Proteus spp. as Putative Gastrointestinal Pathogens

Request for an Opinion: conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980)

The prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) is a later homonym of the protozoan genus name Proteus Müller, 1786 and therefore should be considered illegitimate and in need of replacement according to Rules 51b(4) and 54 of the International Code of Nomenclature of Prokaryotes. However, it would be unwelcome for medical and veterinary community to propose by anyone any replacement name and discontinue the current usage. To prevent from any unfavourable replacement, conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) according to Rules 23a Note 4 and 56b is needed, and therefore, a request for conservation by the Judicial Commission over its earlier protozoan homonym is made here by the author, with Judicial Opinions 9 and 12 serving as precedents.

Medical Device-Associated Biofilm Infections and Multidrug-Resistant Pathogens

Medical devices such as venous catheters (VCs) and urinary catheters (UCs) are widely used in the hospital setting. However, the implantation of these devices is often accompanied by complications. About 60 to 70% of nosocomial infections (NIs) are linked to biofilms. The main complication is the ability of microorganisms to adhere to surfaces and form biofilms which protect them and help them to persist in the host. Indeed, by crossing the skin barrier, the insertion of VC inevitably allows skin flora or accidental environmental contaminants to access the underlying tissues and cause fatal complications like bloodstream infections (BSIs). In fact, 80,000 central venous catheters-BSIs (CVC-BSIs)-mainly occur in intensive care units (ICUs) with a death rate of 12 to 25%. Similarly, catheter-associated urinary tract infections (CA-UTIs) are the most commonlyhospital-acquired infections (HAIs) worldwide.These infections represent up to 40% of NIs.In this review, we present a summary of biofilm formation steps. We provide an overview of two main and important infections in clinical settings linked to medical devices, namely the catheter-asociated bloodstream infections (CA-BSIs) and catheter-associated urinary tract infections (CA-UTIs), and highlight also the most multidrug resistant bacteria implicated in these infections. Furthermore, we draw attention toseveral useful prevention strategies, and advanced antimicrobial and antifouling approaches developed to reduce bacterial colonization on catheter surfaces and the incidence of the catheter-related infections.

Engineering Proteus mirabilis improves antitumor efficacy via enhancing cytotoxic T cell responses

Cancer immunotherapy based on bioengineering of bacteria can effectively increase anticancer immune responses. However, few studies have investigated the antitumor potential of engineering Proteus mirabilis. Here, we genetically engineered P. mirabilis to overexpress Vibrio vulnificus flagellin B (FlaB) protein in a murine CT26 tumor model. We found that a large number of FlaB-expressing P. mirabilis colonized tumor tissues, enhanced T cell infiltration and secretion of cytokines and cytotoxic proteins in tumors, and significantly restrained tumor growth. Our results also showed that programmed death ligand 1 (PD-L1) expression in tumor-infiltrating immune cells was elevated after treatment with FlaB-expressing P. mirabilis. In addition, combination therapy with FlaB-expressing P. mirabilis and PD-L1 blockade synergistically improved antitumor efficacy by enhancing infiltration of CD8+ cells. Furthermore, serum liver biochemical indices of mice increased in the short term in both the P. mirabilis and the FlaB-expressing P. mirabilis treatment groups but gradually recovered in the later stage of treatment so that FlaB protein expression did not increase the toxicity of P. mirabilis in vivo. Taken together, our results suggest that P. mirabilis could serve as an engineered bacterium for bacterium-based cancer immunotherapy.

Proteus appendicitidis sp. nov., isolated from the appendiceal pus of an appendicitis patient in Yongzhou, China

A Gram-negative, facultatively anaerobic, short rod-shaped bacterium, designated as strain HZ0627T, was isolated from the appendiceal pus of a patient with appendicitis in Yongzhou, Hunan, China. This strain was subjected to comprehensive phenotypic, phylogenetic, and genomic analyses using polyphasic taxonomic methods. Phylogenetic analysis of the 16S rRNA gene sequence revealed that this strain belonged to the genus Proteus and the family Morganellaceae, whereas that based on the rpoB gene sequence and phylogenomic analysis demonstrated that this strain was distinctly separated from other type strains of Proteus species. Moreover, whole-genome-based analyses, including in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI), revealed that strain HZ0627T had much lower isDDH rates (24.5-55.6%) and ANI (82.04-93.90%) than those of the thresholds (i.e., 70% and 95%, respectively) for species delineation, when compared to the type strains of other Proteus species. The cellular fatty acid profile of strain HZ0627T was dominated by C16:0 (34.5%), cyclo C17:0 (25.8%), C14:0 (12.6%), C16:1 iso I/14:0 3-OH (7.7%), C18:1ω7c/18:1ω6c (6.5%), and C16:1ω7c/16:1ω6c (4.9%), which clearly differentiated it from the documented type strains of Proteus species. In addition, several specific physiological traits, including optimal growth temperature, tolerance to sodium chloride, and carbon source utilization, differed from those of other Proteus species. Therefore, we propose the name Proteus appendicitidis sp. nov. for strain HZ0627T (= CCTCC AB 2022380T = KCTC 92986T), which represents the type strain of this novel Proteus species.

Antibiotic resistance and virulence profiles of Proteus mirabilis isolated from broiler chickens at abattoir in South Africa

BACKGROUND

Proteus mirabilis has been identified as an important zoonotic pathogen, causing several illnesses such as diarrhoea, keratitis and urinary tract infections.

OBJECTIVE

This study assessed the prevalence of P. mirabilis in broiler chickens, its antibiotic resistance (AR) patterns, ESBL-producing P. mirabilis and the presence of virulence genes.

METHODS

A total of 26 isolates were confirmed as P. mirabilis from 480 pooled broiler chicken faecal samples by polymerase chain reaction (PCR). The disk diffusion method was used to evaluate the antibacterial susceptibility test, while nine virulence genes and 26 AR genes were also screened by PCR.

RESULTS

All 26 P. mirabilis isolates harboured the ireA (siderophore receptors), ptA, and zapA (proteases), ucaA, pmfA, atfA, and mrpA (fimbriae), hlyA and hpmA (haemolysins) virulence genes. The P. mirabilis isolates were resistant to ciprofloxacin (62%) and levofloxacin (54%), while 8 (30.7%) of the isolates were classified as multidrug resistant (MDR). PCR analysis identified the blaCTX-M gene (62%), blaTEM (58%) and blaCTX-M-2 (38%). Further screening for AMR genes identified mcr-1, cat1, cat2, qnrA, qnrD and mecA, 12%, 19%, 12%, 54%, 27% and 8%, respectively for P. mirabilis isolates. The prevalence of the integron integrase intI1 and intI2 genes was 43% and 4%, respectively.

CONCLUSIONS

The rise of ciprofloxacin and levofloxacin resistance, as well as MDR strains, is a public health threat that points to a challenge in the treatment of infections caused by these zoonotic bacteria. Furthermore, because ESBL-producing P. mirabilis has the potential to spread to humans, the presence of blaCTX -M -producing P. mirabilis in broilers should be kept under control. This is the first study undertaken to isolate P. mirabilis from chicken faecal samples and investigate its antibiotic resistance status as well as virulence profiles in South Africa.

Specific gut pathobionts escape antibody coating and are enriched during flares in patients with severe Crohn's disease

OBJECTIVE

Patients with Crohn's disease (CD) exhibit great heterogeneity in disease presentation and treatment responses, where distinct gut bacteria and immune interactions may play part in the yet unresolved disease aetiology. Given the role of antibodies in the barrier defence against microbes, we hypothesised that gut bacterial antibody-coating patterns may influence underlying disease-mediated processes.

DESIGN

Absolute and relative single and multicoating of gut bacteria with IgA, IgG1, IgG2, IgG3 and IgG4 in patients with CD and healthy controls were characterised and compared with disease activity. IgG2-coated and non-coated taxa from patients with severe CD were identified, profiled for pathogenic characteristics and monitored for enrichment during active disease across cohorts.

RESULTS

Patients with severe CD exhibited higher gut bacterial IgG2-coating. Supervised clustering identified 25 bacteria to be enriched in CD patients with high IgG2-coating. Sorting, sequencing and in silico-based assessments of the virulent potential of IgG2-coated and bulk stool bacteria were performed to evaluate the nature and pathogenicity of IgG2-coated and non-coated bacteria. The analyses demonstrated IgG2-coating of both known pathogenic and non-pathogenic bacteria that co-occurred with two non-coated pathobionts, Campylobacter and Mannheimia. The two non-coated pathobionts exhibited low prevalence, rarely coincided and were strongly enriched during disease flares in patients with CD across independent and geographically distant cohorts.

