Single Microorganism Research Articles

Effect of pH on the Abundance and Community Structure of Comammox Nitrospira in Paddy Soils

Soil pH is recognized as an important environmental factor in determining the niche differentiation for ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Species of comammox, a single microorganism capable of the complete oxidation of ammonia to nitrate, have recently been discovered. Metagenomic analysis and quantitative PCR showed that Comammox Nitrospira were found in a wide range of environments, including soil. Comammox bacteria are differentiated into one of two clades (A and B) based on the phylogeny of genes encoding the α-subunit of ammonia monooxygenase genes (amoA). However, all discovered Comammox Nitrospira strains have been isolated and cultured in aquatic ecosystems, including N. inopinata, N. nitrosa, and N. nitrificans, all belonging to clade A. Currently, Comammox Nitrospira has not been obtained from soil environments, which limits our understanding of soil Comammox Nitrospira. Here we hypothesized that, as AOA and AOB, the ecological site of Comammox Nitrospira may also be affected by pH. Therefore, soil samples with differing pH were collected, and the abundances and community structures were studied to elucidate the mechanism of pH effect on the distributions and community compositions of Comammox Nitrospira in soil. Quantitative PCR of comammox clade A and clade B amoA genes in DNA extracts were performed using QuantStudio TM6 Flex Real-Time PCR Systems. The community compositions for Comammox Nitrospira were studied by the cloning libraries of amoA genes method. The results showed that the abundance of Comammox clade A amoA gene in acidic paddy soil was two orders of magnitude higher than that in neutral paddy soil (P<0.05), and the abundance of Comammox clade B in acidic paddy soil was significantly higher than that in neutral paddy soil (P<0.05); the abundance of Comammox clade A amoA gene in acidic paddy soil was 60 times higher than that of clade B, whereas the abundance ratio of Comammox clade A and clade B amoA genes in neutral paddy soil was about two times higher. These results indicated that soil pH significantly affected the abundance of Comammox Nitrospira. The results of cloning and sequencing showed that the Comammox in neutral paddy soil was mainly N. inopinata, which belonged to clade A; no strain belonging to clade B was annotated. Comammox clade A in acidic paddy soil was mainly Composed of N. inopinata and N. nitrosa, and clade B was mainly uncultured bacterium (FN395328). The results indicated that soil pH was an important factor in shaping Comammox Nitrospira community structure. Comammox Nitrospira were detected in all soil samples, and Comammox clade A had a preference for acidic environments. It seemed that species from N. nitrosa possessed the ecological niche of low pH environments, whereas species from N. inopinata preferred to live in neutral environments. In conclusion, pH had a significant effect on the abundance and community structure of Comammox Nitrospira, which was one of the important factors affecting the niche differentiation of Comammox Nitrospira.

Secretome analysis of Trichoderma reesei RUT-C30 and Penicillium oxalicum reveals their synergic potential to deconstruct sugarcane and energy cane biomasses

The conversion of lignocellulosic polymers into monomeric sugars demands a plethora of enzymatic activities generally not produced by a single microorganism and induced by the carbon source. In this vein, this work investigates the synergy between the enzymes secreted by the cellulolytic model fungi Trichoderma reesei RUT-C30 (TR) and Penicillium oxalicum (PO) to deconstruct sugarcane straw (SCS) and energy cane bagasse (ECB). TR and PO secrete a similar profile of cellulose-active enzymes resulting in a comparable conversion of SCS and ECB into glucose. The synergy between the enzymes produced by both fungi to break down the cellulose fraction becomes evident by the improvement of glucose titers from ~35–54% and from ~10–17% in SCS and ECB conditions, respectively, reached with the mixture of the secretomes of both fungi. The effect of a hemicellulase-enriched secretome produced by TR is particularly seen in SCS where the xylose yield reached ~15% compared to 5% by PO, remaining unaltered following the mixture of secretomes. However, the secretion of enzymes active in the decorations of the main chain polymers possibly aid PO to access the hemicellulose fraction of ECB reaching xylose yields similar to TR in this condition.

