Structure and function: Lipid A modifications in commensals and pathogens

Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine

Lipid A, a crucial component of lipopolysaccharides (LPS), plays a pivotal role in the pathogenesis of Gram-negative bacteria. Lipid A patterns are recognized by mammals and can induce immunostimulatory effects. However, the outcome of the interaction is highly dependent on the chemical composition of individual lipid A species. The diversity of potential fatty acyl and polar headgroup combinations in this complex saccharolipid presents a significant analytical challenge. Current mass spectrometry (MS)-based lipid A methods are focused on either direct matrix-assisted laser desorption/ionization (MALDI)-MS screening or comprehensive structural elucidation by tandem mass spectrometry (MS/MS) hyphenated with separation techniques. In this study, we developed an alternative workflow for rapid lipid A profiling covering the entire analysis pipeline from sample preparation to data analysis. This workflow is based on microextraction and subsequent MALDI-MS/MS analysis of uropathogenic Escherichia coli utilizing trapped ion mobility spectrometry (TIMS), followed by mzmine data processing. The additional TIMS dimension served for enhanced sensitivity, selectivity, and structural elucidation through mobility-resolved fragmentation via parallel accumulation-serial fragmentation (PASEF) in parallel reaction monitoring (prm)-mode. Furthermore, mzmine enabled automated MS/MS acquisition by adapting the spatial ion mobility-scheduled exhaustive fragmentation (SIMSEF) strategy for MALDI spot analysis. It also facilitated robust lipid A annotation through a newly developed extension of the rule-based lipid annotation module, allowing for the custom generation of lipid classes, including specific fragmentation rules. In this study, the first publication of lipid A species' collision cross section (CCS) values is reported, which will enhance high-confidence lipid A annotation in future studies.

Dynamics of the canine gut microbiota of a military dog birth cohort

Introduction

We systematically tracked early life stages in a military dog birth cohort to investigate canine gut microbiota dynamics related to environmental exposure during growth. This study utilized 16s rRNA amplicon sequencing-based analysis with molecular epidemiology of Enterococcus faecalis within a controlled environment at a military dog training center.

Methods

We examined shifts in gut microbiota diversity and taxonomic composition across four growth stages (lactation, weaning, starter, puppy) in three littermate groups. Additionally, E. faecalis dynamics was analyzed to confirm strain sharing among littermate groups.

Results

Gut microbiota changed rapidly during early growth, stabilizing at the puppy stage. This is supported by increased similarity in taxonomic composition among littermate groups, as they experienced an increased shared external environment and consumed the identical diets. E. faecalis strain sharing among littermate groups increased as dogs aged. Nine E. faecalis cluster types were identified; three specific types (type I, II, and IX) dominated in each littermate group during lactation. With greater exposure to the shared external environment, cluster type I gradually assumed dominance across all groups. Despite the dynamic shifts in microbiota, we found five genera within the core microbiota, Bacteroides, Peptoclostridium, Fusobacterium, Lactobacillus, and Blautia.

Discussion

This study is the first to explore the dynamic nature of early-life canine gut microbiota, illustrating its transition to stability and its resilience to environmental perturbations within the controlled training environment of a military dog birth cohort.

Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease

Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.

Lipid Nanoparticle-Mediated CRISPR-Cas13a Delivery for the Control of Bacterial Infection

Lipid nanoparticles (LNPs) can assist in the delivery of nucleic acid inside animal cells, as demonstrated by their use in COVID-19 vaccine development. However, LNPs applicable to bacteria have not been reported. Here, the screening of 511 LNPs containing random combinations of different lipid components identified two LNPs, LNP 496 and LNP 470, that efficiently delivered plasmids into Escherichia coli BW25113. Since Gram-negative bacteria have lipid bilayers, the bacteria are pretreated with LNP-helper that weakens the bacterial membrane. The cationic lipid DOTAP improved delivery of LNP-encapsulated plasmid DNA when present at a molar ratio of 10-25 mol% in the LNP. LNP encapsulation of the Cas13a/gRNA expression vector controlled infection by a clinical Escherichia strain in Galleria mellonela larvae and mouse infection models when used in combination with non-cytotoxic concentrations of polymyxin B, a bacterial membrane disruptor. Together, the results show that LNPs can be useful as a delivery platform for agents that counteract pathogenic bacterial infections.

Lipopolysaccharide structural modification in Salmonella Gallinarum targeting lipid a deacylation and O-antigen reduces virulence and endotoxicity with competitive protection against a wild-type challenge in chickens

Fowl typhoid (FT), caused by Salmonella Gallinarum (SG), inflicts a significant economic burden on the poultry industry. Our study focused on a non-reversible gene deletion to develop a safe and effective SG vaccine strain through lipopolysaccharide (LPS) structural modification. The virulence-attenuated SG JOL914 strain, generated by deleting the global regulator lon gene, was engineered by in-frame deletions targeting the LPS structure. Interruption on LPS deacylation was introduced by pagL deletion, JOL2997, to mitigate endotoxicity induced by the live vaccine. The O-antigen was truncated by rfaL deletion, JOL3004, to compromise virulence and facilitate Differentiating Infected from Vaccinated Animals (DIVA). Both genes were depleted in JOL3016 (ΔlonΔpagLΔrfaL) for their compounding effects. Subcutaneous administration of the engineered strains in chickens showed reduced endotoxicity, particularly demonstrated by JOL3016 with 2.55-fold and 3.79-fold reductions in TNF-α and IL-1β, respectively. Furthermore, discernible effects on body weight gain and the absence of pathological signs demonstrated the safety profiles of the inoculated strains. Administration of mutant strains substantially increased antigen-specific IgY, sIgA, CD4+, and CD8+ T cells, supporting immune response elicitation. The absence of antibodies against O-antigen in birds immunized with JOL3004 and JOL3016 demonstrated their DIVA capability. The result was corroborated by improved protection with a rational body weight gain and minimal tissue distortion following an SG WT challenge. JOL2997-immunized birds showed promising survival, and negligible invasion of the challenge strain in vital organs, highlighting its protective efficacy. This study underscores the potential of bioengineered vaccine strains to improve poultry health and productivity, reinforcing the necessity for ongoing vaccine development research.

A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma

Patient responses to immune checkpoint inhibitors can be influenced by the gastrointestinal microbiome. Mouse models can be used to study microbiome-host crosstalk, yet their utility is constrained by substantial anatomical, functional, immunological and microbial differences between mice and humans. Here we show that a gut-on-a-chip system mimicking the architecture and functionality of the human intestine by including faecal microbiome and peristaltic-like movements recapitulates microbiome-host interactions and predicts responses to immune checkpoint inhibitors in patients with melanoma. The system is composed of a vascular channel seeded with human microvascular endothelial cells and an intestinal channel with intestinal organoids derived from human induced pluripotent stem cells, with the two channels separated by a collagen matrix. By incorporating faecal samples from patients with melanoma into the intestinal channel and by performing multiomic analyses, we uncovered epithelium-specific biomarkers and microbial factors that correlate with clinical outcomes in patients with melanoma and that the microbiome of non-responders has a reduced ability to buffer cellular stress and self-renew. The gut-on-a-chip model may help identify prognostic biomarkers and therapeutic targets.

