Hemorrhagic Stroke: A Systematic Review and Meta-Analysis

Periodontitis is a chronic, multifactorial inflammatory condition linked to dysbiotic plaque biofilms and characterized by the gradual destruction of the structures supporting the teeth owing to compromised immune system function. Hemorrhagic stroke, which primarily occurs within the brain tissue or in the subarachnoid space as a blood leak of ruptured vessels, is a sudden neurological impairment caused by vascular damage in the central nervous system, resulting in focal neurological deficits. Chronic periodontitis (CP) and hemorrhagic stroke may share common pathogenic features involving inflammation and immune system activation, prompting researchers to investigate their potential connection. The aim of the study is to systematically review the literature on the epidemiological association between CP and hemorrhagic stroke in adults. The study protocol adhered to the PRISMA 2020 guidelines, and the design followed the Cochrane methodology. A thorough literature search encompassing PubMed, Scopus, and Web of Science databases and a manual search and evaluation of gray literature was conducted. Meta-analysis was performed using Review Manager (RevMan) 5.4, with the effect size represented by the odds ratio (OR) and a 95% confidence interval (CI). Heterogeneity was assessed using the chi-squared and I 2 statistics. The selected articles, written in English without time constraints, focused on observational studies involving patients and controls and included disease diagnostic criteria. Duplicate entries were eliminated. The reliability of each study's results was evaluated using the Newcastle-Ottawa Scale and GRADE tools. Two reviewers conducted the assessments, and a third reviewer resolved any disagreements. The meta-analysis comprised four observational studies involving 1,882 individuals. It revealed that individuals diagnosed with hemorrhagic stroke were notably more likely to have concurrent CP (OR: 6.32; 95% CI: 1.35-29.49; p = 0.02) or severe CP (OR: 3.08; 95% CI: 1.56-6.06; p = 0.001) compared with healthy controls. A notable occurrence of CP was detected in patients with hemorrhagic stroke compared with controls. Health care professionals need to acknowledge the connection between the two conditions, as it allows them to provide optimal holistic care through a thorough approach to diagnosis and treatment.

Structural characteristics, biotechnological production and applications of exopolysaccharides from Bacillus sp.: A comprehensive review

Exopolysaccharides (EPS) produced by Bacillus species display various biological activities and characteristics such as anti-oxidant, immunomodulatory, anti-bacterial, and bioadhesive effects. These attributes confer Bacillus species broad potential applications in diverse fields such as food, medicine, environment, and agriculture. Moreover, Bacillus-derived EPS are easier to produce and yield higher quantities than plant-derived polysaccharides. Despite these advantages, Bacillus-derived EPS still encounter numerous obstacles in industrial production and commercial applications, including elevated costs, the absence of mature fermentation tank production procedures, and the lack of systematic in vivo and in vitro activity and metabolic evaluation. Therefore, it is essential to gain insight into the current status of structure, production, and applications of Bacillus-derived EPS for facilitating their future broader application. This paper provides a comprehensive overview of the current research on the production, separation, characteristics and applications of these related biological products. Furthermore, this paper summarizes the current challenges impeding industrial production of Bacillus-derived EPS, along with potential solutions, and their prospective applications in enhancing the attributes of beneficial biofilms, laying a solid scientific foundation for the applications of Bacillus-derived EPS in industry and agriculture.

Metabolomics for dental caries diagnosis: Past, present, and future

Dental caries, a prevalent global infectious condition affecting over 95% of adults, remains elusive in its precise etiology. Addressing the complex dynamics of caries demands a thorough exploration of taxonomic, potential, active, and encoded functions within the oral ecosystem. Metabolomic profiling emerges as a crucial tool, offering immediate insights into microecosystem physiology and linking directly to the phenotype. Identified metabolites, indicative of caries status, play a pivotal role in unraveling the metabolic processes underlying the disease. Despite challenges in metabolite variability, the use of metabolomics, particularly via mass spectrometry and nuclear magnetic resonance spectroscopy, holds promise in caries research. This review comprehensively examines metabolomics in caries prevention, diagnosis, and treatment, highlighting distinct metabolite expression patterns and their associations with disease-related bacterial communities. Pioneering in approach, it integrates singular and combinatory metabolomics methodologies, diverse biofluids, and study designs, critically evaluating prior limitations while offering expert insights for future investigations. By synthesizing existing knowledge, this review significantly advances our comprehension of caries, providing a foundation for improved prevention and treatment strategies.

Association of Proton Pump Inhibitor Use With Gastric Cancer in Regions With High Prevalence of Gastric Cancer: Systematic Review and Meta-analysis

Background/Aims

Although the association between the use of proton pump inhibitors (PPIs) and the risk of gastric cancer has been postulated in casecontrol and cohort studies, it remains still controversial. We aim to evaluate association of PPI use with gastric cancer in regions with high prevalence of gastric cancer, particularly in patients who underwent eradication of Helicobacter pylori, by systemic review and meta-analysis.

