Two-component regulatory systems in Helicobacter pylori and Campylobacter jejuni: Attractive targets for novel antibacterial drugs

C16 peptide and angiopoietin-1 alleviate the side effects of glucocorticoids in a rat multiple sclerosis model

BACKGROUND

Natural glucocorticoids (GCs) have been widely used to treat acute multiple sclerosis (MS) attacks. However, they also cause significant side effects related to immunosuppression. Our previous study found that C16 peptide combined with angiopoietin-1 (Ang-1) inhibited inflammatory cell infiltration and protected blood vessels in animal models of inflammatory neurodegenerative diseases.

METHODS

An acute experimental autoimmune encephalomyelitis model was established in Lewis rats to explore the effects of these drugs on MS. One hundred rats were equally and randomly assigned into five groups: normal control, vehicle, low-dose methylprednisolone (MP), high-dose MP, and C16 + Ang-1 (C+A). Histological examinations, behavioral tests, and high-throughput 16S rRNA gene sequencing were conducted to determine inflammation levels in the central nervous system, neuronal survival, functional recovery and gut microbiota.

RESULTS

The results illustrated that C+A exerted a neuroprotective effect in MS rats, with fewer side effects observed in the C+A group than in the high-dose MP group. The abundance of Campylobacter was increased in vehicle-treated rats, indicating an imbalance of the gut microbiota after MS. The abundance of probiotic Lactobacillus plantarum was increased in the C+A group. Low-dose MP failed to reverse the gut microbiota imbalance, whereas both the C+A and high-dose MP groups exhibited gut microbiota profiles more similar to those of the normal controls, with C+A displaying superior efficacy.

CONCLUSIONS

C16 plus Ang-1 might serve as a complement to GCs for the treatment of MS. Changes in the abundance of Campylobacter and L. plantarum suggest their essential roles in the pathogenesis of MS.

Novel Drug-like HsrA Inhibitors Exhibit Potent Narrow-Spectrum Antimicrobial Activities against Helicobacter pylori

Helicobacter pylori infection constitutes a silent pandemic of global concern. In the last decades, the alarming increase in multidrug resistance evolved by this pathogen has led to a marked drop in the eradication rates of traditional therapies worldwide. By using a high-throughput screening strategy, in combination with in vitro DNA binding assays and antibacterial activity testing, we identified a battery of novel drug-like HsrA inhibitors with MIC values ranging from 0.031 to 4 mg/L against several antibiotic-resistant strains of H. pylori, and minor effects against both Gram-negative and Gram-positive species of human microbiota. The most potent anti-H. pylori candidate demonstrated a high therapeutic index, an additive effect in combination with metronidazole and clarithromycin as well as a strong antimicrobial action against Campylobacter jejuni, another clinically relevant pathogen of phylum Campylobacterota. Transcriptomic analysis suggests that the in vivo inhibition of HsrA triggers lethal global disturbances in H. pylori physiology including the arrest of protein biosynthesis, malfunction of respiratory chain, detriment in ATP generation, and oxidative stress. The novel drug-like HsrA inhibitors described here constitute valuable candidates to a new family of narrow-spectrum antibiotics that allow overcoming the current resistome, protecting from dysbiosis, and increasing therapeutic options for novel personalized treatments against H. pylori.

CemR atypical response regulator impacts energy conversion in Campylobacteria

Campylobacter jejuni and Arcobacter butzleri are microaerobic food-borne human gastrointestinal pathogens that mainly cause diarrheal disease. These related species of the Campylobacteria class face variable atmospheric environments during infection and transmission, ranging from nearly anaerobic to aerobic conditions. Consequently, their lifestyles require that both pathogens need to adjust their metabolism and respiration to the changing oxygen concentrations of the colonization sites. Our transcriptomic and proteomic studies revealed that C. jejuni and A. butzleri, lacking a Campylobacteria-specific regulatory protein, C. jejuni Cj1608, or a homolog, A. butzleri Abu0127, are unable to reprogram tricarboxylic acid cycle or respiration pathways, respectively, to produce ATP efficiently and, in consequence, adjust growth to changing oxygen supply. We propose that these Campylobacteria energy and metabolism regulators (CemRs) are long-sought transcription factors controlling the metabolic shift related to oxygen availability, essential for these bacteria's survival and adaptation to the niches they inhabit. Besides their significant universal role in Campylobacteria, CemRs, as pleiotropic regulators, control the transcription of many genes, often specific to the species, under microaerophilic conditions and in response to oxidative stress.

