In situ carbothermal synthesis of carbonized bacterial cellulose embedded with nano zero-valent iron for removal of Cr(VI)

Carbonized bacterial cellulose embedded with highly dispersed nano zero-valent iron (nZVI), denoted as nZVI@CBC, was prepared through one-step in situ carbothermal treatment of bacterial cellulose adsorbing iron(III) nitrate. The structure characteristics of nZVI@CBC and its performance in removing hexavalent chromium Cr(VI) were investigated. Results showed the formation of nZVI@CBC with a surface area of 409.61 m2/g at 800 °C, with nZVI particles of mean size 28.2 nm well distributed within the fibrous network of CBC. The stability of nZVI was enhanced by its carbon coating, despite some inevitable oxidation of exposed nZVI. Batch experiments demonstrated that nZVI@CBC exhibited superior removal efficiency compared to bare nZVI and CBC. Under optimal conditions, nZVI@CBC exhibited a high Cr(VI) adsorption capacity of up to 372.42 mg/g. Therefore, nZVI@CBC shows promise as an effective adsorbent for remediating Cr(VI) pollution in water.

Iron decoration in binary graphene oxide and copper iron sulfide nanocomposites boosting catalytic antibacterial activity in acidic microenvironment against antimicrobial resistance

The strong antimicrobial resistance (AMR) of multidrug-resistant (MDR) bacteria and biofilm, especially the biofilm with extracellular polymeric substance (EPS) protection and persister cells, not only renders antibiotics ineffective but also causes chronic infections and makes the infectious tissue difficult to repair. Considering the acidic properties of bacterial infection microenvironment and biofilm, herein, a binary graphene oxide and copper iron sulfide nanocomposite (GO/CuFeSx NC) is synthesized by a surfactant free strategy and utilized as an alternative smart nanozyme to fight against the MDR bacteria and biofilm. For the GO/CuFeSx NC, the iron decoration facilitates the well distribution of bimetallic CuFeSx NPs on the GO surfaces compared to monometallic CuS NPs, providing synergistically enhanced peroxidase (POD)-like activity in acidic medium (pH 4 ∼ 5) and intrinsic strong near infrared (NIR) light responsive photothermal activity, while the ultrathin and sharp structure of 2D GO nanosheet allows the GO/CuFeSx NC to strongly interact with the bacteria and biofilm, facilitating the catalytic and photothermal attacks on the bacterial surfaces. In addition, the GO in GO/CuFeSx NC exhibits a "Pseudo-Photo-Fenton" effect to promote the ROS generation. Therefore, the GO/CuFeSx NC can effectively kill bacteria and biofilm both in vitro and in vivo, finally eliminating the infections and accelerating the tissue repair when treating the biofilm-infected wound. This work paves a new way to the design of novel nanozyme for smart antibacterial therapy against antimicrobial resistance.

Characterization of gut microbiota in patients with stage 3-4 chronic kidney disease: a retrospective cohort study

PURPOSE

Multiple factors, such as dietary patterns, pharmaceutical interventions, and exposure to harmful substances, possess the capacity to influence gut microbiota composition. Gut microbiota dysbiosis has emerged as a significant contributor to the progression of chronic kidney disease (CKD) and its associated complications. By comprehending the intricacies of the intestinal microbiota, this research endeavor holds the potential to offer novel perspectives on potential strategies for mitigating CKD progression.

METHODS

In this retrospective analysis, we assessed gut microbiota composition in CKD patients. Fecal samples were collected from a cohort of 44 patients with stage 3-4 CKD, alongside a control group consisting of 132 healthy volunteers. Subsequently, 16 s rDNA sequencing was conducted to examine the composition of the gut microbiota.

RESULTS

Our findings revealed significant alterations in the diversity of intestinal microbiota in fecal samples between patients with stage 3-4 CKD and healthy subjects. Among the 475 bacterial genera, 164 were shared, while 242 dominant genera were exclusive to healthy subjects and 69 to CKD stages 3-4 samples. Notably, healthy volunteers exhibited a prevalence of intestinal Firmicutes and Bacteroidetes, whereas stage 3-4 CKD patients displayed higher abundance of Proteobacteria and Actinobacteria. The presence of uncultured Coprobacillus sp. notably contributed to distinguishing between the two groups. ROC curve analysis identified distinct microbiota with superior diagnostic efficacy for discriminating stage 3-4 CKD patients from healthy individuals. Metabolic pathway analysis revealed differing dominant pathways between the two groups-the NADH dehydrogenase pathway in healthy individuals and the phosphate acetyltransferase pathway in stage 3-4 CKD patients. Moreover, the CKD cohort displayed a higher proportion of Gram-negative bacteria and facultative anaerobes.

CONCLUSIONS

In conclusion, our study underscores the profound influence of gut microbiota dysbiosis on CKD progression. The distinct microbial profiles observed in CKD patients highlight the potential efficacy of microbiota-based interventions in mitigating CKD advancement.

Phosphate additives promote humic acid carbon and nitrogen skeleton formation by regulating precursors and composting bacterial communities

This study aimed to compare the effect of different phosphate additives including superphosphate (CP) and MP [Mg(OH)2 + H3PO4] on nitrogen conversion, humus fractions formation and bacterial community in food waste compost. The results showed the ratio of humic acid nitrogen in total nitrogen (HA-N/TN) in CP increased by 49 %. Ammonium nitrogen accumulation was increased by 75 % (CP) and 44 % (MP). Spectroscopic techniques proved that phosphate addition facilitated the formation of complex structures in HA. CP enhanced the dominance of Saccharomonospora, while Thermobifida and Bacillus were improved in MP. Structural equation modeling and network analysis demonstrated that ammonium nitrogen can be converted to HA-N and has positive effects on bacterial composition, reducing sugars and amino acids, especially in CP with more clustered network and synergic bacterial interactions. Therefore, the addition of phosphate provides a new idea to regulate the retained nitrogen toward humification in composting.

Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri

Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.

Mechanisms of copper and zinc bioremoval by microalgae and bacteria grown in nutrient rich wastewaters

Swine farming produces large quantities of nutrient-rich wastewater, which often contains metals such as Cu and Zn, used as feed additives for pigs. These metals must be removed from the wastewater before discharge but their retention in the biomass can limit its subsequent utilization. Photobioreactors are a very promising alternative for swine wastewater treatment, as the consortium of microalgae and bacteria growing symbiotically in these reactors allows high nutrient and metal removal efficiency at moderate costs. This work studies the mechanisms of removal of Cu(II) and Zn(II) by the two types of microorganisms growing in these photobioreactors. A microalga commonly used in wastewater treatment (Scenedesmus almeriensis) and an activated sludge were kept in contact with synthetic wastewater containing 100 mg/L of Cu and Zn. After 72 h, Scenedesmus almeriensis removed 43% of Cu and 45% of Zn, while activated sludge removed 78% of Cu and 96% of Zn. Single and sequential extractions of the biomasses using different extracting reagents revealed that biosorption on protonable groups is the dominant removal mechanisms. Mild reagents solubilized 69% of Cu and 94% of Zn from the microalgae and 76% of Cu and 93% of Zn from the activated sludge. Low metal concentrations in the oxidizable and residual fractions evidenced minimal bioaccumulation inside the cells. FTIR and ESEM-EDX analysis confirmed biosorption by ion exchange and complexation as the main metal remediation mechanisms. The weak bonds of the biosorbed Cu and Zn ions are beneficial for the valorization of biomass and the obtaining of safe bioproducts.