Methods

Comprehensive literature search through the PubMed, Embase, and Cochrane database was performed in October 2023. We used random effects model to calculate pooled odds ratios (ORs) with 95% confidence intervals (CIs) between PPI use and gastric cancer. The Cochran Q-statistic and the I2 test were employed for evaluating potential heterogeneity between studies.

Results

Two case-control and 6 cohort studies were identified. PPI use was significantly associated with the development of gastric cancer (OR, 2.02; 95% CI, 1.35-3.01). In subgroup analysis carried out according to the study design, sample size, and adjustment of confounding factors (age, sex, and H. pylori), such association was significant. A meta-analysis of 4 studies performed in patients with H. pylori eradication history showed that the use of PPIs was significantly associated with an elevated incidence of gastric cancer (OR, 2.10; 95% CI, 1.48-2.97).

Conclusions

Long-term use of PPIs is associated with an increased risk of gastric cancer in Asian regions with high prevalence of gastric cancer, particularly in subjects who have eradication history of H. pylori. Optimization of long-term PPI use seems to be necessary in regions where gastric cancer is prevalent.

The synergistic antibacterial effects of allicin nanoemulsion and ε-polylysine against Escherichia coli in both planktonic and biofilm forms

The synergistic effects of allicin nanoemulsion (AcN) and ε-polylysine (ε-PL) against Escherichia coli were investigated in this study. The combination of AcN and ε-PL synergistically inhibited the planktonic growth of E. coli, with a low fractional inhibitory concentration index of 0.252. AcN/ε-PL treatment remarkably promoted the agent-cell contacts compared to AcN or ε-PL treatment, as evidenced by the larger cellular size and lower absolute zeta potential value. Analysis of membrane potential, intracellular ATP and superoxide dismutase activity revealed that the co-treatment induced membrane depolarization and intracellular metabolic disorders. Laser scanning confocal microscope, flow cytometer, and scanning electron microscope revealed that the membrane integrity and cell structure were severely degraded. Further, biofilm formation, cluster motility, and mature biofilm of E. coli were disrupted substantially by AcN/ε-PL. Finally, the application of AcN/ε-PL in raw beef preservation verified the synergy. Therefore, AcN/ε-PL can be used as a potential bacteriostatic agent in food preservation.

Role of a single MCP in evolutionary adaptation of Shewanella putrefaciens for swimming in planktonic and structured environments

Bacteria can adapt to their environments by changing phenotypic traits by mutations. However, improving one trait often results in the deterioration of another one, a trade-off that limits the degree of adaptation. The gammaproteobacterium Shewanella putrefaciens CN-32 has an elaborate motility machinery comprising two distinct flagellar systems and an extensive chemotaxis array with 36 methyl-accepting chemotaxis sensor proteins (MCPs). In this study, we performed experimental selection on S. putrefaciens for increased spreading through a porous environment. We readily obtained a mutant that showed a pronounced increase in covered distance. This phenotype was almost completely caused by a deletion of 24 bp from the chromosome, which leads to a moderately enhanced production of a single MCP. Accordingly, chemotaxis assays under free-swimming conditions and cell tracking in soft agar showed that the mutation improved navigation through nutritional gradients. In contrast, further increased levels of the MCP negatively affected spreading. The study demonstrates how moderate differences in the abundance of a single MCP can lead to an efficient upgrade of chemotaxis in specific environments at a low expense of cellular resources.IMPORTANCEExperimental evolution experiments have been used to determine the trade-offs occurring in specific environments. Several studies that have used the spreading behavior of bacteria in structured environments identified regulatory mutants that increase the swimming speed of the cells. While this results in a higher chemotaxis drift, the growth fitness decreases as the higher swimming speed requires substantial cellular resources. Here we show that rapid chemotaxis adaptation can also be achieved by modifying the chemotaxis signal input at a low metabolic cost for the cell.

Efficient genetic manipulation of Shewanella through targeting defense islands

The Shewanella genus is widely recognized for its remarkable respiratory adaptability in anaerobic environments, exhibiting potential for bioremediation and microbial fuel cell applications. However, the genetic manipulation of certain Shewanella strains is hindered by defense systems that limit their genetic modification in biotechnology processes. In this study, we present a systematic method for predicting, mapping, and functionally analyzing defense islands within bacterial genomes. We investigated the genetically recalcitrant strain Shewanella putrefaciens CN32 and identified several defense systems located on two genomic islands integrated within the conserved chromosomal genes trmA and trmE. Our experimental assays demonstrated that overexpression of excisionases facilitated the excision of these islands from the chromosome, and their removal significantly enhanced the genetic manipulation efficiency of S. putrefaciens CN32. Further analysis revealed that these defense islands are widespread across various Shewanella strains and other gram-negative bacteria. This study presents an effective strategy to circumvent genetic barriers and fully exploit the potential of Shewanella for environmental and microbial engineering applications.