CONCLUSION

Distinct gut bacterial IgG2-coating was demonstrated in patients with severe CD and during disease flares. Co-occurrence of non-coated pathobionts with IgG2-coated bacteria points to an uncontrolled inflammatory condition in severe CD mediated via escape from antibody coating by two gut pathobionts.

Urinary microbiota signatures associated with different types of urinary diversion: a comparative study

Background

Radical cystectomy and urinary diversion (UD) are gold standards for non-metastatic muscle-invasive bladder cancer. Orthotopic neobladder (or Studer), ileal conduit (or Bricker) and cutaneous ureterostomy (CU) are mainstream UD types. Little is known about urinary microbiological changes after UD.

Methods

In this study, urine samples were collected from healthy volunteers and patients with bladder cancer who had received aforementioned UD procedures. Microbiomes of samples were analyzed using 16S ribosomal RNA gene sequencing, and microbial diversities, distributions and functions were investigated and compared across groups.

Results

Highest urine microbial richness and diversity were observed in healthy controls, followed by Studer patients, especially those without hydronephrosis or residual urine, α-diversity indices of whom were remarkably higher than those of Bricker and CU groups. Studer UD type was the only independent factor favoring urine microbial diversity. The urine microflora structure of the Studer group was most similar to that of the healthy individuals while that of the CU group was least similar. Studer patients and healthy volunteers shared many similar urine microbial functions, while Bricker and CU groups exhibited opposite characteristics.

Conclusion

Our study first presented urinary microbial landscapes of UD patients and demonstrated the microbiological advantage of orthotopic neobladder. Microbiota might be a potential tool for optimization of UD management.

Substances Secreted by Lactobacillus spp. from the Urinary Tract Microbiota Play a Protective Role against Proteus mirabilis Infections and Their Complications

Proteus mirabilis urinary tract infections can lead to serious complications such as development of urinary stones. Lactobacillus spp., belonging to the natural microbiota of the urinary tract, exhibit a number of antagonistic mechanisms against uropathogens, including the secretion of organic acids. In this study, we determined the anti-adhesion, anti-cytotoxicity and anti-crystallization properties of the substances secreted by Lactobacillus. For this purpose, membrane inserts with a pore diameter 0.4 μm were used, which prevent mixing of cultured cells, simultaneously enabling the diffusion of metabolic products. The intensity of crystallization was assessed by measuring the levels of Ca2+, Mg2+ and NH3 and by observing crystals using microscopic methods. The cytotoxicity of the HCV-29 cell line was determined using the LDH and MTT assays, and the impact of lactobacilli on P. mirabilis adhesion to the bladder epithelium was assessed by establishing CFU/mL after cell lysis. It was shown that in the presence of L. gasseri the adhesion of P. mirabilis and the cytotoxicity of the cells decreased. The degree of crystallization was also inhibited in all experimental models. Moreover, it was demonstrated that L. gasseri is characterized by the secretion of a high concentration of L-lactic acid. These results indicate that L-lactic acid secreted by L. gasseri has a significant impact on the crystallization process and pathogenicity of P. mirabilis.

Agrocybe aegerita Polysaccharide Combined with Bifidobacterium lactis Bb-12 Attenuates Aging-Related Oxidative Stress and Restores Gut Microbiota

The objective of this study was to examine the impacts of the combing of Agrocybe aegerita polysaccharides (AAPS) with Bifidobacterium lactis Bb-12 (Bb-12) on antioxidant activity, anti-aging properties, and modulation of gut microbiota. The results demonstrated that the AAPS and Bb-12 complex significantly increased the average lifespan of male and female Drosophila melanogaster under natural aging conditions (p < 0.05), with an improvement of 8.42% and 9.79%, respectively. Additionally, the complex enhanced their climbing ability and increased antioxidant enzyme activity, protecting them from oxidative damage induced by H2O2. In D-galactose induced aging mice, the addition of AAPS and Bb-12 resulted in significantly increase in antioxidant enzyme activity, regulation of aging-related biomarker levels, changed gut microbiota diversity, restoration of microbial structure, and increased abundance of beneficial bacteria, particularly lactobacilli, in the intestines. These findings suggested that the complex of AAPS and Bb-12 had the potential to serve as a dietary supplement against organism aging and oxidative stress.

Norfloxacin derivatives as DNA gyrase and urease inhibitors: synthesis, biological evaluation and molecular docking

Background: DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease. Materials & methods: Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (1H NMR, Fourier transform IR, 13C NMR) and carbon, hydrogen, nitrogen and sulfur analysis along with molecular docking. Results & conclusion: The majority of derivatives exhibited significant results but the 3e derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC50 of 0.15 ± 0.24 and 1.14 ± 0.11 μM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.

Antigenic and Structural Properties of the Lipopolysaccharide of the Uropathogenic Proteus mirabilis Dm55 Strain Classified to a New O85 Proteus Serogroup

The aim of the study was the serological and structural characterization of the lipopolysaccharide (LPS) O antigen from P. mirabilis Dm55 coming from the urine of a patient from Lodz. The Dm55 LPS was recognized in ELISA only by the O54 antiserum, suggesting a serological distinction of the Dm55 O antigen from all the 84 Proteus LPS serotypes described. The obtained polyclonal rabbit serum against P. mirabilis Dm55 reacted in ELISA and Western blotting with a few LPSs (including O54), but the reactions were weaker than those observed in the homologous system. The LPS of P. mirabilis Dm55 was subjected to mild acid hydrolysis, and the obtained high-molecular-mass O polysaccharide was chemically studied using sugar and methylation analyses, mass spectrometry, and 1H and 13C NMR spectroscopy, including 1H,1H NOESY, and 1H,13C HMBC experiments. The Dm55 O unit is a branched three-saccharide, and its linear fragment contains α-GalpNAc and β-Galp, whereas α-GlcpNAc occupies a terminal position. The Dm55 OPS shares a disaccharide epitope with the Proteus O54 antigen. Due to the structural differences of the studied O antigen from the other described Proteus O polysaccharides, we propose to classify the P. mirabilis Dm55 strain to a new Proteus O85 serogroup.

Melatonin supplementation protects against traumatic colon injury by regulating SERPINA3N protein expression

Traumatic colon injury (TCI) is a typical injury with high mortality. Prolongation of the intervention time window is a potentially useful approach to improving the outcomes of TCI casualties. This study aimed to identify the pathological mechanisms of TCI and to develop effective strategies to extend the survival time. A semicircular incision was made to prepare a TCI model using C57BL/6 mice. An overview of microbiota dysregulation was achieved by metagenome sequencing. Protein expression reprogramming in the intestinal epithelium was investigated using proteomics profiling. The mice that were subjected to TCI died within a short period of time when not treated. Gut symbiosis showed abrupt turbulence, and specific pathogenic bacteria rapidly proliferated. The protein expression in the intestinal epithelium was also reprogrammed. Among the differentially expressed proteins, SERPINA3N was overexpressed after TCI modeling. Deletion of Serpina3n prolonged the posttraumatic survival time of mice with TCI by improving gut homeostasis in vivo. To promote the translational application of this research, the effects of melatonin (MLT), an oral inhibitor of the SERPINA3N protein, were further investigated. MLT effectively downregulated SERPINA3N expression and mitigated TCI-induced death by suppressing the NF-κB signaling pathway. Our findings prove that preventive administration of MLT serves as an effective regimen to prolong the posttraumatic survival time by restoring gut homeostasis perturbed by TCI. It may become a novel strategy for improving the prognosis of patients suffering from TCI.

Structurally Orientated Rheological and Gut Microbiota Fermentation Property of Mannans Polysaccharides and Oligosaccharides

Three mannan polysaccharides and their oligosaccharides were investigated in terms of physicochemical characteristics and effects on gut microbiota. Oligosaccharides from guar gum had the fastest fermentation kinetics for SCFAs generation at the initial stage, while the locust bean of both polymers and oligosaccharides demonstrated the lowest SCFAs through the whole fermentation process. In contrast, konjac gum steadily increased SCFAs and reached its maximum level at 24 h fermentation, indicating its fermentation character may be associated with its rheological properties. Compared to their corresponding polysaccharides, all the oligosaccharides demonstrated a faster fermentation kinetics, followed by an enriched abundance of propionate-producing bacterial Prevotella and a decreased abundance of Megamonas and Collinsella. Meanwhile, oligosaccharides reduced the Firmicutes/Bacteroidota ratio as well as the abundance of Bacteroidetes and Escherichia-Shigella. The fermentation of konjac substrate significantly promoted the abundance of butyrate-producing bacterial Faecalibacterium. In contrast, although the fermentation of locust bean and guar gum substrates benefited Bifidobacterium abundance due to their similar structure and monosaccharides composition, the fermentation of locust bean gum led to greater Bifidobacterium than the others, which may be associated with its higher mannose composition in the molecules. Interestingly, the partial hydrolysis of the three polysaccharides slightly reduced their prebiotic function.

Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population

High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study-the Chinese Healthy Gut Project (n = 483)-where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.

Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China

The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.

Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges

Bioconversion using insects is a promising strategy to convert organic waste (catering leftovers, harvest waste, food processing byproducts, etc.) into biomass that can be used for multiple applications, turned into high added-value products, and address environmental, societal and economic concerns. Due to its ability to feed on a tremendous variety of organic wastes, the black soldier fly (Hermetia illucens) has recently emerged as a promising insect for bioconversion of organic wastes on an industrial scale. A growing number of studies have highlighted the pivotal role of the gut microbiota in the performance and health of this insect species. This review aims to provide a critical overview of current knowledge regarding the functional diversity of the gut microbiota of H. illucens, highlighting its importance for bioconversion, food safety and the development of new biotechnological tools. After providing an overview of the different strategies that have been used to outline the microbial communities of H. illucens, we discuss the diversity of these gut microbes and the beneficial services they can provide to their insect host. Emphasis is placed on technical strategies and aspects of host biology that require special attention in the near future of research. We also argue that the singular digestive capabilities and complex gut microbiota of H. illucens make this insect species a valuable model for addressing fundamental questions regarding the interactions that insects have evolved with microorganisms. By proposing new avenues of research, this review aims to stimulate research on the microbiota of a promising insect to address the challenges of bioconversion, but also fundamental questions regarding bacterial symbiosis in insects.

Genetic analysis of resistance and virulence characteristics of clinical multidrug-resistant Proteus mirabilis isolates

Objective

Proteus mirabilis is the one of most important pathogens of catheter-associated urinary tract infections. The emergence of multidrug-resistant (MDR) P. mirabilis severely limits antibiotic treatments, which poses a public health risk. This study aims to investigate the resistance characteristics and virulence potential for a collection of P. mirabilis clinical isolates.

Methods and results

Antibiotic susceptibility testing revealed fourteen MDR strains, which showed high resistance to most β-lactams and trimethoprim/sulfamethoxazole, and a lesser extent to quinolones. All the MDR strains were sensitive to carbapenems (except imipenem), ceftazidime, and amikacin, and most of them were also sensitive to aminoglycosides. The obtained MDR isolates were sequenced using an Illumina HiSeq. The core genome-based phylogenetic tree reveals the high genetic diversity of these MDR P. mirabilis isolates and highlights the possibility of clonal spread of them across China. Mobile genetic elements SXT/R391 ICEs were commonly (10/14) detected in these MDR P. mirabilis strains, whereas the presence of resistance island PmGRI1 and plasmid was sporadic. All ICEs except for ICEPmiChn31006 carried abundant antimicrobial resistance genes (ARGs) in the HS4 region, including the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-65. ICEPmiChn31006 contained the sole ARG blaCMY-2 and was nearly identical to the global epidemic ICEPmiJpn1. The findings highlight the important roles of ICEs in mediating the spread of ARGs in P. mirabilis strains. Additionally, these MDR P. mirabilis strains have great virulence potential as they exhibited significant virulence-related phenotypes including strong crystalline biofilm, hemolysis, urease production, and robust swarming motility, and harbored abundant virulence genes.

Conclusion

In conclusion, the prevalence of MDR P. mirabilis with high virulence potential poses an urgent threat to public health. Intensive monitoring is needed to reduce the incidence of infections by MDR P. mirabilis.

Dispersion characteristics of bioaerosols during treatment of rural solid waste in northwest China

In rural China, the release of bioaerosols containing pathogens from solid waste dumps poses a potential health risk to the local population. Here, we sampled bioaerosols from rural solid waste-treatment in four provinces of northwest China to investigate their emission and dispersion characteristics in order to provide a scientific basis for control and risk reduction of bioaerosols released from rural sanitation facilities. The airborne bioaerosol concentrations and particle size distributions were calculated using an Anderson six-stage airborne microbial sampler and counting with its internal Petri dish culture. High-throughput sequencing was used to characterize the microbial composition at different sampling sites and to explore possible influencing factors, while the health risk associated with exposure was estimated based on average daily dose-rate. The highest concentration point values of bacteria and fungi in bioaerosols near the solid waste were 63,617 ± 15,007 and 8044 ± 893 CFU/m³, respectively. Furthermore, the highest concentration point values of Enterobacteriaceae was 502 ± 35 CFU/m³. Most bioaerosols were coarse particles larger than 3.3 μm. Potentially pathogenic genera of winter-indicator species detected in the air were primarily Delftia, Rhodococcus and Aspergillus. The composition of solid waste and environmental conditions are important factors in determining the characteristics of bioaerosols. Local residents are exposed to bioaerosols mainly through inhalation. Children are at a particularly high risk of exposure through both inhalation and skin contact. The results of this study show that bioaerosols in the vicinity of rural solid waste dumps pose a health risk to the surrounding population. More suitable risk assessment criteria for rural areas should be established, and corresponding control and protection measures should be taken from three aspects: generation source and transmission pathway, as well as the recipient.

Porphyran from Porphyra haitanensis Enhances Intestinal Barrier Function and Regulates Gut Microbiota Composition

In this study, the effects of a homogenous porphyran from Porphyra haitanensis (PHP) on the intestinal barrier and gut microbiota were investigated. The results showed that oral administration of PHP resulted in a higher luminal moisture content and a lower pH environment for the growth of beneficial bacteria in the colon of mice. PHP significantly increased the production of total short-chain fatty acids during the fermentation process. PHP made the intestinal epithelial cells of mice arrange more tidily and tightly with a significant increase in mucosal thickness. PHP also increased the amount of mucin-producing goblet cells and the expression of mucin in the colon, which maintained the structure and function of the intestinal mucosal barrier. Moreover, PHP up-regulated the expression of tight junctions including ZO-1 and occludin, improving the intestinal physical barrier function. The results of 16S rRNA sequencing showed that PHP regulated the composition of gut microbiota in mice, increasing the richness and diversity of gut microbiota and the ratio of Firmicutes to Bacteroidetes. This study revealed that the intake of PHP is beneficial for the gastrointestinal tract and PHP could be a potential source of prebiotics in the functional food and pharmaceutical industries.

The influence of antibiotic treatment on the behavior and gut microbiome of adult rats neonatally insulted with lipopolysaccharide

The present study investigated whether neonatal exposure to the proinflammatory endotoxin lipopolysaccharide (LPS) followed by an antibiotic (ATB)-induced dysbiosis in early adulthood could induce neurodevelopmental disorders-like behavioral changes in adult male rats. Combining these two stressors resulted in decreased weight gain, but no significant behavioral abnormalities were observed. LPS treatment resulted in adult rats' hypoactivity and induced anxiety-like behavior in the social recognition paradigm, but these behavioral changes were not exacerbated by ATB-induced gut dysbiosis. ATB treatment seriously disrupted the gut bacterial community, but dysbiosis did not affect locomotor activity, social recognition, and acoustic reactivity in adult rats. Fecal bacterial community analyses showed no differences between the LPS challenge exposed/unexposed rats, while the effect of ATB administration was decisive regardless of prior LPS exposure. ATB treatment resulted in significantly decreased bacterial diversity, suppression of Clostridiales and Bacteroidales, and increases in Lactobacillales, Enterobacteriales, and Burkholderiales. The persistent effect of LPS on some aspects of behavior suggests a long-term effect of early toxin exposure that was not observed in ATB-treated animals. However, an anti-inflammatory protective effect of ATB cannot be assumed because of the increased abundance of pro-inflammatory, potentially pathogenic bacteria (Proteus, Suttrella) and the elimination of the bacterial families Ruminococcaceae and Lachnospiraceae, which are generally considered beneficial for gut health.

