Estimation of bacterial growth rates from turbidimetric and viable count data

An online monitoring device for measuring the concentration of four types of in-situ microorganisms by using the near-infrared band

Using optical density at 600 nm (OD600) to measure the microbial concentration is a popular approach due to its advantages like quick response and non-destructive. However, the OD600 measurement might be affected by the metabolic pigment, and it would become invalid when the solution dilution is insufficient. To overcome these issues, we proposed to adopt a more robust wavelength at 890 nm to quantify the attenuation of transmission light. After selecting this light source, we designed the light path and the circuit of the online monitoring device. Meanwhile, the random forest algorithm was introduced for temperature compensation and improving the stability of the device. This device was verified by monitoring the microbial concentration of four strains (Yeast, Bacillus, Arthrobacter, and Escherichia coli). The experimental result suggested that the mean absolute percentage error reached 4.11 %, 4.28 %, 4.49 %, and 4.53 % respectively, which is helpful to improve the accuracy of microbial concentration measurement.

Uracil hydrazones: design, synthesis, antimicrobial activities, and putative mode of action

BACKGROUND

Crop diseases caused by plant pathogenic fungi and bacteria have led to substantial losses in global food production. Chemical pesticides have been widely used as a primary means to mitigate these issues. Nevertheless, the persistent and excessive use of pesticides has resulted in the emergence of microbial resistance. Moreover, the improper application and excessive utilization of pesticides can contribute to environmental pollution and the persistence of pesticide residues. Consequently, the development of novel and highly effective bactericides and fungicides to combat plant pathogens holds immense practical importance.

RESULTS

A series of uracil hydrazones IV-B was deliberately designed and evaluated for their antimicrobial efficacy. The results of bioassays indicated that most IV-B exhibited >80% inhibition against the fungal species Monilia fructigena and Sclerotium rolfsii, as well as the bacterial species Clavibacter michiganensis subsp. michiganensis, Xanthomonas oryzae pv. oryzae, and Ralstonia solanacearum, at 50 μg/mL in vitro. In vivo, IV-B20 showed 89.9% of curative and 71.8% of protective activities against C. michiganensis subsp. michiganensis at 100 μg/mL superior to thiodiazole copper and copper hydroxide. IV-B20 also showed excellent protective activity against M. fructigena (96.3% at 200 μg/mL) and S. rolfsii (80.4% at 1000 μg/mL), which were greater than chlorothalonil and equivalent to thifluzamide. Mechanistic studies revealed that IV-B20 induced oxidative damage in pathogenic bacteria and promoted the leakage of cellular contents.

CONCLUSION

This study suggests that IV-B20 with uracil hydrazone skeleton has great potential as an antimicrobial candidate. These findings lay a foundation for practical application in agriculture. © 2023 Society of Chemical Industry.

A programmed surface on dental implants sequentially initiates bacteriostasis and osseointegration

Osteogenesis surrounding dental implants is initiated by a series of early physiological events, including the inflammatory response. However, the persistence of an anti-infection surface often results in compromised histocompatibility and osseointegration. Here, we presented a programmed surface containing both silver nanoparticles (AgNPs) and silver ions (Ag+) with a heterogeneous structure and time-dependent functionalities. The AgNPs were located at the surface of the heparin-chitosan polyelectrolyte coating (PEM), whereas Ag+ was distributed at both the surface and inside of the coating under optimized conditions (pH=4). The optimized coating (Ag-4) exhibited potent bactericidal activity at the early stage (12 and 24 h after inoculation) and a sustained antibacterial efficacy in the subsequent stage (one or two weeks), as it gradually depleted. Furthermore, compared to coatings with sustained high silver concentrations in bacteria-cell coculture experiments, the degradable Ag-4 coating demonstrated improved cytocompatibility, better cell viability, and morphology over time. At a later stage (within one month), the in vivo test revealed that Ag-4-coated titanium had superior histocompatibility and osteogenesis outcomes compared to bare titanium in a bacteria-exposed environment. The programmed surface of dental implants presented in this study offers innovative ideas for sequential antibacterial effects and osseointegration.

Biocontrol of Botrytis cinerea as Influenced by Grapevine Growth Stages and Environmental Conditions

The growth of four commercial biocontrol agents (BCAs: Bacillus amyloliquefaciens (BAD), Aureobasidium pullulans (APD), Metschnikowia fructicola (MFN), and Trichoderma atroviride (TAS)) was evaluated using turbidimetric assays on artificial substrates mimicking the chemical berry composition at four stages: pea-sized berries, veraison, softening, and ripe berries. The response of BCA growth differed among BCAs. Subsequently, the BCAs' population size was assessed after 1 to 13 days of incubation on the substrate mimicking ripe berries at 15 to 35 °C. The population size of BAD increased with temperatures, while that of MFN decreased; the population sizes of APD and TAS showed bell-shaped patterns with lower growth at 15 or 35 °C. Finally, the BCAs were applied to ripe berries and then incubated at 15 to 30 °C. After 1 to 13 days, the berries were inoculated with B. cinerea and incubated for 7 days, after which the BCA control efficacy was assessed. The highest control was observed at 25 °C for BAD and APD, at 15 to 20 °C for MFN, and at 25 to 30 °C for TAS. The results confirm that the plant substrates and temperature affect the population size of the BCA following application; temperature also affects the preventative efficacy of BCA against B. cinerea.

