Bacterial metabolism in the host and its association with virulence

The host restricted pathogens are competently dependent on their respective host for nutritional requirements. The bacterial metabolic pathways are surprisingly varied and remarkably flexible that in turn help them to successfully overcome competition and colonise their host. The metabolic adaptation plays pivotal role in bacterial pathogenesis. The understanding of host-pathogen metabolic crosstalk needs to be prioritized to decipher host-pathogen interactions. The review focuses on various aspects of host pathogen interactions that majorly involves adaptation of bacterial metabolism to counteract immune mechanisms by rectifying metabolic cues that provides pathogen the idea of different anatomical sites and the local physiology of the host. The key set of metabolites that are recognized as centre of competition between host and its pathogens are also briefly discussed. The factors that control the timely expression of virulence of bacterial pathogens is poorly understood. The perspective presented herein will facilitate us with a broader view of molecular mechanisms that modulates the expression of virulence factors in bacterial pathogens. The knowledge of crosslinked metabolic pathways of bacteria and their host will serve to develop novel potential therapeutics.

Early life gut microbiome and its impact on childhood health and chronic conditions

The development of the gut microbiome is crucial to human health, particularly during the first three years of life. Given its role in immune development, disturbances in the establishment process of the gut microbiome may have long term consequences. This review summarizes evidence for these claims, highlighting compositional changes of the gut microbiome during this critical period of life as well as factors that affect gut microbiome development. Based on human and animal data, we conclude that the early-life microbiome is a determinant of long-term health, impacting physiological, metabolic, and immune processes. The early-life gut microbiome field faces challenges. Some of these challenges are technical, such as lack of standardized stool collection protocols, inconsistent DNA extraction methods, and outdated sequencing technologies. Other challenges are methodological: small sample sizes, lack of longitudinal studies, and poor control of confounding variables. To address these limitations, we advocate for more robust research methodologies to better understand the microbiome's role in health and disease. Improved methods will lead to more reliable microbiome studies and a deeper understanding of its impact on health outcomes.

Protection acquired upon intraperitoneal group a Streptococcus immunization is independent of concurrent adaptive immune responses but relies on macrophages and IFN-γ

Group A Streptococcus (GAS; Streptococcus pyogenes) is an important bacterial pathogen causing over 700 million superficial infections and around 500.000 deaths due to invasive disease or severe post-infection sequelae yearly. In spite of this major impact on society, there is currently no vaccine available against this bacterium. GAS strains can be separated into >250 distinct emm (M)-types, and protective immunity against GAS is believed to in part be dependent on type-specific antibodies. Here, we analyse the nature of protective immunity generated against GAS in a model of intraperitoneal immunization in mice. We demonstrate that multiple immunizations are required for the ability to survive a subsequent lethal challenge, and although significant levels of GAS-specific antibodies are produced, these are redundant for protection. Instead, our data show that the immunization-dependent protection in this model is induced in the absence of B and T cells and is accompanied by the induction of an altered acute cytokine profile upon subsequent infection, noticeable e.g. by the absence of classical pro-inflammatory cytokines and increased IFN-γ production. Further, the ability of immunized mice to survive a lethal infection is dependent on macrophages and the macrophage-activating cytokine IFN-γ. To our knowledge these findings are the first to suggest that GAS may have the ability to induce forms of trained innate immunity. Taken together, the current study proposes a novel role for the innate immune system in response to GAS infections that potentially could be leveraged for future development of effective vaccines.

Identification of host genetic factors modulating β-lactam resistance in Escherichia coli harbouring plasmid-borne β-lactamase through transposon-sequencing

Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the Escherichia coli genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci skp, gshA, phoPQ and ypfN. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. GshA and phoPQ appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, ypfN, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into Salmonella Typhimurium and Pseudomonas aeruginosa strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.

Nuclear envelope components in vascular mechanotransduction: emerging roles in vascular health and disease

The vascular network, uniquely sensitive to mechanical changes, translates biophysical forces into biochemical signals for vessel function. This process relies on the cell's architectural integrity, enabling uniform responses to physical stimuli. Recently, the nuclear envelope (NE) has emerged as a key regulator of vascular cell function. Studies implicate nucleoskeletal elements (e.g. nuclear lamina) and the linker of nucleoskeleton and cytoskeleton (LINC) complex in force transmission, emphasizing nucleo-cytoskeletal communication in mechanotransduction. The nuclear pore complex (NPC) and its component proteins (i.e. nucleoporins) also play roles in cardiovascular disease (CVD) progression. We herein summarize evidence on the roles of nuclear lamina proteins, LINC complex members, and nucleoporins in endothelial and vascular cell mechanotransduction. Numerous studies attribute NE components in cytoskeletal-related cellular behaviors to insinuate dysregulation of nucleocytoskeletal feedback and nucleocytoplasmic transport as a mechanism of endothelial and vascular dysfunction, and hence implications for aging and vascular pathophysiology.

Scarless excision of an insertion sequence in the OmpK36 promoter restores meropenem susceptibility in a non-carbapenemase-producing Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant global health challenge due to its limited treatment options and high mortality rates. Meanwhile, the prevalence of non-carbapenemase-producing CRKP (NC-CRKP) strains is increasing, but their resistance mechanisms remain less understood compared to those of carbapenemase-producing CRKP (CP-CRKP). In this study, KP-469, an NC-CRKP strain, was found to lack the major porins OmpK35 and Ompk36 but possessed OmpK37, coexisting with ESBL resistance genes CTX-M and SHV. Membrane porin coding sequence alignment revealed a minor deletion in Ompk35 and a 768 bp insertion sequence in the promoter region (IS-PR) of Ompk36, located between the -10 region and the ribosome-binding site (RBS). In the KO-469 strain with scarless excision of IS-PR and the constructed pHSG396-promoter-Ompk36 strain that incorporated wild-type Ompk36 promoter into KP-469, the transcription levels of Ompk36 were significantly higher than that in KP-469 strain, and His-tag antibody quantification further confirmed the regular expression of Ompk36 in KO-469. These results demonstrated that IS-PR markedly reduced the transcriptional and translational efficiency of Ompk36 in the KP-469 strain, leading to decreased permeability to meropenem. Moreover, the restored susceptibility to meropenem in the KO-469 strain was validated by in vitro antimicrobial susceptibility tests and an in vivo intraperitoneal infection model constructed in neutrophil-depleted mice. The novel carbapenem resistance mechanism of NC-CRKP caused by the insertion sequence in the OmpK36 promoter will facilitate the development of antibacterial regimens for treating NC-CRKP infections.