A "plug-and-display" nanoparticle based on attenuated outer membrane vesicles enhances the immunogenicity of protein antigens

As natural nanoparticle, the bacterial outer membrane vesicles (OMV) hold great potential in protein vaccines because of its self-adjuvant properties and good biocompatibility. However, the inherent immunotoxicity seriously hampers the application of OMV as protein antigens delivery carrier. Here, an attenuated OMV was constructed by elimination of the flagella protein from its surface and removal of the phosphate group of LPS at position one via gene-editing strategy. The gene-edited outer membrane vesicles (EMV) effectively reduced the levels of pro-inflammatory factors TNF-α and IL-6 in mouse blood by at least 10-fold and 15-fold respectively, compared to wild type OMV (WT-OMV). Importantly, protein antigens are conveniently displayed on EMV by employing a plug-and-display procedure, whereby the exterior of biotinylated EMV can be readily decorated with a synthetic protein comprised of target antigen fused to a biotin-binding protein. EMV greatly increased the uptake of antigen by dendritic cells (DCs) and promoted their maturation. EMV-antigen complex induces a robust antigen-specific antibody responses and cellular immune responses. We propose that EMV have great potential as protein antigens delivery vehicle for preventing different infectious diseases.

Development of paroxetine loaded nanotransferosomal gel for intranasal delivery with enhanced antidepressant activity in rats

The aim of this study was to develop paroxetine (PXT) loaded nanotransferosomal gel (PXT-NTFG) for intranasal brain delivery. The process involved fabricating PXT-NTFs (paroxetine-loaded nanotransferosomes) through a thin film hydration method and optimizing them based on parameters such as particle size (PS), zeta potential (ZP), polydispersity index (PDI), and entrapment efficiency (EE). The optimized PXT-NTFs exhibited uniform morphology with a PS of 158.30 ± 2.73 nm, low PDI (0.142 ± 0.072), high ZP (21.00 ± 0.75 mV), and excellent EE (88.09 ± 3.40 %). Characterization through various techniques confirmed the incorporation of PXT into the nanotransferosomes and its conversion to amorphous state. Moreover, PXT-NTFG was formulated with suitable viscosity and mucoadhesive properties. In vitro release studies demonstrated sustained drug release from PXT-NTFG at different pH levels as compared to PXT-NTFs and NTF dispersion. Similarly, ex vivo experiments showed 4 folds enhanced drug permeation from PXT-NTFG when compared with PXT conventional gel. Stability studies indicated that the optimized PXT-NTFs remained stable for four months at 4°C and 25°C. Additionally, improved behavioral outcomes, increased neuronal survival rates, and upregulated brain-derived neurotrophic factor (BDNF) expression was observed in lipopolysaccharide (LPS) induced depressed Sprague-Dawley rats after treatment with PXT-NTFG as compared to PXT-dispersion treated and untreated LPS-control groups. Notably, the formulation led to a significant reduction in brain and plasma TNF-α levels. In conclusion, intranasal PXT-NTFG is a promising formulation with sustained drug release, improved brain targeting and enhanced antidepressant activity.

Altering Lipid A Precursor Ion Types in the Gas Phase for In-Depth Structural Elucidation via Tandem Mass Spectrometry

Lipid A, a well-known saccharolipid, acts as the inner lipid-glycan anchor of lipopolysaccharides in Gram-negative bacterial cell membranes and functions as an endotoxin. Its structure is composed of two glucosamines with β(1 → 6) linkages and various fatty acyl and phosphate groups. The lipid A structure can be used for the identification of bacterial species, but its complexity poses significant structural characterization challenges. In this work, we present a comprehensive strategy combining condensed-phase sample preparation, electrospray ionization, and gas-phase ion/ion reactions with tandem mass spectrometry for detailed lipid A structural elucidation. We use proton transfer reactions, charge-inversion reactions, and sequential ion/ion reactions for magnesium transfer to generate targeted lipid A ions. The strategy, established with a synthetic monophosphoryl lipid A (MPLA) and known MPLA and diphosphorylated lipid A (DPLA) from Escherichia coli F583, demonstrated that [MPLA - 2H]2-, [MPLA - H]-, and [MPLA - H + Mg]+ precursor ions offer complementary information for MPLA, while [DPLA - H]-, [DPLA + H]+, and [DPLA - H + Mg]+ precursor ions provide analogous information for DPLA analysis. We validated the strategy using known lipid A species and also successfully applied this strategy to profile unknown MPLA and DPLA in the same E. coli strain.

Biomass-Derived Nanoporous Carbon Honeycomb Monoliths for Environmental Lipopolysaccharide Adsorption from Aqueous Media

After undergoing biological treatment, wastewater still contains substances with endotoxic activity, such as lipopolysaccharide. However, due to the increasing practice of treating wastewater to make it suitable for drinking (potable reuse), the removal of these endotoxic active materials is crucial. These substances can be harmful to human health, leading to a condition called endotoxaemia. Furthermore, environmental endotoxins pose risks to pharmaceutical manufacturing processes and the quality of the final pharmaceutical products. Ultimately, the most significant concern lies with the patient, as exposure to such substances can have adverse effects on their health and well-being. Activated carbon has a proven efficiency for endotoxin removal; rice husk (RH), as a type of natural lignocellulosic agricultural waste, is a unique carbon precursor material in terms of its availability, large-scale world production (over 140 million tons annually), and is characterized by the presence of nanoscale silica phytoliths, which serve as a template to create additional meso/macropore space within the nanoscale range. High surface area RH/lignin-derived honeycomb monoliths were prepared in this study via extrusion, followed by carbonization and physical and chemical activation to develop additional pore space. The nanoporosity of the carbon honeycomb monoliths was established by means of low-temperature nitrogen adsorption studies, using calculations based on QSDFT equilibrium and BJH models, as well as mercury intrusion porosimetry (MIP) and SEM investigations. An alternative method for the elimination of the bacterial lipopolysaccharide (LPS)-a conventional marker-using filtration in flowing recirculation systems and the adsorbent activity of the monoliths towards LPS was investigated. Since LPS expresses strong toxic effects even at very low concentrations, e.g., below 10 EU/mL, its removal even in minute amounts is essential. It was found that monoliths are able to eliminate biologically relevant LPS levels, e.g., adsorption removal within 5, 30, 60, 90, and 120 min of circulation reached the values of 49.8, 74.1, 85.4, 91.3%, and 91.6%, respectively.

Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells

Bacteria assume two distinct lifestyles: the planktonic and biofilm modes of growth. Additionally, dispersion has emerged as a third phenotype, accompanied by the distinct phenotypes and the unique expression of >600 genes. Here, we asked whether the distinct phenotype of dispersed cells is already apparent within minutes of egressing from the biofilm. We used RNA-seq to show that the physiology of freshly dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells, apparent by dispersed cells uniquely expressing 194 genes. Unique and differentially expressed genes relative to planktonic or biofilm cells include genes associated with type IV pili, pyoverdine, type III and type VI secretion systems, and antibiotic resistance that are downregulated in dispersed cells, whereas the transcript abundance of genes involved in swimming motility, Hxc type II secretion system and various other virulence factors, and metabolic and energy-generating pathways are increased, indicative of dispersion coinciding with an awakening and re-energizing of dispersed cells, and a switch in virulence, further apparent by freshly dispersed cells significantly subverting engulfment by macrophages. The findings suggest that dispersed cells display a distinct phenotype within minutes of egressing from the biofilm, with freshly dispersed cells already capable of efficiently evading phagocytosis.

IMPORTANCE

Dispersion is considered a transitionary phenotype, enabling bacteria to switch between the communal, biofilm lifestyle, where cells share resources and are protected from harmful conditions to the planktonic state. Here, we demonstrate that within minutes of leaving the biofilm, dispersed cells express genes and display phenotypic traits that are distinct from biofilms and planktonic cells. Our findings suggest that dispersed cells quickly adapt to a less structured and protected but more nutrient-rich environment, with this trade-off in environment coinciding with an awakening and a switch in virulence, specifically a switch from directly intoxicating host cells and potential competitors toward more broadly active virulence factors and strategies of evasion. To our knowledge, this is the first report of dispersed cells' distinct (trade-off) phenotype and their enhanced resilience so soon after egressing from the biofilm.