IMPORTANCE

Efficiently modifying bacterial genomes is critical for advancing their industrial applications. However, bacteria in complex environments naturally develop defense mechanisms in response to bacteriophages and exogenous DNA, which pose significant challenges to their genetic modification. Several methods have emerged to tackle these challenges, including in vitro methylation of plasmid DNA and targeting specific restriction-modification (R-M) and CRISPR loci. Nevertheless, many bacteria harbor multiple, often uncharacterized defense mechanisms, limiting these strategies. Our study differs from previous approaches by specifically targeting defense islands-clusters of defense systems located within mobile genetic elements. Here, we investigated Shewanella putrefaciens CN32 and identified two key defense islands responsible for these protective functions. By selectively deleting these defense islands, we significantly enhanced the efficiency of genetic manipulation in S. putrefaciens. Our findings not only demonstrate a promising strategy for improving genetic engineering in Shewanella but also suggest broader applicability across other bacterial species. This work opens new opportunities for optimizing microbial processes in biotechnology, highlighting the potential of defense island-targeted genetic modification.

Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering

Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.

IMPORTANCE

This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.

Role of the TPR family protein VPA1365 in regulating type III secretion system 2 and virulence in Vibrio parahaemolyticus

Vibrio parahaemolyticus is a notable seafood-borne pathogen capable of colonizing the intestines of hosts and inducing acute gastroenteritis. The intestinal colonization and enterotoxicity of V. parahaemolyticus are highly reliant on the type III secretion system 2 (T3SS2), encoded within the pathogenicity island (Vp-PAI). The expression of Vp-PAI is strictly regulated by bile acid signals and transcriptional regulators VtrA/VtrB. In this study, we identified a tetratricopeptide repeat (TPR) family protein named VPA1365, which regulates the expression of T3SS2 and is indispensable for the intestinal colonization of V. parahaemolyticus. The expression and secretion of the T3SS2-dependent protein VopD2 were significantly reduced in Δvpa1365 compared to that of the wild type (WT), suggesting that VPA1365 positively regulates the function of T3SS2. Further research indicated that VPA1365 directly binds to the promoters of vtrA, thereby increasing the expression levels of T3SS2-associated genes. Additionally, the deletion of vpa1365 markedly reduced the cytotoxicity, adhesion ability, biofilm formation, and hemolytic activity of V. parahaemolyticus. VPA1365 was found to control the expression levels of these virulence-associated genes by binding to the promoters of scrG, pilA, and mshA. In a zebrafish infection model, the Δvpa1365 infected groups demonstrated a higher survival rate compared to the zebrafish infected with WT. In conclusion, this study identified a TPR family protein VPA1365, which regulates the expression levels of T3SS2 and virulence-associated genes in V. parahaemolyticus, further broadening our understanding of its virulence factors.

IMPORTANCE

The type III secretion system 2 (T3SS2) is of crucial significance for the pathogenicity of Vibrio parahaemolyticus; nevertheless, the biological functions of many genes within the T3SS2 gene cluster and the transcriptional regulatory network of T3SS2 remain ambiguous. In this study, we identified VPA1365, a tetratricopeptide repeat family regulator encoded in the T3SS2 gene cluster, which differs from other known T3SS2 regulatory factors, such as OmpR, ToxR, or LysR family proteins. VPA1365 not only positively regulated the expression and secretion of T3SS2-related proteins but also enhanced the virulence in infant rabbits and zebrafish. Moreover, we identified several novel functions of VPA1365, such as its contribution to hemolytic activity, biofilm formation, cytotoxicity, and adhesion ability, uncovering its global physiological role in V. parahaemolyticus. The putative VPA1365-binding site was predicted and identified through the MEME-Suite tool and electrophoretic mobility shift analysis. Collectively, these results broaden our understanding of the regulatory pathways of T3SS2 and virulence.

