The haemagglutinin gene of bovine-origin H5N1 influenza viruses currently retains receptor-binding and pH-fusion characteristics of avian host phenotype

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Over 891 dairy farms across 16 states have tested positive until 25 December 2024, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0-5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.

Physiological role of bicarbonate in microbes: A double-edged sword?

HCO3- is involved in pH homoeostasis and plays a multifaceted role in human health. HCO3- has been recognized for its antimicrobial properties and is pivotal in bacterial antibiotic susceptibility. Notably, the interconversion between CO2 and HCO3-, facilitated by the enzyme carbonic anhydrase (CA), is crucial in tissues infected by pathogens. Studies have highlighted the antimicrobial potency of CA inhibitors, emphasizing the importance of this enzyme in this area. The potential of HCO3- as an antibiotic adjuvant is evident; its ability to increase virulence in pathogens such as Enterococcus faecalis and Mycobacterium tuberculosis requires meticulous scrutiny. HCO3- modulates bacterial behaviours in diverse manners: it promotes Escherichia coli O157:H7 colonization in the human gut by altering specific gene expression and, with Pseudomonas aeruginosa, amplifies the effect of tobramycin on planktonic cells while promoting biofilm formation. These multifaceted effects necessitate profound mechanistic exploration before HCO3- can be considered a promising clinical adjuvant.

Effect of cold atmospheric plasma on common oral pathogenic microorganisms: a narrative review

BACKGROUND

The oral microbiota is a diverse and complex community that maintains a delicate balance. When this balance is disturbed, it can lead to acute and chronic infectious diseases such as dental caries and periodontitis, significantly affecting people's quality of life. Developing a new antimicrobial strategy to deal with the increasing microbial variability and resistance is important. Cold atmospheric plasma (CAP), as the fourth state of matter, has gradually become a hot topic in the field of biomedicine due to its good antibacterial, anti-inflammatory, and anti-tumor capabilities. It is expected to become a major asset in the regulation of oral microbiota.

METHODS

We conducted a search in PubMed, Medline, and Wiley databases, focusing on studies related to CAP and oral pathogenic microorganisms. We explored the biological effects of CAP and summarized the antimicrobial mechanisms behind it.

RESULTS

Numerous articles have shown that CAP has a potent antimicrobial effect against common oral pathogens, including bacteria, fungi, and viruses, primarily due to the synergy of various factors, especially reactive oxygen and nitrogen species.

CONCLUSIONS

CAP is effective against various oral pathogenic microorganisms, and it is anticipated to offer a new approach to treating oral infectious diseases. The future objective is to precisely adjust the parameters of CAP to ensure safety and efficacy, and subsequently develop a comprehensive CAP treatment protocol. Achieving this objective is crucial for the clinical application of CAP, and further research is necessary.

Ecological drivers of evolution of swine influenza in the United States: a review

Influenza A viruses (IAVs) pose a major public health threat due to their wide host range and pandemic potential. Pigs have been proposed as "mixing vessels" for avian, swine, and human IAVs, significantly contributing to influenza ecology. In the United States, IAVs are enzootic in commercial swine farming operations, with numerous genetic and antigenic IAV variants having emerged in the past two decades. However, the dynamics of intensive swine farming systems and their interactions with ecological factors influencing IAV evolution have not been systematically analysed. This review examines the evolution of swine IAVs in commercial farms, highlighting the role of multilevel ecological factors. A total of 61 articles published after 2000 were reviewed, with most studies conducted after 2009 in Midwestern US, followed by Southeast and South-central US. The findings reveal that ecological factors at multiple spatial scales, such as regional transportation networks, interconnectedness of swine operations, farm environments, and presence of high-density, low-genetic diversity herds, can facilitate virus transmission and enhance virus evolution. Additionally, interactions at various interfaces, such as between commercial swine and feral swine, humans, or wild birds contribute to the increase in genetic diversity of swine IAVs. The review underscores the need for comprehensive studies and improved data collection to better understand the ecological dynamics influencing swine IAV evolution. This understanding is crucial for mitigating disease burden in swine production and reducing the risk of zoonotic influenza outbreaks.

Deciphering novel enzymatic and non-enzymatic lysine lactylation in Salmonella

Lysine lactylation, a novel post-translational modification, is involved in multiple cellular processes. The role of lactylation remains largely unknown, especially in bacteria. Here, we identified 1090 lactylation sites on 469 proteins by mass spectrometry in Salmonella Typhimurium. Many proteins involved in metabolic processes, protein translation, and other biological functions are lactylated, with lactylation levels varying according to the growth phase or lactate supplementation. Lactylation is regulated by glycolysis, and inhibition of L-lactate utilization can enhance lactylation levels. In addition to the known lactylase in E. coli, the acetyltransferase YfiQ can also catalyse lactylation. More importantly, L-lactyl coenzyme A (L-La-CoA) and S,D-lactoylglutathione (LGSH) can directly donate lactyl groups to target proteins for chemical lactylation. Lactylation is involved in Salmonella invasion of eukaryotic cells, suggesting that lactylation is crucial for bacterial virulence. Collectively, we have comprehensively investigated protein lactylome and the regulatory mechanisms of lactylation in Salmonella, providing valuable insights into studying lactylation function across diverse bacterial species.

Urease in acetogenic Lachnospiraceae drives urea carbon salvage in SCFA pools

The gut microbiota produces short-chain fatty acids (SCFA) and acidifies the proximal colon which inhibits enteric pathogens. However, for many microbiota constituents, how they themselves resist these stresses is unknown. The anaerobic Lachnospiraceae family, which includes the acetogenic genus Blautia, produce SCFA, are genomically diverse, and vary in their capacity to acidify culture media. Here, we investigated how Lachnospiraceae tolerate pH stress and found that subunits of urease were associated with acidification in a random forest model. Urease cleaves urea into ammonia and carbon dioxide, however the role of urease in the physiology of Lachnospiraceae is unknown. We demonstrate that urease-encoding Blautia show urea-dependent changes in SCFA production, acidification, growth, and, strikingly, urease encoding Blautia directly incorporate the carbon from urea into SCFAs. In contrast, ureolytic Klebsiella pneumoniae or Proteus mirabilis do not show the same urea-dependency or carbon salvage. In agreement, the combination of urease and acetogenesis functions is rare in gut taxa. We find that Lachnospiraceae urease and acetogenesis genes can be co-expressed in healthy individuals and colonization of mice with a ureolytic Blautia reduces urea availability in colon contents demonstrating Blautia urease activity in vivo. In human and mouse microbial communities, the acetogenic recycling of urea carbon into acetate by Blautia leads to the incorporation of urea carbon into butyrate indicating carbon salvage into broader metabolite pools. Altogether, this shows that urea plays a central role in the physiology of health-associated Lachnospiraceae which use urea in a distinct manner that is different from that of ureolytic pathogens.

Leveraging strain competition to address antimicrobial resistance with microbiota therapies

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

Nonglycosidic C-O bond formation catalyzed by a bifunctional pseudoglycosyltransferase ValL

The C7N antibiotic validamycin A is an antifungal agent widely used as a crop protectant. It comprises a validoxylamine A unit linked to a glucose moiety, which is formed through a nonglycosidic C - N bond connecting a valienol moiety and a validamine moiety, a reaction catalyzed by the pseudoglycosyltransferase ValL. In this study, we analyzed the chemical composition of validamycins in Streptomyces hygroscopicus var. jinggangensis TL01. A series of novel oxygen-bridged analogues, namely, validenomycin, validomycin, and 1,1'-bis-valienol, were identified in the culture supernatants, and their chemical structures were elucidated using a combination of one- and two-dimensional nuclear magnetic resonance and mass spectrometry. Gene disruption and complementation experiments revealed that valL is essential for the biosynthesis of these new oxygen-bridged analogues of validamycins. Biochemical assays further demonstrated that ValL catalyzed the C-O bond formation between GDP-valienol and valienol-7-phosphate, producing 1,1'-bis-valienol-7-phosphate, which was subsequently dephosphorylated by ValO and glycosylated by ValG to yield validenomycin. Collectively, our findings revealed the unique ability of ValL to catalyze nonglycosidic C-O coupling, potentially enabling the generation of various chemical scaffolds for C7N family antibiotics.