The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs

In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.

Pyruvate formate lyase regulates fermentation metabolism and virulence of Streptococcus suis

Streptococcus suis, a zoonotic pathogen, is commonly found as a commensal bacterium in the respiratory tracts of pigs. Under specific conditions, it becomes invasive and enters the blood, causing severe systemic infections. For S. suis, effective acquisition of carbon sources in different host niches is necessary for its survival. However, as of now, our understanding of the metabolism of S. suis within the host is highly restricted. Pyruvate formate lyase (PFL) plays a crucial role in bacterial survival of in glucose-limited and hypoxic host tissues. Here, we investigated the physiological and metabolic functions of PFL PflB in S. suis and elucidated its pivotal role in regulating virulence within the mucosal and blood niches. We demonstrate that PflB is a key enzyme for S. suis to support mixed-acid fermentation under glucose-limited and hypoxic conditions. Additionally, PflB is involved in regulating S. suis morphology and stress tolerance, and its regulation of capsular polysaccharide content depends on dynamic carbon availability. We also found that PflB is associated with the capacity of S. suis to cause bacteremia and persist in the upper respiratory tract to induce persistent infection. Our results provide highly persuasive evidence for the relationship between metabolic regulation and the virulence of S. suis.

Bacterial extracellular vesicles in the initiation, progression and treatment of atherosclerosis

Atherosclerosis is the primary cause of cardiovascular and cerebrovascular diseases. However, current anti-atherosclerosis drugs have shown conflicting therapeutic outcomes, thereby spurring the search for novel and effective treatments. Recent research indicates the crucial involvement of oral and gastrointestinal microbiota in atherosclerosis. While gut microbiota metabolites, such as choline derivatives, have been extensively studied and reviewed, emerging evidence suggests that bacterial extracellular vesicles (BEVs), which are membrane-derived lipid bilayers secreted by bacteria, also play a significant role in this process. However, the role of BEVs in host-microbiota interactions remains insufficiently explored. This review aims to elucidate the complex communication mediated by BEVs along the gut-heart axis. In this review, we summarize current knowledge on BEVs, with a specific focus on how pathogen-derived BEVs contribute to the promotion of atherosclerosis, as well as how BEVs from gut symbionts and probiotics may mitigate its progression. We also explore the potential and challenges associated with engineered BEVs in the prevention and treatment of atherosclerosis. Finally, we discuss the benefits and challenges of using BEVs in atherosclerosis diagnosis and treatment, and propose future research directions to address these issues.

Update on the correlation between mitochondrial function and osteonecrosis of the femoral head osteocytes

Mitochondrial health is maintained in a steady state through mitochondrial dynamics and autophagy processes. Recent studies have identified healthy mitochondria as crucial regulators of cellular function and survival. This process involves adenosine triphosphate (ATP) synthesis by mitochondrial oxidative phosphorylation (OXPHOS), regulation of calcium metabolism and inflammatory responses, and intracellular oxidative stress management. In the skeletal system, they participate in the regulation of cellular behaviors and the responses of osteoblasts, osteoclasts, chondrocytes, and osteocytes to external stimuli. Indeed, mitochondrial damage or dysfunction occurs in the development of a few bone diseases. For example, mitochondrial damage may lead to an imbalance in osteoblasts and osteoclasts, resulting in osteoporosis, osteomalacia, or poor bone production, and chondrocyte death and inflammatory infiltration in osteoarthritis are the main causes of cartilage degeneration due to mitochondrial damage. However, the opposite exists for osteosarcoma, where overactive mitochondrial metabolism is able to accelerate the proliferation and migration of osteosarcoma cells, which is a major disease feature. Bone is a dynamic organ and osteocytes play a fundamental role in all regions of bone tissue and are involved in regulating bone integrity. This review examines the impact of mitochondrial physiological function on osteocyte health and summarizes the microscopic molecular mechanisms underlying its effects. It highlights that targeted therapies focusing on osteocyte mitochondria may be beneficial for osteocyte survival, providing a new insight for the diagnosis, prevention, and treatment of diseases associated with osteocyte death.

Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea

Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.

Effects of bacteriophages on gut microbiome functionality

The gut microbiome, composed of bacteria, fungi, and viruses, plays a crucial role in maintaining the delicate balance of human health. Emerging evidence suggests that microbiome disruptions can have far-reaching implications, ranging from the development of inflammatory diseases and cancer to metabolic disorders. Bacteriophages, or "phages", are viruses that specifically infect bacterial cells, and their interactions with the gut microbiome are receiving increased attention. Despite the recently revived interest in the gut phageome, it is still considered the "dark matter" of the gut, with more than 80% of viral genomes remaining uncharacterized. Today, research is focused on understanding the mechanisms by which phages influence the gut microbiota and their potential applications. Bacteriophages may regulate the relative abundance of bacterial communities, affect bacterial functions in various ways, and modulate mammalian host immunity. This review explores how phages can regulate bacterial functionality, particularly in gut commensals and pathogens, emphasizing their role in gut health and disease.

Stress responsive glycosylphosphatidylinositol-anchored protein SsGSP1 contributes to Sclerotinia sclerotiorum virulence

Fungal cell wall acts as a defense barrier, shielding the cell from varying environmental stresses. Cell wall proteins, such as glycosylphosphatidylinositol (GPI)-anchored proteins, are involved in swift and appropriate responses to minor environmental changes in fungi. However, the roles of these proteins in the pathogenic Sclerotinia sclerotiorum remain largely unexplored. Here, we identified a novel GPI-anchored protein in S. sclerotiorum, SsGSP1, comprising a Kre9_KNH domain. SsGSP1 was upregulated during infection, and the loss-of-function mutants of SsGSP1 exhibited the compromised cell wall integrity and reduced β-glucan content. During inoculation on Arabidopsis thaliana, Nicotiana benthamiana, and Brassica napus, the SsGSP1-deletion strains demonstrated the decreased virulence. The transgenic A. thaliana line carrying the sRNA targeting SsGSP1 enhanced resistance to S. sclerotiorum via Host-Induced Gene Silencing (HIGS). The SsGSP1-deficient strains displayed the heightened sensitivity to various stresses, including osmotic pressure, oxidative stress, and heat shock. The yeast two-hybrid and BiFC assays confirmed that SsGSP1 interacted with the key stress-related proteins catalase SsCat2, heat shock protein Sshsp60, and ABC transporter SsBMR1. Accordingly, transcriptome analysis revealed that the disruption of SsGSP1 downregulated the expression of genes involved in oxidative stress response, heat shock response, and chemical agent resistance. These results collectively delineate the intricate role of GPI-anchored protein SsGSP1 in β-glucan, cell wall integrity, and virulence and may act as a potential surface sensor to elicit signal transduction in response to environmental stresses in S. sclerotiorum.