Assessment of Acaricidal Efficacy of Ivermectin Against Ectoparasitic Skin Lesions in Goats

We have conducted a research experiment to investigate the efficacy of commercial Ivermectin preparations (Ivertin®, Invet®, and A-Mectin®) against skin lesions in goats. The generic Ivermectin is, in fact, a naturally-derived dihydro derivative of avermectin originating exclusively from a single microorganism isolated from Japanese soil, displaying an extensive range of antiparasitic efficacy against internal and external parasites of human and domestic animals. The ectoparasites such as ticks, lice, and mites cause heavy economic losses to the livestock industry due to their blood-sucking habit, which adversely affects economic production. Ectoparasites have been recognized as the notorious threat due to severe irritation, formation of crust, wrinkled, thickened, and or loss of hair, allergy, and toxicosis and eventually brought about financial havoc in goat farming. Presently, this is the best-known drug available for combating ectoparasitic diseases in livestock. After being bound, the drug disrupts parasitic neuro-muscular transmission, causing hyperpolarization of the neuronal membrane, inducing paralysis of somatic muscles, particularly the pharyngeal pump, killing the parasites. To investigate the comparative efficacy of commercially available different ivermectin preparations in the local market against skin lesions in goats, the research work was conducted on 12 goats of both sexes having skin lesions from July to August 2017. Subcutaneous injection of Ivertin® of Chemist Laboratories Ltd, Invet® of Popular Pharmaceuticals Ltd, and A-Mectin® of The Acme Pharmaceuticals Ltd, Bangladesh @ l ml per 50 Kg bwt where each ml contains 10mg of generic Ivermectin on the first day followed by the second dose at 7thday and the third dose at 14th day of experimentation. Our results revealed within 28 days of treatment with these preparations of Ivermectin, both smaller and larger skin lesions in goats of all experimental groups were almost cured at a rate of 99%. No adverse effect was observed following ivermectin therapy. The animals were seen with increased vigor, better growth, and improved coat color. Although the precise mode of action and interactions of Ivermectin is yet to be revealed fully, the drug certainly had a tremendously positive effect in alleviating ectoparasitic diseases from goats.

Surgical Site Infections in Patients after Posterior Lumbar Spine Fusions

Background: Posterior lumbar spine fusions (PLSF) surgery is widely used in the field of spinal surgery for the treatment of lumbar spinal stenosis and spondylolisthesis, because of its surgical effectiveness and simple approach. But in such surgery, surgical site infection (SSI) is a matter of concern. In Bangladesh, we have very few research-oriented information regarding SSI and related complications after posterior lumbar spine fusions (PLSF) among patients. Aim of the study: The aim of to this study was to determine the incidences of postoperative surgical site infection after lumbar spinal surgery and its several characteristics. Methods: This study was a prospective observational study which was conducted in the department of Orthopedics, Holy Family Red Crescent Hospital Dhaka, Bangladesh during the period from March 2019 to December 2019. In total 47 patients of surgical site infections (SSI) following posterior lumbar spine fusions (PLSF) from several age groups were selected as the study people. Data regarding causes of surgery, frequencies of SSIs, associated causative organisms and other clinical status were recorded and analyzed. All data were processed, analyzed and disseminated by MS Office and SPSS programs as per need. Results: In analyzing types of SSI after posterior lumbar surgery among participants we observed 38.30%, 34.04% and 21.28% patients were with lumbar spinal stenosis and lumbar spondylolisthesis and lumbar disc herniation respectively. Among all the participants, among the highest number of patients S. aureus was associated as (19%) were found among noticeable number of patients. a single micro-organism. Besides these, MSSA (19%), S. epidermidis (26%) and MRSE. Conclusion: The pre-assessment of microbiological characteristics should be done in all cases of surgical site infections (SSIs) in patients after posterior lumbar spine fusions. Prompt application of antibiotics may reduce the complications in patients after posterior ........

Bloodstream infections in different stage of reconstitution after first allogeneic hematopoietic stem cell transplantation