Comprehensive phenotyping combined with multi-omics of Salmonella Infantis and its H2S negative variant - Resolving adaption mechanisms to environmental changes

The zoonotic pathogen S. Infantis is of emerging importance, making detection in poultry critical. Phenotypic changes, which are significant for standardized control programs via EN/ISO 6579-1:2017, could lead to pathogens remaining undetected, increasing the risk of food-borne outbreaks. This study investigates an S. Infantis strain with both normal growth (NCP) and atypical H₂S-negative colony variant (ACV) from an Austrian broiler farm. NCP and ACV underwent comprehensive analyses, including stability tests, electron microscopy, whole-genome sequencing, transcriptomics, and proteomics. Our findings demonstrate a stable atypical colony variant exhibiting acquired resistance against cefoxitin in ACV. Genomic analysis identified 9 single nucleotide polymorphisms (SNPs) and two deletions, affecting genes involved in porphyrin and sulfur metabolism. Key factors were a mutation disrupting cysG, which is essential for siroheme biosynthesis and a vital cofactor in sulfur metabolism, and a stop codon in menD (2-oxoglutarate decarboxylase), crucial for small colony variant appearance. Consequently, we hypothesize that these mutations lead to a deficiency in siroheme, as well as anaerobic sulfur respiration altogether resulting in the H₂S-negative phenotype. Functional network analysis highlighted compensatory upregulation of alternative metabolic pathways, including nitrate metabolism, propanoate metabolism and mixed-acid fermentation, which may aid ACV's persistence and adaptation under anaerobic conditions. Reduced flagellin expression suggests a mechanism for immune evasion. These genetic and metabolic adaptations likely respond to environmental stressors, such as oxidative stress from disinfectants or antimicrobial pressure, leading to the emergence of the H₂S-negative phenotype. Consequently, this study provides insights into the genetic and biochemical adaptations of an atypical S. Infantis variant.

Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria

Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2-, N2O, and NH4+, poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4+ and NO2- from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3- from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2- accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2- to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.

Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons

The microbial biodegradation potential of contaminated sites is critical for efficient bioremediation, particularly through bioaugmentation with microorganisms that degrade organic pollutants. The BactoTrapS tool was developed to select and enrich bacteria tolerant to contaminants and capable of biodegradation directly from soils. It comprises a nylon mesh filled with activated carbon or vermiculite spiked with PAHs (phenanthrene, pyrene, dibenzo-a,h-anthracene) or alkanes (n-hexadecane, cyclohexane), while control traps remained unspiked. After five weeks of soil incubation, spiked traps showed significantly higher mineralisation. Bacterial colonisation was evaluated via CFU counts and 16S rDNA qPCR, revealing increased densities in spiked conditions. Alpha diversity analysis showed reduced diversity in spiked traps, while beta diversity confirmed selective enrichment of genera such as Mycobacterium and Polaromonas under PAHs, and Nocardioides and Nocardia under alkanes. These genera were identified as indicator species for the respective contaminants. qPCR of key biodegradation genes (PAH-RHDα, AlkB, CYP153) revealed elevated gene copy numbers in spiked traps. Most isolates from spiked conditions metabolised phenanthrene and hexadecane as sole carbon sources. BactoTrapS offers a rapid, efficient method to enrich biodegrading bacteria for hydrocarbons and other organic contaminants, promising broad applicability for future remediation efforts.

Microplastics in the marine environment: Challenges and the shift towards sustainable plastics and plasticizers

The United Nations (UN) estimate that around 75-199 million tons of plastic is floating in the world's oceans today. Continuous unintentional disposal of plastic waste in marine environments has and continues to cause significant biological impacts to various marine organisms ranging from mild difficulties in swimming or superficial damage to critical organ malfunctions and mortality. Over time, plastics in these environments degrade into microplastics which are now acknowledged as a pervasive harmful pollutant found in the cryosphere, atmosphere and hydrosphere. In response to this issue, the production of bespoke biodegradable bioplastics derived from renewable resources, such as vegetable oils, starch and plant fibres, is emerging to mitigate our reliance on environmentally persistent conventional fossil fuel-based plastics. While bioplastics degrade more readily than conventional plastics, they present new challenges, including leaching of toxic chemical additives and plasticizers into the environment. Consequently, various techniques have been explored in the search for sustainable plasticizers, from cheap, non-toxic compounds, such as vegetable oils and sugars to hyperbranched structures with limited migration. This article seeks to explain the intricate relationship between the problem of microplastics in marine environments and the strategies that have been investigated to address it thus far.

Dimercaptosuccinic acid with membrane-targeting activity against Pseudomonas aeruginosa

BACKGROUND

Multidrug resistant (MDR) gram-negative bacteria (GNB) are a serious health threat. GNB require divalent cations for the integrity of their outer membrane (OM), which can be inhibited by dimercaptosuccinic acid (DMSA), a sulfhydryl-containing metal chelator that has been used as an antidote to heavy metal toxicity. We aim to investigatethe effects and mechanisms of action of DMSA on Pseudomonas aeruginosa.

MAIN METHODS

The inhibition of P. aeruginosa strains by DMSA was determined using growth kinetics analysis. Biofilm formation was evaluated using crystal violet staining after incubation for 24 h. We determined the bacterial OM permeability and cell membrane potential using propidium iodide (PI) and bis-(1,3-dibutylbarbituric acid) trimethineoxonol (DiBAC4(3)) staining, respectively, following DMSA exposure. The bioenergetics-related activity of DMSA-treated bacteria was assessed by determining intracellular ATP levels, bacterial motility and N-phenyl-naphtylamide (NPN) efflux assay.

RESULTS

DMSA inhibited the growth of bacteria in a concentration-dependent manner and repressed biofilm formation by P. aeruginosa. DMSA-treated bacteria exhibited increased PI uptake and enhanced DiBAC4(3) fluorescence intensity compared with untreated cells. Treatment of P. aeruginosa with DMSA reduced the intracellular ATP levels, bacterial motility, and efflux activity in the tested cells.

SIGNIFICANCE

The antibacterial mechanisms of DMSA may be related to alterations in OM permeability, membrane depolarization, and impaired bioenergetics-related activity, which are essential for bacterial viability and infection.

Iron sensing, signalling and acquisition by microbes and plants under environmental stress: Use of iron-solubilizing bacteria in crop biofortification for sustainable agriculture

Iron is very crucial micronutrient prerequisite for growth of all cellular organisms including plants, microbes, animals and humans. Though iron (Fe) is present in abundance in earth's crust, but most of its forms present in soil are biologically unavailable, thus putting a constraint to utilize it. Plants and microorganisms maintain iron homeostasis to balance the supply of enough Fe for metabolism from their surrounding environments and to avoid excessive toxic levels. Microorganisms and plants employ different strategies for sensing, signaling, transportation and uptake of Fe under different types of stressed environments. Microbial communities present in soil and vicinity of roots contribute in biogeochemical cycling and uptake of different nutrients including Fe resulting into improved soil fertility and plant health. In this review, the regulation of iron uptake and transport under different kinds of biotic and abiotic stresses is described. In addition, the insights have been provided for enhancing bioavailability of Fe in sustainable agriculture practices. The inoculation of different crop plants with iron solubilizing microbes improved bioavailablilty of Fe in soil and increased plant growth and crop yield. Insights were provided about possible role of recent bioengineering techniques to improve Fe availability and uptake by plants. However, well-planned and large-scale field trials are required before recommending particular iron solubilizing microbes as biofertilizers for increasing Fe availability, improving plant development and crop yields in sustainable agriculture.