An in-depth investigation of the microbiota and its virulence factors associated with severe udder cleft dermatitis lesions

Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. Proteobacteria, Bacillota, and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, whereas Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples, whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1, and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions, while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network ofpositive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network, which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless or beneficial bacteria, such as Bifidobacterium spp. and Butyrivibrio proteoclasticus, associated with hcnB, hcnC, relB, glyoxalase, and cupin 2. The other network, corresponding to UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB, and haemagglutination activity domain-associated factor. Our results point toward a dysbiotic community with a notable decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.

Synergistic improvement of humus formation in compost residue by fenton-like and effective microorganism composite agents

Improving the humification of compost through a synergistic approach of biotic and abiotic methods is of great significance. This study employed a composite reagent, comprising Fenton-like agents and effective microorganisms (EM) to improve humification. This composite reagent increased humic-acid production by 37.44 %, reaching 39.82 g kg-1, surpassing the control group. The composite reagent synergistically promoted micromolecular fulvic acid and large humic acid production. Collaborative mechanism suggests that Fenton-like agents contributed to bulk residue decomposition and stimulated the evolution of microbial communities, whereas EMs promoted highly aromatic substance synthesis and adjusted the microbial community structure. Sequencing analysis indicates the Fenton-like agent initiated compost decomposition by Firmicutes, and EM reduced the abundance of Virgibacillus, Lentibacillus, and Alcanivorax. Applied as an organic fertilizer in Brassica chinensis L. plantations, the composite reagent considerably improved growth and photosynthetic pigment content. This composite reagent with biotic and abiotic components provides a learnable method for promoting humification.

Improving anammox activity and reactor start-up speed by using CO2/NaHCO3 buffer

Anammox bacteria grow slowly and can be affected by large pH fluctuations. Using suitable buffers could make the start-up of anammox reactors easy and rapid. In this study, the effects of three kinds of buffers on the nitrogen removal and growth characteristics of anammox sludge were investigated. Reactors with CO2/NaHCO3 buffer solution (CCBS) performed the best in nitrogen removal, while 4-(2-hydroxyerhyl)piperazine-1-ethanesulfonic acid (HEPES) and phosphate buffer solution (PBS) inhibited the anammox activity. Reactors with 50 mmol/L CCBS could start up in 20 days, showing the specific anammox activity and anammox activity of 1.01±0.10 gN/(gVSS·day) and 0.83±0.06 kgN/(m3·day), respectively. Candidatus Kuenenia was the dominant anammox bacteria, with a relative abundance of 71.8%. Notably, anammox reactors could also start quickly by using 50 mmol/L CCBS under non-strict anaerobic conditions. These findings are meaningful for the quick start-up of engineered anammox reactors and prompt enrichment of anammox bacteria.

Phage formulations and delivery strategies: Unleashing the potential against antibiotic-resistant bacteria

Bacterial control promoted by bacteriophages (phages) is an attractive tool in the face of the antibiotic crisis triggered by the exacerbated use of these drugs. Despite the growing interest in using these viruses, some gaps still need answers, such as the protection and delivery of phages. Some limitation points involve the degradation of phage proteins by enzymes or inactivation in low-pH environments. In this review, a literature search using keywords related to the field of virus delivery formulations was done to understand the current scenario of using delivery techniques and phage formulations. A total of 2096 raw results were obtained, which resulted in 140 publications after refinement. These studies were analyzed for main application techniques and areas, keywords, and countries. Of the total, 57% of the publications occurred in the last five years, and the encapsulation technique was the most used among the articles analyzed. As excipient agents, lactose, trehalose, mannitol, PEG, and Leucine stand out. The development of phage formulations, protection approaches, their delivery routes, and the knowledge about the best application strategy enables the use of these organisms in several sectors. It can act as a powerful tool against antibiotic-resistant bacteria.

Cooperation of quorum sensing and central carbon metabolism in the pathogenesis of Gram-positive bacteria

Quorum sensing (QS), an integral component of bacterial communication, is essential in coordinating the collective response of diverse bacterial pathogens. Central carbon metabolism (CCM), serving as the primary metabolic hub for substances such as sugars, lipids, and amino acids, plays a crucial role in the life cycle of bacteria. Pathogenic bacteria often utilize CCM to regulate population metabolism and enhance the synthesis of specific cellular structures, thereby facilitating in adaptation to the host microecological environment and expediting infection. Research has demonstrated that QS can both directly or indirectly affect the CCM of numerous pathogenic bacteria, thus altering their virulence and pathogenicity. This article reviews the interplay between QS and CCM in Gram-positive pathogenic bacteria, details the molecular mechanisms by which QS modulates CCM, and lays the groundwork for investigating bacterial pathogenicity and developing innovative infection treatment drugs.

Enhancing wastewater treatment efficiency: A hybrid technology perspective with energy-saving strategies

The study aimed to investigate how hybrid technology, combined with various intermittent aeration (IA) strategies, contributes to reducing the energy costs of wastewater treatment while simultaneously ensuring a high treatment efficiency. Even with IA subphases lasting half as long as those without aeration, and oxygen levels reduced from 3.5 to 1.5 mg O2/L, pollutants removal efficiency remains robust, allowing for a 1.41-fold reduction in energy consumption (EO). Hybrid technology led to a 1.34-fold decrease in EO, along with improved denitrification efficiency from 74.05 ± 4.71 to 81.87 ± 2.43 % and enhanced biological phosphorus removal from 35.03 ± 4.25 to 87.32 ± 3.64 %. The high nitrification efficiency may have been attributed to the abundance of Pseudomonas, Acinetobacter, and Rhodococcus, which outcompeted the genera of autotrophic nitrifying bacteria, suggesting that the hybrid system is favorable for the growth of heterotrophic nitrifiers.

A scoping review of antimicrobial resistance in the Australian dairy cattle industry

INTRODUCTION

Quantification of antimicrobial resistance (AMR) is beneficial to inform policies and direct prudent antimicrobial use.

AIM

This study aimed to assess the current published evidence of AMR from passive and active ad hoc surveillance activities within the Australian dairy cattle industry.

