Identification Of Bacteria Research Articles

Rapid alignment-free bacteria identification via optical scattering with LEDs and YOLOv8

Rapid and accurate bacterial identification is essential for timely treatment of infections like sepsis. While traditional methods are reliable, they lack speed, and advanced molecular techniques often suffer from cost and complexity. The bacterial detection technology based on optical scattering system offers a rapid, label-free alternative but traditionally relies on complex lasers and analysis. Our enhanced approach utilizes RGB light emitting diodes (LEDs) as the light source. Three diffraction images of bacterial colonies from different LED colors are separately captured by a USB camera and combined using an image registration algorithm to enhance image sharpness. Our approach utilizes an object detection model, i.e., YOLOv8, for analysis achieving high-accuracy differentiation between bacterial strains. We demonstrate the effectiveness of this approach, achieving an average accuracy of 97% (mAP50 of 0.97), including accurate discrimination of closely related strains and the significant pathogen Staphylococcus aureus MRSA 1320. Our enhancement offers advantages in affordability, usability, and seamless integration into existing workflows, providing an alternative for rapid bacterial identification.

Molecular Identification of Soil Bacteria

The molecular identity of soil micro-organism is pivotal for expertise soil ecosystems that are important for agricultural productiveness, environmental sustainability, and biogeochemical cycles. This take a look at employs superior molecular techniques, inclusive of high-throughput sequencing and bioinformatics gear, to identify and classify micro-organism in various soil samples. Our comprehensive evaluation discovered a wealthy variety of bacterial species, which include both known and novel taxa, illustrating the complexity of soil micro biomes. These findings emphasize the vast function of soil micro-organism in nutrient cycling and plant health, supplying treasured insights for enhancing soil management practices and agricultural results. Additionally, the observe highlights the efficacy of molecular strategies in microbial ecology, suggesting potential future research instructions to take advantage of soil bacteria for environmental and biotechnological packages. This paintings underscores the crucial importance of molecular identification in unveiling the intricacies of soil bacterial groups and their useful roles within the ecosystem.

Comparison of Zybio Kit and saponin in-house method in rapid identification of bacteria from positive blood cultures by EXS2600 matrix-assisted laser desorption ionization time-of-flightmass spectrometry system.

We evaluated the performance of Zybio EXS2600 matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Zybio Inc., Chongqing, China) for the identification of bacteria from positive blood culture (BC) bottles using Blood Culture Positive Sample Pretreatment Kit (Zybio Inc., Chongqing, China) in comparison to an in-house saponin method. Following a positive signal by the BACTEC™ FX system, confirmation of identification was achieved using subcultured growing biomass used for MALDI-TOF MS analysis. A total of 94 positive BC bottles with 97 bacterial isolates were analyzed. The overall identification rates at the genus and species levels for the saponin method were 89.7% (87/97) and 74.2% (72/97), respectively. With the Zybio Kit, 88.7% (86/97) and 80.4% (78/97) of microorganisms were correctly identified to the genus and species levels, respectively. The saponin method identified 65.3% (32/49) of Gram-positive bacteria at the species level, whereas the Zybio Kit achieved a higher species-level identification rate of 79.6% (39/49) (p= 0.1153). The saponin method with additional on-plate formic acid extraction showed a significantly higher overall identification rate in comparison to the saponin method without that step for both genus (87.6% [85/97] vs. 70.1% [68/97], p= 0.0029) and species level (70.1% [68/97] vs. 46.4% [45/97], p= 0.0008). Identification rates of Gram-negative bacteria showed a higher identification rate, however, not statistically significant with additional Zybio Kit protocol step on both genus (85.4% [41/48] vs. 81.3% [39/48], p= 0.5858) and species level (77.1% [37/48] vs. 75% [36/48], p= 0.8120). Zybio Kit could offer an advantage in species-level identification, particularly for Gram-positive bacteria. The inclusion of on-plate formic acid extraction in the saponin method notably enhanced identification at both genus and species levels for Gram-positive bacteria. The extended protocol provided by the Zybio Kit could potentially offer an advantage in the identification of Gram-negative bacteria at both genus and species levels. Enhancements to the Zybio EXS2600 MALDI-TOF instrument software database are necessary.