Biological methane removal by groundwater trickling biofiltration for emissions reduction

Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.

Synthesis, screening and validation of cysteine-reactive fragments as chikungunya virus protease inhibitors

Alphaviruses like the Chikungunya virus cause severe outbreaks; however, no specific treatments are available. Their viral replication depends on the nsP2 cysteine protease, a promising but underexplored target for drug discovery. In this study, we report a covalent fragment screening against Chikungunya virus nsP2 protease, resulting in the identification of three inhibitors that can serve as starting points for future drug development. Careful validation proved indispensable in eliminating false-positive hits from a Förster resonance energy transfer (FRET)-based inhibition assay, wherein interference was caused by the inner filter effect between the fluorescent substrate and coloured compounds. Jump-dilution experiments accompanied by reactivity studies with cysteine and the recombinant protein indicate covalent inhibition via thia-Michael addition. We further demonstrate cross-inhibition of the related alphavirus nsP2 protease from Sindbis virus. The study provides early insights into nsP2 inhibition by electrophilic fragments featuring non-promiscuous N-arylacrylamides, thus advancing the search for antivirals targeting Chikungunya and other alphaviruses of concern.

Streptococcus suis regulates central carbon fluxes in response to environment to balance drug resistance and virulence

Streptococcus suis, a zoonotic pathogen, must adapt to the distinct nutritional environment of the host microhabitat during infection and the establishment of invasive disease, primarily by modulating its metabolic pathways. Metabolic plasticity endows S. suis with an enhanced capacity for environmental adaptation. Multidrug-resistant S. suis is increasingly prevalent due to the extensive use of antibiotics in swine production. In this study, an environment-dependent evolutionary model demonstrated that S. suis could modulate its metabolism in response to environmental changes, thereby altering its drug resistance and virulence. The central carbon flux regulated by pyruvate dehydrogenase (PDH) was identified as a pivotal node in balancing drug resistance and virulence in S. suis. Within the in vivo host environment, increased carbon flux through PDH enhances the production of capsular polysaccharide (CPS), thereby improving immune evasion. Conversely, in the antibiotic environment, reduced carbon flux through PDH downregulates the bacterial metabolic state, which diminishes the induction of toxic metabolites by antibiotics, thereby augmenting drug resistance. This concept provides a reasonable explanation for the puzzling phenomena observed with S. suis in clinical settings. For instance, antibiotic-resistant S. suis has a survival advantage in pig farms where antibiotics are frequently used but is less frequently associated with invasive infections. Furthermore, this study demonstrates that exogenous pyruvate can enhance the bactericidal effect of gentamicin against clinically multidrug-resistant S. suis, offering new insights and potential strategies for controlling clinical multidrug-resistant S. suis infections.

Synthetic biology of Fusarium for the sustainable production of valuable bioproducts

Synthetic biology offers transformative opportunities to optimise Fusarium species as efficient platforms for the sustainable production of diverse bioproducts. Advanced engineering techniques, including CRISPR/Cas9, RNA interference and synthetic promoters, have enhanced the manipulation of metabolic pathways, enabling higher yields of industrially relevant compounds. Recent insights from next-generation sequencing and omics technologies have significantly expanded our understanding of Fusarium's metabolic networks, leading to more precise strain engineering. Despite these advances, challenges such as metabolic bottlenecks, regulatory complexities and strain stability remain significant barriers to industrial-scale applications. The development of efficient genetic tools, together with the expansion of our knowledge of Fusarium physiology and genetics thanks to systems biology approaches, holds promise to unlock Fusarium's full potential as a sustainable cell factory. This review focuses on the genetic and metabolic tools available to enhance Fusarium's capacity to produce biofuels, pharmaceuticals, enzymes and other valuable compounds. It also highlights key innovations and discusses future directions for leveraging Fusarium as an environmentally friendly bioproduction system.

Recent advances in smart hydrogels derived from polysaccharides and their applications for wound dressing and healing

Owing to their inherent biocompatibility and biodegradability, hydrogels derived from polysaccharides have emerged as promising candidates for wound management. However, the complex nature of wound healing often requires the development of smart hydrogels---intelligent materials capable of responding dynamically to specific physical or chemical stimuli. Over the past decade, an increasing number of stimuli-responsive polysaccharide-based hydrogels have been developed to treat various types of wounds. While a range of hydrogel types and their versatile functions for wound management have been discussed in the literature, there is still a need for a review of the crosslinking strategies used to create smart hydrogels from polysaccharides. This review provides a comprehensive overview of how stimuli-responsive hydrogels can be designed and made using five key polysaccharides: chitosan, hyaluronic acid, alginate, dextran, and cellulose. Various methods, such as chemical crosslinking, dynamic crosslinking, and physical crosslinking, which are used to form networks within these hydrogels, ultimately determine their ability to respond to stimuli, have been explored. This article further looks at different polysaccharide-based hydrogel wound dressings that can respond to factors such as reactive oxygen species, temperature, pH, glucose, light, and ultrasound in the wound environment and discusses how these responses can enhance wound healing. Finally, this review provides insights into how stimuli-responsive polysaccharide-based hydrogels can be developed further as advanced wound dressings in the future.

Emerging structure of chlorovirus PBCV-1

The large plaque-forming chloroviruses infect isolates of eukaryotic chlorella-like green algae. Initial cryo-electron microscopy (cryo-EM) studies revealed that PBCV-1 was icosahedral, with a multilaminate shell surrounding an electron-dense core, and that PBCV-1 particles measured about 1900 Å in diameter with a triangulation number of 169d. However, as described in this review cryo-EM procedures have improved and PBCV-1 is more complex than originally described. A five-fold symmetry reconstruction of cryo-EM images at 8.5 Å revealed that the virus contains a unique vertex with a spike-structure and an internal single lipid bi-layered membrane. Improvement to 3.5 Å resolution revealed that the capsid contains 30 virus-encoded proteins and that it contains six different types of capsomers. The outer surface of three of the six types of capsomers are attached to fiber structures.

Single cell protein production potential of enriched microbial populations from rice paddy soils and roots: Insights into protein yield enhancement by Methylophilaceae

This study aimed to determine key factors for enriching methylotrophic populations for single-cell protein (SCP) production and to determine the predominant active methylotrophs. Microbial populations from rice paddy soils and roots, hotspots for CH4 oxidation, underwent serial incubation by feeding CH4 and O2. The protein content was primarily influenced by the incubation stage, with a lesser effect from the rice plant roots as an inoculum source, reaching a maximum of 20 % in biomass dominated by Methylomonadaceae and Methylophilaceae. While Methylomonadaceae as CH4 oxidizers exhibited lower abundance but high transcription activity, Methylophilaceae as methanol oxidizers were more abundant and strongly correlated with protein content (Pearson's coefficient >0.8, p < 0.05). Enhancing Methylophilaceae in the mixed cultures may improve SCP yields via interactions with Methylomondaceae, likely mediated by methanol. The cooperative relation plausibly offers a promising strategy for sustainable CH4-based SCP production.