Bullfrogs (Lithobates catesbeianus) as a Potential Source of Foodborne Disease

In Mexico, bullfrogs (Lithobates catesbeianus) are produced as gourmet food. However, bullfrogs can be carriers of pathogens because the frogs' preferred living conditions occur in stagnant water. The present study aimed to identify bacteria that cause foodborne diseases or are associated with human diseases. For molecular identification, based on the sequential analysis by 16S rRNA or rpoD was conducted on all isolates obtained from bullfrog. A total of 91 bacterial isolates were obtained from bullfrogs; 14 genera and 23 species were identified, including Acinetobacter johnsonii 16.5%; Aeromonas media 14.3%; Aeromonas veronii 13.2%; Providencia rettgeri 7.7%; Citrobacter freundii 6.6%; Aeromonas caviae 4.4%; Aeromonas hydrophila and Elizabethkingia ursingii 3.3%; Pseudomonas stutzeri, Raoultella ornithinolytica, and Shewanella putrefaciens 2.2%; Acinetobacter guillouiae, Acinetobacter pseudolwoffii, Citrobacter portucalensis, Citrobacter werkmanii, Edwardsiella anguillarum, Klebsiella michiganensis, Kluyvera intermedia, Kocuria rosea, Myroides odoratimimus, Myroides odoratus, Proteus sp., and Proteus hauseri 1.1%. In this study, 49.4% of the isolates obtained cause foodborne disease, 19.8% are bacteria that play an important role in the spoilage of food, 5.5% of isolates have nosocomial significance, 13.2% of bacteria are considered to be pollutants of the ecosystem, and in the case of A. salmonicida and Edwardsiella anguillarum (12.1%) to have a negative impact on aquaculture. Acinetobacter pseudolwoffii and Citrobacter portucalensis have not been reported to cause disease. Lastly of these isolates, 97.8% (89/91) can cause disease by food consumption or by direct contact for immunocompromised persons. The presence of these bacteria in bullfrogs represents a significant problem for human health. There is evidence that these microorganisms are pathogenic and frogs may also be reservoirs.

Infection of Diabetes Foot Caused by Carbapenem-Resistant Proteus penneri Mediated by a Novel Plasmid Containing blaNDM

Objective

A strain of Proteus penneri with carbapenem resistance was found in a patient with a diabetic foot infection. We studied drug resistance, genome, and homology of P. penneri to support clinical prevention and treatment of infection caused by carbapenem-resistant P. penneri (CR-PPE).

Methods

The strains were obtained through bacterial culture from purulence. VITEK 2 compact (GN13) and Kirby-Bauer (K-B) disk diffusion methods were used for antimicrobial susceptibility testing. Ceftriaxone, amikacin, gentamicin, ampicillin, aztreonam, ceftazidime, ciprofloxacin, levofloxacin, cefepime, trimethoprim-sulfamethoxazole, tobramycin, cefotetan, piperacillin-tazobactam, ampicillin-sulbactam, ertapenem, piperacillin, meropenem, cefuroxime, cefazolin, cefoperazone/sulbactam, cefoxitin, and imipenem were used for antimicrobial susceptibility testing. After bacterial genome extraction, sequencing, and sequence assembly, whole-genome sequencing (WGS) was performed to explore the CR-PPE genotype.

Results

CR-PPE was resistant to two carbapenems (imipenem and ertapenem), ceftriaxone, and cefazolin, and was sensitive to aztreonam, piperacillin-tazobactam, and cefotetan. WGS results depict that the resistant phenotype of CR-PPE is consistent with the genotype, without common virulence genes of Enterobacteriaceae bacteria detected (virulence factor database). The carbapenem resistance gene bla_NMD-1 is contained in a new plasmid, pWF127-NDM. The transposon Tn125 in pWF127-NDM carrying bla_NMD-1 has almost the same structure as Tn125 in the reference plasmid pHFK418-NDM (Accession: MH491967). In addition, through phylogenetic analysis, CR-PPE depicts the closest evolutionary relationship with GCF 024129515.1, which was found in Gallus gallus in the Czech Republic in 2019 (downloaded from National Center for Biotechnology Information database). According to the evolutionary tree, CR-PPE has high homology with the two P. penneri strains found in China.

Conclusion

CR-PPE exhibits strong drug resistance owing to the presence of multiple resistance genes. CR-PPE infection should receive more attention, especially in patients with underlying diseases, such as diabetes and weak immunity.

A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis

BACKGROUND

Eosinophilic esophagitis (EoE) is a chronic immune-mediated rare disease, characterized by esophageal dysfunctions. It is likely to be primarily activated by food antigens and is classified as a chronic disease for most patients. Therefore, a deeper understanding of the pathogenetic mechanisms underlying EoE is needed to implement and improve therapeutic lines of intervention and ameliorate overall patient wellness.

METHODS

RNA-seq data of 18 different studies on EoE, downloaded from NCBI GEO with faster-qdump ( https://github.com/ncbi/sra-tools ), were batch-corrected and analyzed for transcriptomics and metatranscriptomics profiling as well as biological process functional enrichment. The EoE TaMMA web app was designed with plotly and dash. Tabula Sapiens raw data were downloaded from the UCSC Cell Browser. Esophageal single-cell raw data analysis was performed within the Automated Single-cell Analysis Pipeline. Single-cell data-driven bulk RNA-seq data deconvolution was performed with MuSiC and CIBERSORTx. Multi-omics integration was performed with MOFA.

RESULTS

The EoE TaMMA framework pointed out disease-specific molecular signatures, confirming its reliability in reanalyzing transcriptomic data, and providing new EoE-specific molecular markers including CXCL14, distinguishing EoE from gastroesophageal reflux disorder. EoE TaMMA also revealed microbiota dysbiosis as a predominant characteristic of EoE pathogenesis. Finally, the multi-omics analysis highlighted the presence of defined classes of microbial entities in subsets of patients that may participate in inducing the antigen-mediated response typical of EoE pathogenesis.

CONCLUSIONS

Our study showed that the complex EoE molecular network may be unraveled through advanced bioinformatics, integrating different components of the disease process into an omics-based network approach. This may implement EoE management and treatment in the coming years.

Gut microbiome signatures reflect different subtypes of irritable bowel syndrome

Irritable bowel syndrome (IBS) is a heterogeneous condition with multifactorial pathogenesis. We studied deeply phenotyped individuals with microbiota sequencing enrolled in the American Gut Project. The IBS subjects were matched by age, gender, body mass index, geography, and dietary patterns with non-IBS controls. A total of 942 subjects with IBS-Diarrhea (IBS-D), IBS-Constipation (IBS-C), unclassified IBS (IBS-U), and 942 non-IBS controls were included. We compared taxonomic and functional composition of gut microbiota based on 16S sequencing data and linked them with clinical characteristics and dietary factors. Subjects with IBS-D or IBS-U but not IBS-C showed significantly reduced bacterial diversity (Shannon; p < .01). Distinct bacterial signatures were associated with different IBS subtypes, and the related functional changes were related to IBS pathogenesis, such as the increased hydrogen sulfide production pathway in IBS-D and the increased palmitoleate biosynthesis pathway in IBS-C. IBS subjects with depression showed lower abundance of Bifidobacterium, Sutterella, Butyricimonas and higher abundance of Proteus than those without depression. The relative abundance of microbial short-chain fatty acid production pathways was significantly lower in IBS patients with depression than those without depression in all three subtypes. Female, younger age in IBS-D, and older age in IBS-C were associated with more severe microbiota dysbiosis, and distinct dietary factors had significant effects on the gut microbiota in different IBS subtypes. Our analysis identified the compositional uniqueness of gut microbiota in different IBS subtypes. Distinct associations of the gut microbiota with depression in IBS provide insights into shared pathways in disease pathogenesis. These findings highlight the importance of personalized gut microbiome modulation approaches in different subtypes for optimal therapeutic effects.

Chemotherapeutic Drugs Induce Different Gut Microbiota Disorder Pattern and NOD/RIP2/NF-κB Signaling Pathway Activation That Lead to Different Degrees of Intestinal Injury