The use of bacteriophages in the identification of bacteria

The use of bacteriophages in the identification of bacteria

Magnetic Fe3O4@MOF@aptamer-mediated entropy-driven fluorescence biosensor for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria

Rapid and early identification of pathogenic bacteria in food and clinical samples is critical for infectious disease control and precision medicine. In this study, we present a novel Magnetic Fe3O4@metal–organic framework (MOF)@Aptamer-based Entropy-driven fluorescence biosensor combined with mesophilic Clostridium butyricumArgonaute (CbAgo) for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria, termed the MAEA biosensor. In this study, magnetic zirconium-based MOF nanoparticles were modified with a phosphorylated aptamer as an efficient signal converter, which recognized the pathogens and released the complementary DNA to activate the entropy-driven circuit reaction. The highly efficient catalytic DNA circuit and isothermal enzyme-free format produce large amounts of guide DNA. CbAgo exerts precise and highly efficient endonuclease activity under the guidance of guide DNA, which makes the MAEA biosensor useful for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria with high sensitivity (<102 CFU/mL). This study demonstrates a highly selective and reliable magnetic Fe3O4@MOF@aptamer-based biosensor using CbAgo for simultaneously detecting multiple pathogenic bacteria, providing a potential tool for other infectious disease pathogens with convenient operation and high sensitivity.

Isolation and identification of rhizospheric, endophytic and epiphytic bacteria from chilli cultivars of telangana and its functional characterization

Isolation and identification of rhizospheric, endophytic and epiphytic bacteria from chilli cultivars of telangana and its functional characterization

Identification of halotolerant Lysinibacillus sphaericus isolated from Indonesian traditional dry-salted fish

Abstract Halotolerant protease-producing bacteria are a potential source of culture starter for the fermentation of fishery products. To find potential culture starter that can be used for fish fermentation, isolation of indigenous halotolerant bacteria is a particularly important step. This study was carried out for the isolation and identification of proteolytic bacteria isolated from traditional dried fish in Indonesia. A total of 32 isolates were obtained from three types of dried salted fish (ikan kotok, ikan belanak, and ikan kepala batu). Out of 30 isolates, six showed casein hydrolysis on skim milk agar (SMA), however, only four isolates showed proteolytic activity on saline SMA (10% w/v NaCl) namely isolates UA10, UA11, UA12, and UA13. All strains were identified as Lysinibacillus sphaericus based on morphological and biochemical tests. Before it can be used for fermentation or other purposes, further characterization of Lysinibacillus sphaericus isolated from traditional Indonesian dried salted fish is required.

Isolation and Identification of Acid-Forming Bacteria in Arabica Coffee Fruit (Coffea arabica) During Wet Fermentation

The distinctive flavor and aroma possessed by Arabica coffee are an attraction for coffee enthusiasts. Post-harvest processing of coffee such as coffee fruit fermentation also contributes to the formation of the flavor and aroma of Arabica coffee. In this study, spontaneous fermentation was conducted by adding distilled water, with treatments on fermentation days 4 and 7 aimed at detecting acid-forming bacteria that played a role in the fermentation process. The bacterial isolates were characterized through macroscopic and microscopic observations, physiological, and biochemical tests. Identification of bacterial isolates was performed using the profile matching method based on Bergey’s Manual of Systematic Bacteriology (Holt et al., 1994) and Axellson (2004) until the genus level. The identified bacterial genera were Asaia, Gluconobacter, Neoasaia, Saccharibacter, and Lactobacillus.