Unveiling the potential bacteriophage therapy: a systematic review

INTRODUCTION

Antimicrobial resistance renders conventional therapy, demanding the need for alternative therapeutic techniques. A potential strategy for treating infections caused by multi-drug-resistant bacteria is using bacteriophages, viruses that only multiply and infect specific bacteria. This review aims to evaluate the findings of clinical studies on phage therapy for bacterial illnesses.

METHODS

A comprehensive search method was utilized to identify 11 appropriate trials, which were then assessed for safety, efficacy, and treatment outcomes. The Joann-Briggs-Institute checklist and PRISMA criteria were used to evaluate these studies thoroughly. The results were summarized by extracting and analyzing data on trial design, treatment outcomes, safety profiles, and therapeutic effectiveness.

RESULTS

Phage treatment had a strong safety profile, with few side effects recorded across many routes, including oral, intravenous, and topical. Clinical studies demonstrated its effectiveness in lowering bacterial loads, resolving infections, and destroying biofilms. However, diversity in trial designs hampered the generalizability of the findings.

CONCLUSION

This study emphasizes the promise of phage therapy as a safe and efficient treatment for bacterial-illnesses. Despite its potential, there are still significant gaps in clinical application, long-term efficacy assessment, and trial standardization. Addressing these issues is critical to developing phage therapy as an effective alternative treatment for multidrug-resistant-illnesses.

Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM12 mice reveals pathogen-specific host and microbiota responses

Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.

Porphyromonas gulae and canine periodontal disease: Current understanding and future directions

Porphyromonas gulae has emerged as a notable pathogen in canine periodontal disease, akin to Porphyromonas gingivalis in human periodontitis. This review examines the initial isolation, phylogenetic analysis, habitat, host range, relationships with host health status and age, and key pathogenic determinants, including fimbriae, proteases, citrullinating enzyme, and lipopolysaccharide. Control strategies discussed include polyphosphate to disrupt haeme/iron utilization, clindamycin with interferon alpha to reduce bacterial load and enhance the immune response, and a protease inhibitor. Further research is needed to understand strain-level diversity of virulence factors and interactions between P. gulae and other oral bacteria, particularly Fusobacterium nucleatum, a common pathogen in both dogs and humans. The potential for interspecies transmission between dogs and humans warrants further research into these interactions. Extensive in vivo studies across various breeds are crucial to validate the effectiveness of proposed treatment strategies. This review emphasizes P. gulae's role in periodontal health and disease, setting the stage for future research and improved management of canine periodontal disease.

Gut-brain axis and environmental factors in Parkinson's disease: bidirectional link between disease onset and progression

Parkinson's disease has long been considered a disorder that primarily affects the brain, as it is defined by the dopaminergic neurodegeneration in the substantia nigra and the brain accumulation of Lewy bodies containing α-synuclein protein. In recent decades, however, accumulating research has revealed that Parkinson's disease also involves the gut and uncovered an intimate and important bidirectional link between the brain and the gut, called the "gut-brain axis." Numerous clinical studies demonstrate that gut dysfunction frequently precedes motor symptoms in Parkinson's disease patients, with findings including impaired intestinal permeability, heightened inflammation, and distinct gut microbiome profiles and metabolites. Furthermore, α-synuclein deposition has been consistently observed in the gut of Parkinson's disease patients, suggesting a potential role in disease initiation. Importantly, individuals with vagotomy have a reduced Parkinson's disease risk. From these observations, researchers have hypothesized that α-synuclein accumulation may initiate in the gut and subsequently propagate to the central dopaminergic neurons through the gut-brain axis, leading to Parkinson's disease. This review comprehensively examines the gut's involvement in Parkinson's disease, focusing on the concept of a gut-origin for the disease. We also examine the interplay between altered gut-related factors and the accumulation of pathological α-synuclein in the gut of Parkinson's disease patients. Given the accessibility of the gut to both dietary and pharmacological interventions, targeting gut-localized α-synuclein represents a promising avenue for developing effective Parkinson's disease therapies.

Glucocorticoid receptor epigenetic activity in the heart

The glucocorticoid receptor (GR) is a critical nuclear receptor that regulates gene expression in diverse tissues, including the heart, where it plays a key role in maintaining cardiovascular health. GR signaling influences essential processes within cardiomyocytes, including hypertrophy, calcium handling, and metabolic balance, all of which are vital for proper cardiac function. Dysregulation of GR activity has been implicated in various cardiovascular diseases (CVDs), highlighting the potential of GR as a therapeutic target. Remarkably, recent insights into GR's epigenetic regulation and its interaction with circadian rhythms reveal opportunities to optimize therapeutic strategies by aligning glucocorticoid administration with circadian timing. In this review, we provide an overview of the glucocorticoid receptor's role in cardiac physiology, detailing its genomic and non-genomic pathways, interactions with epigenetic and circadian regulatory mechanisms, and implications for cardiovascular disease. By dissecting these molecular interactions, this review outlines the potential of epigenetically informed and circadian-timed interventions that could change the current paradigms of CVD treatments in favor of precise and effective therapies.

Pathogenicity and virulence of Helicobacter pylori: A paradigm of chronic infection

Infection with Helicobacter pylori is one of the most common infections of mankind. Infection typically occurs in childhood and persists for the lifetime of the host unless eradicated with antimicrobials. The organism colonizes the stomach and causes gastritis. Most infected individuals are asymptomatic, but infection also causes gastric and duodenal ulceration, and gastric cancer. H. pylori possesses an arsenal of virulence factors, including a potent urease enzyme for protection from acid, flagella that mediate motility, an abundance of outer membrane proteins that can mediate attachment, several immunomodulatory proteins, and an ability to adapt to specific conditions in individual human stomachs. The presence of a type 4 secretion system that injects effector molecules into gastric cells and subverts host cell signalling is associated with virulence. In this review we discuss the interplay of H. pylori colonization and virulence factors with host and environmental factors to determine disease outcome in infected individuals.

