Bacterial Phenotypes Research Articles

Molecular and microbiological methods for the identification of nonreplicating Mycobacterium tuberculosis.

Chronic tuberculosis (TB) disease, which requires months-long chemotherapy with multiple antibiotics, is defined by diverse pathological manifestations and bacterial phenotypes. Targeting drug-tolerant bacteria in the host is critical to achieving a faster and durable cure for TB. In order to facilitate this field of research, we need to consider the physiology of persistent MTB during infection, which is often associated with the nonreplicating (NR) state. However, the traditional approach to quantifying bacterial burden through colony enumeration alone only informs on the abundance of live bacilli at the time of sampling, and provides an incomplete picture of the replicative state of the pathogen and the extent to which bacterial replication is balanced by ongoing cell death. Modern approaches to profiling bacterial replication status provide a better understanding of inter- and intra-population dynamics under different culture conditions and in distinct host microenvironments. While some methods use molecular markers of DNA replication and cell division, other approaches take advantage of advances in the field of microfluidics and live-cell microscopy. Considerable effort has been made over the past few decades to develop preclinical in vivo models of TB infection and some are recognized for more closely recapitulating clinical disease pathology than others. Unique lesion compartments presenting different environmental conditions produce significant heterogeneity between Mycobacterium tuberculosis populations within the host. While cellular lesion compartments appear to be more permissive of ongoing bacterial replication, caseous foci are associated with the maintenance of M. tuberculosis in a state of static equilibrium. The accurate identification of nonreplicators and where they hide within the host have significant implications for the way novel chemotherapeutic agents and regimens are designed for persistent infections.

Association between Turbot (Scophthalmus maximus) Fish Phenotype and the Post-Larval Bacteriome.

Over the past decade, an increasing number of studies have emphasized the importance of the host microbiome in influencing organismal health and development. Aligned with this understanding, our study aimed to investigate the potential association between the turbot (Scophthalmus maximus) phenotypic traits and the post-larval bacteriome. Turbot post-larvae were sampled from twenty randomly selected production cycles thirty days after hatching (DAH) across multiple post-larval production batches over a three-month period (April to June). Fish were selectively sampled based on five phenotypic traits, namely, normal, large, small, malformed, and depigmented. Our results showed that small-sized post-larvae had significantly higher bacterial phylogenetic diversity in their bacterial communities than all other phenotypes. A more in-depth compositional analysis also revealed specific associations between certain bacterial taxa and fish phenotypes. For example, the genera Aliivibrio and Sulfitobacter were enriched in small-sized post-larvae, while the family Micrococcaceae were predominantly found in larger post-larvae. Furthermore, genus Exiguobacterium was linked to depigmented larvae, and genus Pantoea was more prevalent in normal post-larvae. These observations underscore the importance of further research to understand the roles of these bacterial taxa in larval growth and phenotypic differentiation. Such insights could contribute to developing microbiome modulation strategies, which may enhance turbot post-larval health and quality and improve larviculture production.

Does higher ratio of wheat straw addition decrease PAHs degradation in PAHs-contaminated paddy soils and PAHs concentrations in rice?

There are considerable studies focusing on impacts of straw returning on PAHs degradation and bioavailability in PAHs-contaminated upland soils, while similar research in paddy soils is limited. Incubation experiments and pot trials were conducted to study effects of straw returning on PAHs degradation in paddy soils and PAHs accumulation in rice, respectively. There are threshold effects of straw returning on PAHs degradation in PAHs-contaminated paddy soils. The inflection point of PAHs degrading was recorded under 0.8 % wheat straw treatment (conventional (CS) and pretreated wheat straw (PS)), which increased PAHs degradation by 18.13–32.36 %. The lowest PAHs concentrations in rice were recorded under 1 % straw (CS and PS) treatment, which was attributed to the highest PAHs degradation in rhizosphere soils. Compared to CS treatment, PS treatment significantly (p < 0.05) increased PAHs degradation by 7.93–10.28 % and PAHs concentrations in rice by 12.38–45.87 % due to that increasing dissolved organic carbon (DOC) enhanced PAHs concentrations in porewater of rhizosphere soils. Higher diversity enhanced the metabolic pathways and function genes to degrade PAHs by improving bacterial phenotypes and biochemical processes under 1 % wheat straw and PS treatment. The present study firstly demonstrated that the effects of straw returning on PAHs degradation in PAHs-contaminated paddy soils and PAHs concentrations in rice depended on amount and methods of straw returning.