Transcriptional regulation of two redundant 3-bromo-4-hydroxybenzoate catabolic operons via two different regulatory modes in Pigmentiphaga kullae strain H8

Gene redundancy endows bacteria with enhanced adaptability to complex and fluctuating environments but results in genetic costs. Transcriptional regulation is considered an effective strategy for harmonizing adaptive benefits with physiological burdens. In our previous study, two redundant gene clusters (phbh1pcaApcaBorf404bhbR1 and phbh2pcaB2pcaA2bhbR2) involved in 3-bromo-4-hydroxybenzoate (3-Br-4-HB) catabolism were identified in Pigmentiphaga kullae strain H8. The LysR-type transcription regulator BhbR1, encoded by the bhbR1 gene, activated phbh1pcaApcaBorf404 transcription. Through DNase I footprinting assays, the presence of the inducer 3-Br-4-HB was found to shorten the BhbR1-bound region in the promoter, uncovering the protected -35 box, thereby activating transcription. The MarR-family transcription factor (MFTF) BhbR2, encoded by the bhbR2 gene, was different from typical inhibitive MFTFs and activated phbh2pcaB2pcaA2 transcription. BhbR2 was found to bind a 17-bp imperfect palindromic sequence (TTGATT-N5-AATCAA) in the target promoter. Intriguingly, the presence of 3-Br-4-HB neither dissociated BhbR2 from the promoter nor modified its binding site, indicating a novel regulatory mode. Despite a coincident trend in activating their respective operons in response to different concentrations of 3-Br-4-HB, BhbR1 and BhbR2 both showed a significant attenuation of the activation effect at high concentrations (>480 μM), highlighting the requisite co-existence of redundant 3-Br-4-HB catabolic operons and their regulatory genes. This study presents two distinct transcriptional regulation mechanisms of these two redundant 3-Br-4-HB catabolic operons in strain H8, expanding our understanding of the diversity of transcriptional regulation for enhancing adaptation.

IMPORTANCE

In bacteria, catabolic genes for pollutant degradation often possess functionally redundant duplicates, providing a genetic basis for rapid adaptation to complex polluted environments. Synergic regulation plays an important role in balancing the physiological burden of extra genetic material with the adaptive benefits conferred by genetic redundancy. Although the co-existence of two redundant 3-bromo-4-hydroxybenzoate (3-Br-4-HB)-catabolic operons has been proven to enhance the metabolic robustness and adaptability of the host strain Pigmentiphaga kullae H8, how these two inducible catabolic operons are regulated remains unclear. This study identified two regulators, the LysR-type transcription regulator BhbR1 and the MarR-family transcription factor BhbR2, which activated transcription of the two 3-Br-4-HB-catabolic operons using different modes, and also revealed interactions of these two regulators with their effectors and target promoters. These findings not only clarify two distinct transcriptional strategies employed by redundant catabolic operons but also enhance our understanding of the significance of regulatory diversity for bacterial adaptation to complex polluted environments.

Sulfate assimilation regulates antioxidant defense response of the cyanobacterium Synechococcus elongatus PCC 7942 to high concentrations of carbon dioxide

The adaptive evolution of cyanobacteria over a prolonged period has allowed them to utilize carbon dioxide (CO2) at the low concentrations found in the atmosphere (0.04% CO2) for growth. However, whether the exposure of cyanobacteria to high concentrations of CO2 results in oxidative stress and the activation of antioxidant defense response remains unknown, albeit fluctuations in other culture conditions have been reported to exert these effects. The current study reveals the physiological regulation of the model cyanobacterium Synechococcus elongatus PCC 7942 upon exposure to 1% CO2 and the underlying mechanism. Exposure to 1% CO2 was demonstrated to induce oxidative stress and activate antioxidant defense responses in S. elongatus. Further analysis of variations in metabolism between S. elongatus cells grown at 0.04% CO2 and exposed to 1% CO2 revealed that sulfate assimilation was enhanced after the exposure to 1% CO2. A strain of S. elongatus lacking the gene cysR, encoding a global transcriptional regulator for genes involved in sulfate assimilation, was generated by deleting the gene from the genomic DNA. A comparative analysis of the wild-type and cysR-null strains indicated the regulation of the antioxidant response by sulfate assimilation. In addition, lines of evidence were presented that suggest a role of degradation of phycobilisome in the antioxidant response of S. elongatus under conditions of 1% CO2 and sulfate limitation. This study sheds light on the in situ effects of high CO2-induced stress on the ecophysiology of cyanobacteria upon exposure to diverse scenarios from a biotechnological and ecological perspective.IMPORTANCECyanobacteria that grow autotrophically with CO2 as the sole carbon source can be subject to high-CO2 stress in a variety of biotechnological and ecological scenarios. However, physiological regulation of cyanobacteria in response to high-CO2 stress remains elusive. Here, we employed microbial physiological, biochemical, and genetic techniques to reveal the regulatory strategies of cyanobacteria in response to high-CO2 stress. This study, albeit physiological, provides a biotechnological enterprise for manipulating cyanobacteria as the chassis for CO2 conversion and sheds light on the in situ ecological effects of high CO2 on cyanobacteria.