METHODS

Following a scoping review framework 373 articles published before January 2023 were retrieved using the keyword search function from two online databases (PubMed® and Web of Science™ Core Collection). The duplicate articles were removed and the title, abstract, and full text of the remaining articles were reviewed following the study objectives and inclusion criteria (location, subject/theme, and data). Data from the remaining articles were extracted, summarised, interpreted and the study quality assessed using the Grades of Recommendations, Assessment, Development, and Evaluation guidelines.

RESULTS

A total of 29 articles dating from the 1960 s until 2022 were identified to meet the study criteria (passive: n = 15; active: n = 14). Study characteristics such as sampling type, sampling method, and AMR assessment were all common characteristics from both passive and active surveillance articles, being milk samples, individual sampling, and phenotypic assessment respectively. Passive surveillance articles had a wider range in both the type of bacteria and the number of antimicrobials investigated, while active surveillance articles included a higher number of bacterial isolates and sampling from healthy populations. There was an overall low level of clinical AMR across all articles. Higher prevalence of non-wildtype Escherichia coli, Salmonella spp., and Staphylococcus spp., although limited in data, was suggested for commonly used Australian veterinary antimicrobials for these bacteria. The prevalence of phenotypic AMR varied due to the health and age status of the sampled animals. The articles reviewed in this study suggest the prevalence of AMR genes was higher for commonly used antimicrobials, although genes were not always related to the phenotypic AMR profile.

CONCLUSIONS

Published evidence of AMR in the Australian dairy cattle industry is limited as demonstrated by only 29 articles included in this review following selection criteria screening. However, collectively these articles provide insight on industry AMR prevalence. For example, the suggestion of non-wildtype bacteria within the Australian dairy cattle indicating a risk of emerging or increasing industry AMR. Therefore, further surveillance is required to monitor the development of future AMR risk within the industry. Additionally, evidence suggesting that animals varying in health and age differ in prevalence of AMR imply a requirement for further research into animal population demographics to reduce potential bias in data collated in both national and global surveillance activities.

Bacterial profiles detected in ventilator-associated pneumonia in Japan: A systematic review

The primary objective of this study was to identify the predominant organisms associated with ventilator-associated pneumonia (VAP) in Japan. Studies on VAP conducted in Japan were systematically reviewed, and seven studies with a total of 374 cases were included. The detection rate of each bacterium and multidrug-resistant (MDR) pathogen was analyzed using the inverse variance method. Pseudomonas aeruginosa was identified as the predominant pathogen in 29.2 % of cases, followed by methicillin-resistant Staphylococcus aureus (MRSA) (12.0 %), and Klebsiella spp. (9.5 %). An integrated analysis revealed a detection rate of 57.8 % (95 % confidence interval: 48.7%-66.8 %) for MDR pathogens. This review highlights P. aeruginosa and MRSA as the predominant VAP-associated organisms in Japan, with a significant prevalence of MDR pathogens. This analysis provides valuable insights based on the regional distribution of bacteria detected in VAP, which is critical for selecting appropriate empirical therapy.

Carnobacterium maltaromaticum as bioprotective culture against spoilage bacteria in ground meat and cooked ham

This study assessed the bioprotective effect of Carnobacterium maltaromaticum (CM) against Pseudomonas fluorescens (PF) and Brochothrix thermosphacta (BT) in ground beef and sliced cooked ham stored in high- and low-oxygen-modified atmospheres (66/4/30% O2/N2/CO2 and 70/30% N2/CO2, respectively). Both meat products were inoculated with CM, PF, and BT individually or in combination and stored for 7 days (3 days at 4 °C + 4 days at 8 °C) for ground beef and 28 days (10 days at 4 °C + 18 days at 8 °C) for sliced cooked ham. Each food matrix was assigned to 6 treatments: NC (no bacterial inoculation, representing the indigenous bacteria of meat), CM, BT, PF, CM + BT, and CM + PF. Bacterial growth, pH, instrumental color, and headspace gas composition were assessed during storage. CM counts remained stable from inoculation and throughout the shelf-life. CM reduced the population of inoculated and indigenous spoilage bacteria, including BT, PF, and enterobacteria, and showed a negligible impact on the physicochemical quality parameters of the products. Furthermore, upon simulating the shelf-life of ground beef and cooked ham, a remarkable extension could be observed with CM. Therefore, CM could be exploited as a biopreservative in meat products to enhance quality and shelf-life.

The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry

OBJECTIVE

The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.

DESIGN

This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.

RESULTS

Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.

CONCLUSIONS

Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.

Mechanisms of bacterial resistance to environmental silver and antimicrobial strategies for silver: A review

The good antimicrobial properties of silver make it widely used in food, medicine, and environmental applications. However, the release and accumulation of silver-based antimicrobial agents in the environment is increasing with the extensive use of silver-based antimicrobials, and the prevalence of silver-resistant bacteria is increasing. To prevent the emergence of superbugs, it is necessary to exercise rational and strict control over drug use. The mechanism of bacterial resistance to silver has not been fully elucidated, and this article provides a review of the progress of research on the mechanism of bacterial resistance to silver. The results indicate that bacterial resistance to silver can occur through inducing silver particles aggregation and Ag+ reduction, inhibiting silver contact with and entry into cells, efflux of silver particles and Ag+ in cells, and activation of damage repair mechanisms. We propose that the bacterial mechanism of silver resistance involves a combination of interrelated systems. Finally, we discuss how this information can be used to develop the next generation of silver-based antimicrobials and antimicrobial therapies. And some antimicrobial strategies are proposed such as the "Trojan Horse" - camouflage, using efflux pump inhibitors to reduce silver efflux, working with "minesweeper", immobilization of silver particles.

Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea

Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.

Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review

Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.

In vitro evaluation of the susceptibility of bacterial biofilms to hecogenin acetate

Biofilms are a bacterial resistance strategy through which microorganisms organize themselves in the form of a colony fixed to a surface that is protected by a polymer matrix. Infectious diseases that result in biofilm formation have been considered a relevant public health problem due to the potential to increase patient morbidity and mortality, in addition to increasing the burden on health services. Such pathologies are treated with the use of antimicrobial drugs, the indiscriminate use of which has contributed to the process of bacterial resistance, demanding the need to invest in new alternatives to combat them. Based on this, the present work aimed to evaluate the anti-biofilm formation and eradication capacity of Hecogenin Acetate, a steroidal sapogenin of natural origin with important antibacterial properties. For this, we used strains of Streptococcus mutans INCQS 00,446 (ATCC 25,175), Enterococcus faecalis INCQS 00,018 (ATCC 14,506), Staphylococcus epidermidis INCQS 00,016 (ATCC 12,228), Staphylococcus aureus ATCC 25,923, Pseudomonas aeruginosa ATCC 9027 and Escherichia coli ATCC 259,223. The formation, formation inhibition and treatment assays were carried out in microdilution plates and revealed using the crystal violet method. Readings were carried out using absorbance at wavelengths of 492 nm. All tests were performed in triplicate and statistical analyzes were performed using Graphpad Prism v.5.0 software. It was observed that the bacterial strains used have a relevant capacity for biofilm formation, with the Gram positive ones identified in the present study as the best former. In the results of the analyzes with bacterial biofilm, it was identified that Hecogenin Acetate had a relevant antibiofilm capacity, and could therefore serve as a basis for further research into the development of new antimicrobial drugs.