The prevalence of low-level viraemia and its association with virological failure in people living with HIV: a systematic review and meta-analysis

Low-level viraemia (LLV) following antiretroviral therapy (ART) in people living with HIV (PLWH) has not received sufficient attention. To the determine the prevalence of LLV and its association with virological failure (VF), we systematically reviewed evidence-based interventions for PLWH. We searched PubMed, the Cochrane Library, Embase, and Web of Science from inception to 22 May 2024. Cohorts with samples sizes smaller than 1000 in size were excluded. Data from 16 cohort studies, encompassing 13,49,306 PLWH, revealed a pooled prevalence of LLV of 13.81%. Relative risk (RR) and 95% confidence intervals (CI) identified the following risk factors for LLV: viral load (VL) ≥ 105 copies/mL at baseline (1.79, 1.11-2.88), AIDS-defined illness at baseline (1.24, 1.10-1.40), and protease inhibitor-based regimen at ART initiation (1.53, 1.45-1.62) are the risk factors for LLV. Conversely, CD4 count ≥200 cells/μL at baseline (0.90, 0.82-0.98), non-nucleoside reverse transcriptase inhibitor-based regimen (0.81, 0.68-0.96) and the integrase strand transfer inhibitor (INSTI)-based regimen (0.60, 0.42-0.85) were associated with a reduced risk of LLV. Pooling the adjusted hazard ratio (aHR) and the 95% CI, we found that LLV increased the risk of VF with rising VL among 96,711 PLWH (aHR 2.77, 95% CI 2.03-3.76) and increased the risk of all-cause mortality at high VL levels among 14,229 PLWH (aHR 1.66, 95% CI 1.16-2.37). Therefore, the prevalence of LLV in PLWH should not be overlooked. This study aims to guide better management strategies to improve clinical outcomes in patients with LLV.

Characterization and genomic insights into bacteriophages Kpph1 and Kpph9 against hypervirulent carbapenem-resistant Klebsiella pneumoniae

The increasing incidence of infections attributed to hypervirulent carbapenem-resistant Klebsiella pneumoniae (Hv-CRKp) is of considerable concern. Bacteriophages, also known as phages, are viruses that specifically infect bacteria; thus, phage-based therapies offer promising alternatives to antibiotic treatments targeting Hv-CRKp infections. In this study, two isolated bacteriophages, Kpph1 and Kpph9, were characterized for their specificity against the Hv-CRKp K. pneumoniae NUHL30457 strain that possesses a K2 capsule serotype. Both phages exhibit remarkable environmental tolerance, displaying stability over a range of pH values (4-11) and temperatures (up to 50°C). The phages demonstrate potent antibacterial and antibiofilm efficacy, as indicated by their capacity to inhibit biofilm formation and to disrupt established biofilms of Hv-CRKp. Through phylogenetic analysis, it has been revealed that Kpph1 belongs to the new species of Webervirus genus, and Kpph9 to the Drulisvirus genus. Comparative genomic analysis suggests that the tail fiber protein region exhibits the greatest diversity in the genomes of phages within the same genus, which implies distinct co-evolution histories between phages and their corresponding hosts. Interestingly, both phages have been found to contain two tail fiber proteins that may exhibit potential depolymerase activities. However, the exact role of depolymerase in the interaction between phages and their hosts warrants further investigation. In summary, our findings emphasize the therapeutic promise of phages Kpph1 and Kpph9, as well as their encoded proteins, in the context of research on phage therapy targeting hypervirulent carbapenem-resistant Klebsiella pneumoniae.

Interbacterial warfare in the human gut: insights from Bacteroidales' perspective

Competition and cooperation are fundamental to the stability and evolution of ecological communities. The human gut microbiota, a dense and complex microbial ecosystem, plays a critical role in the host's health and disease, with competitive interactions being particularly significant. As a dominant and extensively studied group in the human gut, Bacteroidales serves as a successful model system for understanding these intricate dynamic processes. This review summarizes recent advances in our understanding of the intricate antagonism mechanisms among gut Bacteroidales at the biochemical or molecular-genetic levels, focusing on interference and exploitation competition. We also discuss unresolved questions and suggest strategies for studying the competitive mechanisms of Bacteroidales. The review presented here offers valuable insights into the molecular basis of bacterial antagonism in the human gut and may inform strategies for manipulating the microbiome to benefit human health.

Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance

Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.

The immune response modulated by inoculation of commensal bacteria at birth impacts the gut microbiota and prevents Salmonella colonization

Super- and low-shedding phenomena have been observed in genetically homogeneous hosts infected by a single bacterial strain. To decipher the mechanisms underlying these phenotypes, we conducted an experiment with chicks infected with Salmonella Enteritidis in a non-sterile isolator, which prevents bacterial transmission between animals while allowing the development of the gut microbiota. We investigated the impact of four commensal bacteria called Mix4, inoculated at hatching, on chicken systemic immune response and intestinal microbiota composition and functions, before and after Salmonella infection. Our results revealed that these phenotypes were not linked to changes in cell invasion capacity of bacteria during infection. Mix4 inoculation had both short- and long-term effects on immune response and microbiota and promoted the low-shedder phenotype. Kinetic analysis revealed that Mix4 activated immune response from day 4, which modified the microbiota on day 6. This change promotes a more fermentative microbiota, using the aromatic compounds degradation pathway, which inhibited Salmonella colonization by day 11 and beyond. In contrast, control animals exhibited a delayed TNF-driven pro-inflammatory response and developed a microbiota using anaerobic respiration, which facilitates Salmonella colonization and growth. This strategy offers promising opportunities to strengthen the barrier effect against Salmonella and possibly other pathogens.