Strain-Level Discrimination of Bacteria by Liquid Chromatography and Paper Spray Ion Mobility Mass Spectrometry

Determining bacterial identity at the strain level is critical for public health to enable proper medical treatments and reduce antibiotic resistance. Herein, we used liquid chromatography, ion mobility, and tandem MS (LC-IM-MS/MS) to distinguish Escherichia coli (E. coli) strains. Numerical multivariate statistics (principal component analysis, followed by linear discriminant analysis) showed the capability of this method to perform strain-level discrimination with prediction rates of 96.1% and 100% utilizing the negative and positive ion information, respectively. The tandem MS and LC separation proved effective in discriminating diagnostic lipid isomers in the negative mode, while IM separation was more effective in resolving lipid conformational biomarkers in the positive ion mode. Because of the clinical importance of early detection for rapid medical intervention, a faster technique, paper spray (PS)-IM-MS/MS, was used to discriminate the E. coli strains. The achieved prediction rates of the analysis of E. coli strains by PS-IM-MS/MS were 62.5% and 73.5% in the negative and positive ion modes, respectively. The strategy of numerical data fusion of negative and positive ion data increased the classification rates of PS-IM-MS/MS to 80.5%. Lipid isomers and conformers were detected, which served as strain-indicating biomarkers. The two complementary multidimensional techniques revealed biochemical differences between the E. coli strains confirming the results obtained from comparative genomic analysis. Moreover, the results suggest that PS-IM-MS/MS is a rapid, highly selective, and sensitive method for discriminating bacterial strains in environmental and food samples.

Evaluation of the antibacterial activity of gallic acid anchored phthalocyanine-doped silica nanoparticles towards Escherichia coli and Staphylococcus aureus biofilms and planktonic cells

In this work, we have described the synthesis of phthalocyanine complexes Zn(II) tetrakis 4-(5-formylpyridin-2-yl)oxy) phthalocyanine (2), Zn(II) tetrakis-1-butyl-4-(2-(6- (tetra-phenoxy)pyridin-3-yl) vinyl)pyridin-1-ium phthalocyanine (3) and Zn(II) tetrakis 1-butyl-5-(2-(1-butylpyridin-1-ium-4-yl)vinyl)-2-(tetra-phenoxy)pyridin-1-ium phthalocyanine (4). The effect of a varying number of charges when the Pc complexes are alone or grafted in gallic acid (GA) tagged silica nanoparticles on photodynamic antimicrobial chemotherapy (PACT) is investigated toward Staphylococcus aureus (S.aureus) and Escherichia coli (E.coli) in both planktonic and biofilm forms. Complex 4, bearing a total of 8 cationic charges, displayed the highest activity with log CFU values of 8.60 and 6.42 against E.coli and S.aureus biofilms, respectively. The surface stability of E.coli and S.aureus biofilms in the presence of 4 and its conjugate was analysed using cyclic voltammetry. Scanning electron microscopy (SEM) and Raman spectra are also used to study the conformational and biochemical changes within biofilm upon subjecting them to PACT.

Selective Activity of an Anthocyanin-Rich, Purified Blueberry Extract upon Pathogenic and Probiotic Bacteria

Blueberry extracts have been widely recognized as possessing antimicrobial activity against several potential pathogens. However, the contextualization of the interaction of these extracts with beneficial bacteria (i.e., probiotics), particularly when considering the food applications of these products, may be of importance, not only because their presence is important in the regular gut microbiota, but also because they are important constituents of regular and functional foodstuffs. Therefore, the present work first sought to demonstrate the inhibitory effect of a blueberry extract upon four potential food pathogens and, after identifying the active concentrations, evaluated their impact upon the growth and metabolic activity (organic acid production and sugar consumption) of five potential probiotic microorganisms. Results showed that the extract, at a concentration that inhibited L. monocytogenes, B. cereus, E. coli and S. enteritidis (1000 μg mL^-1), had no inhibitory effect on the growth of the potential probiotic stains used. However, the results demonstrated, for the first time, that the extract had a significant impact on the metabolic activity of all probiotic strains, resulting in higher amounts of organic acid production (acetic, citric and lactic acids) and an earlier production of propionic acid.

Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains

Although closely related, bacterial strains from the same species show significant diversity in their growth and death dynamics. Yet, our understanding of the relationship between the kinetic parameters that dictate these dynamics is still lacking. Here, we measured the growth and death dynamics of 11 strains of Escherichia coli originating from different hosts and show that the growth patterns are clustered into three major classes with typical growth rates, maximal fold change, and death rates. To infer the underlying phenotypic parameters that govern the dynamics, we developed a phenomenological mathematical model that accounts not only for growth rate and its dependence on resource availability, but also for death rates and density-dependent growth inhibition. We show that density-dependent growth is essential for capturing the variability in growth dynamics between the strains. Indeed, the main parameter determining the dynamics is the typical density at which they slow down their growth, rather than the maximal growth rate or death rate. Moreover, we show that the phenotypic landscape resides within a two-dimensional plane spanned by resource utilization efficiency, death rate, and density-dependent growth inhibition. In this phenotypic plane, we identify three clusters that correspond to the growth pattern classes. Overall, our results reveal the tradeoffs between growth parameters that constrain bacterial adaptation.

Novel botanical active component derivatives containing carboxamide and 1,3,4-Thiadiazole thioether moieties: Design, synthesis, and inhibitory activity

In this study, using the botanical active components of carvacrol, thymol, guaiacol, and sesamol as the lead structures, 19 novel botanical active component derivatives containing carboxamide and 1,3,4-thiadiazole thioether moieties (5a−5s) were synthesized and structurally characterized by ¹H NMR, ¹³C NMR, and HRMS. The antibacterial bioassay results in vitro showed that compound 2-(2-methoxyphenoxy)-N-(5-(methylthio)-1,3,4-thiadiazol-2-yl)acetamide (5k) revealed excellent inhibitory activities against Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzicolaby (Xoc), with the median effective concentration (EC₅₀) values of 22 and 15 μg/ml, respectively, which were even better than those of thiodiazole copper and bismerthiazol. Meanwhile, all the target compounds revealed lower in vitro inhibitory effects on Mucor bainieri (M. bainieri), Mucor fragilis (M. fragilis), and Trichoderma atroviride (T. atroviride), than carbendazim.