IMPORTANCE

C. jejuni and A. butzleri are closely related pathogens that infect the human gastrointestinal tract. In order to infect humans successfully, they need to change their metabolism as nutrient and respiratory conditions change. A regulator called CemR has been identified, which helps them adapt their metabolism to changing conditions, particularly oxygen availability in the gastrointestinal tract so that they can produce enough energy for survival and spread. Without CemR, these bacteria, as well as a related species, Helicobacter pylori, produce less energy, grow more slowly, or, in the case of C. jejuni, do not grow at all. Furthermore, CemR is a global regulator that controls the synthesis of many genes in each species, potentially allowing them to adapt to their ecological niches as well as establish infection. Therefore, the identification of CemR opens new possibilities for studying the pathogenicity of C. jejuni and A. butzleri.

Amoebae as training grounds for microbial pathogens

Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.

Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator

Campylobacter jejuni is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, C. jejuni is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant Campylobacter as a serious antibiotic resistance threat in the United States. The C. jejuni CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in C. jejuni that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the cmeABC promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA.

IMPORTANCE

Campylobacter jejuni has emerged as an antibiotic-resistant threat worldwide. CosR is an essential regulator for this bacterium and is important for Campylobacter adaptation to various stresses. Here, we describe the structural basis of CosR binding to target DNA as determined by cryo-electron microscopy and X-ray crystallography. Since CosR is a potential target for intervention, our studies may facilitate the development of novel therapeutics to combat C. jejuni infection.

Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention

Purpose

Polycystic ovary syndrome (PCOS) is a frequent cause of infertility in reproductive-age women. Our work aims to evaluate the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on gut microbiota, with metabolic parameters including body weight and the hormone profile in PCOS.

Patients and Methods

Dehydroepiandrosterone (DHEA)-induced PCOS mice were established and then treated with two GLP-1RAs: liraglutide and novel form semaglutide for four weeks. Changes in body weight and metabolic parameters were measured. Fecal samples were collected and analyzed using metagenomic sequencing.

Results

Liraglutide and semaglutide modulated both alpha and beta diversity of the gut microbiota in PCOS. Liraglutide increased the Bacillota-to-Bacteroidota ratio through up-regulating the abundance of butyrate-producing members of Bacillota like Lachnospiraceae. Moreover, liraglutide showed the ability to reverse the altered microbial composition and the disrupted microbiota functions caused by PCOS. Semaglutide increased the abundance of Helicobacter in PCOS mice (p < 0.01) which was the only bacteria found negatively correlated with body weight. Moreover, pathways involving porphyrin and flavonoids were increased after semaglutide intervention.

Conclusion

Liraglutide and semaglutide improved reproductive and metabolic disorders by modulating the whole structure of gut microbiota in PCOS. The greater efficacy in weight loss compared with liraglutide observed after semaglutide intervention was positively related with Helicobacter. The study may provide new ideas in the treatment and the underlying mechanisms of GLP-1RAs to improve PCOS.

Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts

The perturbations of the gut microbiota and metabolites are closely associated with the progression of inflammatory bowel disease (IBD). However, inconsistent findings across studies impede a comprehensive understanding of their roles in IBD and their potential as reliable diagnostic biomarkers. To address this challenge, here we comprehensively analyze 9 metagenomic and 4 metabolomics cohorts of IBD from different populations. Through cross-cohort integrative analysis (CCIA), we identify a consistent characteristic of commensal gut microbiota. Especially, three bacteria, namely Asaccharobacter celatus, Gemmiger formicilis, and Erysipelatoclostridium ramosum, which are rarely reported in IBD. Metagenomic functional analysis reveals that essential gene of Two-component system pathway, linked to fecal calprotectin, are implicated in IBD. Metabolomics analysis shows 36 identified metabolites with significant differences, while the roles of these metabolites in IBD are still unknown. To further elucidate the relationship between gut microbiota and metabolites, we construct multi-omics biological correlation (MOBC) maps, which highlights gut microbial biotransformation deficiencies and significant alterations in aminoacyl-tRNA synthetases. Finally, we identify multi-omics biomarkers for IBD diagnosis, validated across multiple global cohorts (AUROC values ranging from 0.92 to 0.98). Our results offer valuable insights and a significant resource for developing mechanistic hypotheses on host-microbiome interactions in IBD.