Background. Bloodstream infections (BSI) are common after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The objective of study was to analyze pre- and post-engraftment BSI.Materials and methods. From January 2018 till May 2021242 patients after first allo-HSCT were enrolled in the study. Median age was 35 (17–65) years. The majority of transplants were done for acute leukemias (71.9 %) in remission (91.7 %) with reduced-intensity conditioning regimens (71.5 %) and peripheral blood stem cells (74.4 %) as a graft source.Results. Of 242 patients 95 (39.2 %) developed BSI: 79 (83.2 %) developed 1 BSI episode, 16 (16.8 %) – 2 or more. Overall 113 BSI episodes were registered: 94 (82.7 %) were caused by single microorganism, 19 (17.3 %) were polymicrobial. Probability of pre-engraftment BSI was 31.0 %, post-engraftment – 11.8 %. In total 134 microorganisms were identified: 61.2 % – gram-negative and 38.8 % – gram-positive bacteria. Gram-negative BSI rate was significantly higher during post-engraftment compared to pre-engraftment phase (57.7 % vs. 70.3 %; р = 0.008). Major risk factor for pre-engraftment BSI was mismatched unrelated allo-HSCTs (hazard ratio (HR) 2.55; 95 % confidence interval (CI) 1.32–4.91; р = 0.03), for post-engraftment BSI – secondary poor graft function (HR 21.70; 95 % CI 7.95–59.24; р &lt;0.0001) and graft failure (HR 21.55; 95 % CI 6.27–74.08; р &lt;0.0001), and gut graft-versus-host disease (HR 12.90; 95 % CI 5.77–28.80; р &lt;0.0001). Thirty-day survival after each BSI episode was 90.3 % and was significantly lower in patients with post-engraftment BSI compared to pre-engraftment (71.9 % vs. 97.5 %; р &lt;0.0001).Conclusion. Gram-negative bacteria prevailed in the etiology of BSI. The main risk factors for pre-engraftment BSI was allo-HSCT from mismatched unrelated donors, for post-engraftment BSI – secondary poor graft function and graft failure. Post-engraftment BSI is associated with worse prognosis.

Reconstructing polyaromatic hydrocarbons degrading pathways in the enriched bacterial consortium and their biosurfactants characterization

Due to substantial metabolic burden and low carbon fluxes, a single microorganism cannot utilize multiple classes of hydrocarbons typically found in the polluted environment. A microbial consortium comprising biosurfactants producing strains and hydrocarbon degradative strains could have promising bioremediation capabilities. To address this question, bacteria from non-contaminated soil were enriched in a medium containing polyaromatic hydrocarbons. The metabolic potential and pathways of PAHs degrading bacterial consortia (CON-PAH) that drive energy and carbon from PAHs assimilation were elucidated by metagenomic analysis. CON-PAH degrade more than 90% of PAHs (naphthalene, phenanthrene, and pyrene) with concomitant biosurfactants production. Tween-20 and glucose as a co-substrate suppress the PAHs degradation. Six high-quality metagenome-assembled genomes (MAGs) were assembled with an estimated size of 3.8–6.5 Mb from metagenomic data of CON-PAH. The draft genome of Deliftia tsuruhatensis and Pseudomonas putida contain the entire benzoate and near-complete naphthalene and phenanthrene degradation pathways. For the first time, we reconstruct PAH degrading pathway in D. tsuruhatensis sp. The metagenomic reconstruction of bins indicates the cross-feeding of bacteria within the consortium and suggests that complete PAH degradation pathways may not be obligatory for individual bacteria in the consortium. Biosurfactants structure elucidation via LC/MS showed lipopeptide containing the heptapeptides with different lipid moieties. This work will deepen our understanding of the metabolic capacity of microbial communities and provide new ideas for the engineering of artificial microbial consortia.

Direct microorganism species identification and antimicrobial susceptibility tests from positive blood culture bottles using rapid Sepsityper Kit

IntroductionWe evaluated the performance of Rapid Sepsityper Kit in species identification (ID) and antimicrobial susceptibility testing (AST). MethodsPositive blood culture bottles (n = 227) containing single microorganisms were enrolled. We compared the direct method using Rapid Sepsityper Kit for ID and AST with the conventional method. The analyses of ID and AST were performed using MALDI Biotyper and BD Phoenix platform, respectively. ResultsThe direct ID method correctly identified 89.4% (203/227) of samples, and Gram-negative bacilli (95.2%) had a higher ID rate than Gram-positive cocci (84.4%). Five cases were misidentified, and non-acceptable identification was high among Streptococcus species.Direct AST results were obtained from 168 isolates. Non-acceptable ID occurred among 24 isolates; 4 Streptococcus species, and 31 isolates, which did not grow in the direct AST method, were excluded. A total of 1714 antibiotic susceptibility tests (625 from 69 Gram-positive cocci and 1089 from 99 Gram-negative bacilli) were performed. The direct AST methods showed 98.3% (1685/1714) of categorical agreement (CA), 0.7% (12/1714) of very major errors, 0.2% (4/1714) of major errors, and 0.8% (13/1714) of minor errors. Complete CA was obtained for methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Escherichia coli. ConclusionsThe direct ID method using Rapid Sepsityper Kit and the direct AST method in combination with the BD Phoenix platform, which was associated with a reduction of turnaround time, may be a reliable approach for blood culture bottles. However, additional validation and further improvements, especially for Gram-positive cocci, would have an impact on microbiological diagnoses.