Sludge retention time in anaerobic digestion affects Archaea by a cascade through microeukaryotes

Anaerobic digestion is a crucial process for treating organic waste, such as wastewater sludge, agricultural residues and food waste. While the influence of physicochemical parameters on the prokaryotic community composition in anaerobic digesters has been extensively characterized, the role of biotic interactions in shaping the prokaryotic communities remains poorly understood. This study addresses this knowledge gap by analyzing the complete active microbiome of nine full-scale anaerobic digesters. Our findings reveal that eukaryotes, consisting primarily of protists and fungi, account for approximately 40 % of RNA sequence reads alongside dominant Archaea, indicating their substantial role in the digestion process. Our results suggest that the chosen sludge retention time during anaerobic digestion indirectly affects the archaeal community composition and thus treatment efficacy by cascading through eukaryotes, highlighting their integral role in the system. This study highlights the critical role of eukaryotes in regulating prokaryotic communities and their indirect contribution to the optimization of anaerobic digestion efficiency.

Enzymatic absorption promoters for non-invasive peptide delivery

Peptide drugs offer considerable potential for treating a diverse range of diseases. Yet, their clinical application is generally restricted to injectable therapies. The main challenge hindering their broader use through globally accessible, patient-friendly, and non-invasive delivery routes such as oral or buccal, lies in their poor ability to cross biological barriers effectively. Here, we demonstrate that enzymes can be harnessed to transiently reduce these barriers and improve absorption. As a proof of concept, we employ a mucin-specific protease (mucinase) and a phospholipase to increase mucus diffusivity and epithelial cell membrane permeability, respectively. In a canine model, we show that enteric capsules containing both enzymes, and the peptide drug desmopressin achieved a relative bioavailability of 155 % compared to the drug alone. Additionally, a buccal patch loaded with phospholipase and semaglutide displayed a 5-fold higher bioavailability and lower variability (71.5 % reduction in the coefficient of variation) compared to the commercially available oral tablet. These results suggest that enzymatic modulation of biological barriers holds promise as a strategy to improve non-invasive delivery of peptides and potentially other macromolecular drugs.

Fate reversal: Exosome-driven macrophage rejuvenation and bacterial-responsive drug release for infection immunotherapy in diabetes

Superficial surgical site infection (SSI) is a significant risk factor for the development of periprosthetic joint infection (PJI), particularly in diabetic patients. A high-glucose microenvironment is observed to compromise phagocytosis by inducing cellular senescence, which leads to impaired antibacterial immune function. Exosomes derived from umbilical cord stem cells (H-Exos) can reverse the immunosuppressive microenvironment by rejuvenating senescent cells, thereby terminating excessive, persistent, and ineffective inflammatory responses. Thus, a novel exosome-based immunotherapeutic antibacterial strategy to reverse fate is proposed. Vancomycin & lysostaphin-loaded exosomes are incorporated in a customizable microneedle patch (ExoV-ExoL@MN) for controlled release, enabling tailored treatments for diverse clinical scenarios. While rejuvenating macrophage senescent phenotype, the antibiotics encapsulated within exosomes can be responsively released by the hemolysin secreted by bacteria, triggering rapid bacterial killing. Post-infection clearance, they induce a shift from M1 to M2 macrophage polarization, thereby enhancing anti-inflammatory and reparative responses. Furthermore, the components can be mixed on demand and at any time, allowing for real-time customization and fabrication directly at the clinic (fabrication@clinic). This strategy reverses the immunosuppressive microenvironment by rejuvenating senescent macrophages and effectively combats bacterial invasion into deep tissues through bacteria-responsive antibiotic release, providing a promising approach for preventing and treating SSI-induced PJI.

Structural optimization and discovery of high effective isopropanolamine-based TPS1 inhibitors as promising broad-spectrum fungicide candidates

To address the growing resistance and environmental issues of existing fungicides, the development of novel broad-spectrum fungicides based on new targets, such as TPS1, has been prioritized. However, related research remains limited. In this study, we optimized our previously reported isopropanolamine-based MoTPS1 inhibitor, j11, by replacing its groups on both sides of its isopropanolamine linker with sulfonamide and 1,2,4-triazole fragments through a fragment replacement combining rational design approach. This approach led to the identification of novel isopropanolamine compounds, including g12, g18, o1, and o3, exhibiting significantly improved TPS1 inhibition compared to j11, with IC50 values against MoTPS1 and BcTPS1 of 8.38-14.73 and 38.70-59.99 μM, respectively. The interaction mechanism research confirmed that hydrogen bonds and salt bridges between the novel isopropanolamine compounds and the Glu396 residue in MoTPS1 were crucial during their interaction. Plant leaf and fruit inoculation experiment revealed that these novel isopropanolamine compounds exhibiting substantial inhibition against MoTPS1 and BcTPS1 significantly suppressed the infection of Magnaporthe oryzae and Botrytis cinerea. Preliminary fungicidal mechanism studies indicated that these novel isopropanolamine compounds disrupted various fungal physiological processes including sporulation, conidia germination, appressorium formation, and turgor pressure accumulation within appressorium, while also causing conidia deformation. The hyphal growth inhibition assay against various plant pathogenic fungi suggested that the novel isopropanolamine compounds such as o1 and o3 held the potential as broad-spectrum fungicide candidates with EC50 values of 2.80-17.55 μg/mL. The toxicological assessment suggested that compounds o1 and o3 had no potential toxicity towards diverse non-target organisms. This study provided a valuable insight for optimizing and developing high effective TPS1 inhibitors to be applied in the control of plant diseases.

Efficacy of nitric oxide donors and EDTA against Pseudomonas aeruginosa biofilms: Implications for antimicrobial therapy in chronic wounds

Opportunistic pathogen Pseudomonas aeruginosa plays a crucial role in chronic wound biofilms, increasing infection's morbidity and mortality. In recent years, the signalling molecule nitric oxide (NO) and chelating agent tetrasodium EDTA (T-EDTA) have been applied therapeutically owing to their multifactorial effects including bacterial killing, biofilm dispersal, and wound healing. However, previous studies assessing NO's antibiofilm efficacy have not considered the variable pH and temperature of the wound environment. Here, pH-dependent NO donors N-diazeniumdiolates (NONOates), PAPA NONOate (PA-NO) and Spermine NONOate (SP-NO), and T-EDTA were applied in wound-relevant pH environments (pH 5.5-8.5) and temperatures (32 °C and 37 °C) to P. aeruginosa PAO1 biofilms grown for either 24 or 48 h. At 32 °C and pH 7.5, 250 μM PA-NO reduced 24-h biofilm biomass by 35 %. At 37 °C, 250 μM PA-NO and 4 % w/v T-EDTA caused 21 % and 57 % biomass reduction in 24-h biofilms, respectively. In 48-h biofilms, NONOates did not induce significant biomass reduction, while T-EDTA maintained its efficacy with a 64 % reduction. A subsequent experiment investigated the impact of NONOates and T-EDTA as pre-treatments before exposure to ciprofloxacin. Unexpectedly, NONOate pre-treatment decreased ciprofloxacin's effectiveness, resulting in approximately 1-log increase in viable planktonic and biofilm-residing cells compared to ciprofloxacin alone. It was hypothesized that this protective effect might stem from NO-induced decreased cellular respiration, which inhibits reactive oxygen species (ROS)-mediated bactericidal mechanisms. These findings highlight both the potential and complexities of developing effective antimicrobial strategies for chronic wound infections, emphasizing the need for further research to optimize treatment approaches.