Emergence of extensively drug-resistant hypervirulent Acinetobacter baumannii isolated from patients with bacteremia: bacterial phenotype and virulence analysis

ObjectivesIndividuals infected with extensively drug-resistant (XDR) Acinetobacter baumannii are difficult to cure and have a high mortality rate. In this study, we compared the genomic and phenotypic differences between XDR and non-multidrug-resistant (MDR) A. baumannii and further characterized hypervirulent XDR A. baumannii. MethodsA total of 1,403 Acinetobacter isolates were collected from patients with bacteremia between 1997 and 2015. Antimicrobial susceptibility test was performed to categorize isolates into non-MDR, MDR, and XDR groups. The presence of selected virulence-associated genes was determined by PCR. Bacterial phenotypes, including iron acquisition, biofilm formation, capsule production, and virulence to larvae and mice, were determined. ResultsMultilocus sequence types revealed the high prevalence of ST2 (81.6%) and ST129 (18.4%) among 49 XDR isolates and sequence types of 18 non-MDR isolates were more diverse. Virulence-associated phenotypic assays showed that XDR isolates had higher iron acquisition ability and capsule production and higher virulence to Galleria mellonella larvae. However, their biofilm formation ability was lower compared to that of non-MDR isolates. XDR isolates contained more virulence genes, tonB, hemO, abaI, and ptk, while non-MDR isolates contained more pld and ompA. Twenty-one XDR isolates caused <20% larvae survival rate after 7 days post-infection were defined as hypervirulent XDR isolates. Among them, isolates 1677 (ST129) and 929-1 (ST2) also caused the death of all infected mice within two days. ConclusionSome subpopulations of highly drug-resistant ST2 also exhibit high virulence. Therefore, it is of utmost importance to continue monitoring the spread of hypervirulent XDR A. baumannii isolates.

Fuel fumes and foliage: the fate of speciated gasoline VOCs during phytoremediation and their impact on the bacterial phenotype

The capacity of indoor plants including green walls to capture, deposit and remediate individual volatile organic compounds (VOCs) has been well documented. However, in realistic settings, plant systems are exposed to a complex mixture of VOCs from highly varied various emission sources. Gasoline vapour is one of the major sources of these emissions, containing high concentrations of the carcinogens benzene, toluene, ethylbenzene and xylene (BTEX). Using both solid phase micro extraction (SPME) and quick, easy, cheap, effective, rugged and safe (QuEChERS) sampling techniques, we assessed the dynamics of individual speciated gasoline VOC phytoremediation from the air and uptake within green wall plant species and growth substrates within a small passive green wall system, along with quantifying the phenotypic changes within the plant-associated bacterial communities resulting from gasoline exposure. Over 8 hours the green wall system achieved 100% removal of atmospheric benzene, 1,2,3-trimethyl, eicosane and hexadecane, benzene 1,3-diethyl-; 1,3,5 cycloheptatriene,7- ethyl and carbonic acid eicosyl vinyl ester. All plant species tested demonstrated the accumulation 45 petrochemical VOCs (pVOCs) with Spathiphyllum wallisii successfully accumulating the majority of pVOC functional groups after 24 h of gasoline exposure. Within the plants phyllospheric bacterial communities, changes in both cellular complexity and granularity appeared to increase as a result of gasoline exposure, while cell size diminished. This work provides novel findings on the VOC removal processes of botanical systems for realistic and highly toxic VOC profiles.