Screening oil tank bottom sludge microbial community for identification of native efficient hydrocarbon-degrading bacteria for bioremediation purposes

Screening oil tank bottom sludge microbial community for identification of native efficient hydrocarbon-degrading bacteria for bioremediation purposes

Engineering the bacteriophage 80 alpha endolysin as a fast and ultrasensitive detection toolbox against Staphylococcus aureus

The isolation and identification of pathogenic bacteria from a variety of samples are critical for controlling bacterial infection-related health problems. The conventional methods, such as plate counting and polymerase chain reaction-based approaches, tend to be time-consuming and reliant on specific instruments, severely limiting the effective identification of these pathogens. In this study, we employed the specificity of the cell wall-binding (CBD) domain of the Staphylococcus aureus bacteriophage 80 alpha (80α) endolysin towards the host bacteria for isolation. Amidase 3-CBD conjugated magnetic beads successfully isolated as few as 1 × 102 CFU/mL of S. aureus cells from milk, blood, and saliva. The cell wall hydrolyzing activity of 80α endolysin promoted the genomic DNA extraction efficiency by 12.7 folds on average, compared to the commercial bacterial genomic DNA extraction kit. Then, recombinase polymerase amplification (RPA) was exploited to amplify the nuc gene of S. aureus from the extracted DNA at 37 °C for 30 min. The RPA product activated Cas12a endonuclease activity to cleave fluorescently labeled ssDNA probes. We then converted the generated signal into a fluorescent readout, detectable by either the naked eye or a portable, self-assembled instrument with ultrasensitivity. The entire procedure, from isolation to identification, can be completed within 2 h. The simplicity and sensitivity of the method developed in this study make it of great application value in S. aureus detection, especially in areas with limited resource supply.

Identification of proteotoxic and proteoprotective bacteria that non-specifically affect proteins associated with neurodegenerative diseases

There are no cures for neurodegenerative protein conformational diseases (PCDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Emerging evidence suggests the gut microbiota plays a role in their pathogenesis, though the influences of specific bacteria on disease-associated proteins remain elusive. Here, we reveal the effects of 229 human bacterial isolates on the aggregation and toxicity of Aβ1-42, α-synuclein, and polyglutamine tracts in Caenorhabditis elegans expressing these culprit proteins. Our findings demonstrate that bacterial effects on host protein aggregation are consistent across different culprit proteins, suggesting that microbes affect protein stability by modulating host proteostasis rather than selectively targeting disease-associated proteins. Furthermore, we found that feeding C.elegans proteoprotective Prevotella corporis activates the heat shock response, revealing an unexpected discovery of a microbial influence on host proteostasis. Insight into how individual bacteria affect PCD proteins could open new strategies for prevention and treatment by altering the abundance of microbes.

Molecular identification of lactic acid bacteria from traditional fermented foods and screening exopolysaccharide production by using food wastes.

In this study, lactic acid bacteria (LAB) isolation from fermented foods and molecular identification using magnetic bead technology were performed. And then exopolysaccharide (EPS) production possibility was tested in agar medium, and the positive ones were selected for the next step. The bacteria that could produce higher carbohydrate level were grown in MRS medium fortified with whey and pumpkin waste. In our study, 19 different LAB species were identified from fermented products collected from different places in Hatay(Türkiye) province. In molecular identification, universal primer pairs, p806R/p8FPL, and PEU7/DG74 were used for PCR amplification. After that, PCR products purified using paramagnetic bead technology were sequenced by the Sanger sequencing method. The dominant species, 23.8% of the isolates, were identified as Lactiplantibacillus plantarum. As a technological property of LAB, exopolysaccharide production capability of forty-two LAB isolate was tested in agar medium, and after eleven isolates were selected as positive. Two LAB (Latilactobacillus curvatus SHA2-3B and Loigolactobacillus coryniformis SHA6-3B) had higher EPS production capability when they were grown in MRS broth fortified with pumpkin waste and whey. The highest EPS content (1750mg/L glucose equivalent) was determined in Loigolactobacillus coryniformis SHA6-3B grown in MRS broth fortified with 10% pumpkin waste. Besides the produced EPS samples were validated with FTIR and SEM methods.