Pyrido [1,2-a] Pyrimidinone Mesoionic Compounds Containing Vanillin Moiety: Design, Synthesis, Antibacterial Activity, and Mechanism

Xanthomonas oryzae pv. oryzicola (Xoo) is a plant pathogen responsible for rice bacterial blight disease that remains challenging for prevention and cure. To discover innovative and extremely potent antibacterial agents, vanillin moiety was introduced to develop a series of novel mesoionic derivatives. Compound 15 demonstrated excellent in vitro antibacterial activity against Xoo, with a 50% effective concentration value (EC₅₀) of 27.5 μg/mL, which was superior to that of the positive control agent thiodiazole copper (97.1 μg/mL) and comparable to that of compound "A11" (17.4 μg/mL). The greenhouse pot experiment also revealed that compound 15 had 38.5% curative and 36.8% protective efficacy against rice bacterial leaf blight in vivo at 100 μg/mL, which was higher than those of thiodiazole copper (31.2 and 32.6%, respectively) and compound "A11" (29.6 and 33.2%, respectively). Compound 15 enhanced the activities of related defense enzymes, increased chlorophyll content, and promoted the resistance of rice to bacterial infection by modulating the photosynthetic pathway. This study provides a basis for the subsequent structural modification and mechanism research of mesoionic derivatives.

Synthesis and Antibacterial Activities of 2-Oxo-N-phenylacetamide Derivatives Containing a Dissulfone Moiety Target on Clp

Rice bacterial blight and rice bacterial streak are two serious rice diseases and have caused great harm to the production of rice all over the world. To develop an efficient antibacterial agent with a novel target, a series of novel 2-oxo-N-phenylacetamide derivatives containing a dissulfone moiety were synthesized, and their antibacterial activities were evaluated. Among them, compound D₁₄ exhibited the best antibacterial activities, especially against Xoo and Xoc with EC₅₀ values of 0.63 and 0.79 mg/L, respectively, which were much better than the commercial control of bismerthiazol (BT) (76.59 and 83.35 mg/L, respectively) and thiodiazole copper (TC) (91.72 and 114.00 mg/L, respectively). Meanwhile, compound D₁₄ can interact with a CRP-like protein (Clp) of Pxo99^A and show strong binding activity with Xoo-Clp with a K_d value of 0.52 μM, which was far superior to the corresponding K_d values of BT (183.94 μM) and TC (222.58 μM). Treatment of D₁₄ and deletion of the clp gene could significantly reduce the expression of the clp gene and attenuate the virulence of pathogenic bacteria. These results indicated that compound D₁₄ could be used as a potential novel agricultural bactericide and Clp can be used as a target protein for the control of plant bacterial diseases. This work provided reliable support for developing novel antibacterial agents based on Clp as a target protein.

The Trace Gas Monitoring Method Based on Diode Laser Wavelength-Modulation Spectroscopy Technology for the Detection of Clinical Blood Infection

It is important to monitor and evaluate the growth of microorganisms in order to accurately judge the situation of blood microbial infection. In this paper, diode laser wavelength modulation spectroscopy (DLWMS) technology is used to design a set of low-cost, high sensitivity, fast dynamic responses and a non-invasive trace gas measurement system, which can quickly and accurately assess the concentration of carbon dioxide (CO2) produced by blood microbial reproduction. The measurement principle and spectral processing algorithm of DLWMS are introduced first. The automatic and rapid detection of CO2 is realized through a self-designed optical system. By using the system to detect blood infection, the accuracy of the technology was verified. Therefore, it also indicates that DLWMS CO2 monitoring is a highly sensitive, fast-response and non-invasive technology, which can accurately and quickly determine blood infection and meet the clinical application requirements of human septicemia, bacteremia and other diseases.

Synthesis and Bioactivities of Novel Galactoside Derivatives Containing 1,3,4-Thiadiazole Moiety

A series of novel galactoside derivatives containing 1,3,4-thiadiazole moiety were synthesized, and the structure of them was verified by spectroscopy of NMR and HRMS, and antifungal and antibacterial activities of them were screened. The results showed that the newly synthesized compounds had good antifungal activities. Among them, Ⅲ16, Ⅲ17, and Ⅲ19 exhibited satisfactory activities against Phytophthora infestans (P. infestans), with EC50 values of 5.87, 4.98, and 6.17 μg/ml, respectively, which were similar to those of dimethomorph (5.52 μg/ml). Meanwhile, the title compounds also possessed certain antibacterial activities.

Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely-related protists,however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists.

Active Metabolites From the Endophyte Paenibacillus polymyxa Y-1 of Dendrobium nobile for the Control of Rice Bacterial Diseases

Microbial bactericides have been a research hotspot in recent years. In order to find new microbial fungicides for preventing and treating rice bacterial diseases, Paenibacillus polymyxa Y-1 (P. polymyxa Y-1) was isolated from Dendrobium nobile in this study, and the optimal medium was selected by a single-factor experiment, and then eight metabolites were isolated from P. polymyxa Y-1 fermentation broth by bioactivity tracking separation. The bioassay results showed that 2,4-di-tert-butylphenol, N-acetyl-5-methoxytryptamine, and P-hydroxybenzoic acid have good antibacterial activity against Xanthomonas oryzae pv. Oryzicola (Xoo) and Xanthomonas oryzae pv. oryzae (Xoc), with 50% effective concentration values of 49.45 μg/ml, 64.22 μg/ml, and 16.32 μg/ml to Xoo, and 34.33 μg/ml, 71.17 μg/ml, and 15.58 μg/ml to Xoc, respectively, compared with zhongshengmycin (0.42 and 0.82 μg/ml, respectively) and bismerthiazol (85.64 and 92.49 μg/ml, respectively). In vivo experiments found that 2,4-di-tert-butylphenol (35.9 and 35.4%, respectively), N-acetyl-5-methoxytryptamine (42.9 and 36.7%, respectively), and P-hydroxybenzoic acid (40.6 and 36.8%, respectively) demonstrated excellent protective and curative activity against rice bacterial leaf blight, which were better than that of zhongshengmycin (38.4 and 34.4%, respectively). In addition, after 2,4-di-tert-butylphenol, N-acetyl-5-methoxytryptamine, and P-hydroxybenzoic acid acted on rice, SOD, POD, and CAD defense enzymes increased under the same condition. In conclusion, these results indicated that the activity and mechanism research of new microbial pesticides were helpful for the prevention and control of rice bacterial diseases.