Molecular characterization and transcriptional modulation of stress-responsive genes under heavy metal stress in freshwater ciliate, Euplotes aediculatus.

Heavy metal pollutants in the environment are increasing exponentially due to various anthropogenic factors including mining, industrial and agricultural wastes. Living organisms exposed to heavy metals above a certain threshold level induces deleterious effects in these organisms. To live in such severe environments, microbes have developed a range of tolerance mechanisms which include upregulation of stress-responsive genes and/or antioxidant enzymes to detoxify the metal stress. Single cell eukaryotic microorganisms, i.e., ciliates, are highly sensitive to environmental pollutants mainly due to the absence of cell wall, which make them suitable candidates for conducting ecotoxicological studies. Therefore, the present investigation describes the effects of heavy metals (cadmium and copper) on freshwater ciliate, Euplotes aediculatus. The activities of antioxidant enzymes, i.e., catalase and glutathione peroxidase in E. aediculatus were determined under heavy metal exposure. Besides, the expression of stress-responsive genes, namely, heat-shock protein 70 (hsp70) and catalase (cat), has also been determined in this freshwater ciliate species under metal stress. The present study showed that the enzyme activity and the expression of these genes increased with an increase in the heavy metal concentration and with the duration of metal exposure. Also, these stress-responsive genes were sequenced and characterized to comprehend their role in cell rescue.

One-pot multi-step transformation of D-allose from D-fructose using a co-immobilized biocatalytic system.

In this report, Shinella zoogloeoides NN6 was discovered to produce two rare sugar producing enzymes, D-allulose 3-epimerase (DAE) and L-rhamnose isomerase (LRhI), when cultured with L-rhamnose as the sole carbon source. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of purified DAE and LRhI revealed that the molecular masses of the monomeric subunits are 37 and 43 kDa, respectively, whereas gel filtration analysis showed that purified DAE and LRhI are 148 and 162 kDa, respectively, indicating that both enzymes form tetramers. The activity of DAE was the highest at 80°C in acetate buffer (pH 6.5) with Co2+, whereas LRhI exhibited maximum activity at 60°C in glycine-NaOH buffer (pH 9.0) with Mn2+. A co-immobilized biocatalyst was constructed using DAE (3.2 U) and LRhI (40 U). Activity profile analysis of this co-immobilized biocatalyst revealed that DAE activity was highest at 80°C in acetate buffer (pH 5.5), whereas the highest activity for LRhI was observed at 55°C in sodium phosphate buffer (pH 7.0). D-Allose was produced from 2% (w/w) D-fructose via D-allulose at 60°C and pH 9.0 in a one-pot reaction, providing a mixture of D-glucose, D-fructose, D-allulose and D-allose at a ratio of 1.3:62.7:23.6:12.4. This is the first report describing one-pot D-allose production using LRhI and DAE expressed in a single microorganism.

Sequential Production of ᴅ-xylonate and Ethanol from Non-Detoxified Corncob at Low-pH by Pichia kudriavzevii via a Two-Stage Fermentation Strategy.

Improving the comprehensive utilization of sugars in lignocellulosic biomass is a major challenge for enhancing the economic viability of lignocellulose biorefinement. A robust yeast Pichia kudriavzevii N-X showed excellent performance in ethanol production under high temperature and low pH conditions and was engineered for ᴅ-xylonate production without xylitol generation. The recombinant strain P. kudriavzevii N-X/S1 was employed for sequential production of ᴅ-xylonate and ethanol from ᴅ-xylose, feeding on ᴅ-glucose without pH control in a two-stage strategy of aerobic and shifting micro-aerobic fermentation. Acid-pretreated corncob without detoxification and filtration was used for ᴅ-xylonate production, then simultaneous saccharification and ethanol fermentation was performed with cellulase added at pH 4.0 and at 40 °C. By this strategy, 33.5 g/L ᴅ-xylonate and 20.8 g/L ethanol were produced at yields of 1.10 g/g ᴅ-xylose and 84.3% of theoretical value, respectively. We propose a promising approach for the sequential production of ᴅ-xylonate and ethanol from non-detoxified corncob using a single microorganism.

Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans

BackgroundLignocellulosic biomass is an attractive and sustainable alternative to petroleum-based feedstock for the production of a range of biochemicals, and pretreatment is generally regarded as indispensable for its biorefinery. However, various inhibitors that severely hinder the growth and fermentation of microorganisms are inevitably produced during the pretreatment of lignocellulose. Presently, there are few reports on a single microorganism that can detoxify or tolerate toxic mixtures of pretreated lignocellulose hydrolysate while effectively transforming sugar components into valuable compounds. Alternatively, microbial coculture provides a simpler and more efficacious way to realize this goal by distributing metabolic functions among different specialized strains.ResultsIn this study, a novel synthetic microbial consortium, which is composed of a responsible for detoxification bacterium engineered Pseudomonas putida KT2440 and a lactic acid production specialist Bacillus coagulans NL01, was developed to directly produce lactic acid from highly toxic lignocellulosic hydrolysate. The engineered P. putida with deletion of the sugar metabolism pathway was unable to consume the major fermentable sugars of lignocellulosic hydrolysate but exhibited great tolerance to 10 g/L sodium acetate, 5 g/L levulinic acid, 10 mM furfural and HMF as well as 2 g/L monophenol compound. In addition, the engineered strain rapidly removed diverse inhibitors of real hydrolysate. The degradation rate of organic acids (acetate, levulinic acid) and the conversion rate of furan aldehyde were both 100%, and the removal rate of most monoaromatic compounds remained at approximately 90%. With detoxification using engineered P. putida for 24 h, the 30% (v/v) hydrolysate was fermented to 35.8 g/L lactic acid by B. coagulans with a lactic acid yield of 0.8 g/g total sugars. Compared with that of the single culture of B. coagulans without lactic acid production, the fermentation performance of microbial coculture was significantly improved.ConclusionsThe microbial coculture system constructed in this study demonstrated the strong potential of the process for the biosynthesis of valuable products from lignocellulosic hydrolysates containing high concentrations of complex inhibitors by specifically recruiting consortia of robust microorganisms with desirable characteristics and also provided a feasible and attractive method for the bioconversion of lignocellulosic biomass to other value-added biochemicals.

Introducing a Novel Experimental Model for Osseo-Disintegration of Titanium Dental Implants Induced by Monobacterial Contamination: An In-Vivo Feasibility Study.

Background and Objectives: The aim of the current study was to establish an osseo-disintegration model initiated with a single microorganism in mini-pigs. Materials and Methods: A total of 36 titanium dental implants (3.5 mm in diameter, 9.5 mm in length) was inserted into frontal bone (n: 12) and the basis of the corpus mandible (n: 24). Eighteen implants were contaminated via inoculation of Enterococcus faecalis. Six weeks after implant insertion, bone-to-implant contact (BIC) ratio, interthread bone density (ITBD), and peri-implant bone density (PIBD) were examined. In addition to that, new bone formation was assessed via fluorescence microscopy, histomorphometry, and light microscopical examinations. Results: Compared to the sterile implants, the contaminated implants showed significantly reduced BIC (p < 0.001), ITBD (p < 0.001), and PBD (p < 0.001) values. Around the sterile implants, the green and red fluorophores were overlapping and surrounding the implant without gaps, indicating healthy bone growth on the implant surface, whereas contaminated implants were surrounded by connective tissue. Conclusions: The current experimental model could be a feasible option to realize a significant alteration of dental-implant osseointegration and examine novel surface decontamination techniques without impairing local and systemic inflammatory complications.

Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato.

The use of beneficial microorganisms for the biological control of plant diseases and pests has emerged as a viable alternative to chemical pesticides in agriculture. Traditionally, microbe-based biocontrol strategies for crop protection relied on the application of single microorganisms. However, the design of microbial consortia for improving the reliability of current biological control practices is now a major trend in biotechnology, and it is already being exploited commercially in the context of sustainable agriculture. In the present study, exploiting the microbial library of the biocontrol company Koppert Biological Systems, we designed microbial consortia composed of carefully selected, well-characterized beneficial bacteria and fungi displaying diverse biocontrol modes of action. We compared their ability to control shoot and root pathogens when applied separately or in combination as microbial consortia, and across different application strategies that imply direct microbial antagonism or induced systemic plant resistance. We hypothesized that consortia will be more versatile than the single strains, displaying an extended functionality, as they will be able to control a wider range of plant diseases through diverse mechanisms and application methods. Our results confirmed our hypothesis, revealing that while different individual microorganisms were the most effective in controlling the root pathogen Fusarium oxysporum or the foliar pathogen Botrytis cinerea in tomato, the consortia showed an extended functionality, effectively controlling both pathogens under any of the application schemes, always reaching the same protection levels as the best performing single strains. Our findings illustrate the potential of microbial consortia, composed of carefully selected and compatible beneficial microorganisms, including bacteria and fungi, for the development of stable and versatile biological control products for plant protection against a wider range of diseases.