The epidemiology and gene mutation characteristics of pyrazinamide-resistant Mycobacterium tuberculosis clinical isolates in Southern China

This study investigates the epidemic trend of pyrazinamide (PZA)-resistant tuberculosis in Southern China over 11 years (2012-2022) and evaluates the mutation characteristics of PZA resistance-related genes (pncA, rpsA, and panD) in clinical Mycobacterium tuberculosis (M. tuberculosis) isolates. To fulfil these goals, we analyzed the phenotypic PZA resistance characteristics of 14,927 clinical isolates for which Bactec MGIT 960 PZA drug susceptibility testing (DST) results were available, revealing that 2,054 (13.76%) isolates were resistant to PZA. After evaluating the annual variation in the PZA resistance rate among tuberculosis cases in this region, it was observed that it decreased from 37.21% to 6.45% throughout the initial 7 years (2012-2018) and then increased from 8.01% to 12.12% over the subsequent 4 years (2019-2022). Sequences of pncA were obtained from 402 clinical M. tuberculosis complex isolates. For rpsA and panD, sequences were obtained from 360 clinical M. tuberculosis complex isolates. Mutations in pncA were found in 8 out of 223 PZA-sensitive isolates (3.59%) and 105 of 179 (58.66%) PZA-resistant isolates. Conversely, non-synonymous mutations in rpsA were identified in 5 of 137 (3.65%) PZA-resistant isolates, whereas the mutation ratio of rpsA among PZA-sensitive isolates was high at 14.03% (31/221). This difference in the rpsA mutation rate was statistically significant (P = 0.001, chi-square test). No panD mutations were observed in the 137 PZA-resistant isolates, whereas two PZA-sensitive isolates harboured point mutations in panD, including one nonsense mutation (C433 T) and another C-69 T mutation. These findings indicate that rpsA and panD may not significantly contribute to the development of PZA resistance in clinical M. tuberculosis isolates.

Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.

Preassembled complexes of hAgo2 and ssRNA delivered by nanoparticles: a novel silencing gene expression approach overcoming the absence of the canonical pathway of siRNA processing in the apicomplexan parasite Babesia microti, blood parasite of veterinary and zoonotic importance

Due to the lack of efficacy of the currently used chemical drugs, poor tick control, and lack of effective vaccines against Babesia, novel control strategies are urgently needed. In this regard, searching for anti-Babesia gene therapy may facilitate the control of this infection. Following this pattern, small interfering RNAs (siRNAs) are widely used to study gene function and hence open the way to control the parasite. However, the primary constraint of this approach is the lack of Babesia to RNA-induced silencing complex (RISC) enzymes, making siRNA impractical. In this study, we preassembled complexes with the human enzyme argonaute 2 (hAgo2) and a small interfering RNA (siRNA)/single-stranded RNA (ssRNA) against B. gibsoni and B. microti metabolite transporters. The assembled complexes were generated by developing a gene delivery system with chitosan dehydroascorbic acid nanoparticles. The delivery system effectively protected the loaded RNAi and targeted Babesia-infected RBCs with a relatively high internalization rate. The assembled complexes were successfully transfected into live parasites for specific slicing of Babesia targets. We demonstrated a reduction in the expression of target genes at the mRNA level. Furthermore, this silencing inhibited Babesia growth in vitro and in vivo. For the first time, we used this method to confirm the role of the assembled complexes in manipulating the noncanonical pathway of RNAi in Babesia parasites. This novel method provides a means of silencing Babesia genes to study their role in host-parasite interactions and as potential targets for gene therapy and control.

Maternal consumption of urbanized diet compromises early-life health in association with gut microbiota

Urbanization has significantly transformed dietary habits worldwide, contributing to a globally increased burden of non-communicable diseases and altered gut microbiota landscape. However, it is often overlooked that the adverse effects of these dietary changes can be transmitted from the mother to offspring during early developmental stages, subsequently influencing the predisposition to various diseases later in life. This review aims to delineate the detrimental effects of maternal urban-lifestyle diet (urbanized diet) on early-life health and gut microbiota assembly, provide mechanistic insights on how urbanized diet mediates mother-to-offspring transfer of bioactive substances in both intrauterine and extrauterine and thus affects fetal and neonatal development. Moreover, we also further propose a framework for developing microbiome-targeted precision nutrition and diet strategies specifically for pregnant and lactating women. The establishment of such knowledge can help develop proactive preventive measures from the beginning of life, ultimately reducing the long-term risk of disease and improving public health outcomes.

The crystal structure of the toxin EspC from enteropathogenic Escherichia coli reveals the mechanism that governs host cell entry and cytotoxicity

Enteropathogenic E. coli (EPEC) is a significant cause of diarrhea, leading to high infant mortality rates. A key toxin produced by EPEC is the EspC autotransporter, which is regulated alongside genes from the locus of enterocyte effacement (LEE), which collectively result in the characteristic attaching and effacing lesions on the intestinal epithelium. In this study, we present the crystal structure of the EspC passenger domain (αEspC) revealing a toxin comprised a serine protease attached to a large β-helix with additional subdomains. Using various modified EspC expression constructs, alongside type III secretion system-mediated cell internalization assays, we dissect how the αEspC structural features enable toxin entry into the intestinal epithelium to cause cell cytotoxicity.

The live attenuated varicella-zoster virus vaccine vOka: Molecular and cellular biology of its skin attenuation

Infection with varicella-zoster virus (VZV) causes chickenpox and shingles, both manifesting as a blistering skin rash. The skin is central to VZV, as the site of viral replication, transmission from cell-free virus in blisters and as the gateway to sensory nerves for establishing latency. The existing chickenpox vaccine is based on the live attenuated vOka strain and is impaired for replication in skin. While the genetics of the vOka vaccine have been extensively studied, critical gaps exist in understanding the molecular and cellular mechanisms of vOka attenuation, particularly in human skin models. This review aims to explore the molecular biology of vOka vaccine, focusing on its genetic diversity, interaction with host skin pathways, and the impact of vOka mutations in key VZV genes on attenuation mechanisms in human skin models. Insights from this review may guide the development of next-generation varicella vaccines and enhance the understanding of VZV pathogenesis.

Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs

Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.

Effects of ex situ conservation on commensal bacteria of crocodile lizard and conservation implications

Ex situ conservation is an important wildlife conservation strategy, but endangered wildlife in captivity often exhibit high disease rates. Commensal microorganisms are vital for homeostasis, immunity, and linked to diseases. This study analyzed the structure, assembly, variations of the symbiotic microbiota of the endangered crocodile lizard, and their relationship with environment, as well as the effects of captivity on them, to explore why captive reptiles face high dermatosis rates. Results showed that the reptile's microbiota significantly differ from that of its habitat, demonstrating niche specificity. While species richness among organs showed no significant differences, microbial diversity varied considerably. Skin microbiota showed no site-specific clustering. The assembly of skin, oral, and intestinal bacterial communities was dominated by homogeneous selection. The gut and oral bacterial networks were resilient to disturbances, while the skin bacterial network was sensitive. Captivity primarily affected the skin microbiota, reducing its diversity and stability, thereby increasing disease risk, and these effects were not solely attributable to environmental changes. These findings suggested that skin microbial changes in captive reptiles may be responsible for their increased susceptibility to dermatosis in ex situ conservation. This study underscored the importance of understanding reptile-associated microbes for effective conservation strategies and offers potential solutions.