TolC facilitates the intracellular survival and immunomodulation of Salmonella Typhi in human host cells

Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic infection that affects millions of people worldwide. S. Typhi can invade and survive within host cells, such as intestinal epithelial cells and macrophages, by modulating their immune responses. However, the immunomodulatory capability of S. Typhi in relation to TolC-facilitated efflux pump function remains unclear. The role of TolC, an outer membrane protein that facilitates efflux pump function, in the invasion and immunomodulation of S. Typhi, was studied in human intestinal epithelial cells and macrophages. The tolC deletion mutant of S. Typhi was compared with the wild-type and its complemented strain in terms of their ability to invade epithelial cells, survive and induce cytotoxicity in macrophages, and elicit proinflammatory cytokine production in macrophages. The tolC mutant, which has a defective outer membrane, was impaired in invading epithelial cells compared to the wild-type strain, but the intracellular presence of the tolC mutant exhibited greater cytotoxicity and induced higher levels of proinflammatory cytokines (IL-1β and IL-8) in macrophages compared to the wild-type strain. These effects were reversed by complementing the tolC mutant with a functional tolC gene. Our results suggest that TolC plays a role in S. Typhi to efficiently invade epithelial cells and suppress host immune responses during infection. TolC may be a potential target for the development of novel therapeutics against typhoid fever.

Application of lipopolysaccharide in establishing inflammatory models

Lipopolysaccharide (LPS), a unique component of the outer membrane of Gram-negative bacteria, possesses immune-activating properties. It induces an immune response by stimulating host cells to produce a lot of inflammatory cytokines with a thermogenic effect, which may cause an inflammatory response. In the past few decades, the structure and function of LPS and its mechanism leading to inflammation have been extensively analyzed. Since LPS can cause inflammation, it is often used to establish inflammation models. These models are crucial in the study of inflammatory diseases that pose a serious threat to human health. In addition, the non-pro-inflammatory effects of LPS under certain circumstances are also being studied widely. This review summarizes the methods by which LPS has been used to establish inflammatory models at the cellular and animal levels to study related diseases. It also introduces in detail the evaluation indicators necessary for the successful establishment of these models, providing a reference for future research.

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia

BACKGROUND

Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS

Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm2) and n = 25 with high VAT area (177.5 ± 31.3 cm2). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS

Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS

Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.

A Novel Bifidobacterium longum Subsp. longum T1 Strain from Cow's Milk: Homeostatic and Antibacterial Activity against ESBL-Producing Escherichia coli

Background/Objectives: The global emergence of antibiotic-resistant zooanthroponotic Escherichia coli strains, producing extended-spectrum beta-lactamases (ESBL-E) and persisting in the intestines of farm animals, has now led to the development of a pandemic of extra-intestinal infectious diseases in humans. The search for innovative probiotic microorganisms that eliminate ESBL-E from the intestines of humans and animals is relevant. Previously, we received three isolates of bifidobacteria: from milk of a calved cow (BLLT1), feces of a newborn calf (BLLT2) and feces of a three-year-old child who received fresh milk from this calved cow (BLLT3). Our goal was to evaluate the genetic identity of BLLT1, BLLT2, BLLT3 isolates using genomic DNA fingerprinting (GDF), to study the tolerance, adhesion, homeostatic and antibacterial activity of BLLT1 against ESBL-E. Methods: We used a complex of microbiological, molecular biological, and immunological methods, including next generation sequencing (NGS). Results: GDF showed that DNA fragments of BLLT2 and BLLT3 isolates were identical in number and size to DNA fragments of BLLT1. These data show for the first time the possibility of natural horizontal transmission of BLLT1 through with the milk of a calved cow into the intestines of a calf and the intestines of a child. BLLT1 was resistant to gastric and intestinal stresses and exhibited high adhesive activity to calf, pig, chicken, and human enterocytes. This indicates the unique ability of BLLT1 to inhabit the intestines of animals and humans. We are the first to show that BLLT1 has antibacterial activity against ESBL-E strains that persist in humans and animals. BLLT1 produced 145 ± 8 mM of acetic acid, which reduced the pH of the nutrient medium from 6.8 to 5.2. This had an antibacterial effect on ESBL-E. The genome of BLLT1 contains ABC-type carbohydrate transporter gene clusters responsible for the synthesis of acetic acid with its antibacterial activity against ESBL-E. BLLT1 inhibited TLR4 mRNA expression induced by ESBL-E in HT-29 enterocytes, and protected the enterocyte monolayers used in this study as a bio-model of the intestinal barrier. BLLT1 increased intestinal alkaline phosphatase (IAP) as one of the main molecular factors providing intestinal homeostasis. Conclusions: BLLT1 shows promise for the creation of innovative functional nutritional products for humans and feed additives for farm animals that will reduce the spread of ESBL-E strains in the food chain.

Phylogenetic Lineages and Diseases Associated with Moraxella catarrhalis Isolates Recovered from Bulgarian Patients

Moraxella catarrhalis has been recognized as an important cause of upper respiratory tract and middle ear infections in children, as well as chronic obstructive pulmonary disease and chronic bronchitis in adults. We aim to study the clonal structure, antimicrobial resistance, and serotypes of M. catarrhalis strains recovered from patients of different ages. Nasopharyngeal swabs, middle ear fluid, and sputum samples were collected. In vitro susceptibility testing was performed according to EUCAST criteria. The monoclonal Ab hybridoma technique was used for serotyping. All strains were subjected to MLST. The studied population demonstrated susceptibility to all tested antimicrobials M. catarrhalis strains, with the majority being serotype A (90.4%), followed by B (6.8%), and C (2.7%). We observed a predominant clonal complex CC224 (21.9%) along with other clusters including CC141 (8.2%), CC184 (8.2%), CC449 (6.8%), CC390 (5.5%), and CC67 (2.7%). Two primary founders, namely, ST224 and ST141, were identified. The analyzed genetic lineages displayed diversity but revealed the predominance of two main clusters, CC224 and CC141, encompassing multidrug-resistant sequence types distributed in other regions. These data underscore the need for ongoing epidemiological monitoring of successfully circulating clones and the implementation of adequate antibiotic policies to limit or delay the spread of multidrug-resistant strains in our region.

Navigating commensal dysbiosis: Gastrointestinal host-pathogen interplay orchestrating opportunistic infections

The gut commensals, which are usually symbiotic or non-harmful bacteria that live in the gastrointestinal tract, have a positive impact on the health of the host. This review, however, specifically discuss distinct conditions where commensals aid in the development of pathogenic opportunistic infections. We discuss that the categorization of gut bacteria as either pathogens or non-pathogens depends on certain circumstances, which are significantly affected by the tissue microenvironment and the dynamic host-microbe interaction. Under favorable circumstances, commensals have the ability to transform into opportunistic pathobionts by undergoing overgrowth. These conditions include changes in the host's physiology, simultaneous infection with other pathogens, effective utilization of nutrients, interactions between different species of bacteria, the formation of protective biofilms, genetic mutations that enhance pathogenicity, acquisition of genes associated with virulence, and the ability to avoid the host's immune response. These processes allow commensals to both initiate infections themselves and aid other pathogens in populating the host. This review highlights the need of having a detailed and sophisticated knowledge of the two-sided nature of gut commensals. Although commensals mostly promote health, they may also become harmful in certain changes in the environment or the body's functioning. This highlights the need of acknowledging the intricate equilibrium in interactions between hosts and microbes, which is crucial for preserving intestinal homeostasis and averting diseases. Finally, we also emphasize the further need of research to better understand and anticipate the behavior of gut commensals in different situations, since they play a crucial and varied role in human health and disease.