Composting of Cow-Dung-Amended Soil by the Dung Beetle Catharsius molossus L. Improves Bacterial Ecological Functions Related to Nitrogen Mineralization and Human and Plant Pathogenesis

The Asian dung beetle (Catharsius molossus L.; Coleoptera: Scarabeidae) has been shown to positively affect soil bacterial diversity and the agronomic features of crop plants. In this study, we used bioinformatic tools to investigate the differences in bacterial functional phenotypes and ecological functions between control soil, cow dung-amended soil (CD), and cow dung-amended soil composted by dung beetles (DB). The soil bacterial metagenomes were sequenced and analyzed with the bioinformatic packages BugBase, PICRUSt2, Tax4Fun, and FAPROTAX to evaluate the effects of dung beetle-mediated composting on bacterial functions such as human and plant pathogenicity, trophic strategies, and soil nutrient transformation. BugBase proved useful for the determination of differences in major functional phenotypes, whereas FAPROTAX was effective at identifying differences in bacterial ecological functions between the treatments. Both tools suggested a relative decrease in human pathogens in the DB soil. This was corroborated by the pairwise comparison of abundances in bacterial species, which showed a significant reduction in the abundance of the broad-host-range pathogen Pseudomonas aeruginosa in the DB soil. In addition, FAPROTAX suggested a decrease in plant pathogens and an increase in chitinolytic bacteria, meaning that the DB treatment might be beneficial to the plant-growth-promoting bacteria involved in biological control. Finally, FAPROTAX revealed an array of ecological functions related to trophic strategies and macro- and micronutrient metabolism. According to these results, the activity of C. molossus beetles enhanced methanotrophy, ammonification, nitrification, sulfate reduction, and manganese oxidation, whereas iron respiration was decreased in the DB-treated soil. Our results represent a collection of general insights into the effects of C. molossus beetles on soil bacterial functions, which also reflect on the nutrient composition of dung beetle-composted soil.

Enhanced Nitric Oxide Delivery Through Self-Assembling Nanoparticles for Eradicating Gram-Negative Bacteria.

In the current battle against antibiotic resistance, the resilience of Gram-negative bacteria against traditional antibiotics is due not only to their protective outer membranes but also to mechanisms like efflux pumps and enzymatic degradation of drugs, underscores the urgent need for innovative antimicrobial tactics. Herein, this study presents an innovative method involving the synthesis of three furoxan derivatives engineered to self-assemble into nitric oxide (NO) donor nanoparticles (FuNPs). These FuNPs, notably supplied together with polymyxin B (PMB), achieve markedly enhanced bactericidal efficacy against a wide spectrum of bacterial phenotypes at considerably lower NO concentrations (0.1-2.8µgmL-1), which is at least ten times lower than the reported data for NO donors (≥200µgmL-1). The bactericidal mechanism is elucidated using confocal, scanning, and transmission electron microscopy techniques. Neutron reflectometry confirms that FuNPs initiate membrane disruption by specifically engaging with the polysaccharides on bacterial surfaces, causing structural perturbations. Subsequently, PMB binds to lipid A on the outer membrane, enhancing permeability and resulting in a synergistic bactericidal action with FuNPs. This pioneering strategy underscores the utility of self-assembly in NO delivery as a groundbreaking paradigm to circumvent traditional antibiotic resistance barriers, marking a significant leap forward in the development of next-generation antimicrobial agents.

Methicillin resistant Staphylococcus aureus mazEF expression promotes infections by influencing cellular growth, antibiotic sensitivity, and formation of biofilms

Staphylococcus aureus infections are hard to treat due to the emergence of antibiotic resistant strains, as well as their ability to form biofilms. The MazEF toxin–antitoxin system is thought play a role in bacterial biofilm phenotype as well as antibiotic resistance. In S. aureus, the physiologic function of the mazEF gene in the disease transition from acute to chronic infection is not well understood. In methicillin resistant S. aureus (MRSA), loss of mazF expression results in loss of resistance to first generation cephalosporins. mazF::tn displayed sensitivity while the isogenic wild type (WT) remained resistant. mazF::tn displayed significantly increased growth of biofilms on metal implants over 48 h compared to WT and the complemented transposon mutant. mazF::tn biofilms displayed significantly decreased antibiotic tolerance to vancomycin and cefazolin in comparison to WT and complement biofilms. Mice given mazF::tn in a sepsis model displayed less abscess burden and increased survival (100%) when treated with cefazolin compared to WT bacteremia treated with cefazolin (20%). mazF::tn periprosthetic joint infections displayed increased biofilm burden at acute time points and decreased biofilm burden at chronic time points. Our data suggests MazEF in MRSA is responsible for controlling growth of biofilms, antibiotic tolerance, and influence chronic infections in vivo.