Polymyxin B1 and E2 From Paenibacillus polymyxa Y-1 for Controlling Rice Bacterial Disease

To discover novel microbial pesticide for controlling rice bacterial disease, polymyxin B₁ and E₂ were firstly isolated from the supernatant of fermentation broth of Paenibacillus polymyxa Y-1 by bioactivity tracking separation. It is shown that polymyxin B₁ and E₂ had remarkable in vitro inhibitory activities to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) with the EC₅₀ values of 0.19 μg/ml and 0.21 μg/ml against Xoo, and 0.32 μg/ml and 0.41 μg/ml against Xoc, respectively, which were better than those of Zhongshengmycin (0.31 μg/ml and 0.73 μg/ml) and Bismerthiazol (77.48 μg/ml and 85.30 μg/ml). Polymyxins B₁ and E₂ had good protection and curative activities against rice bacterial leaf blight (BLB) and rice bacterial leaf streak (BLS) in vivo. The protection and curative activities of polymyxins B₁ (45.8 and 35.8%, respectively) and E₂ (41.2 and 37.0%, respectively) to BLB were superior to those of Zhongshengmycin (34.8 and 29.8%, respectively) and Bismerthiazol (38.0 and 33.5%, respectively). Meanwhile, the protection and curative activities of polymyxins B₁ (44.8 and 39.8%, respectively) and E₂ (42.9 and 39.9%, respectively) to BLS were also superior to those of Zhongshengmycin (39.7 and 32.0%, respectively) and Bismerthiazol (41.5 and 34.3%, respectively). Polymyxin B₁ exerted the anti-pesticide properties via destroying the cell integrity of Xoo, reducing its infectivity and enhancing rice resistance against pathogens through activating the phenylpropanoid biosynthesis pathway of rice. It is indicated that polymyxin B₁ and E₂ were potential microbial pesticides for controlling rice bacterial disease.

Synthesis and Bioactivity Evaluation of Novel Thiochroman-4-One Derivatives Incorporating Carboxamide and 1, 3, 4-Thiadiazole Thioether Moieties

A series of novel thiochroman-4-one derivatives incorporating carboxamide and 1, 3, 4-thiadiazole thioether moieties were synthesized. Bioassay results indicated that the EC50 values of compound 6-chloro-N-(5-(methylthio)-1, 3, 4-thiadiazol-2-yl)-4-oxothiochromane-2-carboxamide (5a) against Xanthomonas oryzae pv. Oryzae (Xoo) and Xanthomonas axonopodis pv. Citri (Xac) were 24 and 30 μg/mL, respectively, which were even better than those of bismerthiazol and thiadiazole copper. Meanwhile, compound 6-methyl-4-oxo-N-(5-(propylthio)-1, 3, 4-thiadiazol-2-yl)thiochromane-2-carboxamide (5m) showed a better antifungal activity against Botrytis cinerea (B. cinerea), with an inhibition rate of 69%, than carbendazim. As far as we know, this is the first report on the antibacterial and antifungal activities of this series of novel thiochroman-4-one derivatives incorporating carboxamide and 1, 3, 4-thiadiazole thioether moieties.

Hand-powered vacuum-driven microfluidic gradient generator for high-throughput antimicrobial susceptibility testing

The growth of bacterial resistance to antimicrobials is a serious problem attracting much attention nowadays. To prevent the misuse and abuse of antimicrobials, it is important to carry out antibiotic susceptibility testing (AST) before clinical use. However, conventional AST methods are relatively laborious and time-consuming (18-24 h). Here, we present a hand-powered vacuum-driven microfluidic (HVM) device, in which a syringe is used as the only vacuum source for rapid generating concentration gradient of antibiotics in different chambers. The HVM device can be preassembled with various amounts of antibiotics, lyophilized, and stored for ready-to-use. Bacterial samples can be loaded into the HVM device through a simple suction step. With the assistance of Alamar Blue, the AST assay and the minimum inhibitory concentration (MIC) of different antibiotics can be investigated by comparing the growth results of bacteria in different culture chambers. In addition, a parallel HVM device was proposed, in which eight AST assays can be performed simultaneously. The results of MIC of three commonly used antibiotics against E. coli K-12 in our HVM device were consistent with those obtained by traditional method while the detection time was shortened to less than 8 h. We believe that our platform is high-throughput, cost-efficient, easy to use, and suitable for POCT applications.

Trifluoromethylpyridine 1,3,4-Oxadiazole Derivatives: Emerging Scaffolds as Bacterial Agents

A new class of trifluoromethylpyridine 1,3,4-oxadiazole derivatives (6a-6v) was obtained, and their antibacterial activities were evaluated. Some of them exhibited good activity, particularly 6a, which had the highest in vitro activity against Ralstonia solanacearum (R. solanacearum) and Xanthomonas axonopodis pv. citri (Xac). The half-maximal effective concentrations (EC50) were 26.2 and 10.11 μg/mL, respectively, which were lower than those of commercial thiodiazole copper (97.2 and 35.3 μg/mL, respectively). Furthermore, 6q showed much higher activity against Xanthomonas oryzae pv. oryzae (Xoo) with an EC50 value of 7.2 μg/mL; this was superior to bismerthiazol (57.2 μg/mL). Collectively, our findings provide a foundation for the development of trifluoromethylpyridine 1,3,4-oxadiazole derivatives.