5-Fluorouracil (5-FU), irinotecan (CPT-11), oxaliplatin (L-OHP), and calcium folinate (CF) are widely used chemotherapeutic drugs to treat colorectal cancer. However, chemotherapeutic use is often accompanied by intestinal inflammation and gut microbiota disorder. Changes in gut microbiota may destroy the intestinal barrier, which contributes to the severity of intestinal injury. However, intestinal injury and gut microbiota disorder have yet to be compared among 5-FU, CPT-11, L-OHP, and CF in detail, thereby limiting the development of targeted detoxification therapy after chemotherapy. In this study, a model of chemotherapy-induced intestinal injury in tumor-bearing mice was established by intraperitoneally injecting chemotherapeutic drugs at a clinically equivalent dose. 16S rRNA gene sequencing was used to detect gut microbiota. We found that 5-FU, CPT-11, and l-OHP caused intestinal injury, inflammatory cytokine (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], interleukin-1β [IL-1β], and IL-6) secretion, and gut microbiota disorder. We established a complex but clear network between the pattern of changes in gut microbiota and degree of intestinal damage induced by different chemotherapeutic drugs. L-OHP caused the most severe damage in the intestine and disorder of the gut microbiota and showed a considerable overlap of the pattern of changes in microbiota with 5-FU and CPT-11. Analysis by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt v.1.0) showed that the microbiota disorder pattern induced by 5-FU, CPT-11, and L-OHP was related to the NOD-like signaling pathway. Therefore, we detected the protein expression of the NOD/RIP2/NF-κB signaling pathway and found that L-OHP most activated this pathway. Redundancy analysis/canonical correlation analysis (RDA/CCA) revealed that Bifidobacterium, Akkermansia, Allobaculum, Catenibacterium, Mucispirillum, Turicibacter, Helicobacter, Proteus, Escherichia Shigella, Alloprevotealla, Vagococcus, Streptococcus, and "Candidatus Saccharimonas" were highly correlated with the NOD/RIP2/NF-κB signaling pathway and influenced by chemotherapeutic drugs. IMPORTANCE Chemotherapy-induced intestinal injury limits the clinical use of drugs. Intestinal injury involves multiple signaling pathways and gut microbiota disruption. Our results suggested that the degree of intestinal injury caused by different drugs of the first-line colorectal chemotherapy regimen is related to the pattern of changes in microbiota. The activation of the NOD/RIP2/NF-κB signaling pathway was also related to the pattern of changes in microbiota. l-OHP caused the most severe damage to the intestine and showed a considerable overlap of the pattern of changes in microbiota with 5-FU and CPT-11. Thirteen bacterial genera were related to different levels of intestinal injury and correlated with the NOD/RIP2/NF-κB pathway. Here, we established a network of different chemotherapeutic drugs, gut microbiota, and the NOD/RIP2/NF-κB signaling pathway. This study likely provided a new basis for further elucidating the mechanism and clinical treatment of intestinal injury caused by chemotherapy.

Construction of an Ordered Transposon Library for Uropathogenic Proteus mirabilis HI4320

Ordered transposon libraries are a valuable resource for many bacterial species, especially those with difficult methods for generating targeted genetic mutations. Here, we present the construction of an ordered transposon library for the bacterial urinary tract pathogen Proteus mirabilis strain HI4320. This library will facilitate future studies into P. mirabilis biology. For large experimental screens, it may be used to overcome bottleneck constraints and avoid biased outcomes resulting from gene length. For smaller studies, the library allows sidestepping the laborious construction of single targeted mutants. This library, containing 18,432 wells, was condensed into a smaller library containing 1,728 mutants. Each selected mutant had a single transposon insertion in an open reading frame, covering 45% of predicted genes encoded by P. mirabilis HI4320. This coverage was lower than expected and was due both to library wells with no mapped insertions and a surprisingly high proportion of mixed clones and multiple transposon insertion events. We offer recommendations for improving future library construction and suggestions for how to use this P. mirabilis library resource. IMPORTANCE Ordered libraries facilitate large genetic screens by guaranteeing high genomic coverage with a minimal number of mutants, and they can save time and effort by reducing the need to construct targeted mutations. This resource is now available for P. mirabilis, a common and complicating agent of catheter-associated urinary tract infection. We also present obstacles encountered during library construction with the goal to aid others who would like to construct ordered transposon libraries in other species.

Health-related quality of life is associated with fecal microbial composition in breast cancer survivors

PURPOSE

To investigate relationships between body size, gut microbiome, and health-related quality of life (QOL) in breast cancer survivors (BCS) in a clinical trial.

METHODS

A cross-sectional substudy was conducted using baseline data from 70 BCS participating in a randomized controlled trial of a lifestyle intervention. Measures included anthropometrics, QOL (Short Form Health-related QOL Survey-36 [SF-36]), and 16S rRNA gene sequencing of fecal microbes. Participants were categorized by body mass index (BMI) into without obesity (≤ 29.9 kg/m²; n = 38) and with obesity (≥ 30.0 kg/m²; n = 32) groups. Differences in bacterial taxa between groups were assessed using Kruskal-Wallis one-way analysis of variance. Spearman and partial correlations explored associations between taxa and SF-36 subscales. Mediation analysis explored the relationship between BMI and SF-36 mental health summary score with alpha diversity as a mediator.

RESULTS

Most BCS (72.9%) were non-Hispanic White with average age of 61.6 (± 8.7) years. No differences were observed for SF-36 subscales between groups. Physical functioning, vitality, and mental health subscales were negatively associated with Ruminococcus (ρ =  - 0.304, p = 0.036; ρ =  - 0.361, p = 0.012; ρ =  - 0.495, p < 0.001) and Dorea (ρ =  - 0.378, p = 0.028; ρ =  - 0.33, p = 0.022; ρ =  - 0.388, p = 0.006) abundance controlling for BMI. BCS without obesity had a significantly higher relative abundance of Ruminococcus (p = 0.003), Streptococcus (p = 0.049), Roseburia (p = 0.035), and Dorea (p = 0.003).

CONCLUSIONS

Fecal microbial composition differed between BCS with and without obesity, with associations between QOL and several microbial taxa. Several of these genera, previously identified as potentially beneficial, may also influence QOL in BCS. These results support further studies to determine the role of individual microbiota in QOL and obesity in cancer survivors.

Drug-Resistant Proteus Virulence Factors Characterization and Their Inhibition Using Probiotic Bacteria

Background: The genus Proteus is a Gram-negative bacterium with a unique characteristic of swarming. Mainly three species are involved in initiating urinary tract infections in the community and in immunocompromised patients, particularly in patients going through long-term catheterization. Due to their strong virulence factors like biofilm formations, protease, and hemolysin, they can lead to lengthening infections in affected individuals. Probiotics are live bacteria and yeasts that are beneficial to human health and can be used as an alternative for the control of nosocomial diseases. Lactobacilli are one of the common probiotics mostly found in yogurt and other fermented foods that have been used as a substitute for infection control. Objectives: The current study was designed to screen potential probiotic bacteria to encounter antibiotic-resistant and virulent Proteus species. Methods: In the current study, using probiotics, already known antibiotic-resistant isolates (n = 25) of Proteus were processed to characterize their virulence factors and their inhibition. Biofilm formation, protease, and hemolysin activities were studied using different phenotypic detection methods. Further, their virulence genes zapA, flg, hmpA, mrp, and rsbA were explored using their genomic DNA. These isolates were found resistant to different classes of antibiotics, and a strategy was designed to inhibit their growth by using probiotic bacteria isolated from the soil. Results: Virulence factors first, all isolates were subjected to biofilm detection, and they were 32% (n = 8) strong, 40% (n = 10) moderate, 16% (n = 4) weak, and 12% (n = 3) non-biofilm producers. All isolates were positive for swarming activity by showing a differentiated ring form of growth. Protease activity showed 56% (n = 14) isolates. Only 24% (n = 6) of isolates were positive for hemolysin. Virulence factors and molecular mechanisms were studied, and gene rsbA responsible for swarming was amplified in 17 (68%) Proteus isolates, and mrp responsible for fimbria was detected in 19 (76%) bacterial isolates. Further, these isolates were subjected to flagella, protease, and hemolysin, and it was revealed that flg 11 (44%), 13 (52%) protease coding zapA, and hmA gene coding hemolysin were amplified in 2 (8%) Proteus isolates. Probiotic bacteria isolated from soil samples were probed for antagonistic activity against Proteus species. The probiotic bacteria were identified as Lactobacillus plantarum, Bacillus subtilis, and B. licheniformis. Due to their strong growth inhibitory effects against Proteus, it is crucial to characterize further the metabolites that have shown suppressive results against Proteus. Conclusions: Findings from the current study will provide new avenues for drug development and also help clinicians manage resistant pathogens in healthcare settings. Probiotic applications for infection control can be useful in treating resistant pathogens. Further purification and characterization of metabolites will provide alternative options for managing resistance issues in microbes.

The in Vitro Fermentation of Cordyceps militaris Polysaccharides Changed the Simulated Gut Condition and Influenced Gut Bacterial Motility and Translocation

The motility ability of intestinal lipopolysaccharide (LPS)-producing bacteria determines their translocation to the enterohepatic circulation and works as an infectious complication. In this study, the health effects of Cordyceps militaris polysaccharides (CMPs) were re-evaluated based on whether these polysaccharides could affect the motility of gut commensal LPS-producing bacteria and impede their translocation. The results showed that CMP-m fermentation in the gut could change the chemical environment, leading to a decrease in velocity and a shift in the motility pattern. Further study suggested that detachment/fragmentation of flagella, decreased motor forces, and changed chemical conditions might account for this weakened motility. The adhesion and invasion abilities of gut bacteria were also reduced, with lower expression of virulence-related genes. These results indicated that the health regulation effects of CMP-m might be through decreasing the motility of LPS-producing bacteria, hindering their translocation and therefore reducing the LPS level in the enterohepatic circulation.