Depth-dependent responses of soil bacterial communities to salinity in an arid region

Soil salinization adversely affects soil fertility and plant growth in arid region worldwide. However, as the drivers of nutrient cycling, the response of microbial communities to soil salinization is poorly understood. This study characterized bacterial communities in different soil layers along a natural salinity gradient in the Karayulgun River Basin, located northwest of the Taklimakan desert in China, using the 16S rRNA Miseq-sequencing technique. The results revealed a significant filtering effect of salinity on the bacterial community in the topsoil. Only the α-diversity (Shannon index) in the topsoil (0–10 cm) significantly decreased with increasing salinity levels, and community dissimilarity in the topsoil was enhanced with increasing salinity, while there was no significant relationship in the subsoil. BugBase predictions revealed that aerobic, facultatively anaerobic, gram-positive, and stress-tolerant bacterial phenotypes in the topsoil was negatively related to salinity. The average degree and number of modules of the bacterial co-occurrence network in the topsoil were lower under higher salinity levels, which contrasted with the trends in the subsoil, suggesting an unstable bacterial network in the topsoil caused by higher salinity. The average path length among bacterial species increased in both soil layers under high salinity conditions. Plant diversity and available nitrogen were the main drivers affecting community composition in the topsoil, while available potassium largely shaped community composition in the subsoil. This study provides solid evidence that bacterial communities adapt to salinity through the adjustment of microbial composition based on soil depth. This information will contribute to the sustainable management of drylands and improved predictions and responses to changes in ecosystems caused by climate change.

Emergence of heteroresistance to carbapenems in Gram-negative clinical isolates from two Egyptian hospitals

BackgroundAntimicrobial resistance is a global concern, linking bacterial genotype and phenotype. However, variability in antibiotic susceptibility within bacterial populations can lead to misclassification. Heteroresistance exemplifies this, where isolates have subpopulations less susceptible than the main population. This study explores heteroresistance in Gram-negative bacteria, distinguishing between carbapenem-sensitive isolates and stable heteroresistant isolates (SHIs).MethodsA total of 151 Gram-negative clinical isolates including Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii and Proteus mirabilis from various sources were included. Heteroresistant isolates and their stability were detected by disc-diffusion technique while genotypic analysis was carried out by PCR and efflux activity was assessed by ethidium bromide (EtBr)-agar cartwheel method.ResultsA total of 51 heteroresistant subpopulations were detected, producing 16 SHIs upon stability-detection. Amplified resistance genes and EtBr-agar cartwheel method showed a significant difference between resistant subpopulations and their corresponding-sensitive main populations.ConclusionGenotypic analysis confirmed that genetic mutation can lead to resistance development although the main populations were sensitive, thereby leading to treatment failure. This is a neglected issue which should be highly considered for better treatment outcomes.

Co-occurrence of ST412 Klebsiella pneumoniae isolates with hypermucoviscous and non-mucoviscous phenotypes in a short-term hospitalized patient.

K. pneumoniae with a hypermucoviscosity (HMV) phenotype is a community-acquired pathogen that is associated with increased invasiveness and pathogenicity, and underlying diseases are the most common comorbid risk factors inducing metastatic complications. HMV was earlier attributed to the overproduction of capsular polysaccharide, and more data point to the possibility of several causes contributing to this bacterial phenotype. Here, we describe a unique event in which the same clonal population showed both HMV and non-HMV characteristics. Studies have demonstrated that this process is influenced by mutational processes and genes related to transport and central metabolism. These findings provide fresh insight into the mechanisms behind co-occurrence of HMV and non-HMV phenotypes in monoclonal populations as well as potentially being critical in developing strategies to control the further spread of HMV K. pneumoniae.