Lacticaseibacillus paracasei AD22 Stress Response in Brined White Cheese Matrix: In Vitro Probiotic Profiles and Molecular Characterization

Functionalizing foods involve discovering and integrating new candidate health-promoting bacteria into the food matrix. This study aimed (i) to reveal the probiotic potential of autochthonous Lacticaseibacillus paracasei AD22 by a series of in vitro tests and molecular characterization and (ii) to evaluate its application to the matrix of brined white cheese, which is the most common cheese in Türkiye, in terms of survival and stress response. To evaluate in vitro probiotic characteristics, L. paracasei AD22 was exposed to functional, technological, and safety tests. Pilot scale production was conducted to integrate L. paracasei AD22 into the brined white cheese matrix. The expression levels of stress-related genes (dnaK, groES, ftsH, argH, and hsp20) were detected by reverse-transcriptase polymerase chain reaction to determine the transcriptional stress response during ripening. The presence of genes encoding stress-related proteins was determined by whole-genome sequence analysis using a subsystem approach; the presence of antibiotic resistance and virulence genes was determined by ResFinder4.1 and VirulenceFinder 2.0 databases. The BAGEL4 database determined the presence of bacteriocin clusters. L. paracasei AD22 was found to survive in pH 2 and medium with 12% NaCl and did not cause hemolysis. Adhesion of the strain to Caco2 cells was 76.26 ± 4.81% and it had coaggregation/autoaggregation properties. It was determined that L. paracasei AD22 exceeded 7 log cfu/g in the cheese matrix at the end of the ripening period. Total mesophilic aerobes decreased in the cheese inoculated with L. paracasei AD22 after the 45th day of ripening. While hsp20 and groES genes were downregulated during ripening, argH was upregulated. Both downregulation and upregulation were observed in dnaK and ftsH. Fold changes indicating the expression levels of dnaK, groES, ftsH, argH, and hsp20 genes were not statistically significant during ripening (p > 0.05). Whole-genome sequence profiles revealed that the strain did not contain antibiotic and virulence genes but bacteriocin clusters encoding Enterolysin A (Class III bacteriocin), Carnosine CP52 (class II bacteriocin), Enterocin X beta chain (Class IIc bacteriocin), and the LanT region. Subsystems approach manifested that the most functional part of the genomic distribution belonged to metabolism, protein processing, and stress response functions. The study findings highlight that L. paracasei AD22 will provide biotechnological innovation as a probiotic adjunct because it contains tolerance factors and probiotic characteristics to produce new functional foods.

Oligomer assembly of Bacillus thuringiensis Cyt2Aa2 on lipid membranes reveals a thread-like structure

Bacillus thuringiensis, a well-known insecticidal bacterium, produces several insecticidal proteins, including cytolytic (Cyt) proteins. Cyt proteins bind directly to the lipid membrane and form large protein complexes. In addition to the protein ladder bands, information on the oligomeric structure in lipid membranes is necessary to understand the mechanism of Cyt proteins on target cells. In this work, we have investigated the oligomeric Cyt2Aa2 complex with synthetic lipid and with erythrocyte membranes. When the activated Cyt2Aa2 protein was incubated with these lipid membranes, the protein ladder pattern relevant to hemolytic activity was detected in SDS-PAGE. Moreover, AFM topographic images revealed a fusilli-like structure and a ring-like structure for synthetic POPC and POPC/Chol, respectively. Furthermore, TEM micrographs provided an additional information on the oligomeric structure of Cyt2Aa2 in erythrocytes. Cyt2Aa2 appears to oligomerise/aggregate into mixed structures between the filamentous structure and small protein complexes in erythrocytes. In addition, a nanopore was found to be a substructure of the filamentous structure. These results strengthen the understanding of Cyt2Aa2 behavior in these two membrane systems, the fusilli and ring-like structures, depending on the type of lipid membrane. Furthermore, the structure of Cyt2Aa2 in insect target membranes remains to be investigated.

Quantitative microbial risk assessment of Legionella pneumophila in a drinking water distribution system: A case study

Background

Legionella pneumophila poses a significant health risk in hospital water systems. This study assessed the risk associated with Legionella contamination in a hospital drinking water system in Sari, Iran, over one year.

Methods

Water samples were collected seasonally from various hospital taps, including patient room showers and toilet faucets. Both cold and warm water sources were analyzed. Water quality parameters, including pH, chlorine levels, and temperature, were measured. Legionella spp. were isolated and enumerated using standard microbiological techniques, and species identification was confirmed via 16S rRNA gene sequencing. A Quantitative Microbial Risk Assessment (QMRA) model was employed to estimate the infection risk from shower and faucet use.

Results

Legionella counts were significantly higher in warm water samples and during the summer season. A positive correlation was observed between Legionella counts and water pH, whereas negative correlations were found with chlorine levels and water temperature. QMRA results indicated that the estimated annual infection risk exceeded the acceptable limits set by the World Health Organization (WHO) and the United States Environmental Protection Agency (USEPA), particularly during summer.

Conclusions

The findings suggest that existing water management practices may be inadequate for controlling Legionella growth and transmission. Seasonal variations significantly impact infection risk, emphasizing the need for improved monitoring and control strategies. However, limitations related to sampling methodology, geographic specificity, and dose-response modeling should be considered when interpreting the results.

Detoxification techniques for bacterial toxins: A pathway to effective toxoid vaccines

Bacterial toxins play a critical role in the virulence of many pathogens, leading to serious diseases such as tetanus, diphtheria, botulism, and entrotoxemia. As key virulence factors, these toxins cause significant tissue damage and disease manifestations in infected hosts. Vaccination against these toxins through toxoid vaccines, composed of inactivated forms of the toxins, represents a vital strategy for preventing toxin-mediated diseases. However, creating effective toxoid vaccines necessitates meticulous detoxification processes that ensure the loss of toxicity while retaining the immunogenic properties inherent in the native toxins. This review offers a comprehensive evaluation of the diverse methodologies employed for detoxifying bacterial toxins, highlighting their advantages, limitations, and implications for vaccine development. By detailing comparisons of efficacy, stability, residual toxicity, and clinical applicability, we demonstrate that while traditional methods utilizing chemical reagents (such as formaldehyde) remain widely used, emerging technologies like genetic inactivation and protein engineering present significant advantages. These innovations promise to advance the development of durable and irreversible toxoid vaccines that protect public health and contribute to future vaccine formulation improvements. Ultimately, this knowledge synthesis aims to guide future research efforts and facilitate the design of safer and more effective toxoid vaccines to combat the public health threats posed by toxin-producing bacteria.

Counterintuitive method improves yields of isotopically labelled proteins expressed in flask-cultured Escherichia coli

NMR is a powerful tool for the structural and dynamic study of proteins. One of the necessary conditions for the study of these proteins is their isotopic labelling with 15N and 13C. One of the most widely used methods to obtain these labelled proteins is heterologous expression of the proteins in E. coli using 13C-D-glucose and 15NH4Cl as the sole nutrient sources. In recent years, the price of 13C-D-glucose has almost tripled, making it essential to develop labelling methods that are as cost effective as possible. In this work, different parameters were studied to achieve the most rational use of 13C-D-glucose, and an optimized method was developed to obtain labelled proteins with high labelling and low 13C-D-glucose consumption. Surprisingly, the optimized method is also simple and does not require monitoring of culture growth.

Efficacy of oxidative disinfectants, quaternary ammonium compounds and dry heat on the inactivation of Salmonella Enteritidis in different cellular states

The investigation of disinfection methods with different antimicrobial mechanisms is of utmost importance in determining inactivation kinetics pertaining to various cellular states of Salmonella. The present study evaluated the effectiveness of different conventional and novel disinfectants against the inactivation of suspended and desiccated Salmonella enterica Enteritidis FUA1946. A comparative study was conducted to evaluate the efficacy of various disinfection methods, including dry heat, membrane-acting benzalkonium chloride (BAC), conventional oxidizing agents such as peracetic acid (PAA) and hydrogen peroxide (H2O2) in the inactivation of S. Enteritidis. Further, the efficacy of novel oxidizers such as plasma-activated water bubbles (PAWB) and plasma-activated hydrogen peroxide water bubbles (PAHP-WB) was evaluated against the suspended and desiccated S. Enteritidis. The results showed that the disinfectant concentration, treatment temperature, and treatment time significantly affected the susceptibility of the S. Enteritidis to disinfection methods. Compared to the surface-dried cells, the S. Enteritidis suspensions displayed a higher lethality to the tested disinfectants. The results revealed a greater resistance of the air-dried and equilibrated S. Enteritidis on the stainless steel to dry heat, BAC, H2O2, and PAWB. The PAA treatment 40 °C displayed high efficacy against the S. Enteritidis on the stainless steel. This emphasizes the need to incorporate effective disinfection programmes to prevent the spread of S. Enteritidis in dry processing environments. Moreover, conducting a comparative analysis of the diverse cellular states of bacteria is crucial in the context of disinfection of the low-aw food processing industry.