Effect of an Enteroprotective Complementary Feed on Faecal Markers of Inflammation and Intestinal Microbiota Composition in Weaning Puppies

Weaning entails numerous modifications of the intestinal structure and microbiota composition, making puppies at high risk of sickness during this delicate life stage. The aim of this study was to investigate the effects of a four-week administration of a supplement composed of ultramicronised Palmitoylethanolamide, bovine colostrum and Bacillus subtilis (Normalia® Extra, Innovet Italia Srl, Saccolongo, Italy) on markers of gut health and microbiome of weaning puppies. Twenty-nine four-week-old Golden Retriever puppies were randomly assigned to control (CG, n = 13) and treated (TG, n = 16) groups. During the whole experimental time, there were no differences between the groups with regard to average daily gain and faecal score. In TG, faecal calprotectin and zonulin values were statistically significantly decreased compared to CG, especially at week 8 (zonulin: 42.8 ± 1.54 ng/mL and 55.3 ± 42.8 ng/mL, and calprotectin: 2.91 ± 0.38 µg/g and 5.71 ± 0.43 µg/g, in TG and CG, respectively; p < 0.0001 for both comparisons). Bacteria belonging to phylum Campylobacterota decreased (p = 0.04), while those referring to genera Coprococcus and Pseudomonas increased (p = 0.01 and p = 0.04, respectively). The supplementation of the tested complementary feed can promote the intestinal health of puppies and therefore facilitate weaning by lowering gut inflammation.

Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria

In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.

Effect of Cyberlindnera jadinii supplementation on growth performance, serum immunity, antioxidant status, and intestinal health in winter fur-growing raccoon dogs (Nyctereutes procyonoides)

Introduction

This study aimed to investigate the effects of Cyberlindnera jadinii supplementation on the growth performance, nutrient utilization, serum biochemistry, immunity, antioxidant status, and intestinal microbiota of raccoon dogs during the winter fur-growing period.

Methods

Forty-five 135 (±5) day-old male raccoon dogs were randomly assigned to three dietary groups supplemented with 0 (group N), 1 × 10⁹ (group L) and 5 × 10⁹ CFU/g (group H) Cyberlindnera jadinii, with 15 raccoon dogs per group.

Results

The results showed that Cyberlindnera jadinii in groups L and H improved average daily gain (ADG) and decreased feed-to-weight ratio (F/G) (P < 0.05). No significant difference was found in nutrient digestibility and nitrogen metabolism among the three groups (P > 0.05). Compared with group N, serum glucose levels were lower in groups L and H (P < 0.05). The levels of serum immunoglobulins A and G in group L were higher than those in the other two groups (P < 0.05), and the levels of serum immunoglobulins A and M in group H were higher than those in group N (P < 0.05). Supplementation with Cyberlindnera jadinii in groups L and H increased serum superoxide dismutase activity, and the total antioxidant capacity in group H increased compared with group N (P < 0.05). The phyla Bacteroidetes and Firmicutes were dominant in raccoon dogs. The results of principal coordinate analysis (PCoA) showed that the composition of microbiota in the three groups changed significantly (P < 0.05). The relative abundance of Campylobacterota was increased in the H group compared to the N and L groups (P < 0.05). The relative abundance of Sarcina was increased in group L compared with the other two groups (P < 0.05), while the relative abundance of Subdoligranulum and Blautia were decreased in group H compared with the other two groups (P < 0.05). Also, the relative abundance of Prevotella, Sutterella and Catenibacterium was higher in group L (P < 0.05) compared with group H.

Discussion

In conclusion, dietary supplementation with Cyberlindnera jadinii improved growth performance, antioxidant activity, immune status, and improved intestinal microbiota in winter fur-growing raccoon dogs. Among the concentrations tested, 1 × 10⁹ CFU/g was the most effective level of supplementation.

Insights into the Orchestration of Gene Transcription Regulators in Helicobacter pylori

Bacterial pathogens employ a general strategy to overcome host defenses by coordinating the virulence gene expression using dedicated regulatory systems that could raise intricate networks. During the last twenty years, many studies of Helicobacter pylori, a human pathogen responsible for various stomach diseases, have mainly focused on elucidating the mechanisms and functions of virulence factors. In parallel, numerous studies have focused on the molecular mechanisms that regulate gene transcription to attempt to understand the physiological changes of the bacterium during infection and adaptation to the environmental conditions it encounters. The number of regulatory proteins deduced from the genome sequence analyses responsible for the correct orchestration of gene transcription appears limited to 14 regulators and three sigma factors. Furthermore, evidence is accumulating for new and complex circuits regulating gene transcription and H. pylori virulence. Here, we focus on the molecular mechanisms used by H. pylori to control gene transcription as a function of the principal environmental changes.