Gut bacterial profiles in Parkinson's disease: A systematic review

INTRODUCTION

Recent advances have highlighted the relationships between gut dysbiosis and Parkinson's disease (PD). Microbiota transplantation from PD patients to mice can induce increased alpha-synuclein-mediated motor deficits. Human studies have identified differences in the gut microbiota of PD patients compared to healthy controls. We undertook a systematic review to evaluate the available evidence for the involvement of gut bacteria in the etiology of PD.

METHODS

The PubMed databank, the China National Knowledge Infrastructure databank, and Wanfang Data were searched from inception until June 2021 to identify human case-control studies that investigated relationships between PD and microbiota quantified from feces. We evaluated the resulting studies focusing on bacterial taxa that were different between PD patients and healthy controls.

RESULTS

Twenty-six studies were found in which 53 microbial families and 98 genera exhibited differences between patients with PD and healthy controls. The genera identified by more than two studies as increased in PD were Bifidobacterium, Alistipes, Christensenella, Enterococcus, Oscillospira, Bilophila, Desulfovibrio, Escherichia/Shigella, and Akkermansia, while Prevotella, Blautia, Faecalibacterium, Fusicatenibacter, and Haemophilus had three or more reports of being lower in PD patients. More than one report demonstrated that Bacteroides, Odoribacter, Parabacteroides, Butyricicoccus, Butyrivibrio, Clostridium, Coprococcus, Lachnospira, Lactobacillus, Megasphaera, Phascolarctobacterium, Roseburia, Ruminococcus, Streptococcus, and Klebsiella were altered in both directions.

CONCLUSION

Our review shows that the involvement of the gut microbiome in the etiology of PD may involve alterations of short-chain fatty acids (SCFAs)-producing bacteria and an increase in putative gut pathobionts. SCFAs-producing bacteria may vary above or below an "optimal range," causing imbalances. Considering that Bifidobacterium, Lactobacillus, and Akkermansia are beneficial for human health, increased Bifidobacterium and Lactobacillus in the PD gut microbiome may be associated with PD medications, especially COMT inhibitors, while a high level of Akkermansia may be associated with aging.

Colorimetric Detection of Urease-Producing Microbes Using an Ammonia-Responsive Flexible Film Sensor

Urease-producing (ureolytic) microbes have given rise to environmental and public health concerns because they are thought to contribute to emissions of ammonia and to be a virulence factor for infections. Therefore, it is highly important to have the ability to detect such microbes. In this study, a poly(dimethylsiloxane) (PDMS)-based colorimetric film sensor was employed for the detection of urease-producing microbes. The sensor was able to detect the enzyme activity of commercially available urease, as the color and absorbance spectrum of the sensor was observed to change upon being exposed to the reaction catalyzed by urease. The ratio of the absorbance of the sensor at 640 nm to that at 460 nm (A₆₄₀/A₄₆₀) was linearly proportional to the amount of urease present. The performance of the sensor was validated by the results of a sensitivity and selectivity analysis towards thirteen different bacterial strains. Based on the development of blue color of the sensor, the tested bacteria were classified as strongly positive, moderately positive, weakly positive, or negative urease producers. The response of the sensor to ureolytic bacteria was verified using the urease inhibitor phenyl phosphorodiamidate (PPDA). Additionally, the sensor achieved the selective detection of ureolytic bacteria even in the presence of non-ureolytic bacteria. In addition, a used sensor could be reverted to its original state by being subjected to simple aeration, and in this way the same sensor could be used at least five times for the detection of bacterial urease activity.

Play the plug: How bacteria modify recognition by host receptors?

The diverse microbial community that colonizes the gastrointestinal tract has remarkable effects on the host immune system and physiology resulting in homeostasis or disease. In both scenarios, the gut microbiota interacts with their host through ligand-receptor binding whereby the downstream signaling processes determine the outcome of the interaction as disease or the counteractive immune responses of the host. Despite several studies on microbe-host interactions and the mechanisms by which this intricate process happens, a comprehensive and updated inventory of known ligand-receptor interactions and their roles in disease is paramount. The ligands which originate as a result of microbial responses to the host environment contribute to either symbiotic or parasitic relationships. On the other hand, the host receptors counteract the ligand actions by mounting a neutral or an innate response. The varying degrees of polymorphic changes in the host receptors contribute to specificity of interaction with the microbial ligands. Additionally, pathogenic microbes manipulate host receptors with endogenous enzymes belonging to the effector protein family. This review focuses on the diversity and similarity in the gut microbiome-host interactions both in health and disease conditions. It thus establishes an overview that can help identify potential therapeutic targets in response to critically soaring antimicrobial resistance as juxtaposed to tardy antibiotic development research.

Structural and functional alterations of intestinal flora in mice induced by halonitromethanes exposure

Halonitromethanes (HNMs) as one typical class of nitrogenous disinfection byproducts (DBPs) have been widely found in drinking water and are receiving more and more attentions because of their high cytotoxicity, genotoxicity, and developmental toxicity. However, the effects of HNMs exposure on the intestinal tract and intestinal flora remain unknown. This study comprehensively determined the effects of trichloronitromethane, bromonitromethane, and bromochloronitromethane exposure on the intestinal tract and intestinal flora. Results showed that the three HNMs induced intestinal oxidative stress and inflammatory response. Further, HNMs exposure could change the diversities and community structure of intestinal flora, thereby triggering intestinal flora dysbiosis, which might be associated with the intestinal damage such as oxidative stress and inflammation. The intestinal flora dysbiosis was accompanied with mark alterations in function of intestinal flora, such as carbohydrate, lipid, and amino acid metabolisms. This research provides a new insight into studying the toxicity of HNMs exposure based on intestinal flora, which will further improve the health risk assessment of DBPs in drinking water.

Gut Microbiota, Plasma Metabolomic Profiles, and Carotid Artery Atherosclerosis in HIV Infection

BACKGROUND

Alterations in gut microbiota and blood metabolomic profiles have been implicated in HIV infection and cardiovascular disease. However, it remains unclear whether alterations in gut microbiota may contribute to disrupted host blood metabolomic profiles in relation to atherosclerosis, especially in the context of HIV infection.

METHODS

We analyzed cross-sectional associations between gut microbiota features and carotid artery plaque in 361 women with or at high risk of HIV (67% HIV+), and further integrated plaque-associated microbial features with plasma lipidomic/metabolomic profiles. Furthermore, in 737 women and men, we examined prospective associations of baseline gut bacteria-associated lipidomic and metabolomic profiles with incident carotid artery plaque over 7-year follow-up.

RESULTS

We found 2 potentially pathogenic bacteria, Fusobacterium and Proteus, were associated with carotid artery plaque; while the beneficial butyrate producer Odoribacter was inversely associated with plaque. Fusobacterium and Proteus were associated with multiple lipids/metabolites which were clustered into 8 modules in network. A module comprised of 9 lysophosphatidylcholines and lysophosphatidylethanolamines and a module comprised of 9 diglycerides were associated with increased risk of carotid artery plaque (risk ratio [95% CI], 1.34 [1.09-1.64] and 1.24 [1.02-1.51] per SD increment, respectively). Functional analyses identified bacterial enzymes in lipid metabolism associated with these plasma lipids. In particular, phospholipase A1 and A2 are the key enzymes in the reactions producing lysophosphatidylcholines and lysophosphatidylethanolamines.

CONCLUSIONS

Among individuals with or at high risk of HIV infection, we identified altered gut microbiota and related functional capacities in the lipid metabolism associated with disrupted plasma lipidomic profiles and carotid artery atherosclerosis.

Fecal Microbes Associated with the Outcomes After Esophagectomy in Patients with Esophageal Cancer

BACKGROUND

Although accumulating evidence suggests that an imbalanced gut microbiota leads to cancer progression, few studies demonstrated the implication in patients who underwent oncologic esophagectomy. This study aimed to elucidate the association between gut microbes and the outcomes after oncologic esophagectomy, as well as the host's inflammatory/nutritional status.

METHODS

Overall, 783 consecutive patients who underwent oncologic esophagectomy were eligible. We investigated the microbiota detected by fecal culture tests and then assessed the association between the gut microbiota and patient characteristics, short-term outcomes, and long-term survival.