Epigenetic regulation of the inflammatory response in stroke

Stroke is classified as ischemic or hemorrhagic, and there are few effective treatments for either type. Immunologic mechanisms play a critical role in secondary brain injury following a stroke, which manifests as cytokine release, blood-brain barrier disruption, neuronal cell death, and ultimately behavioral impairment. Suppressing the inflammatory response has been shown to mitigate this cascade of events in experimental stroke models. However, in clinical trials of anti-inflammatory agents, long-term immunosuppression has not demonstrated significant clinical benefits for patients. This may be attributable to the dichotomous roles of inflammation in both tissue injury and repair, as well as the complex pathophysiologic inflammatory processes in stroke. Inhibiting acute harmful inflammatory responses or inducing a phenotypic shift from a pro-inflammatory to an anti-inflammatory state at specific time points after a stroke are alternative and promising therapeutic strategies. Identifying agents that can modulate inflammation requires a detailed understanding of the inflammatory processes of stroke. Furthermore, epigenetic reprogramming plays a crucial role in modulating post-stroke inflammation and can potentially be exploited for stroke management. In this review, we summarize current findings on the epigenetic regulation of the inflammatory response in stroke, focusing on key signaling pathways including nuclear factor-kappa B, Janus kinase/signal transducer and activator of transcription, and mitogen-activated protein kinase as well as inflammasome activation. We also discuss promising molecular targets for stroke treatment. The evidence to date indicates that therapeutic targeting of the epigenetic regulation of inflammation can shift the balance from inflammation-induced tissue injury to repair following stroke, leading to improved post-stroke outcomes.

A novel coumarin-incorporated lanthanide coordination nanoprobe for ratiometric sensing of tetracycline

Tetracycline (Tc), a broad-spectrum antibiotic for treating bacterial infections, poses significant risks to human health and the environment. This study presents a novel lanthanide coordination probe, AMP/Eu/CMP, for the ratiometric detection of Tc. The pyridine-appended coumarin derivative, CMP, acting as a stable internal reference, combines with AMP and Eu3+ to form the robust ratiometric probe AMP/Eu/CMP. Upon binding to Tc, Eu3+ fluorescence (emission at 616 nm) is sensitized while CMP fluorescence (emission at 505 nm) remains unchanged, resulting in a clear fluorescence shift from blue-green to red, enabling effective ratiometric detection of Tc. By integrating a smartphone color recognition app, rapid and visual detection of tetracycline concentrations is achieved. Additionally, paper-based test strips were developed for on-site Tc detection, exhibiting a linear response across a wide concentration range, making this method suitable for applications in food safety, pharmaceutical analysis, and environmental monitoring. The use of a fluorescent molecule with unique photophysical properties as an internal reference enables the construction of a high-performance, ratiometric lanthanide coordination polymer probe that is rapid, simple, and cost-effective, providing valuable insights for the development of future fluorescence sensors.

Mucus-penetrating nanomotor system strengthens mucosal immune response to in situ bacterial vaccine against severe bacterial pneumonia

Pathogens causing major infectious diseases primarily invade through mucosal tissues. Promptly killing these pathogens at the mucosal site and constructing mucosal vaccines in situ can prevent further infections and induce robust mucosal immune responses and memory to prevent reinfection. In this study, we utilized chemotherapy, sonodynamic therapy, and gas therapy to eliminate Streptococcus pneumoniae (S. pneumoniae) colonizing the nasal mucosa. Simultaneously, an in situ pneumococcal vaccine was constructed to elicit specific immune responses and memory. Poly-l-arginine (PArg)-modified ZIF-8 metal-organic frameworks (MOFs) loaded with the ultrasonic sensitizer protoporphyrin IX (PpIX) killed S. pneumoniae in the nasal cavity by multiple mechanisms in the presence of ultrasound. When stimulated by ultrasound, PpIX not only generates reactive oxygen species (ROS) for antimicrobial effect, but these ROS also catalyze the release of nitric oxide (NO) from PArg. NO exerts a motor-like effect that facilitates more efficient passage of nanoparticles through the mucus layer of the alveoli. The immunogenic bacterial debris formed a vaccine formulation by complexing with PArg, which adhered electrostatically to the mucosal surface, facilitating in situ vaccination and inducing mucosal immune responses and memory. This cascade-based combination therapy enabled rapid bacterial eradication and long-term immune prevention. It shortens the traditional vaccine development process, eliminates the spatial distance from pathogen invasion to vaccine development, significantly cuts costs, and addresses vaccine failure due to pathogen mutations. This approach offers a groundbreaking strategy for mucosal vaccine development and the prevention of major infectious diseases.

Bioinoculant substitution enhances rhizosphere soil quality and maize growth by modulating microbial communities and host gene expression in alkaline soils

The application of plant growth-promoting bacteria (PGPB) as bioinoculants is widely recognized for improving crop yields and soil fertility. However, the precise mechanisms underlying their impact on rhizosphere soil quality and crop productivity remain insufficiently understood. This study elucidates how a solid bioinoculant, comprising Bacillus velezensis FZB42 and attapulgite clay, enhances rhizosphere soil quality and maize (Zea mays) growth in nutrient-deficient alkaline calcareous soils. Pot experiments reveal that bioinoculant application promotes extensive root colonization under nitrogen-deficient conditions, with significantly higher colonization rates observed in the half-nitrogen (HN) and zero-nitrogen (ZN) treatments compared to full-nitrogen conditions. Notably, bioinoculant application in ZN and HN significantly increases phosphorus availability and soil quality in the rhizosphere. Furthermore, maize growth parameters, including plant height, stem diameter, and kernel yield, are markedly enhanced, with optimal biomass accumulation achieved under HN conditions. High-throughput sequencing of rhizosphere microbiomes uncovers significant shifts in microbial community composition, with enrichment of key taxa involved in nutrient cycling and plant-microbe interactions. Transcriptomic analysis of maize tissues demonstrates the upregulation of genes associated with nutrient transport, photosynthesis, fatty acid biosynthesis, and kernel development, with a pronounced enrichment in metabolic pathways linked to growth and productivity. Structural equation modeling indicates that increased microbial diversity and gene expression collectively account for 69 % of the variance in the soil quality index and 45 % of the variance in maize yield. These findings provide critical mechanistic insights into the role of solid bioinoculant in enhancing soil fertility and crop performance, highlighting their potential as a sustainable agricultural strategy for improving productivity in low-fertility alkaline soils.