Diversity and genomics of bacteriome-associated symbionts in treehopper Darthula hardwickii (Hemiptera: Aetalionidae) and implications of their nutritional functions

Symbionts play important roles in insect nutritional ecology, and the phylogenies of some vertically transmitted symbionts mirror the host phylogeny. Here we report the diversity, distribution, transmission, and potential functions of symbionts harbored in the aetalionid treehopper Darthula hardwickii (Aetalionidae) using multiple methods and compare the potential functions of its obligate symbiont Karelsulcia with that of the related aetalionid Aetalion reticulatum. D. hardwickii harbors Karelsulcia in bacteriomes, a yeast-like fungal symbiont (YLS) in fat bodies, and Tisiphia in both the bacteriomes and fat bodies. Karelsulcia and YLS are vertically transmitted to the ovaries but do not cluster to form a "symbiont ball" in terminal oocytes, as is the case in other auchenorrhynchan insects. YLS harbored in D. hardwickii represents the first known instance of a fungal symbiont being associated with treehoppers. Phylogenetic analysis revealed that Aetalionidae are derived from within Membracidae. Gene truncation and absence were revealed in the tryptophan biosynthetic pathway of Karelsulcia from D. hardwickii, suggesting this symbiont is no longer capable of providing this essential amino acid (EAA) to its host. Tryptophan is presumed to be supplied to D. hardwickii by YLS since tryptophan-related genes are either absent or degraded in Karelsulcia and Tisiphia. No truncated genes were found in Karelsulcia from A. reticulatum, but it has lost genes related to the synthesis of other EAAs, as in some leafhoppers. This study sheds new light on the diversity and functions of the nutritional endosymbionts of Membracoidea and processes that may have precipitated symbiont replacement in this diverse insect lineage.IMPORTANCESymbionts in sap-feeding insects play important roles related to nutrition of their hosts, which may change through evolutionary time and vary across host and symbiont lineages. This comparative genomic study indicates that, compared to the related symbionts of other leaf- and treehoppers, the Karelsulcia symbiont of the treehopper Darthula hardwickii has lost the ability to provide the EAA tryptophan to its host. This function is apparently being performed by a coexisting yeast-like symbiont (YLS). This is the first report of a YLS in a species of treehopper, which suggests that the processes involved in symbiont replacement in treehoppers are similar to those observed in other sap-sucking auchenorrhynchan insects. Phylogenetic analyses of Karelsulcia lineages of Membracoidea largely mirror the host insect phylogeny but suggest that Aetalionidae may have originated from Membracidae, in contrast to some recent phylogenies based on the genomic data from the host insects.

The GCN4-Swi6B module mediates low nitrogen-induced cell wall remodeling in Ganoderma lucidum

In natural habitats, microorganisms encounter various unfavorable environmental stresses, including nitrogen deficiency. As the outermost barrier, the cell wall plays a crucial role in the interaction between the cell and the external environment. However, the effect of low nitrogen on cell wall thickness, especially the underlying molecular mechanism, is unclear. Here, we found that compared with those under normal nitrogen conditions, both the cell wall thickness and polysaccharide content of Ganoderma lucidum are increased under low nitrogen conditions. Furthermore, the abundance of SWI6B, a transcription factor that participates in cell wall remodeling, is also increased in low-nitrogen environments. The thickness and polysaccharide content of the cell wall increased in SWI6B-overexpression strains (SWI6B-OEs) but decreased in SWI6-knockdown strains (swi6-kds). Moreover, although the cell wall thickness of all the genotypes increased under nitrogen-limited conditions, the percentage of upregulated swi6-kds was significantly lower than that of the WT, and the percentage of increased SWI6B-OEs was the highest. Moreover, GCN4, a key transcription factor of the low-nitrogen signaling pathway, was found to directly bind to the promoter of SWI6. The transcriptional and translational levels of SWI6B were reduced in GCN4-knockdown strains (gcn4-kds), indicating a positive regulation of SWI6B by GCN4. Consistently, the cell wall thickness of gcn4-kds was also lower than that of the wild type. Taken together, our results revealed that the GCN4-Swi6B module regulates cell wall remodeling in G. lucidum under nitrogen deficiency conditions.

IMPORTANCE

To survive in stressful environments, fungi initiate cell wall remodeling pathways to adaptively modify the cell wall composition and structure. Here, we found that nitrogen deficiency upregulated the cell wall polysaccharide content and cell wall thickness through the GCN4-SWI6B signaling pathway. Our findings provide valuable insights into the environmental adaptation of fungal cell walls, contributing to a deeper understanding of fungal responses to environmental stress.