Cryo-EM structure of a phosphotransferase system glucose transporter stalled in an intermediate conformation

The phosphotransferase system glucose-specific transporter IICBGlc serves as a central nutrient uptake system in bacteria. It transports glucose across the plasma membrane via the IICGlc domain and phosphorylates the substrate within the cell to produce the glycolytic intermediate, glucose-6-phosphate, through the IIBGlc domain. Furthermore, IICGlc consists of a transport (TD) and a scaffold domain, with the latter being involved in dimer formation. Transport is mediated by an elevator-type mechanism within the IICGlc domain, where the substrate binds to the mobile TD. This domain undergoes a large-scale rigid-body movement relative to the static scaffold domain, translocating glucose across the membrane. Structures of elevator-type transporters are typically captured in either inward- or outward-facing conformations. Intermediate states remain elusive, awaiting structural determination and mechanistic interpretation. Here, we present a single-particle cryo-EM structure of purified, n-dodecyl-β-D-maltopyranoside-solubilized IICBGlc from Escherichia coli. While the IIBGlc protein domain is flexible remaining unresolved, the dimeric IICGlc transporter is found trapped in a hitherto unobserved intermediate conformational state. Specifically, the TD is located halfway between inward- and outward-facing states. Structural analysis revealed a specific n-dodecyl-β-D-maltopyranoside molecule bound to the glucose binding site. The sliding of the TD is potentially impeded halfway due to the bulky nature of the ligand and a shift of the thin gate, thereby stalling the transporter. In conclusion, this study presents a novel conformational state of IICGlc, and provides new structural and mechanistic insights into a potential stalling mechanism, paving the way for the rational design of transport inhibitors targeting this critical bacterial metabolic process.

Hydrogel and fish mucus mediated semi-biofloc formation, nitrogenous stress mitigation and growth performance of fish in integrated bioremediation system of aquaculture

Intensive aquaculture system tends to produce excessive ammonia and other nitrogenous metabolites and microbial load, which lead to abiotic and biotic stresses in fish. Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. In the present study, 90-days experiments were conducted at two stocking densities 80 and 160 per m3 fish (7.15 ± 0.05 g) coupled with xanthan gum (ED1) and sweet potato powder (ED2) for mitigation of priority stresses in Labeo rohita. Highest average body weight (17.71 ± 0.15 g), average daily gain (0.12 ± 0.01 g), specific growth rate (1.02 ± 0.01 g day-1), percentage weight gain (150.73 ± 1.01) and feed efficiency ratio (1.00 ± 0.01) were found in 80 fish per m3 coupled with ED2. Bacterial counts (2.6 × 106 CFU ml-1) and removal efficiency of total ammonia-N (97.6 %) and nitrite-N (99.99 %) were significantly(P < 0.05) higher in 160 fish per m3 coupled with ED2. Maturation of biofloc bacterial biomass and bio-stimulatory effects were found to be the major mechanism. Fish mucus was found to be bactericidal mostly against fish pathogenic bacteria Aeromonas hydrophila and Edwardsiella tarda due to antagonistic effect of probiotic microbiome of green slime. Bacteria as safe candidate probionts in fish health management have been isolated and identified as Bacillus spp based on 16S rDNA and FAME approaches. Low level of catalase and SOD was observed in gill, muscle and liver in treatments, indicating stress alleviation to the culture organisms. For the first time, coupling of fish green slime with hydrogel has newly been coined an integrated hydrogel-mucus-based bioremediation system. The investigation of fish mucus has a very important biological and environmental roles in potential applications in species diversification and climate-resilient aquaculture and culture-based fisheries.

Peering into the Bacterial Cell: From Transcription to Functional Genomics

I started my faculty career in 1981 at the UW-Madison in the Department of Bacteriology and moved to the University of California, San Francisco in 1993, where I am a Professor in the Departments of Microbiology and Immunology and Cell and Tissue Biology. In this article, I first review my contributions to understanding the molecular biology of the bacterial transcriptional apparatus and the global role of alternative sigmas (σs), a major pillar of bacterial transcriptional control. I then discuss my role in spearheading the development of bacterial systems biology, specifically to the genome-wide phenotyping approaches necessary for rapid understanding of gene function and the molecular basis of pathway connections across the bacterial universe.

Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling

Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5 % w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.

Identification of a Snf7-domain-containing protein that exhibits high affinity and synergistic activity for Cry13Aa1 toxin in Bursaphelenchus xylophilus

Pine wilt disease, caused by the pinewood nematode Bursaphelenchus xylophilus (Rhabditida: Aphelenchoididae), results in significant global economic and ecological impacts. Although the Cry13Aa1 toxin from Bacillus thuringiensis shows nematicidal activity, its mechanism of action against B. xylophilus remains unclear. This study aimed to identify and characterize the receptors for Cry13Aa1 in B. xylophilus. We cloned the cDNAs encoding an Snf7 domain-containing protein (BxSnf7) from B. xylophilus. Far-western blot analysis revealed a specific binding interaction between BxSnf7 and Cry13Aa1, showing a dissociation constant (Kd) of 20.8 ± 4.2 nM. Interestingly, bioassay results indicated that silencing BxSnf7 increased the susceptibility of nematodes to Cry13Aa1 at higher concentrations, although the difference was not statistically significant. Besides, the combined application of BxSnf7 with Cry13Aa1 significantly enhanced nematicidal mortality (95.9 %) after 24 h of treatment, which higher than the expected mortality (42.8 %) (χ2 = 16.118, P = 0.048), indicating that the exogenous BxSnf7 synergistically enhances the activity of Cry13Aa1 toxin. These findings identify BxSnf7 as a novel Cry13Aa1 binding protein and reveal a unique mechanism by which BxSnf7 synergistically enhances the activity of Cry13Aa1. However, BxSnf7 does not function as the primary receptor, and further research is needed to investigate its role in modulating nematode susceptibility to Cry13Aa1.

Microbial communities and fatty acid markers across acidification and eutrophication extremes in a river influenced by mining activities

Microbial communities in combination with fatty acid and isotopic markers were studied seasonally to assess the effects of acid mine drainage (AMD) and nutrient loads in the Spree river. Negative values of δ15N, the bacterial and detrital markers 18: 1(n-7) and 18:1(n-9), pH values ∼3 and bacteria of the genera Ferrovum, Thiomonas, Acidocella, Acidiphilum, Syderoxydans and Galionella were characteristic of the AMD extreme. Potential iron-oxidizers may produce ferric ions and their precipitates may influence biogeochemical processes, while potential sulfur-oxidizers may contribute to elevated sulphate concentrations and challenge drinking water production in the Spree catchment. In this river, eutrophication was linked with polyunsaturated fatty acids (PUFA) enrichment and not with PUFA depletion as occurs in other freshwater systems. Elevated concentrations and proportions of PUFA as well as higher relative sequence abundance of cyanobacteria were characteristic of the highly eutrophic station, particularly during the phytoplankton bloom. The 18:5(n-3) from flagellates or dinoflagellates may indicate lipid anabolism and trophic upgrading processes. The dominance of the classes Bacteroidia, Gammaproteobacteria and Actinobacteria suggested eutrophic and changing hydrological conditions in the river. The microbial communities were better markers of seasonality than the biogeochemical markers and their combination offers an excellent resolution for the study of the ecology and biogeochemistry of water courses. The expected decreased runoff under climate-driven scenarios may worsen the AMD pollution and eutrophication problems and signify a considerable challenge for water management.