Microbial Characterization of Yellow Curing Process of Codfish

Yellow cured codfish has a typical yellow colour, distinctive taste, and low salt content due to its special curing process of the raw salted codfish involving several soaks in water of the raw salted codfish, alternated with drying steps. The purpose of this study was to assess the main functional groups of bacteria involved in this process and relate them with physicochemical properties of the product. A total of 28 codfish from Iceland were supplied by two local companies. Seven stages of the curing process were analyzed. From each of these seven stages, four fish samples were collected to carry out the microbial and physicochemical analyses (moisture, salt content, pH, total volatile basic nitrogen (TVB-N), and trimethylamine nitrogen (TMA-N)). Bacteria counts were performed using the MPN method and adequate culture media for aerobic, proteolytic, sulphite-reducing, biogenic amine, and trimethylamine-producing and ammonifying bacteria. Strains isolated from the highest dilutions with microbial growth were used to characterize the predominant bacteria. The results showed that total aerobic counts increased from 3.9 log MPN/g in raw salted codfish to 5.9 log MPN/g in the final. Proteolytic, ammonifying, and trimethylamine bacteria producers also increased to 8, 7.5, and 6.5 log MPN/g, respectively. The salt content decreases (from 17% until 8%) and moisture increases (53% until 67%) during the salted-raw-codfish soaking, favoring sulphite-reducing and biogenic amine-producing species, confirming that desalting enhances potential spoilers. The subsequent drying step benefits proteolytic, ammonifying, and trimethylamine-producing bacteria, with a corresponding non-protein-nitrogen content (TVB-N and TMA-N) increase. The dominant bacteria during yellow curing belong to the genera Staphylococcus, Psychrobacter, Pseudomonas, and Alcaligenes with a clear positive correlation between the content of Staphylococcus and Psychrobacter and TVB-N and TMA-N concentration. Staphylococcus spp. are the dominant bacteria in the steps where the product has a higher salt concentration; thus, it could be particularly useful as an indicator to control the industrially yellow curing process and could have an important role in the development of the final characteristics of this product.

Staphylococcus singaporensis sp. nov., a new member of the Staphylococcus aureus complex, isolated from human clinical specimens

Staphylococcus argenteus and Staphylococcus schweitzeri are the newest members of the Staphylococcus aureus complex. The number of clinical reports attributed to these new S. aureus complex members is limited. In a retrospective clinical laboratory study conducted over a 4-month period investigating the prevalence of S. argenteus and S. schweitzeri, a total of 43 isolates were selected. Phylogeny based on core-gene multilocus sequence typing (MLST) analysis confirmed that 37 were S. argenteus but a genetically distinct clade of six isolates was identified. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses further supported the classification of these six isolates as a separate species. When compared to S. aureus complex reference genomes, the ANI values were ≤94 % and the dDDH values were <53 %. Based on the seven-gene S. aureus MLST scheme, the six isolates belong to five novel allelic profiles (ST6105, ST6106, ST6107, ST6108 and ST109). Their clinical infection features were similar to S. aureus. Skin and soft tissue infections presented in four out of the six cases. Routine clinical diagnostic identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and biochemical profiling does not differentiate these new members from the rest of the complex. Genotypic analysis suggests that the six isolates belong to a novel species, Staphylococcus singaporensis sp. nov. with isolate SS21^T (=DSM 111408^T=NCTC14419^T) designated as the type strain.

A comprehensive review of image analysis methods for microorganism counting: from classical image processing to deep learning approaches

Microorganisms such as bacteria and fungi play essential roles in many application fields, like biotechnique, medical technique and industrial domain. Microorganism counting techniques are crucial in microorganism analysis, helping biologists and related researchers quantitatively analyze the microorganisms and calculate their characteristics, such as biomass concentration and biological activity. However, traditional microorganism manual counting methods, such as plate counting method, hemocytometry and turbidimetry, are time-consuming, subjective and need complex operations, which are difficult to be applied in large-scale applications. In order to improve this situation, image analysis is applied for microorganism counting since the 1980s, which consists of digital image processing, image segmentation, image classification and suchlike. Image analysis-based microorganism counting methods are efficient comparing with traditional plate counting methods. In this article, we have studied the development of microorganism counting methods using digital image analysis. Firstly, the microorganisms are grouped as bacteria and other microorganisms. Then, the related articles are summarized based on image segmentation methods. Each part of the article is reviewed by methodologies. Moreover, commonly used image processing methods for microorganism counting are summarized and analyzed to find common technological points. More than 144 papers are outlined in this article. In conclusion, this paper provides new ideas for the future development trend of microorganism counting, and provides systematic suggestions for implementing integrated microorganism counting systems in the future. Researchers in other fields can refer to the techniques analyzed in this paper.

Lemongrass and cinnamon oil nanoemulsions: Formulation and study of their physical stability and activity against Zygosaccharomyces bailii

The optimal conditions for elaborating oil/water nanoemulsions of lemongrass (LG), cinnamon bark (CB) and cinnamon leaves (CL) essential oils and their antimicrobial activity against Zygosaccharomyces bailii at pH 4.00 were studied. The effect of the emulsification methodology on the physical stability and antimicrobial activity of the nanoemulsions were also evaluated. Furthermore, the sensory impact of nanoemulsions added to an apple juice was tested. LG and CL nanoemulsions were elaborated by ultrasonication and CB nanoemulsion, by high-speed homogenization. They were stable for at least 120 days at 25 °C. They exhibited antimicrobial activity against Z. bailii being CB the most effective since it showed the smallest MIC value (156.3 mg/l), followed by LG (468.8 mg/l) and CL (1250.0 mg/l). A slight increase in growth rate was observed due to ultrasonication. An additive interaction in relation to the inhibitory effect between LG and CB nanoemulsions against Z. bailii was observed. While nanoemulsions obtained would be used as natural antimicrobial agents in food and beverage products, only LG nanoemulsion at MIC concentration diluted was acceptable in juice showing the sensory impact of essential oils on foods.