The lipopolysaccharide structure affects the detoxifying ability of intestinal alkaline phosphatases

Lipopolysaccharide (LPS) is one of the most potent mediators of inflammation. In swine husbandry, weaning is associated with LPS-induced intestinal inflammation, resulting in decreased growth rates due to malabsorption of nutrients by the inflamed gut. A potential strategy to treat LPS-mediated disease is administering intestinal alkaline phosphatase (IAP). The latter can detoxify lipid A, the toxic component of LPS, by removal of phosphate groups. Currently, 183 LPS O-serotypes from E. coli have been described, however, comparative experiments to elucidate functional differences between LPS serotypes are scarce. In addition, these functional differences might affect the efficacy of LPS detoxifying enzymes. Here, we evaluated the ability of four LPS serotypes (O26:B6, O55:B5, O111:B4 and O127:B8) derived from Escherichia coli to trigger the secretion of pro-inflammatory cytokines by porcine PBMCs. We also tested the ability of three commercially available IAPs to detoxify these LPS serotypes. The results show that LPS serotypes differ in their ability to trigger cytokine secretion by immune cells, especially at lower concentrations. Moreover, IAPs displayed a different detoxification efficiency of the tested serotypes. Together, this study sheds light on the impact of LPS structure on the detoxification by IAPs. Further research is however needed to elucidate the LPS serotype-specific effects and their implications for the development of novel treatment options to alleviate LPS-induced gut inflammation in weaned piglets.

Identification of a Chimera Mass Spectrum of Isomeric Lipid A Species Using Negative Ion Tandem Mass Spectrometry

The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation of lipid A, used independently or in combination with separation techniques. However, it is challenging to accurately characterize constitutional isomers of lipid A extracts by direct mass spectrometry, as the elemental composition and molecular mass of these molecules are identical. Thus, their simultaneous fragmentation leads to a composite, so-called chimera mass spectrum. The present study focuses on the phosphopositional isomers of the classical monophosphorylated, hexaacylated Escherichia coli-type lipid A. Collision-induced dissociation (CID) was performed in an HPLC-ESI-QTOF system. Energy-resolved mass spectrometry (ERMS) was applied to uncover the distinct fragmentation profiles of the phosphorylation isomers. A fragmentation strategy applying multi-levels of collision energy has been proposed and applied to reveal sample complexity, whether it contains only a 4'-phosphorylated species or a mixture of 1- and 4'-phosphorylated variants. This comparative fragmentation study of isomeric lipid A species demonstrates the high potential of ERMS-derived information for the successful discrimination of co-ionized phosphorylation isomers of hexaacylated lipid A.

The individual response to antibiotics and diet - insights into gut microbial resilience and host metabolism

Antibiotic use disrupts microbial composition and activity in humans, but whether this disruption in turn affects host metabolic health is unclear. Cohort studies show associations between antibiotic use and an increased risk of developing obesity and type 2 diabetes mellitus. Here, we review available clinical trials and show the disruptive effect of antibiotic use on the gut microbiome in humans, as well as its impact on bile acid metabolism and microbial metabolites such as short-chain fatty acids. Placebo-controlled human studies do not show a consistent effect of antibiotic use on body weight and insulin sensitivity at a population level, but rather an individual-specific or subgroup-specific response. This response to antibiotic use is affected by the resistance and resilience of the gut microbiome, factors that determine the extent of disruption and the speed of recovery afterwards. Nutritional strategies to improve the composition and functionality of the gut microbiome, as well as its recovery after antibiotic use (for instance, with prebiotics), require a personalized approach to increase their efficacy. Improved insights into key factors that influence the individual-specific response to antibiotics and dietary intervention may lead to better efficacy in reversing or preventing antibiotic-induced microbial dysbiosis as well as strategies for preventing cardiometabolic diseases.

The root canal microbiome diversity and function. A whole-metagenome shotgun analysis

AIM

To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.

METHODOLOGY

Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.

RESULTS

Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.

CONCLUSIONS

Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.

Metabolic Endotoxemia: From the Gut to Neurodegeneration

Metabolic endotoxemia is a severe health problem for residents in developed countries who follow a Western diet, disrupting intestinal microbiota and the whole organism's homeostasis. Although the effect of endotoxin on the human immune system is well known, its long-term impact on the human body, lasting many months or even years, is unknown. This is due to the difficulty of conducting in vitro and in vivo studies on the prolonged effect of endotoxin on the central nervous system. In this article, based on the available literature, we traced the path of endotoxin from the intestines to the blood through the intestinal epithelium and factors promoting the development of metabolic endotoxemia. The presence of endotoxin in the bloodstream and the inflammation it induces may contribute to lowering the blood-brain barrier, potentially allowing its penetration into the central nervous system; although, the theory is still controversial. Microglia, guarding the central nervous system, are the first line of defense and respond to endotoxin with activation, which may contribute to the development of neurodegenerative diseases. We traced the pro-inflammatory role of endotoxin in neurodegenerative diseases and its impact on the epigenetic regulation of microglial phenotypes.

Lipid A modification of colistin-resistant Klebsiella pneumoniae does not alter innate immune response in a mouse model of pneumonia

Polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae bacteria is associated with high morbidity and mortality in vulnerable populations throughout the world. Ineffective antimicrobial activity by these last resort therapeutics can occur by transfer of mcr-1, a plasmid-mediated resistance gene, causing modification of the lipid A portion of lipopolysaccharide (LPS) and disruption of the interactions between polymyxins and lipid A. Whether this modification alters the innate host immune response or carries a high fitness cost in the bacteria is not well established. To investigate this, we studied infection with K. pneumoniae (KP) ATCC 13883 harboring either the mcr-1 plasmid (pmcr-1) or the vector control (pBCSK) ATCC 13883. Bacterial fitness characteristics of mcr-1 acquisition were evaluated. Differentiated human monocytes (THP-1s) were stimulated with KP bacterial strains or purified LPS from both parent isolates and isolates harboring mcr-1. Cell culture supernatants were analyzed for cytokine production. A bacterial pneumonia model in WT C57/BL6J mice was used to monitor immune cell recruitment, cytokine induction, and bacterial clearance in the bronchoalveolar lavage fluid (BALF). Isolates harboring mcr-1 had increased colistin MIC compared to the parent isolates but did not alter bacterial fitness. Few differences in cytokines were observed with purified LPS from mcr-1 expressing bacteria in vitro. However, in a mouse pneumonia model, no bacterial clearance defect was observed between pmcr-1-harboring KP and parent isolates. Consistently, no differences in cytokine production or immune cell recruitment in the BALF were observed, suggesting that other mechanisms outweigh the effect of these lipid A mutations in LPS.

A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development

With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.

PmrAB, the two-component system of Acinetobacter baumannii, controls the phosphoethanolamine modification of lipooligosaccharide in response to metal ions

Acinetobacter baumannii is highly resistant to antimicrobial agents, and XDR strains have become widespread. A. baumannii has developed resistance to colistin, which is considered the last resort against XDR Gram-negative bacteria, mainly caused by lipooligosaccharide (LOS) phosphoethanolamine (pEtN) and/or galactosamine (GalN) modifications induced by mutations that activate the two-component system (TCS) pmrAB. Although PmrAB of A. baumannii has been recognized as a drug resistance factor, its function as TCS, including its regulatory genes and response factors, has not been fully elucidated. In this study, to clarify the function of PmrAB as TCS, we elucidated the regulatory genes (regulon) of PmrAB via transcriptome analysis using pmrAB-activated mutant strains. We discovered that PmrAB responds to low pH, Fe2+, Zn2+, and Al3+. A. baumannii selectively recognizes Fe2+ rather than Fe3+, and a novel region ExxxE, in addition to the ExxE motif sequence, is involved in the environmental response. Furthermore, PmrAB participates in the phosphoethanolamine modification of LOS on the bacterial surface in response to metal ions such as Al3+, contributing to the attenuation of Al3+ toxicity and development of resistance to colistin and polymyxin B in A. baumannii. This study demonstrates that PmrAB in A. baumannii not only regulates genes that play an important role in drug resistance but is also involved in responses to environmental stimuli such as metal ions and pH, and this stimulation induces LOS modification. This study reveals the importance of PmrAB in the environmental adaptation and antibacterial resistance emergence mechanisms of A. baumannii.