Antimicrobials and antiseptics: Lowering effect on ocular surface bacterial flora - A systematic review

Topical antimicrobials and antiseptics are used perioperatively to reduce the ocular surface bacteria flora (OSBF) that are involved in the development of post-operative infectious complications. However, their effectiveness is still a controversial topic. This systematic review, performed according to the PRISMA guidelines and registered in PROSPERO, aims to provide an overview of the efficacy of the agents currently used in peri-cataract surgery and -intravitreal injections (IVI) in lowering the OSBF. Although effective in lowering OSBF, perioperative topical antimicrobials are associated with the risk of resistance development, with no obvious additional benefit compared with topical antisepsis. Conversely, the effectiveness of topical antiseptics before cataract surgery and IVI is strongly supported. Based on the available evidence, perioperative antimicrobials are not recommended, whereas the perioperative use of antiseptics is strongly recommended as prophylactic treatment for lowering the infection due to OSBF. Post-operative antimicrobials may be considered in eyes at higher risk for infection.

Dietary methanotroph bacteria meal alleviates soybean meal-induced enteritis by improving immune tolerance and intestinal flora profile of juvenile turbot (Scophthalmus maximus L.)

An 8-week growth trial was performed to investigate the protective effects of methanotroph bacteria meal (MBM) produced from methane against soybean meal-induced enteritis (SBMIE) in juvenile turbot (Scophthalmus maximus L.). Five isonitrogenous and isolipidic diets were formulated: fishmeal-based diet (FM, the control group); FM with approximate 50% of fishmeal substituted by 399.4 g/kg soybean meal (SBM); SBM supplemented with 63.6, 127.2 and 190.8 g/kg MBM (named MBM1, MBM2 and MBM3), each diet was randomly assigned to triplicate fibreglass tanks. Results showed that fish fed with SBM exhibited enteritis, identified by reduced relative weight of intestine (RWI), as well as expanded lamina propria width and up-regulated gene expression of pro-inflammatory cytokines (tnf-α, il-6 and il-8) in intestine. While the above symptoms were reversed when diet SBM supplemented with MBM at the levels of 63.6 and 127.2 g/kg, as well as characterized by up-regulated gene expression of anti-inflammatory cytokines (tgf-β and il-10) and tight junction protein (claudin3, claudin4 and claudin7) in intestine. Intestinal transcriptome analysis showed that the differentially expressed genes between groups FM and SBM predominantly enriched in the JAK-STAT signaling pathway, and the enrichment of differentially expressed genes between groups SBM and SBM supplemented with 63.6 g/kg MBM was in the inflammatory bowel disease (IBD) and JAK-STAT signaling pathway. To be specific, the expression of jak1, jak2b, stat1 and stat5a was significantly up-regulated when fish fed with SBM, suggested the activation of JAK-STAT signaling pathway, while the expression of these above genes was depressed by providing MBM to diet SBM, and the gene expression of toll-like receptors tlr2 and tlr5b showed a similar pattern. Moreover, intestinal flora analysis showed that community richness and abundance of beneficial bacteria (Cetobacterium and acillus_coagulans) were improved when fish fed with SBM supplemented with 63.6 g/kg MBM. Overall, methanotroph bacteria meal may alleviate SBMIE by regulating the expression of tight junction protein, toll-like receptors and JAK-STAT signaling pathway, as well as improving intestinal flora profile, which would be beneficial for enhancing the immune tolerance and utilization efficiency of turbot to dietary soybean meal.

Dielectric barrier discharge plasma promotes disinfection-residual-bacteria inactivation via electric field and reactive species

Traditional disinfection processes face significant challenges such as health and ecological risks associated with disinfection-residual-bacteria due to their single mechanism of action. Development of new disinfection processes with composite mechanisms is therefore urgently needed. In this study, we employed liquid ground-electrode dielectric barrier discharge (lgDBD) to achieve synergistic sterilization through electric field electroporation and reactive species oxidation. At a voltage of 12 kV, Pseudomonas fluorescens (ultraviolet and ozone-resistant) and Bacillus subtilis (chlorine-resistant) were completely inactivated within 8 and 6 min, respectively, surpassing a 7.0-log reduction. The lgDBD process showed good disinfection performance across a wide range of pH values and different practical water samples. Staining experiments suggest that cellular membrane damage contributes to this inactivation. In addition, we used a two-dimensional parallel streamer solver with kinetics code to fashion a representative model of the basic discharge unit, and discovered the presence of a persistent electric field during the discharge process with a peak value of 2.86 × 106 V/m. Plasma discharge generates excited state species such as O(1D) and N2(C3Πu), and further forms reactive oxygen and nitrogen species at the gas-liquid interface. The physical process, which is driven by electric field-induced cell membrane electroporation, synergizes with the bactericidal effects of reactive oxygen and nitrogen species to provide effective disinfection. Adopting the lgDBD process enhances sterilization efficiency and adaptability, underscoring its potential to revolutionize physicochemical synergistic disinfection practices.

Mechanistic insight into the aggregation ability of anammox microorganisms: Roles of polarity, composition and molecular structure of extracellular polymeric substances

The chemical characteristics of extracellular polymeric substances (EPS) of anammox bacteria (AnAOB) play a crucial role in the rapid enrichment of AnAOB and the stable operation of wastewater anammox processes. To clarify the influential mechanisms of sludge EPS on AnAOB aggregation, multiple parameters, including the polarity distribution, composition, and molecular structure of EPS, were selected, and their quantitative relationship with AnAOB aggregation was analyzed. Compared to typical anaerobic sludge (anaerobic floc and granular sludge), the anammox sludge EPS exhibited higher levels of tryptophan-like substances (44.82-56.52 % vs. 2.57-39.81 %), polysaccharides (40.02-53.49 mg/g VSS vs. 30.22-41.69 mg/g VSS), and protein structural units including α-helices (20.70-23.98 % vs. 16.48-19.32 %), β-sheets (37.43-42.98 % vs. 25.78-36.72 %), and protonated nitrogen (Npr) (0.065-0.122 vs. 0.017-0.061). In contrast, it had lower contents of β-turns (20.95-27.39 % vs. 28.17-39.04 %). These biopolymers were found to originate from different genera of AnAOB. Specifically, the α-helix-rich proteins were mainly derived from Candidatus Kuenenia, whereas the extracellular proteins related to tryptophan and Npr were closely associated with Candidatus Brocadia. Critically, these EPS components could drive anammox aggregation through interactions. Substantial amounts of tryptophan-like substances facilitated the formation of β-sheet structures and the exposure of internal hydrophobic clusters, which benefited the anammox aggregation. Meanwhile, extracellular proteins with high Npr content played a pivotal role in the formation of mixed protein-polysaccharide gel networks with the electronegative regions of polysaccharides, which could be regarded as the key component in the maintenance of anammox sludge stability. These findings provide a comprehensive understanding of the multifaceted roles of EPS in driving anammox aggregation and offer valuable insights into the development of EPS regulation strategies aimed at optimizing the anammox process.

Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents

Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.

The color of biodegradable mulch films is associated with differences in peanut yield and bacterial communities

Biodegradable mulch films (BDMs) are increasingly used in agricultural production as desirable alternatives to the current widespread use of polyethylene (PE) mulch films in China. However, potential effects of different colors of BDMs on field crop production and microbiomes remain unexplored. Here, the differences in bacterial communities of peanut rhizosphere soil (RS) and bulk soil (BS) under non-mulching (CK), PE, and three different colors of BDMs were studied. The results indicated that all treatments could increase the soil temperature, which positively affected the growth of the peanut plants. Moreover, mulching affected the bacterial community structure in RS and BS compared to CK. Furthermore, certain BDM treatments significantly enriched N-fixing bacteria (Bradyrhizobium and Mesorhizobium) and functional groups, increased the closeness of bacterial networks, and harbored more beneficial bacteria as keystone taxa in the RS. This in turn facilitated the growth and development of the peanut plants under field conditions. Our study provides new insights into the micro-ecological effects of mulch films, which can be affected by both the mulch type and color. The observed effects are likely caused by temperature and prevalence of specific microbial functions under the employed films and could guide the development of optimized mulching materials.

Biochar and zero-valent iron alleviated sulfamethoxazole and tetracycline co-stress on the long-term system performance of bioretention cells: Insights into microbial community, antibiotic resistance genes and functional genes

Antibiotics and antibiotic resistance genes (ARGs), known as emerging contaminants, have raised widespread concern due to their potential environmental and human health risks. In this study, a conventional bioretention cell (C-BRC) and three modified bioretention cells with biochar (BC-BRC), microbial fuel cell coupled/biochar (EBC-BRC) and zero-valent iron/biochar (Fe/BC-BRC) were established and two antibiotics, namely sulfamethoxazole (SMX) and tetracycline (TC), were introduced into the systems in order to thoroughly investigate the co-stress associated with the long-term removal of pollutants, dynamics of microbial community, ARGs and functional genes in wastewater treatment. The results demonstrated that the SMX and TC co-stress significantly inhibited the removal of total nitrogen (TN) (C-BRC: 37.46%; BC-BRC: 41.64%; EBC-BRC: 55.60%) and total phosphorous (TP) (C-BRC: 53.11%; BC-BRC: 55.36%; EBC-BRC: 62.87%) in C-BRC, BC-BRC and EBC-BRC, respectively, while Fe/BC-BRC exhibited profoundly stable and high removal efficiencies (TN: 89.33%; TP: 98.36%). Remarkably, greater than 99% removals of SMX and TC were achieved in three modified BRCs compared with C-BRC (SMX: 30.86 %; TC: 59.29%). The decreasing absolute abundances of denitrifying bacteria and the low denitrification functional genes (nirK: 2.80 × 105-5.97 × 105 copies/g; nirS: 7.22 × 105-1.69 × 106 copies/g) were responsible for the lower TN removals in C-BRC, BC-BRC and EBC-BRC. The amendment of Fe/BC successfully detoxified SMX and TC to functional bacteria. Furthermore, the co-stress of antibiotics stimulated the propagation of ARGs (sulI, sulII, tetA and tetC) in substrates of all BRCs and only Fe/BC-BRC effectively reduced all the ARGs in effluent by an order of magnitude. The findings contribute to developing robust ecological wastewater treatment technologies to simultaneously remove nutrients and multiple antibiotics.

Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization

Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.

Continuous valorization of food waste and oily food waste using bacteria-pumice and bacteria-smectite nanocomposites: Alternative cell immobilization and zooplankton lifespan impact

Recycling waste into commercial products is a profitable strategy but the lifetime of immobilized cells for long-term waste treatment remains a problem. This study presents alternative cell immobilization methods for valorizing food waste (FW) and oily food waste (OFW) to microbial carotenoids and proteins. Carriers (pumice or smectite), magnetite nanoparticles, and isolated photosynthetic bacteria were integrated to obtain magnetically recoverable bacteria-pumice and bacteria-smectite nanocomposites. After recycling five batches (50 d), chemical oxygen demand removal from FW reached 76% and 78% with the bacteria-pumice and bacteria-smectite nanocomposite treatments, respectively, and oil degradation in OFW reached 71% and 62%, respectively. Destructive changes did not occur, suggesting the durability of nanocomposites. The used nanocomposites had no impact on the lifespan of Moina macrocopa or water quality as assessed by toxicity analysis. Bacteria-pumice and bacteria-smectite nanocomposites are efficient for food waste recycling and do not require secondary treatment before being discharged into the environment.

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Phage-Based antibacterial hydrogels for bacterial targeting and Ablation: Progress and perspective

The emergence of drug-resistant bacteria makes antibiotics inadequate to treat bacterial infections, which is now a global problem. Phage as a virus with specific recognition ability can effectively kill the bacteria, which is an efficacious antibacterial material to replace antibiotics. Phage-based hydrogels have good biocompatibility and antibacterial effect at the site of infection. Phage hydrogels have remarkable antibacterial effects on targeted bacteria because of their specific targeted bactericidal ability, but there are few reports and reviews on phage hydrogels. This paper discusses the construction method of phage-based antibacterial hydrogels (PAGs), summarizes the advantages related to PAGs and their applications in the direction of wound healing, treating bone bacterial infections, gastrointestinal infection treatment and other application, and finally gives an outlook on the development and research of PAGs.