SGBP-B-like bimodular cellulose-binding protein CHU_1279 is essential for cellulose utilization by Cytophaga hutchinsonii

The widespread cellulolytic specialist Cytophaga hutchinsonii belonging to the phylum Bacteroidetes adopted a unique cellulose utilization strategy that did not conform to the known cellulose-degrading paradigms involving free cellulases or cellulosomes. The strategy used by C. hutchinsonii still remains largely unclear. In this study, we showed that chu_1279 within the chu_1276-chu_1280 gene cluster, which has been previously shown to be important for cellulose utilization by C. hutchinsonii, encodes an outer membrane protein, and its elimination prohibited bacterial growth on cellulose. Structural prediction revealed that CHU_1279 is a surface glycan-binding protein B (SGBP-B)-like protein comprising two putative carbohydrate-binding module (CBM)-like domains. Further analyses verified that recombinant CHU_1279 displayed significant cellulose-binding protein, and its C-terminal domain is predominantly responsible for cellulose binding. Expression of the C-terminal domain but not the N-terminal domain restored cellulose utilization of ∆chu_1279. Moreover, site-directed mutagenesis analyses identified three aromatic residues important for cellulose binding of the recombinant CHU_1279 protein. The defective cellulose utilization of ∆chu_1279 cells otherwise could be recovered by CHU_1279 variants with significantly damaged cellulose-binding capability. Sequence analyses revealed that orthologs of CHU_1279 as well as the atypical polysaccharide utilization loci (PUL) constituted by the gene cluster chu_1276-chu_1280 are also present in two other cellulolytic Bacteroidetes bacteria, Cytophaga aurantiaca and Sporocytophaga myxococcoides, which are closely related to C. hutchinsonii. Our results contribute to unveiling the unique mechanism underlying the efficient cellulose utilization by C. hutchinsonii and similar cellulolytic bacteria.IMPORTANCEMost members of the phylum Bacteroidetes are highly competitive and efficient degraders of complex polysaccharides largely ascribed to their employment of a SusC-like system encoded by a polysaccharide utilization locus (PUL). However, characterization of PULs is limited to those responsible for utilization of (semi)soluble glycans. PULs involved in the utilization of cellulose, the most abundant renewable polymer, have not been identified and functionally characterized yet. We demonstrated that chu_1279 in the cellulolytic specialist C. hutchinsonii encodes an SGBP-B-like protein that is required for cellulose utilization, supporting that the gene cluster chu_1276-chu_1280 in C. hutchinsonii encodes an atypical PUL system dedicated to cellulose assimilation. Further analyses showed that this atypical PUL system is also present in two other cellulolytic Bacteroidetes bacteria. This study not only contributes to unveiling the unusual cellulose utilization strategy adopted by C. hutchinsonii and similar cellulolytic bacteria but also helps expand our understanding of atypical PULs for nutrient acquisition by cellulolytic bacteria.

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment.IMPORTANCERhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

Dynamic coexistence driven by physiological transitions in microbial communities

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.

Unveiling the role of phages in shaping the periodontal microbial ecosystem

The oral microbiome comprises various species and plays a crucial role in maintaining the oral ecosystem and host health. Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.IMPORTANCEIn the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.

Reconsidering Stochasticity in Modeling of Bacterial Population Growth and Inactivation With Technical and Biological Variability

Considering variability in microbial behavior has been recognized as a crucial element for predictive microbiology and quantitative microbial risk assessment. Although some sources of variability have been listed so far, a mathematical description of the variability in bacterial population behavior has not yet been realized. The present paper illustrates stochastic bacterial population growth and/or inactivation behavior from a mathematical point of view. Among various stochastic factors, sampling for the quantification of bacterial numbers and single-cell division/inactivation responses to food environments are highlighted as sources of technical and biological variability. Furthermore, the variability in sampling and single-cell division/inactivation responses emerges as variability in both number and time from the viewpoint of population dynamics. The aforementioned mathematical description of variability enables combining Poisson, binomial, and negative binomial distributions into traditional kinetic equations as its residual distribution. The primary focus is on the stochastic nature of variability, while it also includes discussions on incorporating parameter uncertainty into mathematical models. The traditional kinetic equation integrated with technical and biological variability and uncertainty enables a precise estimate of variation in population behavior, which would facilitate exposure assessment in quantitative microbial risk assessment.

Cleavage cascade of the sigma regulator FecR orchestrates TonB-dependent signal transduction