Biomarker defined infective and inflammatory asthma exacerbation phenotypes in hospitalized adults: clinical impact and phenotype stability at recurrent exacerbation

Objective Acute exacerbations (AEs) of asthma are heterogeneous in terms of triggers, outcomes, and treatment response. This study investigated biomarker defined infective and inflammatory AE phenotypes in hospitalized adult asthma patients, and their impact on clinical outcomes and phenotype stability at AE recurrence. Method Patients with asthma admitted with an AE between January 2010 and December 2011 with a 3-year follow-up were retrospectively studied. AEs were categorized into infective (CRP >10 mg/L) vs non-infective, eosinophilic (blood eosinophils ≥ 0.2 × 109 cells/L) vs non-eosinophilic, and viral (CRP >10 to <40 mg/L) vs bacterial (CRP ≥40 mg/L) phenotypes. Clinical impact of the index AE, the risk and time to a second AE and AE phenotype stability were analyzed using Kaplan-Meier survival curves and McNamar’s test. Result 294 asthma patients were included: 47% had infective AE with a longer length of stay than non-infective AE (2.0 vs. 1.0 days, p = 0.01). The proportion of patients with eosinophilic AEs was evenly distributed across infective and non-infective AE (40% vs. 46%), although more patients with viral had eosinophilia than bacterial AE (46% vs. 26%). During follow-up, 18% had recurrent AE; with a higher risk in viral AE than bacterial AE (25% vs. 8%, p = 0.02). Both inflammatory and infective AE phenotype were stable at recurrent AE. Conclusion AE phenotyping in hospitalized asthma patients, based on CRP and blood eosinophils, revealed prolonged hospital stay in infective AEs and a higher risk of recurrent AE requiring hospitalization in viral versus bacterial AEs. Moreover, infective, and inflammatory AE phenotypes were rather stable at recurrent AE. Our results suggest a role for biomarker guided phenotyping of AEs of asthma.

Integrating Multiple Bacterial Phenotypes and Bayesian Network for Analyzing Health Risks of Pathogens in Plastisphere.

Plastic pollution represents a critical threat to soil ecosystems and even humans, as plastics can serve as a habitat for breeding and refuging pathogenic microorganisms against stresses. However, evaluating the health risk of plastispheres is difficult due to the lack of risk factors and quantification model. Here, DNA sequencing, single-cell Raman-D2O labeling, and transformation assay were used to quantify key risk factors of plastisphere, including pathogen abundance, phenotypic resistance to various stresses (antibiotic and pesticide), and ability to acquire antibiotic resistance genes. A Bayesian network model was newly introduced to integrate these three factors and infer their causal relationships. Using this model, the risk of pathogen in the plastisphere is found to be nearly 3 magnitudes higher than that in free-living state. Furthermore, this model exhibits robustness for risk prediction, even in the absence of one factor. Our framework offers a novel and practical approach to assessing the health risk of plastispheres, contributing to the management of plastic-related threats to human health.

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes.

Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of P. aeruginosa clinical isolates. To better understand the metabolic repertoire of P. aeruginosa in infection, we deeply profiled a representative set from a library of 971 clinical P. aeruginosa isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multilocus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective P. aeruginosa pangenome metabolic repertoire. Characterizing this rich set of clinical P. aeruginosa isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.

RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae.

Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.

Disrupting quorum sensing as a strategy to inhibit bacterial virulence in human, animal, and plant pathogens.

The development of sustainable alternatives to conventional antimicrobials is needed to address bacterial virulence while avoiding selecting resistant strains in a variety of fields, including human, animal, and plant health. Quorum sensing (QS), a bacterial communication system involved in noxious bacterial phenotypes such as virulence, motility, and biofilm formation, is of utmost interest. In this study, we harnessed the potential of the lactonase SsoPox to disrupt QS of human, fish, and plant pathogens. Lactonase treatment significantly alters phenotypes including biofilm formation, motility, and infection capacity. In plant pathogens, SsoPox decreased the production of plant cell wall degrading enzymes in Pectobacterium carotovorum and reduced the maceration of onions infected by Burkholderia glumae. In human pathogens, lactonase treatment significantly reduced biofilm formation in Acinetobacter baumannii, Burkholderia cepacia, and Pseudomonas aeruginosa, with the cytotoxicity of the latter being reduced by SsoPox treatment. In fish pathogens, lactonase treatment inhibited biofilm formation and bioluminescence in Vibrio harveyi and affected QS regulation in Aeromonas salmonicida. QS inhibition can thus be used to largely impact the virulence of bacterial pathogens and would constitute a global and sustainable approach for public, crop, and livestock health in line with the expectations of the One Health initiative.