Prevalence and Antibiotic Resistance of Klebsiella pneumoniae in Diabetic Foot Ulcer.

Introduction A serious global threat of antimicrobial resistance has emerged due tothe improper use of antibiotics, including polypharmacy and inappropriate prescribing. This misuse has led bacteria to develop immunity against these drugs.Klebsiella pneumoniae, a concerning gram-negative bacterium, has become resistant, especially among immunocompromised diabetic patients for multiple antibiotics. To fight effectively this growing crisis and regain control of these infections, it is crucial to comprehend the resistance mechanisms utilized by the bacteria anddevelop a new therapeutic strategy to prevent antibiotic resistance. Materials and methods A five-month study from January 2023 to May 2023 was conducted at the tertiary healthcare facility of Saveetha Medical Collegeby collecting 122 clinical specimens from patients with diabetic foot ulcers (DFUs) and ulcer-related infections. The microbiological testing methods followed by the identification of bacteria using matrix-assisted laser desorption/ionizationtime-of-flight mass spectrometry (MALDI-TOF) and antimicrobial susceptibility testing (AST) by the VITEK 2 Compact system were performed. Results A stout, rod-shaped, gram-negative bacilli was observed in gram staining, and growth of mucoid γ-hemolytic colonies and lactose-fermenting mucoid colonies were seen in blood and MacConkey agar plates. MALDI-TOF analysis confirmed the presence ofKlebsiella pneumoniaealong with other bacteria such as Klebsiella oxytoca, Staphylococcus spp., Proteus spp., and​​Escherichia ​coli. VITEKshowed high resistance rates to commonly used antibiotics, including carbapenems. Notably, isolates showed sensitivity and intermediate to tigecycline and colistin. Resistance patterns varied across specimen types, emphasizing the importance of considering clinical sources when interpreting data. Conclusion Hence, this study underscores the urgent need for novel antimicrobial agents and effective infection control measures to combat multidrug-resistant Klebsiella pneumoniae infections. Understanding resistance mechanisms is essential for the incorporation of treatment strategies and preserving antibiotic efficacy.

The Isolation and Identification of Novel Arsenic-Resistant Bacteria from an Arsenic-Contaminated Region—A Study to Understand the Efficiency of Bacteria for Arsenic Removal from Aqueous Media

Drinking water sources with groundwater arsenic (As) contamination face multifaceted challenges in the removal and supply of fresh drinking water resources. To eradicate this problem, bioremediation has evolved to become more effective than other chemical and physical removal processes in its cost-effectiveness, high removal efficiency, and lesser production of secondary by-products or waste. Thus, this study aimed to treat As from aqueous media and to detoxify highly toxic forms of As by the isolated bacteria from As-affected areas. We isolated two new Gram-positive bacteria, which are reported here (Bacillus sp. and Bacillus cereus), with As5+ minimum inhibitory concentrations (MICs) of 4500 mg/L for the Bacillus sp. and 1000 mg/L for Bacillus cereus; meanwhile, for As3+, the MICs are 600 mg/L for both isolates. Bacillus sp. and Bacillus cereus can also effectively convert the highly toxic and easily mobile As3+ to As5+ in aqueous media. This study also demonstrates that these bacteria can remove a significant proportion of As3+ and As5+ (averaging 50% for both) from aqueous media. These As-resistant bacteria from the As-affected area can be used and upscaled for the treatment of As for a safer drinking water supply.