TonB-dependent signal transduction is a versatile mechanism observed in gram-negative bacteria that integrates energy-dependent substrate transport with signal relay. In Escherichia coli, the TonB-ExbBD motor complex energizes the TonB-dependent outer membrane transporter FecA, facilitating ferric citrate import. FecA also acts as a sensor, transmitting signals to the cytoplasmic membrane protein FecR, which eventually activates the cytoplasmic sigma factor FecI, driving transcription of the fec operon. Building on our previous finding that FecR undergoes functional maturation through a three-step cleavage process [T. Yokoyama et al., J. Biol. Chem. 296, 100673 (2021)], we here describe the complete mechanism of FecR-mediated ferric citrate signaling involving FecA and TonB. The cleavage cascade begins with FecR autoproteolysis prior to membrane integration. The soluble C-terminal domain (CTD) fragment of FecR is cotranslocated with the N-terminal domain (NTD) fragment through a twin-arginine translocation (Tat) system-mediated process. In the periplasm, the interaction between the CTD and NTD fragments prevents further cleavage. Binding of ferric citrate induces a conformational change in FecA, exposing its TonB box to the periplasmic space. This structural alteration is transmitted to the interacting FecR CTD via the motor function of TonB, resulting in the release of the CTD blockage from the NTD. Consequently, the successive cleavage of FecR's NTD is initiated, culminating in the ferric citrate signal-induced activation of fec gene expression. Our findings reveal that the regulation of FecR cleavage, controlled by the TonB-FecA axis, plays a central role in the bacterial response to ferric citrate signals.

Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State

Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.

Diverse evolutionary trajectories of Klebsiella pneumoniae carbapenemase: unraveling the impact of amino acid substitutions on β-lactam susceptibility and the role of avibactam in driving resistance

Klebsiella pneumoniae carbapenemases (KPCs) have evolved into over 245 distinct variants, with over one-third of variants exhibiting reduced susceptibility to ceftazidime-avibactam, while the underlying selection mechanisms remain elusive. To better elucidate these resistant phenotypes, we cloned 33 clinically described KPC variants (from KPC-2 to KPC-36) and 8 artificially created variants into a common plasmid vector and assessed their impact on β-lactam susceptibility. Strains expressing KPC-14, KPC-28, and KPC-31 exhibited increased resistance to ceftazidime and ceftazidime-avibactam but decreased resistance to carbapenems. We further studied the catalytic mechanism of β-lactam hydrolysis by KPC-4, KPC-14, KPC-15, KPC-16, KPC-21, KPC-25, KPC-28, KPC-31, and the ancestral KPC-2 and KPC-3 enzymes. Antimicrobial susceptibility test, enzyme kinetics, and molecular modeling revealed diverse selective pressures, including but not limited to aztreonam and ceftriaxone, driving KPC evolution, with ceftazidime playing a central role. Substitutions within the KPC hydrolytic active sites notably reduced the inhibitory effect of avibactam on KPC, demonstrated by isothermal titration calorimetry analysis, resulting in enhanced hydrolysis of ceftazidime by enzyme kinetics. This highlights that avibactam may serve as an additional driving force in KPC evolution.IMPORTANCEThe rapid evolution of KPC carbapenemases, including resistance to ceftazidime-avibactam, threatens the effectiveness of last-resort antibiotics against Klebsiella pneumoniae infections, necessitating understanding of of the underlying selection pressures. This study investigates the evolutionary mechanisms driving KPC diversification and resistance to ceftazidime-avibactam, providing crucial information for developing effective strategies to combat carbapenem-resistant Klebsiella pneumoniae (CRKP) infections and preserve antibiotic efficacy.

Selection of MDM2-binding peptides in Escherichia coli using an engineered split intein and aminoglycoside phosphotransferase

A protein trans-splicing (PTS)-based method for screening the peptides capable of binding to a target protein was developed using an engineered split intein and an aminoglycoside phosphotransferase. Two peptides selected against MDM2 bind to MDM2 with high affinity and a peptide can induce apoptosis in SJSA-1 cells.

Electrochemistry and Molecular Compositions Reflect Electron Shuttling of Dissolved Organic Matter in High Arsenic Groundwater

Little is known about the electron shuttle ability of dissolved organic matter (DOM) and its effects on arsenic (As) mobilization, which makes the underlying mechanism of groundwater As enrichment elusive. In this study, both the electrochemical properties and molecular compositions of DOM in high As groundwater were quantified in the Hetao Basin, China. We found that, along the flow path, the average electron-transferring capacity (ETC) of DOM, including the capacities of electron-accepting and electron-donating, continuously increased from 2.85 to 3.59 mmole-/gC along with As concentrations. The increasing ETC reflected an increase in electron shuttle ability of DOM. Furthermore, the increasing electron shuttle ability was mainly attributed to the recalcitrant compounds in DOM, especially CHOS and CHONS formulas in highly unsaturated structures with high oxygen (HUSHO) and CHO and CHON formulas in aromatic structures (AS). The significantly positive correlation between As concentration and ETC indicated that recalcitrant DOM promoted groundwater As enrichment through electron shuttling for inducing the reductive dissolution of As-containing Fe(III) oxide minerals, which was further supported by our culture experiments showing that goethite was more reduced [133 μM Fe(II)] in the presence of DOM with a higher ETC (3.35 mmole-/gC) as electron shuttling than that [65.2 μM Fe(II)] with a relatively lower ETC (2.41 mmole-/gC). Our study highlights that recalcitrant DOM compounds with unsaturated and AS have high electron shuttle ability, promoting As enrichment in groundwater.