Fluorescent Protein Expression as a Proxy for Bacterial Fitness in a High-Throughput Assay

Bacterial growth is classically assessed by measuring the increases in optical density of pure cultures in shaken liquid media. Measuring growth using optical density has severe limitations when studying multistrain interactions, as it is not possible to measure the growth of individual strains within mixed cultures. Here, we demonstrated that constitutively expressed fluorescent proteins can be used to track the growth of individual strains in different liquid media. Fluorescence measurements were highly correlated with optical density measurements and cell counts. This allowed us to assess bacterial growth not only in pure cultures but also in mixed bacterial cultures and determine the impact of a competitor on a focal strain, thereby assessing relative fitness. Furthermore, we were able to track the growth of two different strains simultaneously by using fluorescent proteins with differential excitation and emission wavelengths. Bacterial densities measured by fluorescence yielded more consistent data between technical replicates than optical density measurements. Our setup employs fluorescence microplate readers that allow high throughput and replication. IMPORTANCE We expand on an important limitation of the concept of measuring bacterial growth, which is classically limited to one strain at a time. By adopting our approach, it is possible to measure the growth of several bacterial strains simultaneously with high temporal resolution and in a high-throughput manner. This is important to investigate bacterial interactions, such as competition and facilitation.

The In Vitro and In Vivo Synergistic Antimicrobial Activity Assessment of Vacuum Microwave Assisted Aqueous Extracts from Pomegranate and Avocado Fruit Peels and Avocado Seeds Based on a Mixtures Design Model

The present study aimed to assess the antimicrobial properties of encapsulated lyophilized powdered extracts of pomegranate peels (PP), avocado peels (AP) and avocado seeds (AS) in vitro and in vivo. Minimum Inhibitory Concentration (MIC) and Minimal Bactericidal Concentration (MBC) methods, optical density measurement, and well diffusion assay were used to determine antimicrobial activity against food borne bacteria (Gram− Escherichia coli, Salmonella typhimurium, Campylobacter jejuni, Pseudomonas putida), (Gram+ Staphylococcus aureus, Listeria monocytogenes, Clostridium perfringens, Lactobacillus plantarum), and fungi (Penicillium expansum and Aspergillus niger) based on a mixture design model. Additionally, the most effective powder was studied in vivo in yogurt, cream cheese, and minced meat burger. The samples that contained high polyphenol content also exhibited higher antioxidant, antimicrobial, and antifungal activity. From the results of the well diffusion, the MIC/MBC, and the cell optical density assays, the antimicrobial activity of the extracts was found to be correlated to the total phenolic content (TPC) of the samples and the type of the microorganism. The pomegranate peels extract presented the higher TPC and antioxidant activity and constitute the highest percentage in the most active antimicrobial mixture. The powders that were tested in vitro showed microbial type-dependent effects in each food model. The results presented here can be further studied in the large-scale industrial production of natural food preservatives.

Broad-Spectrum Bactericidal Activity of a Synthetic Random Copolymer Based on 2-Methoxy-6-(4-Vinylbenzyloxy)-Benzylammonium Hydrochloride

Low-molecular-weight organic ammonium salts exert excellent antimicrobial effects by interacting lethally with bacterial membranes. Unfortunately, short-term functionality and high toxicity limit their clinical application. On the contrary, the equivalent macromolecular ammonium salts, derived from the polymerization of monomeric ammonium salts, have demonstrated improved antibacterial potency, a lower tendency to develop resistance, higher stability, long-term activity, and reduced toxicity. A water-soluble non-quaternary copolymeric ammonium salt (P7) was herein synthetized by copolymerizing 2-methoxy-6-(4-vinylbenzyloxy)-benzylammonium hydrochloride monomer with N, N-di-methyl-acrylamide. The antibacterial activity of P7 was assessed against several multidrug-resistant (MDR) clinical isolates of both Gram-positive and Gram-negative species. Except for colistin-resistant Pseudomonas aeruginosa, most isolates were susceptible to P7, also including some Gram-negative bacteria with a modified charge in the external membrane. P7 showed remarkable antibacterial activity against isolates of Enterococcus, Staphylococcus, Acinetobacter, and Pseudomonas, and on different strains of Escherichia coli and Stenotrophomonas maltophylia, regardless of their antibiotic resistance. The lowest minimal inhibitory concentrations (MICs) observed were 0.6-1.2 µM and the minimal bactericidal concentrations (MBC) were frequently overlapping with the MICs. In 24-h time-kill and turbidimetric studies, P7 displayed a rapid non-lytic bactericidal activity. P7 could therefore represent a novel and potent tool capable of counteracting infections sustained by several bacteria that are resistant to the presently available antibiotics.

Synthesis and Bioactivities of Novel 1,3,4-Thiadiazole Derivatives of Glucosides

A series of novel 1,3,4-thiadiazole derivatives of glucosides were synthesized by the starting materials d-glucose and 5-amino-1,3,4-thiadiazole-2-thiol in good yields with employing a convergent synthetic route. The results of bioactivities showed that some of the target compounds exhibited good antifungal activities. Especially, compounds 4i showed higher bioactivities against Phytophthora infestans (P. infestans), with the EC₅₀ values of 3.43, than that of Dimethomorph (5.52 μg/ml). In addition, the target compounds exhibited moderate to poor antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas campestris pv. citri (Xcc).