IMPORTANCE

Antimicrobial resistance (AMR) is a pressing global issue in human health. Acinetobacter baumannii is notably high on the World Health Organization's list of bacteria for which new antimicrobial agents are urgently needed. Colistin is one of the last-resort drugs used against extensively drug-resistant (XDR) Gram-negative bacteria. However, A. baumannii has become increasingly resistant to colistin, primarily by modifying its lipooligosaccharide (LOS) via activating mutations in the two-component system (TCS) PmrAB. This study comprehensively elucidates the detailed mechanism of drug resistance of PmrAB in A. baumannii as well as its biological functions. Understanding the molecular biology of these molecules, which serve as drug resistance factors and are involved in environmental recognition mechanisms in bacteria, is crucial for developing fundamental solutions to the AMR problem.

The conceptual foundations of innate immunity: Taking stock 30 years later

While largely neglected over decades during which adaptive immunity captured most of the attention, innate immune mechanisms have now become central to our understanding of immunology. Innate immunity provides the first barrier to infection in vertebrates, and it is the sole mechanism of host defense in invertebrates and plants. Innate immunity also plays a critical role in maintaining homeostasis, shaping the microbiota, and in disease contexts such as cancer, neurodegeneration, metabolic syndromes, and aging. The emergence of the field of innate immunity has led to an expanded view of the immune system, which is no longer restricted to vertebrates and instead concerns all metazoans, plants, and even prokaryotes. The study of innate immunity has given rise to new concepts and language. Here, we review the history and definition of the core concepts of innate immunity, discussing their value and fruitfulness in the long run.

Dose-Dependent Effects of Lipopolysaccharide on the Endothelium-Sepsis versus Metabolic Endotoxemia-Induced Cellular Senescence

The endothelium, the innermost cell layer of blood vessels, is not only a physical barrier between the bloodstream and the surrounding tissues but has also essential functions in vascular homeostasis. Therefore, it is not surprising that endothelial dysfunction is associated with most cardiovascular diseases. The functionality of the endothelium is compromised by endotoxemia, the presence of bacterial endotoxins in the bloodstream with the main endotoxin lipopolysaccharide (LPS). Therefore, this review will focus on the effects of LPS on the endothelium. Depending on the LPS concentration, the outcomes are either sepsis or, at lower concentrations, so-called low-dose or metabolic endotoxemia. Sepsis, a life-threatening condition evoked by hyperactivation of the immune response, includes breakdown of the endothelial barrier resulting in failure of multiple organs. A deeper understanding of the underlying mechanisms in the endothelium might help pave the way to new therapeutic options in sepsis treatment to prevent endothelial leakage and fatal septic shock. Low-dose endotoxemia or metabolic endotoxemia results in chronic inflammation leading to endothelial cell senescence, which entails endothelial dysfunction and thus plays a critical role in cardiovascular diseases. The identification of compounds counteracting senescence induction in endothelial cells might therefore help in delaying the onset or progression of age-related pathologies. Interestingly, two natural plant-derived substances, caffeine and curcumin, have shown potential in preventing endothelial cell senescence.

Exploring the Gut-Mitochondrial Axis: p66Shc Adapter Protein and Its Implications for Metabolic Disorders

This review investigates the multifaceted role of the p66Shc adaptor protein and the gut microbiota in regulating mitochondrial function and oxidative stress, and their collective impact on the pathogenesis of chronic diseases. The study delves into the molecular mechanisms by which p66Shc influences cellular stress responses through Rac1 activation, Forkhead-type transcription factors inactivation, and mitochondria-mediated apoptosis, alongside modulatory effects of gut microbiota-derived metabolites and endotoxins. Employing an integrative approach, the review synthesizes findings from a broad array of studies, including molecular biology techniques and analyses of microbial metabolites' impacts on host cellular pathways. The results underscore a complex interplay between microbial metabolites, p66Shc activation, and mitochondrial dysfunction, highlighting the significance of the gut microbiome in influencing disease outcomes through oxidative stress pathways. Conclusively, the review posits that targeting the gut microbiota-p66Shc-mitochondrial axis could offer novel therapeutic strategies for mitigating the development and progression of metabolic diseases. This underscores the potential of dietary interventions and microbiota modulation in managing oxidative stress and inflammation, pivotal factors in chronic disease etiology.

Engineering Escherichia coli for constitutive production of monophosphoryl lipid A vaccine adjuvant

During the COVID-19 pandemic, expedient vaccine production has been slowed by the shortage of safe and effective raw materials, such as adjuvants, essential components to enhance the efficacy of vaccines. Monophosphoryl lipid A (MPLA) is a potent and safe adjuvant used in human vaccines, including the Shingles vaccine, Shingrix. 3-O-desacyl-4'-monophosphoryl lipid A (MPL), a representative MPLA adjuvant commercialized by GSK, was prepared via chemical conversion of precursors isolated from Salmonella typhimurium R595. However, the high price of these materials limits their use in premium vaccines. To combat the scarcity and high cost of safe raw materials for vaccines, we need to develop a feasible MPLA production method that is easily scaled up to meet industrial requirements. In this study, we engineered peptidoglycan and outer membrane biosynthetic pathways in Escherichia coli and developed a Escherichia coli strain, KHSC0055, that constitutively produces EcML (E. coli-produced monophosphoryl lipid A) without additives such as antibiotics or overexpression inducers. EcML production was optimized on an industrial scale via high-density fed-batch fermentation, and obtained 2.7 g of EcML (about 135,000 doses of vaccine) from a 30-L-scale fermentation. Using KHSC0055, we simplified the production process and decreased the production costs of MPLA. Then, we applied EcML purified from KHSC0055 as an adjuvant for a COVID-19 vaccine candidate (EuCorVac-19) currently in clinical trial stage III in the Philippines. By probing the efficacy and safety of EcML in humans, we established KHSC0055 as an efficient cell factory for MPLA adjuvant production.

Effects of ruminal lipopolysaccharide exposure on primary bovine ruminal epithelial cells