Predictive statistical models for monitoring antimicrobial resistance spread in the environment using Apis mellifera (L. 1758) colonies

The rise of antimicrobial resistance (AMR) is one of the most relevant problems for human and animal health. According to One Health Approach, it is important to regulate the use of antimicrobials and monitor the spread of AMR in the environment as well. Apis mellifera (L. 1758) colonies were used as bioindicators thanks to their physical and behavioural characteristics. During their foraging flights, bees can intercept small particles, including atmospheric particulate matter, etc., and also microorganisms. To date, the antimicrobial surveillance network is limited to the sanitary level but lacks into environmental context. This study aimed to evaluate the use of A. mellifera colonies distributed throughout the Emilia-Romagna region (Italy) as indicators of environmental antimicrobial-resistant bacteria. This was performed by creating a statistical predictive model that establishes correlations between environmental characteristics and the likelihood of isolating specific bacterial genera and antimicrobial-resistant strains. A total of 608 strains were isolated and tested for susceptibility to 19 different antimicrobials. Aztreonam-resistant strains were significantly related to environments with sanitary structures, agricultural areas and wetlands, while urban areas present a higher probability of trimethoprim/sulfamethoxazole-resistant strains isolation. Concerning genera, environments with sanitary structures and wetlands are significantly related to the genera Proteus spp., while the Escherichia spp. strains can be probably isolated in industrial environments. The obtained models showed maximum values of Models Accuracy and robustness (R2) of 55 % and 24 %, respectively. The results indicate the efficacy of utilizing A. mellifera colonies as valuable bioindicators for estimating the prevalence of AMR in environmentally disseminated bacteria. This survey can be considered a good basis for the development of further studies focused on monitoring both sanitary and animal pathology, creating a specific network in the environments of interest.

Dual disintegration of microalgae biomass for cost-effective biomethane production: Energy and cost assessment

The present study aims to enhance the biomethane production potential of microalgae via a dual disintegration process. During this process, the microalgae biomass was firstly subjected to cell wall weakening by thermochemical disintegration (TC) (50 to 80 °C), pH adjustment with alkali, NaOH (6 to 10) and time (0 to 10 min) and, secondly, by bacterial disintegration (BD). TC-BD disintegration was comparatively higher (33 %) than BD (24 %), TC (8.5 %), and control (7 %). A more significant VFA accumulation of 2816 mg/L was recorded for TC-BD. Similarly, a greater substrate anaerobic biodegradability was achieved in TC-BD (0.32 g COD /g COD) than BD (0.21 g COD /g COD), TC alone (0.09 gCOD/g COD) and control (0.08 g COD /g COD), respectively. The TC-BD achieves a positive net profit and an energy ratio of + 0.12 GJ/d and 1.03. The proposed dual disintegration has a promising future for commercialization.

Bacterial abscesses in whitespotted bamboo sharks (Chiloscyllium plagiosum) in managed care

Sixteen whitespotted bamboo sharks (Chiloscyllium plagiosum) with histologically similar bacterial abscesses were submitted to Northwest ZooPath from nine zoo and aquarium institutions over a 17-year period. These abscesses were characterized by inflammatory cell infiltrates and necrosis with intralesional small, Gram-positive, acid-fast negative, cocci bacteria. The clinical presentation, histologic findings, and culture results indicate that Enterococcus faecalis is a relatively common cause of these lesions in whitespotted bamboo sharks. This organism also provides a treatment challenge due to its inherent antibiotic-resistant properties and ability to form biofilms, confounding the host's immune response. Enterococcus faecalis represents an important cause for abscess formation and cellulitis in captive whitespotted bamboo sharks.

Microbial community structure in a constructed wetland based on a recirculating aquaculture system: Exploring spatio-temporal variations and assembly mechanisms

The diversity, composition and performance of microbial communities within constructed wetlands (CW) were markedly influenced by spatio-temporal variations. A pilot-scale integrated vertical-flow constructed wetland (IVCW) as the biological purification unit within a recirculating aquaculture system (RAS) was established and monitored in this study. The investigation aimed to elucidate the responses of community structure, co-occurrence networks, and assembly mechanisms of the microbial community to spatial and temporal changes. Spatially, all a-diversity indices and microbial networks complexity were significantly higher in the upstream pool of the IVCW than in the downstream pool. Temporally, the richness increased over time, while the evenness showed a decreasing trend. The number of nodes and edges of microbial networks increased over time. Notably, the stable pollutant removal efficiencies were observed during IVCW operations, despite a-diversity and bacterial community networks exhibited significant variations across time. Functional redundancy emerged as a likely mechanism contributing to the stability of microbial ecosystem functions. Null model and neutral model analyses revealed the dominance of deterministic processes shaping microbial communities over time, with deterministic influences being more pronounced at lower a-diversity levels. DO and inorganic nitrogen emerged as the principal environmental factor influencing microbial community dynamics. This study provides a theoretical foundation for the regulation of microbial communities and environmental factors within the context of IVCW.

Implications of PM2.5 chemical composition in modulating microbial community dynamics during spring in Seoul

Particulate matter with an aerodynamic diameter of 2.5 μm or less (PM2.5) harbors a diverse microbial community. To assess the ecological dynamics and potential health risks associated with airborne microorganisms, it is crucial to understand the factors influencing microbial communities within PM2.5. This study investigated the influence of abiotic parameters, including air pollutants, PM2.5 chemical composition (water-soluble ions and organics), and meteorological variables, on microbial communities in PM2.5 samples collected in Seoul during the spring season. Results revealed a significant correlation between air pollutants and water-soluble ions of PM2.5 with microbial α-diversity indices. Additionally, air pollutants exerted a dominant effect on the microbial community structure, with stronger correlations observed for fungi than bacteria, whereas meteorological variables including temperature, pressure, wind speed, and humidity exerted a limited influence on fungal α-diversity. Furthermore, the results revealed specific water-soluble ions, such as SO42-, NO3-, and NH4+, as important factors influencing fungal α-diversity, whereas K+ negatively correlated with both microbial α-diversity. Moreover, PM2.5 microbial diversity was affected by organic compounds within PM2.5, with fatty acids exhibited a positive correlation with fungal diversity, while dicarboxylic acids exhibited a negative correlation with it. Furthermore, network analysis revealed direct links between air pollutants and dominant bacterial and fungal genera. The air pollutants exhibited a strong correlation with bacterial genera, such as Arthrospira and Clostridium, and fungal genera, including Aureobasidium and Cladosporium. These results will contribute to our understanding of the ecological dynamics of airborne microorganisms and provide insights into the potential risks associated with PM2.5 exposure.

Biofilm-producing Bacteria and Quality of Life after Endoscopic Sinus Surgery in Patients with Chronic Rhinosinusitis with Nasal Polyposis

BACKGROUND

Chronic rhinosinusitis (CRS) is one of the most common health disorders in humans and has a major impact on health-related quality of life (HRQoL). Of the many factors contributing to the etiology of CRS, less is known about the correlation between CRS and bacterial biofilms and their impact on HRQoL.

OBJECTIVE

The aim of this prospective study was to investigate the relationship between biofilm-producing bacteria and patients' objective findings and HRQoL.

METHODS

Forty-eight patients with CRSwNP were enrolled in a 12-month prospective study. The Lund-Mackay (LM) CT and endoscopic Lund-Kennedy (LK) scores were obtained before endoscopic sinus surgery (ESS), and patients completed the HRQoL instruments: the 22-item Sinonasal Outcome Test (SNOT-22), the 36-item Short Questionnaire (SF-36), and the visual analog scale (VAS). A sinus culture was obtained at ESS, bacteria were isolated, and in vitro quantification of the biofilm was performed. The LK score and HRQoL were determined postoperatively at months 1, 3, 6, and 12.