Growing a Cystic Fibrosis-Relevant Polymicrobial Biofilm to Probe Community Phenotypes.

Most in vitro models lack the capacity to fully probe bacterial phenotypes emerging from the complex interactions observed in real-life environments. This is particularly true in the context of hard-to-treat, chronic, and polymicrobial biofilm-based infections detected in the airways of individuals living with cystic fibrosis (CF), a multiorgan genetic disease. While multiple microbiome studies have defined the microbial compositions detected in the airway of people with CF (pwCF), no in vitro models thus far have fully integrated critical CF-relevant lung features. Therefore, a significant knowledge gap exists in the capacity to investigate the mechanisms driving the pathogenesis of mixed species CF lung infections. Here, we describe a recently developed four-species microbial community model, including Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica grown in CF-like conditions. Through the utilization of this system, clinically relevant phenotypes such as antimicrobialrecalcitrance of several pathogens were observed and explored at the molecular level. The usefulness of this in vitro model resides in its standardized workflow that can facilitate the study of interspecies interactions in the context of chronic CF lung infections.

Impact of antibiotic therapy on cutaneous and gut microbiota in Rana dybowskii amphibians: Insights and implications

Antibiotics are key in combating bacterial infections and halting disease spread, yet their effects on amphibian gut microbiomes remain poorly understood. Amphibian survival depends on their skin microbiota. Drugs used to treat amphibians may affect gut microbiota but has yet to have unexplored impacts on skin microbiota. We used Illumina sequencing to analyze the cutaneous (C) and gut (G) microbiota of healthy (H) frogs and diseased (D) frogs treated with antibiotics and evaluate their functional characteristics. The result showed that antibiotics lowered gut microbiota alpha diversity but not skin microbiota. Bray-Curtis and UniFrac measures demonstrate the significant variations in skin and gut microbiota between healthy and antibiotic-treated frogs. Bacteroidota, Firmicutes, and Proteobacteria predominated in DC and HC; Proteobacteria, Firmicutes, and Bacteroidota dominated DG and HG. Linear discriminant analysis and effect size (LEfSe) analysis identified specific bacterial taxa enriched in antibiotic-treated versus healthy frogs. Maximum likelihood (ML) analysis revealed close evolutionary relationships among certain bacterial taxa. Functional predictions indicated significant differences in metabolic pathways between groups, and BugBase analysis showed variations in bacterial phenotypes, suggesting altered microbial functions following antibiotic treatment. Antibiotic treatment in frogs significantly altered gut microbiota diversity and impacts functional pathways in both gut and skin microbiota without affecting skin microbiota alpha diversity. Antibiotics' complex effects on frog microbiota showed R. dybowskii's delicate balance between therapeutic advantages and ecological changes, which might affect conservation and health initiatives.

Ensilage using Leuconostoc lactis and Weissella confusa reduces microbial risk and enhances hygienic quality of whole-crop corn

This study combined applied PICRUSt2 and BugBase tools to evaluate the effects of these two strains on the fermentation characteristics, microbial community, potential microbial risk and hygienic quality of whole-crop corn (WCC) silage. Fresh WCC harvested at the dough stage was ensiled with distilled water (CON), Leuconostoc lactis (LS) and Weissella confusa (WA) for 2, 4, 8, 15 and 30 days. After ensiling, all WCC silages presented desirable fermentation with high lactic acid and Lactobacillus proportions, low pH and ammonia nitrogen levels and absent butyric acid. Ensiling decreased the complexity of bacterial co-occurrence networks, and the Lc. lactis and W. confusa inoculation further decreased the complexity. The inoculation of W. confusa suppressed the most pathogenic pathways and related modules associated with zoonosis. In bacterial phenotype predicted analysis, although CON had lower proportions of ‘Potentially pathogenic’ than fresh material, this undesirable phenotype declined to negligible levels via LS and WA inoculation. Even for well-fermented WCC silages, the risk of pathogens remained after 30 days of ensiling. Therefore, WA could be developed as a promising fast start-up inoculant for reducing pathogenic contamination and improving hygienic quality of silage.Graphical

Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform.

Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.