16S rRNA metabarcoding for the identification of tick-borne bacteria in ticks in the Republic of Korea

Ticks are blood-sucking ectoparasites that act as vectors for transmission of various pathogens. The purpose of this study was to assess tick-borne bacteria, whether pathogenic or not, in ticks distributed in Korea using 16S rRNA metabarcoding and to confirm the results by PCR. Questing ticks were collected from four provinces in Korea in 2021 using the flagging method. After pooling the DNAs from the 61 tick pools (including 372 ticks), the bacterial 16S rRNA V3–V4 hypervariable region was amplified and sequenced using the MiSeq platform. Rickettsia, Ehrlichia, and the endosymbiont Wolbachia were confirmed by conventional PCR and molecular analysis. In total, 6907 ticks (534 pools) were collected and identified as belonging to five species (Haemaphysalis spp., H. longicornis, H. flava, I. nipponensis, and A. testudinarium). Through 16S rRNA metabarcoding, 240 amplicon sequence variants were identified. The dominant taxa were Rickettsiella and Coxiella. Additionally, pathogenic bacteria such as Rickettsia and Ehrlichia, endosymbiotic bacteria such as Wolbachia and Spiroplasma were identified. Polymerase chain reaction (PCR) was performed to confirm the presence of Rickettsia, Ehrlichia, Bartonella, and Wolbachia in individual ticks. Overall, 352 (65.92%) of 534 pools tested positive for at least one of the screened tick-borne bacteria. Rickettsia was the most prevalent (61.42%), followed by Wolbachia (5.05%). Ehrlichia was detected in 4.86% of tested samples, whereas Bartonella was not detected. In this study, 16S rRNA metabarcoding revealed the presence of Rickettsia, Wolbachia, and Ehrlichia, in that order of abundance, while showing absence of Bartonella. These results were confirmed to exhibit the same trend as that of the conventional PCR. Therefore, large-scale screening studies based on pooling, as applied in this study, will be useful for examining novel or rare pathogens present in various hosts and vectors.

New insights on entomopathogenic bacteria isolated from soil of citrus crops to combat the polyphagus aphid pest Hyalopterus pruni (Geoffroy 1762) (Hemiptera, Aphididae)

BackgroundThe employment of entomopathogenic microorganisms is a promising approach for ensuring optimal phytosanitary protection in the framework of biological management of insect crop pests. Among these microbes, entomopathogenic soil-borne bacteria are preferred over pesticides because they help successfully in the natural regulation of arthropod populations, as soil has a favorable ecology for the availability and richness of many beneficial bacterial species. In this study, it was focused on the isolation, identification and characterization of entomopathogenic bacteria isolated from cultivated citrus soils and on the evaluation of their insecticidal potential in the laboratory against the mealy plum aphid, Hyalopterus pruni (Geoffroy 1762) (Hemiptera: Aphididae), a polyphagous and major pest attacking and virus-transmitting of several Prunus crops.ResultsIsolation results gave 11 bacterial isolates, which were more than 50% effective in selection tests on H. pruni aphids at 1 × 108 CFU/ml. A total of seven isolates generated significant insecticidal potential at different concentrations, and their molecular identification based on 16S rRNA genome sequencing yielded the following results: Lysinibacillus fusiformis (B4), Bacillus thuringiensis (B13), B. thuringiensis (B22), B. thuringiensis (B23), B. thuringiensis (B24), Pseudomonas sp. (P2) and Enterococcus gallinarum (P4). The most pathogenic potential of these strains was for E. gallinarum (P4), which induced 100% H. pruni mortality after 72 h of treatment at the concentration (C3 = 1 × 106 CFU/ml), followed by B. thuringiensis (B23), (B22), (B4), (P2), (B13) and (B24) isolates, which caused 96, 91, 85, 83, 65 and 50% mortality rates, respectively, at the lowest concentration (C4 = 1 × 105 CFU/ml). The LC50 and LT50 values were calculated for the entomopathogenic isolates of (P2), (P4), (B23) and (B24). A lowest LC50 value was 1.08 × 102 CFU/ml for (P4) E. gallinarum after 72 h of treatment, whereas (P2) Pseudomonas sp. presented the shortest LT50 of 33.6 h at concentration (C4 = 1 × 105 CFU/ml).ConclusionsThe present study's outcomes have confirmed the existence, abundance, and variety of entomopathogenic bacteria at the soil level in citrus groves. Interestingly, these bacteria could be useful for aphids’ population control on a wide scale through the utilization of their toxins and enzymes, even against insect pests of a broad order.