RESULTS

The most common bacterial isolates in patients with CRSwNP were Staphylococcus aureus (28%), coagulase-negative staphylococci (52%), and Pseudomonas aeruginosa (8%). Preoperatively, the highest LM and LK scores were found in patients with strong biofilm producers. Postoperative LK scores were significantly reduced in all patients. Postoperative VAS scores were significantly reduced from month 1 to month 12 postoperatively. Patients with strong biofilm producers had significantly worse nasal blockage, secretion, headache, facial pressure and pain, and loss of smell preoperatively, compared to patients with low biofilm producers. The most significant reduction in preoperative scores SNOT-22 and SF-36 (excluding physical functioning) was seen in patients with S. aureus and P. aeruginosa.

CONCLUSIONS

Patients with strong biofilm producers had higher LK and LM scores preoperatively, and greater improvement in LK and HRQoL scores postoperatively. Microbiologic surveillance of all CRS patients is recommended.

Caspase-like activity is associated with bacterial infection of the urine in urinary tract diseases

Urinary tract infections (UTIs) are a serious public health problem. They can be caused by a number of pathogens, but the most common are Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis and Staphylococcus saprophyticus. Bacterial infection is diagnosed by examining a urine sample. The presence of bacteria or white blood cells is determined under a microscope or a urine culture is performed. In this study, we used a panel of chromogenic substrates for the qualitative determination of specific enzyme activity in the urine of patients with confirmed bacterial infection and/or urinary tract disease. Healthy patients were used as a control group. It turned out that in the case of Escherichia coli infection, we observed the activity of the caspase subunit of the human 20S proteasome. We did not observe similar correlations for infections with other types of bacteria.

2,3-Dichloronaphthoquinone derivatives: Synthesis, antimicrobial activity, molecular modelling and ADMET studies

In the present study, an intermediate namely 2-(3-bromopropylamino)-3-chloronaphthalene-1,4-dione was initially synthesized via the nucleophilic addition-elimination reaction between 2,3-dichloro-1,4-naphthoquinone and 3-bromo-1-aminopropane. Then a coupling reaction between the intermediate and piperazine derivatives yielded a number of 1,4-naphthoquinone derivatives. Spectroscopic analysis successfully characterized the products that were obtained in good yields. In vitro antibacterial properties of the compounds were examined against different bacterial strains. In vitro antibacterial properties of the compounds were examined against the bacterial strains S. Aureus, E. Faecalis, E. Coli and P. Aeruginosa. While compound 9 was found to be effective against all bacterial strains used, compound 12 was active against three strains and compounds 10 and 11 were effective against the two. None of the compounds are effective against C. albicans strain. In silico molecular docking studies revealed that all compounds had docking scores comparable to the antibacterial drugs ciprofloxacin and gentamicin and might be considered as DNA gyrase B inhibitors. Molecular dynamics simulations were also conducted for a better understanding of the stability and the selected docked complexes. Additionally, the drug similarity of the synthesized compounds and ADMET characteristics were examined in conjunction with the antibiotic ciprofloxacin, and drug potentials were then evaluated. Compatible predictions were found with the drug similarity and ADMET parameters.

Dissolving microneedle system containing Ag nanoparticle-decorated silk fibroin microspheres and antibiotics for synergistic therapy of bacterial biofilm infection

Most cases of delayed wound healing are associated with bacterial biofilm infections due to high antibiotic resistance. To improve patient compliance and recovery rates, it is critical to develop minimally invasive and efficient methods to eliminate bacterial biofilms as an alternative to clinical debridement techniques. Herein, we develop a dissolving microneedle system containing Ag nanoparticles (AgNPs)-decorated silk fibroin microspheres (SFM-AgNPs) and antibiotics for synergistic treatment of bacterial biofilm infection. Silk fibroin microspheres (SFM) are controllably prepared in an incompatible system formed by a mixture of protein and carbohydrate solutions by using a mild all-aqueous phase method and serve as biological templates for the synthesis of AgNPs. The SFM-AgNPs exert dose- and time-dependent broad-spectrum antibacterial effects by inducing bacterial adhesion. The combination of SFM-AgNPs with antibiotics breaks the limitation of the antibacterial spectrum and achieves better efficacy with reduced antibiotic dosage. Using hyaluronic acid (HA) as the soluble matrix, the microneedle system containing SFM-AgNPs and anti-Gram-positive coccus drug (Mupirocin) inserts into the bacterial biofilms with sufficient strength, thereby effectively delivering the antibacterial agents and realizing good antibiofilm effect on Staphylococcus aureus-infected wounds. This work demonstrates the great potential for the development of novel therapeutic systems for eradicating bacterial biofilm infections.

Fungi and tumors: The role of fungi in tumorigenesis (Review)

Fungi inhabit different anatomic sites in the human body. Advances in omics analyses of host‑microbiome interactions have tremendously improved our understanding of the effects of fungi on human health and diseases such as tumors. Due to the significant enrichment of specific fungi in patients with malignant tumors, the associations between fungi and human cancer have attracted an increasing attention in recent years. Indeed, cancer type‑specific fungal profiles have been found in different tumor tissues. Importantly, fungi also influence tumorigenesis through multiple factors, such as host immunity and bioactive metabolites. Microbiome interactions, host factors and fungal genetic and epigenetic factors could be involved in fungal enrichment in tumor tissues and/or in the conversion from a commensal fungus to a pathogenic fungus. Exploration of the interactions of fungi with the bacterial microbiome and the host may enable them to be a target for cancer diagnosis and treatment. In the present review, the associations between fungi and human cancer, cancer type‑specific fungal profiles and the mechanisms by which fungi cause tumorigenesis were discussed. In addition, possible factors that can lead to the enrichment of fungi in tumor tissues and/or the conversion of commensal fungi to pathogenic fungi, as well as potential therapeutic and preventive strategies for tumors based on intratumoral fungi were summarized.

The performance of a Fully Automated Urine Particle Analyzer, Sysmex UF-5000, in detecting fastidious bacteria in urine samples

Several types of fastidious bacteria can cause tract infections. We evaluated the performance of counting fastidious bacteria using a Fully Automated Urine Particle Analyzer UF-5000. The results showed that UF-5000 counts fastidious bacteria in urine without the need for culture using measurement principles based on flow cytometry.

Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal

BACKGROUND

The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese.

METHODS

Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR.

RESULTS

In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554).

CONCLUSIONS

Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.