The objective of this study was to investigate the immunopotential of ruminal lipopolysaccharides (LPS) on cultured primary bovine rumen epithelial cells (REC). Primary bovine REC were isolated from 6 yearling steers and grown in culture for 3 experiments. Experiment 1 aimed to determine the immunopotential of ruminal LPS, experiment 2 aimed to assess tolerance to chronic LPS exposure, and experiment 3 aimed to evaluate antagonistic interactions between ruminal and Escherichia coli LPS. In experiments 1 and 2, REC were exposed to nonpyrogenic water, 20 μg/mL E. coli LPS (EC20), 10 μg/mL ruminal LPS, 20 μg/mL ruminal LPS, and 40 μg/mL ruminal LPS, either continuously or intermittently. For the continuous exposure, REC underwent a 6 h exposure, whereas for the intermittent exposure, the procedure was: (1) a 12 h continuous exposure to treatments followed by LPS removal for 24 h and then another 12 h of exposure (RPT), and (2) a 12 h continuous exposure to treatments followed by LPS removal and a recovery period of 36 h (RCV). In experiment 3, REC were exposed to nonpyrogenic water, 1 μg/mL E. coli LPS, 1 μg/mL ruminal LPS to 1 μg/mL E. coli LPS, 10 μg/mL ruminal LPS to 1 μg/mL E. coli LPS, and 50 μg/mL ruminal LPS to 1 μg/mL E. coli LPS. Each experiment was done as a complete randomized block design with 6 REC donors. The REC-donor was used as blocking factor. Each treatment had 2 technical replicates, and treatment responses for all data were analyzed with the MIXED procedure of SAS. For all experiments, total RNA was extracted from REC and real-time quantitative PCR was performed to determine the relative expression of genes for toll-like receptors (TLR2 and TLR4), proinflammatory cytokines (TNF, IL1B, and IL6), chemokines (CXCL2 and CXCL8), growth factor-like cytokines (CSF2 and TGFB1), and a lipid mediator (PTGS2). In experiment 1, the targeted genes were upregulated by EC20, whereas all ruminal LPS treatments resulted in a lower transcript abundance. Regarding RPT, and RCV condition, in experiment 2, the expression of targeted genes was not affected or was at a lower abundance to EC20 when compared with ruminal LPS treatments. Lastly, in experiment 3, all targeted genes resulted in lower or similar transcript abundance on all ruminal LPS ratios. Overall, our results indicate that ruminal LPS have a limited capacity to activate the TLR4/NF-kB pathway and to induce the expression of inflammatory genes.

Advances in Development of Novel Therapeutic Strategies against Multi-Drug Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) with multi-drug resistance (MDR) is a major cause of serious healthcare-associated infections, leading to high morbidity and mortality. This opportunistic pathogen is responsible for various infectious diseases, such as those seen in cystic fibrosis, ventilator-associated pneumonia, urinary tract infection, otitis externa, and burn and wound injuries. Due to its relatively large genome, P. aeruginosa has great diversity and can use various molecular mechanisms for antimicrobial resistance. For example, outer membrane permeability can contribute to antimicrobial resistance and is determined by lipopolysaccharide (LPS) and porin proteins. Recent findings on the regulatory interaction between peptidoglycan and LPS synthesis provide additional clues against pathogenic P. aeruginosa. This review focuses on recent advances in antimicrobial agents and inhibitors targeting LPS and porin proteins. In addition, we explore current and emerging treatment strategies for MDR P. aeruginosa, including phages, vaccines, nanoparticles, and their combinatorial therapies. Novel strategies and their corresponding therapeutic agents are urgently needed for combating MDR pathogens.

Deciphering Lipid Arrangement in Phosphatidylserine/Phosphatidylcholine Mixed Membranes: Simulations and Experiments

Phosphatidylserine (PS) exposure on the plasma membrane is crucial for many cellular processes including apoptotic cell recognition, blood clotting regulation, cellular signaling, and intercellular interactions. In this study, we investigated the arrangement of PS headgroups in mixed PS/phosphatidylcholine (PC) bilayers, serving as a simplified model of the outer leaflets of mammalian cell plasma membranes. Combining atomistic-scale molecular dynamics (MD) simulations with Langmuir monolayer experiments, we unraveled the mutual miscibility of POPC and POPS lipids and the intricate intermolecular interactions inherent to these membranes as well as the disparities in position and orientation of PC and PS headgroups. Our experiments revealed micrometer-scale miscibility at all mole fractions of POPC and POPS, marked by modest deviations from ideal mixing with no apparent microscale phase separation. The MD simulations, meanwhile, demonstrated that these deviations were due to strong electrostatic interactions between like-lipid pairs (POPC-POPC and POPS-POPS), culminating in lateral segregation and nanoscale clustering. Notably, PS headgroups profoundly affect the ordering of the lipid acyl chains, leading to lipid elongation and subtle PS protrusion above the zwitterionic membrane. In addition, PC headgroups are more tilted with respect to the membrane normal, while PS headgroups align at a smaller angle, making them more exposed to the surface of the mixed PC/PS membranes. These findings provide a detailed molecular-level account of the organization of mixed PC/PS membranes, corroborated by experimental data. The insights gained here extend our comprehension of the physiological role of PSs.

Photoinduced force microscopy as a novel method for the study of microbial nanostructures

A detailed comparison of the capabilities of electron microscopy and nano-infrared (IR) microscopy for imaging microbial nanostructures has been carried out for the first time. The surface sensitivity, chemical specificity, and non-destructive nature of spectroscopic mapping is shown to offer significant advantages over transmission electron microscopy (TEM) for the study of biological samples. As well as yielding important topographical information, the distribution of amides, lipids, and carbohydrates across cross-sections of bacterial (Escherichia coli, Staphylococcus aureus) and fungal (Candida albicans) cells was demonstrated using PiFM. The unique information derived from this new mode of spectroscopic mapping of the surface chemistry and biology of microbial cell walls and membranes, may provide new insights into fungal/bacterial cell function as well as having potential use in determining mechanisms of antimicrobial resistance, especially those targeting the cell wall.

Bacterial extracellular vesicles: an emerging avenue to tackle diseases

A growing body of research, especially in recent years, has shown that bacterial extracellular vesicles (bEVs) are one of the key underlying mechanisms behind the pathogenesis of various diseases like pulmonary fibrosis, sepsis, systemic bone loss, and Alzheimer's disease. Given these new insights, bEVs are proposed as an emerging vehicle that can be used as a diagnostic tool or to tackle diseases when used as a therapeutic target. To further boost the understanding of bEVs in health and disease we thoroughly discuss the contribution of bEVs in disease pathogenesis and the underlying mechanisms. In addition, we speculate on their potential as novel diagnostic biomarkers and how bEV-related mechanisms can be exploited as therapeutic targets.

Endotoxic Septic Shock: Diagnosis and Treatment

Endotoxin, also referred to as lipopolysaccharide (LPS), is a potent stimulator of the inflammatory cascade which may progress to sepsis and septic shock. The term endotoxic septic shock has been used for patients who have a clinical phenotype that is characterized by high endotoxin activity in addition to a high burden of organ failure; especially a pattern of organ failure including hepatic dysfunction, acute kidney injury, and various forms of endothelial dysfunction. Endotoxic septic shock has been a target for drug therapy for decades with no success. A likely barrier to their success was the inability to quantify endotoxin in the bloodstream. The Endotoxin Activity Assay (EAA) is positioned to change this landscape. In addition, medical devices using adsorptive technology in an extra-corporeal circulation has been shown to remove large quantities of endotoxin from the bloodstream. Focusing on the use of EAA to determine high concentrations of endotoxin will allow patients with endotoxic septic shock to be identified quickly and these patients may benefit most from removal of endotoxin using extracorporeal methods.

The opportunistic nature of gut commensal microbiota

The abundance of gut commensals has historically been associated with health-promoting effects despite the fact that the definition of good or bad microbiota remains condition-specific. The beneficial or pathogenic nature of microbiota is generally dictated by the dimensions of host-microbiota and microbe-microbe interactions. With the increasing popularity of gut microbiota in human health and disease, emerging evidence suggests opportunistic infections promoted by those gut bacteria that are generally considered beneficial. Therefore, the current review deals with the opportunistic nature of the gut commensals and aims to summarise the concepts behind the occasional commensal-to-pathogenic transformation of the gut microbes. Specifically, relevant clinical and experimental studies have been discussed on the overgrowth and bacteraemia caused by commensals. Three key processes and their underlying mechanisms have been summarised to be responsible for the opportunistic nature of commensals, viz. improved colonisation fitness that is dictated by commensal-pathogen interactions and availability of preferred nutrients; pathoadaptive mutations that can trigger the commensal-to-pathogen transformation; and evasion of host immune response as a survival and proliferation strategy of the microbes. Collectively, this review provides an updated concept summary on the underlying mechanisms of disease causative events driven by gut commensal bacteria.