Targeted inhibition of oral biofilm formation using phage-derived high-affinity peptides

Dental caries, commonly known as tooth decay, poses a significant oral health challenge affecting individuals of all age groups. While dietary factors play a role, tooth decay primarily results from the activity of various oral bacteria that form biofilms in the oral cavity. In this study, we employed the phage display technique to identify high-affinity peptides capable of binding specifically to three oral bacteria strains: Streptococcus mutans, Streptococcus oralis, and Lactobacillus casei. Four selected peptides underwent binding affinity testing for each target bacterium, revealing that three of them exhibited specific binding capabilities, effectively inhibiting biofilm formation. This study demonstrates the efficacy of engineered phages in identifying high-affinity peptides that selectively target oral bacteria. These peptides hold promise for preventing oral biofilm formation, a significant contributor to oral diseases and dental caries. This innovative approach opens doors to novel therapeutic strategies for addressing oral health issues. The findings may spur further research into the utilization of phages and peptides as potential anti-biofilm agents, potentially revolutionizing the field of oral health.

Soil Organic Matter and Total Nitrogen Reshaped Root-Associated Bacteria Community and Synergistic Change the Stress Resistance of Codonopsis pilosula

The stress resistance of medicinal plants is essential to the accumulation of pharmacological active ingredients, but the regulation mechanism of biological factors and abiotic factors on medicinal plants is still unclear. To investigate the mechanism of soil nutrient and microecology on the stress resistance of C. pilosula, rhizosphere soil and roots were collected across the four seasons in Minxian, Gansu, and their physicochemical properties, as well as root-associated microorganisms, were examined. The results showed that the bacterial α-diversity indexes increased in the endosphere and rhizosphere from summer to autumn. At the same time, the community composition and function changed considerably. The stability of the endophytic bacterial community was higher than that rhizospheric bacteria, and the complexity of the endophytic bacterial community was lower than rhizospheric bacteria. Soil organic matter (OM), water content (WC), total potassium (TK), and total nitrogen (TN) have been identified as the key factors affecting bacterial community diversity and stress resistance of C. pilosula. WC, TN, and OM showed significant differences from summer to autumn (P < 0.5). Four key soil physiochemical factors changed significantly between seasons (P < 0.01). TN and OM change the stress resistance of C. pilosula mainly by changing the activity of antioxidant enzymes. Changes of OM and endophytic bacterial diversity affect the accumulation of soluble sugars to alter stress resistance. These four key soil physicochemical factors significantly influenced the diversity of endophytic bacteria. WC and OM were identified as the most important factors for endophytic and rhizospheric bacteria, respectively. This study provided the research basis for the scientific planting of C. pilosula.

Be a GEM: Biocontained, environmentally applied, genetically engineered microbes

Technological advances in engineering biology or synthetic biology have enabled practical applications of genetically engineered microbes (GEMs), including their use as living diagnostics and vehicles for therapeutics. However, technological and non-technological issues associated with biocontainment of GEMs have yet to be addressed before fully realizing their potential. In this short perspective, I briefly discuss the relevant technologies for GEM biocontainment as well as environmental impacts, regulatory issues, and public perception of GEMs.

In silico DFT and molecular modeling of novel pyrazine-bearing thiazolidinone hybrids derivatives: elucidating in vitro anti-cancer and urease inhibitors

In the present work, one of the leading health issues i.e. cancer was targeted by synthesizing and biologically investigating the potential of pyrazine-based thiazolidinone derivatives (1-13). The basic structure of the synthesized compounds was determined using a variety of spectroscopic techniques, including 1H NMR, 13C NMR, and HREI-MS. These scaffolds were studied for their biological profiles as anti-cancer as well as anti-urease agents. The biological effectiveness of these compounds was compared using the reference tetrandrine (IC50 = 4.50 ± 0.20 µM) and thiourea (IC50 = 5.10 ± 0.10 µM), respectively. Among novel compounds, scaffold 3, 6, 7 and 10 demonstrated an excellent potency with highest inhibitory potential (IC50 = 1.70 ± 0.10 and 1.30 ± 0.20 µM), (IC50 = 4.20 ± 0.10 and 5.10 ± 0.30 µM), (IC50 = 2.10 ± 0.10 and 3.20 ± 0.20 µM) and (IC50 = 2.70 ± 0.20 and 4.20 ± 0.20 µM), respectively, out of which scaffold 3 emerged as the leading compound due to the presence of highly reactive -CF3 moiety which interacts via hydrogen bonding. Molecular docking investigations of the potent compounds was also carried out which revealed the binding interactions of ligands with the active sites of enzyme. Moreover, the electronic properties, nucleophilic and electrophilic sited of the lead compounds were also studied under density functional theory (DFT).

Temporal patterns and influences of monthly, seasonal and annual temperatures on methane emissions in Greece, Armenia and Russia over two decades

This study explores methane emission trends across Greece, Armenia, and Rostov Oblast region of Russia from 2004 to 2023. Our analyses, based on remote sensing and advanced statistical techniques, showed a 1.3-1.8 °C increase in mean annual temperature over this 20-year period in all these three regions, with the highest and the lowest rates of annual warming in Armenia (0.104 °C) and Rostov Oblast of Russia (0.052 °C), respectively. Mean annual methane concentrations increased distinctly in these regions over this period. Greece showed the trend of highest correlations between methane emissions and temperatures, including mean annual and seasonal temperatures, highlighting substantial role of climate change in emission trends. The emission trends with on-ground observations revealed intricate connections between reduced precipitations, farming practices, waste disposal methods, and naturally occurring emissions in Greece. In contrast, Armenia exhibited weak correlations between temperature and methane emissions, with its farming, waste management, energy and manufacturing sectors playing a significant role in determining emission quantities. The Rostov Oblast of Russia demonstrated weaker association between methane emissions and temperatures than Greece and Armenia, with emission trends being primarily shaped by agricultural activities and natural discharges from wetlands. The forecast models predicted further rise in methane emissions over the 7-year period (2024-2030), with the highest elevation rate estimated for Russia. This study emphasizes the need for tailored mitigation strategies to address methane emissions effectively, considering region-specific factors. Advanced monitoring technologies provide crucial insights into the assessment and management of methane emissions in these diverse geomorphological regions.

Biochemical basis of endogenous bioluminescent springtail Lobella sauteri (Collembola)

Bioluminescence plays important roles among animals in both intra- and inter-species communication. A variety of bioluminescent organisms inhabit soil environments, even in areas where light penetration is minimal. However, due to the lack of a model system to study underground bioluminescence, the biology and molecular mechanisms underlying this phenomenon remain largely unknown. Springtails (Collembola) are representative soil animals, and we recently identified Lobella sauteri (Neanuridae) as a bioluminescent species. L. sauteri can be maintained over multiple generations under laboratory conditions on a single food source, the plasmodium Fuligo septica, with a generation time of approximately 3 months. Bioluminescence was observed in all developmental stages of L. sauteri in laboratory-raised populations. The light emission exhibited periodic changes and increased before ecdysis, coinciding with the whitening of its tubercles. The bioluminescent reaction in vitro requires a small molecular (luciferin) fraction, an enzyme (luciferase) fraction, adenosine triphosphate (ATP), and Mg2+. Comparative transcriptomic and biochemical analyses suggest that L. sauteri employs a novel endogenous bioluminescent molecular mechanism. We propose that L. sauteri provides a valuable research opportunity for investigating novel bioluminescence systems and underground light-based communication.