Virovory: control of viral pathogenesis by the protists and the way forward

The interactions between viruses and protists have been crucially impacting the ecosystem. In recent studies, it has been found that the protists are not only able to consume, ingest or inactivate a variety of viruses, resulting in a reduction of the viral load, but instead, they can treat viruses as the exclusive source of nutrients, exhibiting "Virovory" (virus-only diet). These small protists can act as virosomes (organisms harnessing nutrients from the viruses) and utilize the viruses as the only source of nourishment, implying the protist to multiply and grow. The viral reduction was previously thought to be only because of the action of abiotic factors (temperature, ultraviolet light, chemicals, membrane adsorption, etc.). However, virovory suggests that organic material flow in microbial communities, the impact of viruses on the food web and, the role of protists in regulating viral populations are crucial factors in ecosystem dynamics. In this review, ingestion, digestion, and inactivation of a variety of viruses by protists are discussed. Several questions can be answered by further research on understanding the mechanisms behind the inactivation of viruses, the impact of reduced viral load on other microbial populations, and the large-scale employability of these little protists in removing pathogenic viruses from the environment.

Nanoplastics-mediated physiologic and genomic responses in pathogenic Escherichia coli O157:H7

The widespread occurrence of microplastics (MP) and nanoplastics (NP) in the environment is commonly thought to negatively impact living organisms; however, there remains a considerable lack of understanding regarding the actual risks associated with exposure. Microorganisms, including pathogenic bacteria, frequently interact with MPs/NPs in various ecosystems, triggering physiological responses that warrant a deeper understanding. The present study experimentally demonstrated the impact of surface-functionalized differentially charged polystyrene (PS) NPs on the physiology of human pathogenic Escherichia coli O157:H7 and their influence on biofilm formation. Our results suggest that charged NPs can influence the growth, viability, virulence, physiological stress response, and biofilm lifestyle of the pathogen. Positively-charged NPs were found to have a bacteriostatic effect on planktonic cell growth and affect cellular viability and biofilm initiation compared to negatively charged and uncharged NPs. The transcriptomic and gene expression data indicated significant changes in the global gene expression profile of cells exposed to NPs, including the differential expression of genes encoding several metabolic pathways associated with stress response and virulence. Significant upregulation of Shiga-like toxin (stx1a), quorum sensing, and biofilm initiation genes was observed in NP-exposed biofilm samples. Overall, exposure to NPs did not significantly affect the survival of pathogens but affected their growth and biofilm development pattern, and most importantly, their virulence traits.

Chemical Synthetic Lethality Screens Identify Selective Drug Combinations against Pseudomonas aeruginosa

The emergence of bacterial ESKAPE pathogens presents a formidable challenge to global health, necessitating the development of innovative strategies for antibiotic discovery. Here, we leverage chemical synthetic lethality to locate therapeutic combinations of small molecules against multidrug-resistant Pseudomonas aeruginosa. Using a transposon screen, we identify PyrD as a target for sensitizing P. aeruginosa to subinhibitory doses of ceftazidime. High-throughput inhibitor screens identify two PyrD inhibitors, nordihydroguaiaretic acid (NDGA) and chlorhexidine (CHX), each of which does not significantly affect growth in isolation but exhibits chemical synthetic lethality when combined with low-dose ceftazidime. Downstream biochemical studies elucidate the mechanism of inhibition by NDGA and CHX. Remarkably, this combination is toxic to P. aeruginosa but leaves commensal bacteria, which are more susceptible to antibiotics, unscathed. Aside from advancing drug combinations that may be explored further in the future, our results offer a new approach for devising potent and specific drug combinations against recalcitrant pathogens.

Live tracking of replisomes reveals nutrient-dependent regulation of replication elongation rates in Caulobacter crescentus

In bacteria, commitment to genome replication (initiation) is intricately linked to nutrient availability. Whether growth conditions affect other stages of replication beyond initiation remains to be systematically studied. To address this, we assess the replication dynamics of Caulobacter crescentus, a bacterium that undergoes only a single round of replication per cell cycle, by tracking the replisome across various growth phases and nutrient conditions. We find that the replication elongation rates slow down as cells transition from exponential (high-nutrient) to stationary (low-nutrient) phase, and this contributes significantly to the overall cell-cycle delay. Although elongation rates are correlated with growth rates, both properties are differentially influenced by nutrient status. This slowdown in replication progression is reversed via supplementation with dNTPs and is not associated with increased mutagenesis or upregulation of the DNA damage responses. We conclude that growth conditions not only dictate the commitment to replication but also the rates of genome duplication. Such regulation appears to be distinct from stress-induced replication slowdown and likely serves as an adaptive mechanism to cope with fluctuations in nutrient availability in the environment.