Unveiling the role of ferrous ion in driving microalgae granulation from salt-tolerant strains for mariculture wastewater treatment

Development of microalgal-bacterial granular sludge (MBGS) from saline-adapted microalgae is a promising approach for efficient mariculture wastewater treatment, whereas the elusive mechanisms governing granulation have impeded its widespread adoption. In this study, spherical and regular MBGS were successfully developed from mixed culture of pure Spirulina platensis and Chlorella sp. GY-H4 at 10 mg/L Fe2+ concentration. The addition of Fe2+ was proven to induce the formation of Fe-precipitates which served as nucleation sites for microbial attachment and granulation initiation. Additionally, Fe2+ increased the prevalence of exopolysaccharide-producing cyanobacteria, i.e. Synechocystis and Leptolyngbya, facilitating microbial cell adhesion. Furthermore, it stimulated the secretion of extracellular proteins (particularly tryptophan and aromatic proteins), which acted as structural backbone for the development of spherical granule form microalgal flocs. Lastly, it fostered the accumulation of exogenous heterotrophic functional genera, resulting in the efficient removal of DOC (98 %), PO43--P (98 %) and NH4+-N (87 %). Nevertheless, inadequate Fe2+ hindered microalgal floc transformation into granules, excessive Fe2+ expanded the anaerobic zone within the granules, almost halved protein content in the TB-EPS, and inhibited the functional genes expression, ultimately leading to an irregular granular morphology and diminished nutrient removal. This research provides valuable insights into the mechanisms by which Fe2+ promotes the granulation of salt-tolerant microalgae, offering guidance for the establishment and stable operation of MBGS systems in mariculture wastewater treatment.

Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Isolation, identification and characterisation of Pseudomonas koreensis CM-01 isolated from diseased Malaysian mahseer (Tor tambroides)

Pseudomonas species are one of the most threatening fish pathogens which reside a wide range of environments. In this study, the dominant bacteria were isolated from diseased Malaysian mahseer (Tor tambroides) and tentatively named CM-01. It was identified as Pseudomonas koreensis based on its biochemical, morphological, genetic and physiological information. Its pathogenicity was found to be correlated with twelve virulence genes identified including iron uptake, protease, acylhomoserine lactone synthase gacS/gacA component regulation system, type IV secretion system, hydrogen cyanide production, exolysin, alginate biosynthesis, flagella and pili. The median lethal dose (LD50) for the CM-01 isolate on Malaysian mahseer was documented at 5.01 × 107 CFU/mL. The experimental infection revealed that CM-01 led to significant histological lesions in the fish, ultimately resulting in death. These lesions comprise necrosis, tissue thickening and aggregation. Drug sensitivity tests had shown its susceptibility to beta-lactam combination agents and further suggest its drug of choice. Its growing features had shown its growth at optimal temperature and pH. To the best of our knowledge, this is the first report of P. koreensis linked to diseased T. tambroides. STATEMENT OF RELEVANCE: In this research, a novel strain of Pseudomonas koreensis, CM-01 was isolated from diseased T. tambroides for the first time. The antimicrobial susceptibility, pathogenicity, virulence genes and growth characteristics of CM-01 were studied. These findings established a scientific foundation for the recognition of P. koreensis and the management of fish infections caused by this pathogen.

Why is HSO5- so effective against bacteria? Insights into the mechanisms of Escherichia coli disinfection by unactivated peroxymonosulfate

This study examined the antimicrobial efficacy of peroxymonosulfate (PMS) against bacteria, using Escherichia coli (E. coli) as a model organism. Our investigation delineates the complex mechanisms exerted by unactivated PMS. Thus, an initial redox reaction between PMS and the target biomolecules of bacteria generates SO4•- as the pivotal reactive species for bacterial inactivation; to a lesser extent, •OH, 1O2, or O2•- may also participate. Damage generated during oxidation was identified using an array of biochemical techniques. Specifically, redox processes are promoted by PMS and SO4•- targets and disrupt various components of bacterial cells, predominantly causing extracellular damage as well as intracellular lesions. Among these, external events are the key to cell death. Finally, by employing gene knockout mutants, we uncovered the role of specific gene responses in the intracellular damage induced by radical pathways. The findings of this study not only expand the understanding of PMS-mediated bacterial inactivation but also explain the ten-fold higher effectiveness of PMS than that reported for H2O2. Hence, we provide clear evidence that unactivated PMS solutions generate SO4•- in the presence of bacteria, and consequently, should be considered an effective disinfection method.

Efficacy of exopolysaccharide in dye-laden wastewater treatment: A comprehensive review

The discharge of dye-laden wastewater into the water streams causes severe water and soil pollution, which poses a global threat to aquatic ecosystems and humans. A diverse array of microorganisms such as bacteria, fungi, and algae produce exopolysaccharides (EPS) of different compositions and exhibit great bioflocculation potency to sustainably eradicate dyes from water bodies. Nanomodified chemical composites of EPS enable their recyclability during dye-laden wastewater treatment. Nevertheless, the selection of potent EPS-producing strains and physiological parameters of microbial growth and the remediation process could influence the removal efficiency of EPS. This review will intrinsically discuss the fundamental importance of EPS from diverse microbial origins and their nanomodified chemical composites, the mechanisms in EPS-mediated bioremediation of dyes, and the parametric influences on EPS-mediated dye removal through sorption/bioflocculation. This review will pave the way for designing and adopting futuristic green and sustainable EPS-based bioremediation strategies for dye-laden wastewater in situ and ex situ.

Fractional order model of MRSA bacterial infection with real data fitting: Computational Analysis and Modeling

Bacterial infections in the health-care sector and social environments have been linked to the Methicillin-Resistant Staphylococcus aureus (MRSA) infection, a type of bacteria that has remained an international health risk since the 1960s. From mild colonization to a deadly invasive disease with an elevated mortality rate, the illness can present in many different forms. A fractional-order dynamic model of MRSA infection developed using real data for computational and modeling analysis on the north side of Cyprus is presented in this paper. Initially, we tested that the suggested model had a positively invariant region, bounded solutions, and uniqueness for the biological feasibility of the model. We study the equilibria of the model and assess the expression for the most significant threshold parameter, called the basic reproduction number (ℛ0). The reproductive number's parameters are also subjected to sensitivity analysis through mathematical methods and simulations. Additionally, utilizing the power law kernel and the fixed-point approach, the existence, uniqueness, and generalized Ulam-Hyers-Rassias stability are presented. Chaos Control was used to regulate the linear responses approach to bring the system to stabilize according to its points of equilibrium, taking into account a fractional-order system with a managed design where solutions are bound in the feasible domain. Finally, numerical simulations demonstrating the effects of different parameters on MRSA infection are used to investigate the impact of the fractional operator on the generalized form of the power law kernel through a two-step Newton polynomial method. The impact of fractional orders is emphasized in the study so that the numerical solutions support the importance of these orders on MRSA infection. With the application of fractional order, the significance of cognizant antibiotic usage for MRSA infection is verified.