Synthesis, Characterization, and Bactericidal Activity of a 4-Ammoniumbuthylstyrene-Based Random Copolymer

The growing resistance of bacteria to current chemotherapy is a global concern that urgently requires new and effective antimicrobial agents, aimed at curing untreatable infection, reducing unacceptable healthcare costs and human mortality. Cationic polymers, that mimic antimicrobial cationic peptides, represent promising broad-spectrum agents, being less susceptible to develop resistance than low molecular weight antibiotics. We, thus, designed, and herein report, the synthesis and physicochemical characterization of a water-soluble cationic copolymer (P5), obtained by copolymerizing the laboratory-made monomer 4-ammoniumbuthylstyrene hydrochloride with di-methyl-acrylamide as uncharged diluent. The antibacterial activity of P5 was assessed against several multi-drug-resistant clinical isolates of both Gram-positive and Gram-negative species. Except for strains characterized by modifications of the membrane charge, most of the tested isolates were sensible to the new molecule. P5 showed remarkable antibacterial activity against several isolates of genera Enterococcus, Staphylococcus, Pseudomonas, Klebsiella, and against Escherichia coli, Acinetobacter baumannii and Stenotrophomonas maltophilia, displaying a minimum MIC value of 3.15 µM. In time-killing and turbidimetric studies, P5 displayed a rapid non-lytic bactericidal activity. Due to its water-solubility and wide bactericidal spectrum, P5 could represent a promising novel agent capable of overcoming severe infections sustained by bacteria resistant the presently available antibiotics.

A novel concentration gradient microfluidic chip for high-throughput antibiotic susceptibility testing of bacteria

Antibiotic resistance has become a serious threat to food safety and public health globally. Therefore, the development of a sensitive, quick, and simple method for antibiotic susceptibility testing is an urgent and crucial need. A novel concentration gradient microfluidic chip was designed in this work to generate antibiotic concentration gradient, culture bacteria, and produce fluorescence emission. An in-house-assembled fluorescence detection platform was constructed, and experiments were conducted to verify the linearity of the generated concentration gradient, explore the appropriate incubation time and flow rate for the microfluidic chip, and study the effect of long-term acid-based food processing on antibiotic susceptibility testing. Experimental results show that the concentration gradient generated by the microfluidic chip exhibited good linearity, stability, and controllability. The appropriate flow rate and incubation time for the microfluidic chip were 2 μL/min and 5 h, respectively. The use of this microfluidic chip for testing antibiotic resistance of Salmonella to ofloxacin and ampicillin generated results that were completely consistent with test results obtained using the gold-standard method. Furthermore, Salmonella showed greater sensitivity to antibiotics under strong acid conditions, confirming the potential influence of acid-based food processing on antibiotic susceptibility testing of real samples. The designed microfluidic chip provides a high-throughput, sensitive, and rapid antibiotic susceptibility testing method that combines the microfluidic chip and the fluorescence detection platform. The application of this method would facilitate determination of antibiotic-resistant bacterial strains for clinicians and researchers, and enable monitoring of changes in bacterial resistance during food processing.

CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli

Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a P_emrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD₆₀₀) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.

Synthesis and biological activities of novel trifluoromethylpyridine amide derivatives containing sulfur moieties

A series of trifluoromethylpyridine amide derivatives containing sulfur moieties (thioether, sulfone and sulfoxide) was designed and synthesized. Their antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo), Ralstonia solanacearum (R. solanacearum) and insecticidal activities against P. xylostella were evaluated. Notably, the half-maximal effective concentration (EC50) value of sulfone-containing compound F10 is 83 mg L-1 against Xoo, which is better than that of commercial thiodiazole copper (97 mg L-1) and bismerthiazol (112 mg L-1). Thioether-containing compounds E1, E3, E5, E6, E10, E11 and E13 showed much higher activities against R. solanacearum with the EC50 value from 40 to 78 mg L-1, which are much lower than that of thiodiazole copper (87 mg L-1) and bismerthiazol (124 mg L-1). Generally, most of the sulfone-containing compounds and sulfoxide-containing compounds showed higher activities against Xoo than that of the corresponding thioether-containing compound, but most of the thioether-containing compounds contributed higher antibacterial activities against R. solanacearum. Furthermore, title compounds E3, E11, E24 and G2 showed good insecticidal activities of 75%, 70%, 70% and 75%, respectively.

Bacterial Isolation Microwell-Plug (μWELLplug) for Rapid Antibiotic Susceptibility Testing Using Morphology Analysis

The rapid and accurate diagnosis of infectious diseases with high morbidity rates is crucial because it can minimize the misuse and overuse of antibiotics and increase survival rates in dreadful conditions. The conventional antibiotic susceptibility test (AST) systems used to choose appropriate antibiotics require long wait times to obtain results and cannot prevent the misuse or overuse of antibiotics by clinicians who need to quickly treat patients and cannot wait to identify the underlying cause of their symptoms. Therefore, several rapid AST (rAST) methods have been developed to provide quick test results, but they are complicated to operate, require additional equipment or materials, and give less accurate results than the conventional AST methods. In this study, we propose an rAST method that can obtain precise outcomes from a simple process with a short running time using a bacterial isolation microwell-plug (μWELLplug) in a conventional 96-well plate. The specifically designed hydrogel component of the μWELLplug provides a simple process for cell isolation and the observation of bacterial growth and morphological changes induced by a variety of antibiotic concentrations. The μWELLplug is placed over each well of the 96-well plate, and then bacterial or eukaryotic cells are isolated in the microwells and treated with different antibiotic concentrations to observe their effects. Saccharomyces cerevisiae (yeast, eukaryote), Streptomyces atratus (actinomycetes, prokaryote), Escherichia coli, Staphylococcus aureus, and methicillin-resistant S. aureus were cultivated and tested using the μWELLplug. The minimum inhibitory concentration values from this system were obtained in 3-4 h and correlated well with those from the conventional AST methods whose running time is 18-24 h.