Plant growth-promoting microorganisms: New insights and the way forward

In the context of global challenges such as climate change, soil degradation, and food security, understanding the modes of action of Plant Growth-Promoting Microorganisms (PGPMs), their formulation, and their application is crucial and can be more focused in future research projects. This editorial paper aims to elucidate diverse modes of action employed by different types of PGPMs, including nitrogen fixation, phosphorus solubilization, production or regulation of phytohormones, and plant protection against environmental and biotic stresses as demonstrated and discussed in the Special Issue entitled "Plant Growth-Promoting Microorganisms: new insights and the way forward".

Listeria monocytogenes gut interactions and listeriosis: Gut modulation and pathogenicity

Following ingestion via contaminated food, Listeria monocytogenes faces multiple hurdles through the human digestive system, thereby influencing its capacity to cause infection. This review provides a comprehensive overview of the multifaceted mechanisms employed by L. monocytogenes to overcome gastrointestinal hurdles and interact with the host's microbiota, facing chemical and physical barriers such as saliva, stomach acidity, bile salts and mechanical clearance. Proposed evasion strategies will be highlighted, exploring the bacteriocins produced by L. monocytogenes, such as the well-described bacteriocin Listeriolysin S (LLS), a bacteriocin that inhibits inflammogenic species - Lmo2776, and a phage tail-like bacteriocin, monocin. The competitive dynamic interactions within the gut microbiota, as well as the modulation of microbiota composition and immune responses, will also be explored. Finally, the adhesion and invasion of the intestinal epithelium by L. monocytogenes is described, exploring the mechanism of pathogenesis, biofilm and aggregation capacities and other virulence factors. Unlike previous reviews that may focus on individual aspects of L. monocytogenes pathogenicity, this review offers a holistic perspective on the bacterium's ability to persist and cause infection, integrating information about survival strategies, including bacteriocin production, immune modulation, and virulence factors. By connecting recent findings on microbial interactions and infection dynamics, this review incorporates recent developments in the field and connects various lines of research that explore both host and microbial factors influencing infection outcomes.

Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment

The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.

Deciphering the role of the distal pocket in Staphylococcus aureus coproheme decarboxylase

Coproheme decarboxylase (ChdC) catalyzes the sequential oxidative decarboxylation of coproheme III propionate side chains at positions 2 and 4 to form heme b by activation of two molecules of H2O2 at its substrate's iron center. The coproheme III binding pocket lacks the distal His-Arg pair that polarizes and acts as a catalytic base toward activation of coordinated H2O2 in canonical heme-dependent peroxidases. Instead ChdC from Staphylococcus aureus has a Gln (Q185). This report presents thermodynamic, kinetic, and spectroscopic results that provide comparative insight into how wild type (WT) and Q185A and Q185R variant ChdCs activate H2O2. Reactivities with H2O2 and cyanide affinities at pH 7.5 follow the trend: WT > Q185R > Q185A. Both variants exhibited greater catalase efficiency than WT ChdC. Vibrational resonance Raman signatures of ferric coproheme-CN- and ferrous coproheme-CO complexes of WT, Q185A, and Q185R SaChdCs revealed that the Arg mutation does not significantly alter the distal environment while Q185A has a more open active site. Together these data are consistent with a modest role for Q185 in promoting the decarboxylation reaction. A model for the proton transfer required for H2O2 activation that involves the Gln185 iminol tautomer is presented. The three ChdCs reacted with chlorite to generate harderoheme III and heme b to varying extents. In reaction with chlorite, coproheme III:SaChdC was cleanly converted to harderoheme III:SaChdC, which exhibited vinyl bending and stretching modes at 423 and 1622 cm-1, respectively. Differences in SaChdC reactivity with ClO2- and H2O2 relative to those of chlorite dismutase and peroxidases, respectively, are discussed.

Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress

Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress, but its structure and functions in heavy metal-hyperaccumulating plants remain elusive. Here, the phyllosphere microbiome, inhabiting hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii grown in soils with varying heavy metal concentration, was characterized. Compared with NHE, the microbial community α-diversity was greater in HE. Core phyllosphere taxa with high relative abundance (>10 %), including Streptomyces and Nocardia (bacteria), Cladosporium and Acremonium (fungi), were significantly related to cadmium (Cd) and zinc (Zn) concentration and biomass of host plants. Moreover, microbial co-occurrence networks in HE exhibited greater complexity than those in NHE. Additionally, proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration, indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress. Furthermore, in contrast to NHE, microbial community functions, primarily involved in heavy metal stress resistance, were more abundant in HE, in which microbiome assisted hosts to resist heavy metal stress better. Collectively, this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress, and provided new insights into phyllosphere microbial application potential in phytoremediation.

Application of pulsed electric field (PEF) as a strategy to enhance aminoglycosides efficacy against Gram-negative bacteria

In this study, two aminoglycosides (AGs), Kanamycin and Gentamicin, with similar modes of action and molecular weights, were combined with PEF treatment to enhance the inactivation of E. coli cells. Various PEF strengths were applied to assess the combined effect. To compare the inactivation efficacy of different AGs, bacterial growth measurements in suspension were performed at 3 and 10 h intervals over a 10-h period after PEF treatment. Interestingly, it was found that the additive effect of PEF treatment on E. coli growth inhibition was significantly greater with Kanamycin (IC50) than with Gentamicin (IC50). Further analysis revealed that the combined treatment with Kanamycin (IC50) was most effective within a timeframe of around 3 h. Our findings suggest that PEF treatment can significantly enhance the efficacy of AGs against Gram-negative bacteria; however, the extent of the additive effect varies depending on the specific antibiotic and the intensity of the applied PEF treatment.