RESULTS

Seventeen different species could be cultivated. We comprehensively examined the impact of each detected microbe on survival. The presence of Bacillus species (Bacillus sp.; 26.8%) was associated with favorable prognosis on overall and cancer-specific survival (p = 0.02 and 0.02, respectively). Conversely, the presence of Proteus mirabilis (P. mirabilis; 3.4%) was associated with unfavorable overall and recurrence-free survivals (p = 0.02 and < 0.01, respectively). Multivariate analysis showed that the presence of P. mirabilis was one of the independent prognostic factors for poor recurrence-free survival (p < 0.01). Patients with Bacillus sp. had lower modified Glasgow prognostic score and better response to preoperative treatment than those without (p = 0.01 and 0.03, respectively). Meanwhile, patients with P. mirabilis were significantly associated with higher systemic inflammation scores and increased postoperative pneumonia incidence than those without (p = 0.01 and 0.02, respectively).

CONCLUSIONS

Preoperative fecal microbiota was associated with the host's inflammatory and nutritional status and may influence the outcomes after oncologic esophagectomy.

Clinical data from studies involving novel antibiotics to treat multidrug-resistant Gram-negative bacterial infections

Multidrug-resistant (MDR) Gram-negative bacteria (GNB) are a critical threat to healthcare worldwide, worsening outcomes and increasing mortality among infected patients. Carbapenemase- and extended-spectrum β-lactamase-producing Enterobacterales, as well as carbapenemase-producing Pseudomonas and Acinetobacter spp., are common MDR pathogens. To address this threat, new antibiotics and combinations have been developed. Clinical trial findings support several combinations, notably ceftazidime-avibactam (CZA, a cephalosporin-β-lactamase inhibitor combination) which is effective in treating complicated urinary tract infections (cUTI), complicated intra-abdominal infections and hospital-acquired and ventilator-associated pneumonia caused by GNBs. Other clinically effective combinations include meropenem-vaborbactam (MVB), ceftolozane-tazobactam (C/T) and imipenem- relebactam (I-R). Cefiderocol is a recent siderophore β-lactam antibiotic that is useful against cUTIs caused by carbapenem-resistant Enterobacterales (CRE) and is stable against many β-lactamases. CRE are a genetically heterogeneous group that vary in different world regions and are a substantial cause of infections, among which Klebsiella pneumoniae are the most common. Susceptible CRE infections can be treated with fluoroquinolones, aminoglycosides or fosfomycin, but alternatives include CZA, MVB, I-R, cefiderocol, tigecycline and eravacycline. MDR Acinetobacter baumannii and Pseudomonas aeruginosa are increasingly common pathogens producing a range of different carbapenemases, and infections are challenging to treat, often requiring novel antibiotics or combinations. Currently, no single agent can treat all MDR-GNB infections, but new β-lactam-β-lactamase inhibitor combinations are often effective for different infection sites, and, when used appropriately, have the potential to improve outcomes. This article reviews clinical studies investigating novel β-lactam approaches for treatment of MDR-GNB infections.

Flagellotropic Bacteriophages: Opportunities and Challenges for Antimicrobial Applications

Bacteriophages (phages) are the most abundant biological entities in the biosphere. As viruses that solely infect bacteria, phages have myriad healthcare and agricultural applications including phage therapy and antibacterial treatments in the foodservice industry. Phage therapy has been explored since the turn of the twentieth century but was no longer prioritized following the invention of antibiotics. As we approach a post-antibiotic society, phage therapy research has experienced a significant resurgence for the use of phages against antibiotic-resistant bacteria, a growing concern in modern medicine. Phages are extraordinarily diverse, as are their host receptor targets. Flagellotropic (flagellum-dependent) phages begin their infection cycle by attaching to the flagellum of their motile host, although the later stages of the infection process of most of these phages remain elusive. Flagella are helical appendages required for swimming and swarming motility and are also of great importance for virulence in many pathogenic bacteria of clinical relevance. Not only is bacterial motility itself frequently important for virulence, as it allows pathogenic bacteria to move toward their host and find nutrients more effectively, but flagella can also serve additional functions including mediating bacterial adhesion to surfaces. Flagella are also a potent antigen recognized by the human immune system. Phages utilizing the flagellum for infections are of particular interest due to the unique evolutionary tradeoff they force upon their hosts: by downregulating or abolishing motility to escape infection by a flagellotropic phage, a pathogenic bacterium would also likely attenuate its virulence. This factor may lead to flagellotropic phages becoming especially potent antibacterial agents. This review outlines past, present, and future research of flagellotropic phages, including their molecular mechanisms of infection and potential future applications.

Augmented Enterocyte Damage During Candida albicans and Proteus mirabilis Coinfection

The human gut acts as the main reservoir of microbes and a relevant source of life-threatening infections, especially in immunocompromised patients. There, the opportunistic fungal pathogen Candida albicans adapts to the host environment and additionally interacts with residing bacteria. We investigated fungal-bacterial interactions by coinfecting enterocytes with the yeast Candida albicans and the Gram-negative bacterium Proteus mirabilis resulting in enhanced host cell damage. This synergistic effect was conserved across different P. mirabilis isolates and occurred also with non-albicans Candida species and C. albicans mutants defective in filamentation or candidalysin production. Using bacterial deletion mutants, we identified the P. mirabilis hemolysin HpmA to be the key effector for host cell destruction. Spatially separated coinfections demonstrated that synergism between Candida and Proteus is induced by contact, but also by soluble factors. Specifically, we identified Candida-mediated glucose consumption and farnesol production as potential triggers for Proteus virulence. In summary, our study demonstrates that coinfection of enterocytes with C. albicans and P. mirabilis can result in increased host cell damage which is mediated by bacterial virulence factors as a result of fungal niche modification via nutrient consumption and production of soluble factors. This supports the notion that certain fungal-bacterial combinations have the potential to result in enhanced virulence in niches such as the gut and might therefore promote translocation and dissemination.

Mechanisms of Kwashiorkor-Associated Immune Suppression: Insights From Human, Mouse, and Pig Studies

Malnutrition refers to inadequate energy and/or nutrient intake. Malnutrition exhibits a bidirectional relationship with infections whereby malnutrition increases risk of infections that further aggravates malnutrition. Severe malnutrition (SM) is the main cause of secondary immune deficiency and mortality among children in developing countries. SM can manifest as marasmus (non-edematous), observed most often (68.6% of all malnutrition cases), kwashiorkor (edematous), detected in 23.8% of cases, and marasmic kwashiorkor, identified in ~7.6% of SM cases. Marasmus and kwashiorkor occur due to calorie-energy and protein-calorie deficiency (PCD), respectively. Kwashiorkor and marasmic kwashiorkor present with reduced protein levels, protein catabolism rates, and altered levels of micronutrients leading to uncontrolled oxidative stress, exhaustion of anaerobic commensals, and proliferation of pathobionts. Due to these alterations, kwashiorkor children present with profoundly impaired immune function, compromised intestinal barrier, and secondary micronutrient deficiencies. Kwashiorkor-induced alterations contribute to growth stunting and reduced efficacy of oral vaccines. SM is treated with antibiotics and ready-to-use therapeutic foods with variable efficacy. Kwashiorkor has been extensively investigated in gnotobiotic (Gn) mice and piglet models to understand its multiple immediate and long-term effects on children health. Due to numerous physiological and immunological similarities between pigs and humans, pig represents a highly relevant model to study kwashiorkor pathophysiology and immunology. Here we summarize the impact of kwashiorkor on children's health, immunity, and gut functions and review the relevant findings from human and animal studies. We also discuss the reciprocal interactions between PCD and rotavirus-a highly prevalent enteric childhood pathogen due to which pathogenesis and immunity are affected by childhood SM.

Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus

The purpose of this study was to explore the relationship between the characteristics of gut microbiome and the effect of medical nutrition therapy (MNT) on glycemic control in pregnant women with gestational diabetes mellitus (GDM). Seventy-four pregnant women newly diagnosed with GDM received MNT for one-week. The effect of glycemic control was evaluated by fasting and 2-hour postprandial blood glucose; and stool samples of pregnant women were collected to detect the gut microbiome before and after MNT. We used a nested case-control study design, with pregnant women with GDM who did not meet glycemic standards after MNT as the ineffective group and those with an age difference of ≤5 years, matched for pre-pregnancy body mass index (BMI) 1:1, and meeting glycemic control criteria as the effective group. Comparison of the gut microbiome characteristics before MNT showed that the ineffective group was enriched in Desulfovibrio, Aeromonadales, Leuconostocaceae, Weissella, Prevotella, Bacillales_Incertae Sedis XI, Gemella and Bacillales, while the effective group was enriched in Roseburia, Clostridium, Bifidobacterium, Bifidobacteriales, Bifidobacteriaceae, Holdemania and Proteus. After treatment, the effective group was enriched in Bifidobacterium and Actinomycete, while the ineffective group was enriched in Holdemania, Proteus, Carnobacteriaceae and Granulicatella. In conclusion, the decrease in the abundance of characteristic gut microbiome positively correlated with blood glucose may be a factor influencing the poor hypoglycemic effect of MNT in pregnant women with GDM. Abundance of more characteristic gut microbiome negatively correlated with blood glucose could help control blood glucose in pregnant women with GDM.