Resolvin D1 promotes the resolution of inflammation in the ACLF rat model by increasing the proportion of Treg cells

OBJECTIVE

Acute-on-chronic liver failure (ACLF) causes organ system failures in patients and increases the risk of mortality. One of the main predictors of ACLF development in patients is the severity of systemic inflammation. The purpose of this study was to explore the effects of resolvin D1 (RvD1) on the rat model of ACLF.

METHODS

The ACLF rats were induced by first intraperitoneally (ip) injecting CCl4 and porcine serum for 6 weeks to establish the chronic liver injury, followed by once administration (ip) of lipopolysaccharide and d-galactose d-GalN to cause acute liver injury (ALI). An hour before the ALI-induced treatment, rats were administrated (ip) with 0.9% saline or different doses of RvD1 (0.3 or 1 µg/kg). Afterward, the control and treated rats were killed and samples were collected. Biochemical analysis, hematoxylin-eosin and Sirius red staining, flow cytometry assay, and real-time polymerase chain reaction were used to assess the rat liver histopathological injury, the percentage of Treg cells in the spleen, and the messenger RNA (mRNA) levels of transcription factors and immunologic cytokines in liver.

RESULTS

The necroinflammatory scores and the serum levels of transaminase significantly increased in ACLF rats compared with those in control rats. These impaired changes observed in ACLF rats could be attenuated by the administration of a low dose of RvD1 before the induction of ALI, which was associated with the increased proportion of regulatory T cells (Treg) in the spleen together with the increased gene expression ratio of Foxp3/RORγt and decreased mRNA level of Il-17a and Il-6 in the liver.

CONCLUSION

A low dose of RvD1 can promote the resolution of inflammation in ACLF rats by increasing the proportion of Treg cells. RvD1, therefore, may be used as a potential drug for the treatment of patients with ACLF.

Phage-targeting bimetallic nanoplasmonic biochip functionalized with bacterial outer membranes as a biorecognition element

The use of phages-a natural predator of bacteria-has emerged as a therapeutic strategy for treating multidrug-resistant bacterial infections; thus, the isolation and detection of phages from the environment is crucial for advancing phage therapy. Herein, for the first time, we propose a nanoplasmonic-based biodetection platform for phages that utilizes bacterial outer membranes (OMs) as a biorecognition element. Conventional biosensors based on phage-bacteria interactions encounter multiple challenges due to the bacteriolytic phages and potentially toxic bacteria, resulting in instability and risk in the measurement. Therefore, instead of whole living bacteria, we employ a safe biochemical OMs fraction presenting phage-specific receptors, allowing the robust and reliable phage detection. In addition, the biochip is constructed on bimetallic nanoplasmonic islands through solid-state dewetting for synergy between Au and Ag, whereby sensitive detection of phage-OMs interactions is achieved by monitoring the absorption peak shift. For high detection performance, the nanoplasmonic chip is optimized by systematically investigating the morphological features, e.g., size and packing density of the nanoislands. Using our optimized device, phages are detected with high sensitivity (≥∼104 plaques), specificity (little cross-reactivity), and affinity (stronger binding to the host OMs than anti-bacterial antibodies), further exhibiting the cell-killing activities.

Collab or Cancel? Bacterial Influencers of Inflammasome Signaling

The immune system of multicellular organisms protects them from harmful microbes. To establish an infection in the face of host immune responses, pathogens must evolve specific strategies to target immune defense mechanisms. One such defense is the formation of intracellular protein complexes, termed inflammasomes, that are triggered by the detection of microbial components and the disruption of homeostatic processes that occur during bacterial infection. Formation of active inflammasomes initiates programmed cell death pathways via activation of inflammatory caspases and cleavage of target proteins. Inflammasome-activated cell death pathways such as pyroptosis lead to proinflammatory responses that protect the host. Bacterial infection has the capacity to influence inflammasomes in two distinct ways: activation and perturbation. In this review, we discuss how bacterial activities influence inflammasomes, and we discuss the consequences of inflammasome activation or evasion for both the host and pathogen.

In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis

The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.

Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism

Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.

Investigation of Immune Responses in Giant African Snail, Achatina immaculata, against a Two-Round Lipopolysaccharide Challenge

As one of the 100 most-threatening invasive alien species, the giant African snail (Achatina immaculata) has successfully invaded and established itself in most areas of southern China. Protection against recurrent pathogen infections is vital to biological invasion. Enhanced immune protection has been previously found in other invertebrates, but not in the unique immune system of the giant African snail. In the present study, the survival rate of the giant African snail was recorded following a second infection with lethal doses of Escherichia coli after a previous first injection using lipopolysaccharide (LPS), and the mechanism of immune enhancement was investigated by examining the cellular and transcriptomic response of the giant African snail after two successive stimuli using LPS. Snails injected first with LPS, sterilized physiologic (0.9%) saline (SPS), phosphate-buffered saline (PBS) or untreated (Blank) were rechallenged at 7d with E. coli (Ec), and were named as LPS + Ec, SPS + Ec, PBS + Ec, Ec, and Blank. The log-rank test shows the survival rate of the LPS + Ec group as significantly higher than that of other control groups after the second injection (p < 0.05). By performing cell counting and BrdU labeling on newly generated circulating hemocytes, we found that the total hemocyte count (THC) and the ratio of BrdU-positive cells to total cells increased significantly after primary stimulation with LPS and that they further increased after the second challenge. Then, caspase-3 of apoptosis protease and two antioxidant enzyme activities (CAT and SOD) increased significantly after infection, and were significantly higher in the second response than they had been in the first round. Moreover, transcriptome analysis results showed that 84 differentially expressed genes (DEGs) were expressed at higher levels in both the resting and activating states after the second immune response compared to the levels observed after the first challenge. Among them, some DEGs, including Toll-like receptor 4 (TLR4) and its downstream signaling molecules, were verified using qRT-PCR and were consistent with the transcriptome assay results. Based on gene expression levels, we proposed that these genes related to the TLR signaling cascade participate in enhanced immune protection. All results provide evidence that enhanced immune protection exists in the giant African snail.

The Vegetable 'Kale' Protects against Dextran-Sulfate-Sodium-Induced Acute Inflammation through Moderating the Ratio of Proinflammatory and Anti-Inflammatory LPS-Producing Bacterial Taxa and Augmenting the Gut Barrier in C57BL6 Mice

Kale (Brassica oleracea var. acephala), a food rich in bioactive phytochemicals, prevents diet-induced inflammation and gut dysbiosis. We hypothesized that the phytochemicals protect against the lipopolysaccharide (LPS)-induced acute inflammation which results from gut dysbiosis and loss of gut barrier integrity. We designed this study to test the protective effects of the whole vegetable by feeding C57BL/6J mice a rodent high-fat diet supplemented with or without 4.5% kale (0.12 g per 30 g mouse) for 2 weeks before administering 3% dextran sulfate sodium (DSS) via drinking water. After one week, DSS increased the representation of proinflammatory LPS (P-LPS)-producing genera Enterobacter and Klebsiella in colon contents, reduced the representation of anti-inflammatory LPS (A-LPS)-producing taxa from Bacteroidales, reduced the expression of tight junction proteins, increased serum LPS binding protein, upregulated molecular and histopathological markers of inflammation in the colon and shortened the colons. Mice fed kale for 2 weeks before the DSS regime had a significantly reduced representation of Enterobacter and Klebsiella and instead had increased Bacteroidales and Gram-positive taxa and enhanced expression of tight junction proteins. Downstream positive effects of dietary kale were lack of granuloma in colon samples, no shortening of the colon and prevention of inflammation; the expression of F4/80, TLR4 and cytokines 1L-1b, IL-6, TNF-a and iNOS was not different from that of the control group. We conclude that through reducing the proliferation of P-LPS-producing bacteria and augmenting the integrity of the gut barrier, kale protects against DSS-induced inflammation.