Antibacterial Activity of Non-Cytotoxic, Amino Acid-Modified Polycationic Dendrimers against Pseudomonas aeruginosa and Other Non-Fermenting Gram-Negative Bacteria

Due to the rapid increase of antimicrobial resistance with ensuring therapeutic failures, the purpose of this study was to identify novel synthetic molecules as alternatives to conventional available, but presently ineffective antibiotics. Variously structured cationic dendrimers previously reported have provided promising outcomes. However, the problem of their cytotoxicity towards eukaryotic cells has not been completely overcome. We have now investigated the antibacterial activities of three not cytotoxic cationic dendrimers (G5Ds: G5H, G5K, and G5HK) against several multidrug-resistant (MDR) clinical strains. All G5Ds displayed remarkable activity against MDR non-fermenting Gram-negative species such as P. aeruginosa, S. maltophilia, and A. baumannii (MICs = 0.5-33.2 µM). In particular, very low MIC values (0.5-2.1 µM) were observed for G5K, which proved to be more active than the potent colistin (2.1 versus 3.19 µM) against P. aeruginosa. Concerning its mechanism of action, in time-killing and turbidimetric studies, G5K displayed a rapid non-lytic bactericidal activity. Considering the absence of cytotoxicity of these new compounds and their potency, comparable or even higher than that provided by the dendrimers previously reported, G5Ds may be proposed as promising novel antibacterial agents capable of overcoming the alarming resistance rates of several nosocomial non-fermenting Gram-negative pathogens.

Capillary-Driven Flow Microfluidics Combined with Smartphone Detection: An Emerging Tool for Point-of-Care Diagnostics

Point-of-care (POC) or near-patient testing allows clinicians to accurately achieve real-time diagnostic results performed at or near to the patient site. The outlook of POC devices is to provide quicker analyses that can lead to well-informed clinical decisions and hence improve the health of patients at the point-of-need. Microfluidics plays an important role in the development of POC devices. However, requirements of handling expertise, pumping systems and complex fluidic controls make the technology unaffordable to the current healthcare systems in the world. In recent years, capillary-driven flow microfluidics has emerged as an attractive microfluidic-based technology to overcome these limitations by offering robust, cost-effective and simple-to-operate devices. The internal wall of the microchannels can be pre-coated with reagents, and by merely dipping the device into the patient sample, the sample can be loaded into the microchannel driven by capillary forces and can be detected via handheld or smartphone-based detectors. The capabilities of capillary-driven flow devices have not been fully exploited in developing POC diagnostics, especially for antimicrobial resistance studies in clinical settings. The purpose of this review is to open up this field of microfluidics to the ever-expanding microfluidic-based scientific community.

Design, Synthesis, and Bioactivity of α-Ketoamide Derivatives Bearing a Vanillin Skeleton for Crop Diseases

A series of novel α-ketoamide derivatives bearing a vanillin skeleton were designed and synthesized. Bioactivity tests on virus and bacteria were performed. The results indicated that some compounds exhibited excellent antitobacco mosaic virus (TMV) activities, such as compound 34 exhibited an inactivation activity of 90.1% and curative activity of 51.8% and compound 28 exhibited a curative activity of 54.8% at 500 μg mL^-1, which is equivalent to that of the commercial ningnanmycin (inactivation of 91.9% and curative of 51.9%). Moreover, the in vitro antibacterial activity test illustrated that compounds 2, 22, and 33 showed much higher activities than commercial thiodiazole copper, which could be used as lead compounds or potential candidates. The findings of transmission electron microscopy and molecular docking indicated that the synthesized compounds exhibited strong and significant binding affinity to the TMV coat protein and could obstruct the self-assembly and increment of TMV particles. This study revealed that α-ketoamide derivatives bearing a vanillin skeleton could be used as a novel potential pesticide for controlling the plant diseases.

Discovery of novel bis-sulfoxide derivatives bearing acylhydrazone and benzothiazole moieties as potential antibacterial agents

On the basis of the active substructure combination principle, 24 novel synthesis of novel bis-sulfoxide derivatives bearing acylhydrazone and benzothiazole moieties as potential antibacterial agents were designed and synthesized. The bioactivity assay results showed that many compounds had significant in vitro inhibitory effects against Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas citri pv. citri (Xac). Notably, compound 4b had the best in vitro antibacterial activity against Xoo at an half-maximal effective concentration value of 11.4 μg/mL, which was superior to those of thiodiazole copper (TDC) and bismerthiazol (BMT). Compared with TDC and BMT, compound 4b was more effective in vivo controlling rice bacterial leaf blight with curative and protection activities of 42.5% and 40.3%, respectively. In addition, compound 4b can influence biofilm formation, inhibit extracellular polysaccharide production, and ultimately reduce the pathogenicity of Xoo. All the results indicated that bis-sulfoxide derivatives bearing acylhydrazone and benzothiazole moieties can be used for the development of small-molecule pesticides with high antibacterial activity.

Profiling of gene expression in methicillin-resistant Staphylococcus aureus in response to cyclo-(L-Val-L-Pro) and chloramphenicol isolated from Streptomyces sp., SUK 25 reveals gene downregulation in multiple biological targets

Chloramphenicol (CAP) and cyclo-(L-Val-L-Pro) were previously isolated from Streptomyces sp., SUK 25 which exhibited a high potency against methicillin-resistant Staphylococcus aureus (MRSA). This study aimed to profile gene expression of MRSA treated with CAP and cyclo-(L-Val-L-Pro) compounds using DNA microarray. Treatment of MRSA with CAP resulted in upregulation of genes involved in protein synthesis, suggesting the coping mechanism of MRSA due to the inhibition of protein synthesis effect from CAP. Most upregulated genes in cyclo-(L-Val-L-Pro) were putative genes with unknown functions. Interestingly, genes encoding ribosomal proteins, cell membrane synthesis, DNA metabolism, citric acid cycle and virulence were downregulated in MRSA treated with cyclo-(L-Val-L-Pro) compound, suggesting the efficacy of this compound in targeting multiple biological pathways. Contrary to CAP, with only a single target, cyclo-(L-Val-L-Pro) isolated from this study had multiple antimicrobial targets that can delay antibiotic resistance and hence is a potential antimicrobial agent of MRSA.