Comparative Analysis of the Fecal Microbiota of Relict Gull (Larus relictus) in Mu Us Desert (Hao Tongcha Nur) and Bojiang Haizi in Inner Mongolia, China

The gut microbiota contributes to host health by improving digestive efficiency and maintaining homeostasis. The relict gull (Larus relictus), a national first-class protected bird in China, is listed as vulnerable in the International Union for Conservation of Nature Red List. Here, 16S rRNA gene sequencing was performed to characterize and compare the community composition and diversity of the gut microbiota sampled from relict gulls in two breeding sites. In total, 418 operational taxonomic units (OUTs) were obtained and classified into 15 phyla and 228 genera. Alpha diversity analysis revealed no significant differences in community diversity among the two breeding sites. Beta diversity analyses showed that the microbial communities at the two sites were different. Six dominant phyla and fourteen dominant genera were identified. The most abundant bacterial genera had a significant relationship with the diet and living environment, and some bacterial genera were found to adapt to the plateau environment in which relict gulls live, which enables the relict gulls to use local resources effectively to accumulate energy. Simultaneously, a variety of highly abundant pathogenic bacteria were found, suggesting that these gulls may spread diseases among the local gull population. Certain measures should be taken to protect this species and to prevent the spread of diseases.

Evidence for long-lasting alterations in the fecal microbiota following prenatal alcohol exposure

BACKGROUND

There is growing evidence that the gut microbiota can be shaped by early-life experiences/exposures, with long-term consequences for brain, behavior, and health. Changes in the gut microbiota have also been identified in neurodevelopmental disorders including Autism Spectrum Disorder and schizophrenia. In contrast, no studies to date have investigated whether the gut microbiota is altered in individuals with Fetal Alcohol Spectrum Disorder (FASD), the neurodevelopmental disorder that results from prenatal alcohol exposure (PAE). The current study was designed to assess the impact of PAE on the fecal microbiota.

METHODS

We used a rodent model in which pregnant Sprague-Dawley rats were provided with an EtOH-containing diet or a control diet throughout gestation. Fecal samples were collected from adult male and female animals and 16s rRNA sequencing was performed.

RESULTS

Overall, PAE rats showed greater richness of bacterial species, with community structure investigations demonstrating distinct clustering by prenatal treatment. In addition, prenatal treatment and sex-specific alterations were observed for many specific microbes. For example, in males, Bacteroides and Bifidobacterium, and in females, Faecalitalea and Proteus, differed in abundance between PAE and control rats.

CONCLUSIONS

Taken together, these results show for the first time that PAE has a long-lasting and sex-specific impact on the fecal microbiota. Further research is needed that considers fetal microbiota in the development of new interventions in FASD.

Mucosal microbiome associates with progression to gastric cancer

Background & Aims: Dysbiosis is associated with gastric cancer (GC) development. However, no longitudinal study was carried out to identify key bacteria that could predict for GC progression. Here, we aimed to investigate changes in bacterial metagenome prior to GC and develop a microbiome-based predictive model to accurately classify patients at risk of GC.

Methods: Bacterial 16S rDNA was sequenced from 89 gastric antral biopsies obtained from 43 participants. This study was nested in a prospective, longitudinal study, whereby study participants underwent screening gastroscopy, with further 1-2 yearly surveillance gastroscopies for at least 5 years. Putative bacterial taxonomic and functional features associated with GC carcinogenesis were identified by comparing between controls, patients with gastric intestinal metaplasia (IM) and patients with early gastric neoplasia (EGN).

Results: Patients with EGN had enrichment of Proteobacteria (in particular Proteus genus) and depletion of Bacteroidetes (in particular S24-7 family) in their gastric mucosa. Sequencing identified more patients with Helicobacter pylori compared to histopathological assessment, while H. pylori was also significantly enriched in EGN. Furthermore, a total of 261 functional features, attributing to 97 KEGG pathways were differentially abundant at baseline between patients who subsequent developed EGN (n = 13/39) and those who did not. At the same time, a constellation of six microbial taxonomic features present at baseline, provided the highest classifying power for subsequent EGN (AUC = 0.82).

Conclusion: Our study highlights early microbial changes associated with GC carcinogenesis, suggesting a potential role for prospective microbiome surveillance for GC.

Does Anti-TNF-α Therapy Affect the Bacteriological Profile of Specimens Collected from Perianal Lesions? A Retrospective Analysis in Patients with Crohn's Disease

Anal abscesses and fistulas are potential complications of Crohn’s disease (CD). Chronic immunosuppression, loose stools, and poor wound healing in this population present challenges to the management of perianal diseases. The purpose of the study was to determine the predominant bacterial species found in specimens from perianal lesions causing anal abscess and/or fistula drainage in hospitalized patients, and to compare the number and type of microorganisms isolated from samples taken from patients undergoing biological therapy or traditionally treated. The outcomes of studies of patients treated for anal abscesses or fistulas from 2017 to 2019 were evaluated. Data obtained from medical records included culture and antibiotic sensitivity results of swabs from perianal lesions of isolated microorganisms. A total of 373 swabs were collected from perianal lesions during the analysis period, including 51 (49 positive samples) from patients with CD. The predominant pathogen was Escherichia coli (55%, p < 0.001), the second most common microorganism was Staphylococcus aureus (14.3%, p < 0.001). In vitro susceptibility testing showed E. coli, ESBL (strain with Extended Spectrum Beta-Lactamase) in five cases, S. aureus, MRSA (methicillin-resistant S. aureus -resistant to all beta-lactam antibiotics: penicillins with inhibitors, cephalosporins, monobactams, carbapenems, except for ceftaroline) in one sample. Biologic therapy does not affect the type of microorganisms isolated from perianal abscesses in patients with CD.

Antibacterial and Sporicidal Activity Evaluation of Theaflavin-3,3'-digallate

Theaflavin-3,3'-digallate (TFDG), a polyphenol derived from the leaves of Camellia sinensis, is known to have many health benefits. In this study, the antibacterial effect of TFDG against nine bacteria and the sporicidal activities on spore-forming Bacillus spp. have been investigated. Microplate assay, colony-forming unit, BacTiter-Glo^TM, and Live/Dead Assays showed that 250 µg/mL TFDG was able to inhibit bacterial growth up to 99.97%, while 625 µg/mL TFDG was able to inhibit up to 99.92% of the spores from germinating after a one-hour treatment. Binding analysis revealed the favorable binding affinity of two germination-associated proteins, GPR and Lgt (GerF), to TFDG, ranging from -7.6 to -10.3 kcal/mol. Semi-quantitative RT-PCR showed that TFDG treatment lowered the expression of gpr, ranging from 0.20 to 0.39 compared to the control in both Bacillus spp. The results suggest that TFDG not only inhibits the growth of vegetative cells but also prevents the germination of bacterial spores. This report indicates that TFDG is a promising broad-spectrum antibacterial and anti-spore agent against Gram-positive, Gram-negative, acid-fast bacteria, and endospores. The potential anti-germination mechanism has also been elucidated.

Intestinal Microbiota and Serum Metabolic Profile Responded to Two Nutritional Different Diets in Mice

There is an interaction and bidirectional selection between dietary intake and gut microbiota due to the different efficiency of nutrients in the gut. The nutritional composition of germ-free (GF) diets differs significantly from specific pathogen-free (SPF) diets. There is, however, no data revealing how SPF animals from the same microbial background respond to them and if they affect the host. We examined the growth of SPF mice on the GF diet and found that it reduced body weight, intestinal length and intestinal morphology. Interestingly, the GF diet increased the level of pro-inflammatory bacteria in the gut of SPF mice, including Proteobacteria, Burkholderiaceae, Alloprevotella and Parasutterella. Furthermore, GF diets caused significant increases in malondialdehyde (MDA), IL-1β, IL-6, and D-lactate levels in the serum of SPF mice and significantly altered their serum metabolic profile, especially amino acid metabolism. In conclusion, GF diets are not suitable for the growth and development of SPF mice. These findings, based on the role of gut microbiota in diet selection, provide new insights into the scientific and rational use of experimental animal diets.