Horizontal Gene Transfer Systems for Spread of Antibiotic Resistance in Gram-Negative Bacteria

Antibiotic-resistant bacteria have become a significant global threat to public health due to the increasing difficulty in treatment. These bacteria acquire resistance by incorporating various antibiotic resistance genes (ARGs) through specialized gene transfer mechanisms, allowing them to evade antibiotic attacks. Conjugation, transformation, and transduction are well-established mechanisms that drive the acquisition and dissemination of ARGs in Gram-negative bacteria. In particular, the horizontal transfer of plasmids carrying multiple ARGs is highly problematic, as it can instantly convert susceptible bacteria into multidrug-resistant ones. Transduction, mediated by bacteriophages that package ARG-containing chromosomal DNA from host cells, also plays a crucial role in ARG spread without requiring direct cell-to-cell contact. Recently, a novel horizontal gene transfer (HGT) mechanism involving outer membrane vesicles (OMVs) has been identified as a key player in ARG dissemination. OMVs-nanoscale, spherical structures produced by bacteria during growth-have been found to carry small plasmids and chromosomal DNA fragments containing ARGs from their host bacteria. This newly discovered transfer process, termed "vesiduction," enables intercellular DNA exchange and further contributes to the spread of antibiotic resistance. Additionally, mobile genetic elements such as transposons, insertion sequences, and site-specific recombination systems like integrons facilitate rearrangement of ARGs, including their translocation between chromosomes and plasmids. This review explores the molecular mechanisms underlying the HGT of ARGs, with a particular focus on clinically isolated antibiotic-resistant Gram-negative bacteria.

Excess A-subunits of Shiga toxin 2a are produced in enterohemorrhagic Escherichia coli

Shiga toxins (Stx) produced by Shiga toxin-producing Escherichia coli (STEC) and enterohemorrhagic E. coli (EHEC) are ribosome-inactivating AB5 proteins that consist of one enzymatic active A-subunit (StxA) and a pentamer of non-covalently linked B-subunits (StxB). The description of Stx as an AB5 protein and the observation that A-subunits without their corresponding B-subunits also intoxicate eukaryotic cells, led to the question whether A- and B-subunits are produced in the bacteria in a 1:5 ratio or whether the A-subunit of the clinically most prominent subtype Stx2a is transcribed in excess revealing free A-subunits released in the bacterial environment. The aim of this study was therefore, to investigate the genetic and protein-based background for this observation in six Stx2a-encoding STEC and EHEC wildtype strains. For this purpose, transcriptional analysis of the Stx2a subunit genes, stxA2a and stxB2a, was performed by quantitative real-time PCR in one foodborne O113:H21 STEC isolate (strain TS18/08) and five HUS-associated EHEC strains with the serotypes O157:H7/H- (HUSEC003, HUSEC004), O103:H- (HUSEC008), O26:H11 (HUSEC018), and O104:H4 (LB226692). Contrary to the hypothesis that the A- and B-subunit genes are expressed in a ratio of 1:5 comparable to the holotoxin structure or in a ratio of 1:1 based on the operon structure, the results showed that stxA2a was expressed 1.90 ± 0.55-times stronger than the gene encoding the B-subunit, possibly indicating the presence of free A-subunits. In addition, strain-specific differences regarding the mRNA fold-changes of the A-subunit gene were observed. By use of native polyacrylamide gel electrophoresis and subsequent Western blot analysis, those single A-subunits were indeed detected in the culture supernatants of all six strains. To investigate whether the transcription ratios between A- and B-subunits observed are in a similar range as the amount of subunit proteins present after translation, a quantitative ELISA specific for StxA2a and StxB2a was established. Quantification of the subunits on protein level by use of ELISA revealed that the subunit ratio of StxA2a:StxB2a is 1.10 ± 0.20 for the strains HUSEC003, HUSEC004 and HUSEC008, but 4.63 ± 0.31 for the strains TS18/08, LB226692, and HUSEC018. The results of this study demonstrated that on both, the transcriptional and the translational level, the established 1:5 subunit ratio is not present in all investigated strains. In addition, the ratios observed after translation indicate that in some strains StxA2a subunits are even produced in higher amounts than B-subunits.

Terminal complement complexes with or without C9 potentiate antimicrobial activity against Neisseria gonorrhoeae

The complement cascade is a front-line defense against pathogens. Complement activation generates the membrane attack complex (MAC), a 10-11 nm diameter pore formed by complement proteins C5b through C8 and polymerized C9. The MAC embeds within the outer membrane of Gram-negative bacteria and displays bactericidal activity. In the absence of C9, C5b-C8 complexes can form 2-4 nm pores on membranes, but their relevance to microbial control is poorly understood. Deficiencies in terminal complement components uniquely predispose individuals to infections by pathogenic Neisseria, including N. gonorrhoeae (Gc). Increasing antibiotic resistance in Gc makes new therapeutic strategies a priority. Here, we demonstrate that MAC formed by complement activity in human serum disrupts the Gc outer and inner membranes, potentiating the activity of antimicrobials against Gc and re-sensitizing multidrug-resistant Gc to antibiotics. C9-depleted serum also exerts bactericidal activity against Gc and, unlike other Gram-negative bacteria, disrupts both the outer and inner membranes. C5b-C8 complex formation potentiates Gc sensitivity to azithromycin and ceftriaxone, but not lysozyme or nisin. These findings expand our mechanistic understanding of complement lytic activity, suggest a size limitation for terminal complement-mediated enhancement of antimicrobials against Gc, and suggest that complement manipulation can be used to combat drug-resistant gonorrhea.

IMPORTANCE

The complement cascade is a front-line arm of the innate immune system against pathogens. Complement activation results in membrane attack complex (MAC) pores forming on the outer membrane of Gram-negative bacteria, resulting in bacterial death. Individuals who cannot generate MAC are specifically susceptible to infection by pathogenic Neisseria species including N. gonorrhoeae (Gc). High rates of gonorrhea, its complications like infertility, and high-frequency resistance to multiple antibiotics make it important to identify new approaches to combat Gc. Beyond direct anti-Gc activity, we found that the MAC increases the ability of antibiotics and antimicrobial proteins to kill Gc and re-sensitizes multidrug-resistant bacteria to antibiotics. The most terminal component, C9, is needed to potentiate the anti-Gc activity of lysozyme and nisin, but azithromycin and ceftriaxone activity is potentiated regardless of C9. These findings highlight the unique effects of MAC on Gc and suggest novel translational avenues to combat drug-resistant gonorrhea.

Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives

Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.

Plasmid-bacteria associations in the clinical context

Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid-bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid-host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid-bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid-host associations and to design strategies to prevent and predict future high-risk associations.

From microbial proteins to cultivated meat for alternative meat-like products: a review on sustainable fermentation approaches

The global demand for protein is rapidly increasing due to population growth and changing dietary preferences, highlighting the need for sustainable alternatives to traditional animal-based proteins. This review explores cultivated meat and microbial alternative proteins, focusing on their potential to meet nutritional needs while mitigating environmental impacts. It also examines the production of cultivated meat as well as various sources of microbial proteins, including mycoproteins, bacterial proteins, and microalgae, highlighting their nutritional profiles, production methods, and commercial applications. This includes an evaluation of the state of commercialization of mycoproteins and the innovative use of agricultural and industrial by-products as substrates for microbial fermentation. The integration of microbial protein production with the bioenergy sector is evaluated as a relevant alternative to attain a synergetic effect between energy and food production systems. Ultimately, this work aims to underscore the importance of microbial proteins in advancing towards a more sustainable protein production system, offering insights into current challenges and future opportunities in the field of fermentation to produce alternative proteins.