Boosting Rhizobium-legume symbiosis: The role of nodule non-rhizobial bacteria in hormonal and nutritional regulation under stress

Legumes are vital for sustainable agriculture due to their unique ability to fix atmospheric nitrogen through symbiosis with rhizobia. Recent research has highlighted the significant role of non-rhizobial bacteria (NRB) within root nodules in enhancing this symbiotic relationship, particularly under stress conditions. These NRB exhibit plant growth-promoting (PGP) metabolites by modulating phytohormones and enhancing nutrient availability, thereby improving nodule development and function. Bacteria produce essential hormones, such as auxin (indole-3-acetic acid), cytokinins, gibberellic acids abscisic acid, jasmonic acid, and salicylic acid, and enzymes like 1-aminocyclopropane-1-carboxylate deaminase, which mitigate ethylene's inhibitory effects on nodulation. Furthermore, NRB contribute to nutrient cycling by solubilizing minerals like phosphate, potassium, silicate, zinc, and iron, essential for effective nitrogen fixation. The co-inoculation of legumes with both rhizobia and NRB with multiple PGP metabolites has shown synergistic effects on plant growth, yield, and resilience against environmental stresses. This review emphasizes the need to further explore the diversity and functional roles of nodule-associated non-rhizobial endophytes, aiming to optimize legume productivity through improved nutrient and hormonal management. Understanding these interactions is crucial for developing sustainable agricultural practices that enhance the efficiency of legume-rhizobia symbiosis, ultimately contributing to food security and ecosystem health.

Anaerobic digestion at high-pH and alkalinity for biomethane production: Insights into methane yield, biomethane purity, and process performance

The role of high-pH conditions in anaerobic digestion (AD) has traditionally been confined to it's use in pre-treatment processes. However, operating AD at elevated pH and alkalinity offers significant advantages, including in-situ upgrading of biogas to biomethane. This study examines the potential and scalability of AD under these conditions (pH ∼ 9.3; alkalinity ∼ 0.5 eq/L). The substrate used was the alkaline waste generated from the extraction of extracellular polymeric substances (EPS) from aerobic granular sludge (AGS), and the inoculum used was a haloalkaliphile microbial community from soda lake sediments. To evaluate the system's performance, the organic loading rate (OLR) was incrementally increased. The highest methane production obtained was 8.4 ± 0.1 mL/day/gVSadded at a hydraulic retention time (HRT) of 15 days and an OLR of 1 kgVS/day/m3. At this loading rate, methanogenesis became the rate limiting conversion. The maximum volatile solids conversion was 48.1 ± 1.1 %. Throughout the reactor operation, methane purity in the biogas consistently exceeded 90 % peaking at 96.0 ± 0.2 %, showcasing the potential for in-situ biogas purification under these conditions. In addition, no ammonia inhibition was observed, even with free-ammonia (NH3) concentrations reaching up to 14 mM. This study underscores the potential of high-pH anaerobic digestion as a sustainable method for both waste treatment and energy recovery.

Gaseous ligand binding to Porphyromonas gingivalis HmuY hemophore-like protein in complex with heme

Porphyromonas gingivalis is the main pathogenic player in the development of periodontitis. To acquire heme, being an essential source of iron and protoporphyrin IX, P. gingivalis utilizes TonB-dependent outer membrane heme receptor (HmuR) and heme-binding hemophore-like protein (HmuY) as the main system for heme uptake from host hemoproteins. In this work, we present an extensive spectroscopic characterization of the binding of exogenous gaseous ligands to the holo-form of the HmuY (HmuY-heme) to unravel the mechanistic basis of heme release. Our data are consistent with a scenario where heme release from HmuY-heme is a multistep process that requires the initial rupture of one of the two heme‑iron coordination bonds with endogenous histidines.

Heme dependent activity of the Streptomyces c-di-GMP-metabolizing enzyme CdgA

Streptomyces species are vital for producing natural products like antibiotics, with c-di-GMP playing a key role in regulating processes such as differentiation. C-di-GMP metabolism is controlled by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), which synthesize and hydrolyze c-di-GMP, respectively, to modulate cellular levels. To improve our understanding of c-di-GMP-regulated processes in Streptomyces, we have characterized a c-di-GMP-metabolizing enzyme CdgA from Streptomyces ghanaensis that contains both a diguanylate cyclase and a phosphodiesterase domain. Our studies demonstrate that the enzyme is purified in a form without heme and is only able to degrade c-di-GMP. When reconstituted with heme, it enables c-di-GMP synthesis, and depending on the redox state the synthesis rate is changed. To our knowledge, this is the first heme-dependent activity reported for a c-di-GMP-metabolizing enzyme in Streptomyces and has major implications for understanding the way c-di-GMP is metabolized in vivo in Streptomyces.

Real-time monitoring method of microbial growth using a simple pressure-based respiration detection system

Dry cell weight (DCW) and optical density (OD) measurement methods provide useful data for assessing microbial growth. However, their sampling process is labor-intensive and time-consuming. Therefore, we aimed to evaluate a method for measuring microbial growth through continuous CO2 measurement under aerobic conditions using a pressure-based respiration detection system, which is traditionally used in anaerobic environments and applies measurement of reduced pressure by capturing CO2 with KOH. The pressure reduction rate, OD, and DCW values were compared during Ralstonia eutropha H16 culture, which revealed a correlation of R2 of 0.99 between the pressure reduction and DCW and a change of DCW (g/L) per pressure (1 mbar) of -0.02 g/L. It showed theoretical limit of detection at 14.67 mbar corresponding to 0.0428 g/L of DCW and theoretical limit of quantification at 48.9 mbar as lower limits. When the pressure-based method was applied to compare carbon source utilization and growth of different strains, such as E. coli sp., Pseudomonas sp., Burkholderia sp., and Bacillus sp., it showed a high correlation with DCW. Overall, these results demonstrate that the pressure-based respiration detection system is a reliable tool for microbial growth monitoring and offers significant advantages by providing real-time data with less labor.

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Mechanisms of exopolysaccharide synthesis by Streptococcus thermophilus IMAU20246 determined by the carbon source

Our study characterized exopolysaccharide production by Streptococcus thermophilus IMAU20246 with lactose, glucose, galactose, or sucrose as sole carbon sources, and conducted comparative transcriptomics to unravel EPS synthesis mechanisms. The yield, molecular weight, monosaccharide composition and structure of EPSs were significantly affected by carbon sources. The yield of EPSs was highest (617 ± 5.9 mg/L), and Mw the smallest (3.789 × 104 Da) in sucrose; it was 1.5, 1.2 and 1.8 times higher than with lactose, glucose and galactose, respectively. Transcriptomic analysis identified 21 key enzymes for EPS synthesis, and S. thermophilus IMAU20246 preferentially regulated sucrose utilization through ABC transporters, phosphotransferase system (PTS), amino sugar and nucleotide sugar metabolism; and upregulated expression of EPS biosynthesis genes to increase EPS production. This study provides a theoretical basis for enhancing EPS content and reveals the dynamics of EPS synthesis in S. thermophilus which may be significant for further EPS production and application.