Diet, commensal microbiota-derived extracellular vesicles, and host immunity

The gut microbiota has co-evolved with its host, and commensal bacteria can influence both the host's immune development and function. Recently, a role has emerged for bacterial extracellular vesicles (BEVs) as potent immune modulators. BEVs are nanosized membrane vesicles produced by all bacteria, possessing the membrane characteristics of the originating bacterium and carrying an internal cargo that may include nucleic acid, proteins, lipids, and metabolites. Thus, BEVs possess multiple avenues for regulating immune processes, and have been implicated in allergic, autoimmune, and metabolic diseases. BEVs are biodistributed locally in the gut, and also systemically, and thus have the potential to affect both the local and systemic immune responses. The production of gut microbiota-derived BEVs is regulated by host factors such as diet and antibiotic usage. Specifically, all aspects of nutrition, including macronutrients (protein, carbohydrates, and fat), micronutrients (vitamins and minerals), and food additives (the antimicrobial sodium benzoate), can regulate BEV production. This review summarizes current knowledge of the powerful links between nutrition, antibiotics, gut microbiota-derived BEV, and their effects on immunity and disease development. It highlights the potential of targeting or utilizing gut microbiota-derived BEV as a therapeutic intervention.

Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203^T at the concentration of 10¹ cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r² = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.

Structure Determination of Lipid A with Multiple Glycosylation Sites by Tandem MS of Lithium-Adducted Negative Ions

FLATn is a tandem mass spectrometric technique that can be used to rapidly generate spectral information applicable for structural elucidation of lipids like lipid A from Gram-negative bacterial species from a single bacterial colony. In this study, we extend the scope and capability of FLATn by tandem MS fragmentation of lithium-adducted molecular lipid A anions and fragments (FLATn-Li) that provides additional structural and diagnostic data from FLATn samples allowing for the discrimination of terminal phosphate modifications in a variety of pathogenic and environmental species. Using FLATn-Li, we elucidated the lipid A structure from several bacterial species, including novel structures from arctic bacterioplankton of the Duganella and Massilia genera that favor 4-amino-4-deoxy-l-arabinopyranose (Ara4N) modification at the 1-phosphate position and that demonstrate double glycosylation with Ara4N at the 1 and 4' phosphate positions simultaneously. The structures characterized in this work demonstrate that some environmental psychrophilic species make extensive use of this structural lipid A modification previously characterized as a pathogenic adaptation and the structural basis of resistance to cationic antimicrobial peptides. This observation extends the role of phosphate modification(s) in environmental species adaptation and suggests that Ara4N modification can functionally replace the positive charge of the phosphoethanolamine modification that is more typically found attached to the 1-phosphate position of modified lipid A.

Association between lipid-A-producing oral bacteria of different potency and fractional exhaled nitric oxide in a Norwegian population-based adult cohort

BACKGROUND

Lipid A is the primary immunostimulatory part of the lipopolysaccharide (LPS) molecule. The inflammatory response of LPS varies and depends upon the number of acyl chains and phosphate groups in lipid A which is specific for a bacterial species or strain. Traditional LPS quantification assays cannot distinguish between the acylation degree of lipid A molecules, and therefore little is known about how bacteria with different inflammation-inducing potencies affect fractional exhaled nitric oxide (F_eNO). We aimed to explore the association between pro-inflammatory hexa- and less inflammatory penta-acylated LPS-producing oral bacteria and F_eNO as a marker of airway inflammation.

METHODS

We used data from a population-based adult cohort from Norway (n = 477), a study center of the RHINESSA multi-center generation study. We applied statistical methods on the bacterial community- (prediction with MiRKAT) and genus-level (differential abundance analysis with ANCOM-BC) to investigate the association between the oral microbiota composition and F_eNO.

RESULTS

We found the overall composition to be significantly associated with increasing F_eNO levels independent of covariate adjustment, and abundances of 27 bacterial genera to differ in individuals with high F_eNO vs. low F_eNO levels. Hexa- and penta-acylated LPS producers made up 2.4% and 40.8% of the oral bacterial genera, respectively. The Bray-Curtis dissimilarity within hexa- and penta-acylated LPS-producing oral bacteria was associated with increasing F_eNO levels independent of covariate adjustment. A few single penta-acylated LPS producers were more abundant in individuals with low F_eNO vs. high F_eNO, while hexa-acylated LPS producers were found not to be enriched.

CONCLUSIONS

In a population-based adult cohort, F_eNO was observed to be associated with the overall oral bacterial community composition. The effect of hexa- and penta-acylated LPS-producing oral bacteria was overall significant when focusing on Bray-Curtis dissimilarity within each of the two communities and F_eNO levels, but only penta-acylated LPS producers appeared to be reduced or absent in individuals with high F_eNO. It is likely that the pro-inflammatory effect of hexa-acylated LPS producers is counteracted by the dominance of the more abundant penta-acylated LPS producers in this population-based adult cohort involving mainly healthy individuals.

Emerging role of bacterial outer membrane vesicle in gastrointestinal tract

Bacteria form a highly complex ecosystem in the gastrointestinal (GI) tract. In recent years, mounting evidence has shown that bacteria can release nanoscale phospholipid bilayer particles that encapsulate nucleic acids, proteins, lipids, and other molecules. Extracellular vesicles (EVs) are secreted by microorganisms and can transport a variety of important factors, such as virulence factors, antibiotics, HGT, and defensive factors produced by host eukaryotic cells. In addition, these EVs are vital in facilitating communication between microbiota and the host. Therefore, bacterial EVs play a crucial role in maintaining the GI tract's health and proper functioning. In this review, we outlined the structure and composition of bacterial EVs. Additionally, we highlighted the critical role that bacterial EVs play in immune regulation and in maintaining the balance of the gut microbiota. To further elucidate progress in the field of intestinal research and to provide a reference for future EV studies, we also discussed the clinical and pharmacological potential of bacterial EVs, as well as the necessary efforts required to understand the mechanisms of interaction between bacterial EVs and gut pathogenesis.

Undesirable consequences of the metallic nanoparticles action on the properties and functioning of Escherichia coli, Bacillus cereus and Staphylococcus epidermidis membranes

Controversial and inconsistent findings on the toxicity of metallic nanoparticles (NPs) against many bacteria are common in recorded studies; therefore, further advanced experimental work is needed to elucidate the mechanisms underlying nanotoxicity. This study deciphered the direct effects of Ag-NPs, Cu-NPs, ZnO-NPs and TiO₂-NPs on membrane permeability, cytoplasmic leakage, ATP level, ATPase activity and fatty acid profiling of Escherichia coli, Bacillus cereus and Staphylococcus epidermidis as model microorganisms. A multifaceted analysis of all collected results indicated the different influences of individual NPs on the measured parameters depending on their type and concentration. Predominantly, membrane permeability was correlated with increased cytoplasmic leakage, reduced total ATP levels and ATPase activity. The established fatty acid profiles were unique and concerned various changes in the percentages of hydroxyl, cyclopropane, branched and unsaturated fatty acids. Decisively, E. coli was more susceptible to changes in measured parameters than B. cereus and S. epidermidis. Also, it was established that ZnO-NPs and Cu-NPs had a major differentiating impact on studied parameters. Additionally, bacterial cell imaging using scanning electron microscopy elucidated different NPs distributions on the cell surface. The presented results are believed to provide novel, valuable and accumulated knowledge in the understanding of NPs action on bacterial membranes.