Assessing the impact of triiodothyronine treatment on the lung microbiome of mice with pulmonary fibrosis

BackgroundIdiopathic pulmonary fibrosis (IPF), an interstitial lung disease, is characterized by the exacerbation of progressive pulmonary fibrosis (PF). IPF primarily affects older individuals and can lead to respiratory failure. This study aimed to assess the effects of triiodothyronine (T3) treatment on the lung microbiome of mice with PF.MethodsMice were perfused with bleomycin (BLM) to establish a PF model. Using a randomized design, 40 female specific pathogen-free (SPF) C57BL6/N mice were divided into four groups: saline, saline + T3, BLM, and BLM + T3. Histological morphology was assessed through Hematoxylin and Eosin staining as well as Masson’s Trichrome staining. For the identification of lung bacteria, 16S rRNA gene sequencing was employed. An Enzyme-Linked Immunosorbent Assay was used to measure total T3 (TT3), free T3 (FT3, and reverse T3 (rT3) levels in the peripheral serum.ResultsT3 treatment ameliorated BLM-induced lung fibrosis and structural damage. The microbiome experienced a decrease in the abundance of Proteobacteria, Bacteroides, and Actinomycetes and an increase in the abundance of Firmicutes when exposed to BLM; however, T3 treatment reversed this effect. The four groups showed no significant difference in alpha microbiome diversity (P > 0.05). Serum concentrations of TT3 and FT3 were positively correlated with microbiome abundance (P < 0.05). Administration of T3 enhanced the microbiota in PF without affecting the diversity and biological functions of the microbiome (P > 0.05).ConclusionThe administration of T3 demonstrated a favorable impact on the lung microbiota of mice afflicted with PF, thereby partially substantiating the potential role of T3 as a therapeutic agent in the management of PF.

RESIST ACINETO test for the rapid detection of NDM and OXA acquired carbapenemases directly from blood culture in Acinetobacter species.

The incidence of bloodstream infections with carbapenem-resistant Acinetobacter baumannii (CRAB) could be very high in some countries such as the Balkans or Southeast Asia. In case of positive blood cultures with Gram-negative bacteria, the use of the RESIST ACINETO test could prove highly beneficial for the rapid identification of these imipenem-resistant bacteria and their antibiotic resistance mechanisms. In addition, it is now well established that New-Delhi Metallo-beta-lactamase (NDM) carbapenemase-producing isolates can have increased MICs of cefiderocol, which is an alternative treatment for these infections. This test may also allow the optimization of treatment based on the type of carbapenemase present. Finally, the RESIST ACINETO test is a rapid, easy-to-use, and cost-effective assay that demonstrates excellent performance in detecting the major acquired carbapenemases present in the Acinetobacter species.

Isolation and Identification of Pathogenic Bacteria from Ready to Eat Fast Foods from Kothanur, Bangalore.

Isolation and Identification of Pathogenic Bacteria from Ready to Eat Fast Foods from Kothanur, Bangalore.

Personalized identification of autism-related bacteria in the gut microbiome using explainable artificial intelligence

Autism spectrum disorder (ASD) affects social interaction and communication. Emerging evidence links ASD to gut microbiome alterations, suggesting that microbial composition may play a role in the disorder. This study employs explainable artificial intelligence (XAI) to examine the contributions of individual microbial species to ASD. By using local explanation embeddings and unsupervised clustering, the research identifies distinct ASD subgroups, underscoring the disorder's heterogeneity. Specific microbial biomarkers associated with ASD are revealed, and the best classifiers achieved an AU-ROC of 0.965± 0.005 and an AU-PRC of 0.967± 0.008. The findings support the notion that gut microbiome composition varies significantly among individuals with ASD. This work's broader significance lies in its potential to inform personalized interventions, enhancing precision in ASD management and classification. These insights highlight the importance of individualized microbiome profiles for developing tailored therapeutic strategies for ASD.