Parallelism of intestinal secretory IgA shapes functional microbial fitness.

Dimeric IgA secreted across mucous membranes in response to nonpathogenic taxa of the microbiota accounts for most antibody production in mammals. Diverse binding specificities can be detected within the polyclonal mucosal IgA antibody response1-10, butlimited monoclonal hybridomas have been studied to relate antigen specificity or polyreactive binding to functional effects on microbial physiologyin vivo11-17. Here we use recombinant dimeric monoclonal IgAs (mIgAs) to finely map the intestinal plasma cell responseto microbial colonization with a single microorganism in mice. We identify a range of antigen-specific mIgA molecules targeting defined surface and nonsurface membrane antigens. Secretion of individual dimeric mIgAs targeting different antigens in vivo showed distinct alterations in the function and metabolism of intestinal bacteria, largely through specific binding. Even in cases in which the same microbial antigen is targeted, microbial metabolic alterations differed depending on IgA epitopespecificity. By contrast, bacterial surface coating generally reduced motility and limited bile acid toxicity. The overall intestinal IgA response to a single microbe therefore contains parallel components with distinct effects on microbial carbon-source uptake, bacteriophage susceptibility, motility and membrane integrity.

Nitrate modulation of Bacillus sp. biofilm components: a proposed model for sustainable bioremediation.

The presence of different pollutants in wastewater hinder microbial growth, compromise enzymatic activity or compete for electrons required for bioremediation pathway. Therefore, there is a need to use a single microorganism that is capable of tolerating different toxic compounds and can perform simultaneous bioremediation. In the present study, nitrate reducing bacteria capable of decolorizing azo dye was identified as Bacillus subtillis sp. DN using protein profiling, morphological and biochemical tests X-ray diffraction pattern, Raman spectroscopy and cyclic voltammetry confirm that the bacterium under study possesses membrane-bound nitrate reductase and that is capable of direct electron transfer. The addition of nitrate concentrations (0-50mM) resulted in increased biofilm formation with variable exopolysaccharides, protein, and eDNA. Fourier Transform Infrared spectrum revealed the presence of a biopolymer at high nitrate concentrations. Effective capacitance and conductivity of the cells grown in different nitrate concentrations suggest changes in the relative position of polar groups, their relative orientation and permeability of cell membrane as detected by dielectric spectroscopy. The increase in biofilm shifted the removal of the azo dye from biodegradation to bioadsorption. Our results indicate that nitrate modulates biofilm components. Bacillus sp. DN granular biofilm can be used for simultaneous nitrate and azo dye removal from wastewater.

Enhancing the weighted voting ensemble algorithm for tuberculosis predictive diagnosis

Tuberculosis has the most considerable death rate among diseases caused by a single micro-organism type. The disease is a significant issue for most third-world countries due to poor diagnosis and treatment potentials. Early diagnosis of tuberculosis is the most effective way of managing the disease in patients to reduce the mortality rate of the infection. Despite several methods that exist in diagnosing tuberculosis, the limitations ranging from the cost in carrying out the test to the time taken to obtain the results have hindered early diagnosis of the disease. This work aims to develop a predictive model that would help in the diagnosis of TB using an extended weighted voting ensemble method. The method used to carry out this research involved analyzing tuberculosis gene expression data obtained from GEO (Transcript Expression Omnibus) database and developing a classification model to aid tuberculosis diagnosis. A classifier combination of Naïve Bayes (NB), and Support Vector Machine (SVM) was used to develop the classification model. The weighted voting ensemble technique was used to improve the classification model's performance by combining the classification results of the single classifier and selecting the group with the highest vote based on the weights given to the single classifiers. Experimental analysis indicates a performance accuracy of the enhanced ensemble classifier as 0.95, which showed a better performance than the single classifiers, which had 0.92, and 0.87 obtained from SVM and NB, respectively. The developed model can also assist health practitioners in the timely diagnosis of tuberculosis, which would reduce the mortality rate caused by the disease, especially in developing countries.

Effectiveness of indigenous local microorganisms in degrading hexavalent chromium (Cr(VI)) in Batik liquid waste

The batik industry in Indonesia has an IKM (Small and Medium Industry) scale so that it does not yet have adequate waste treatment. In the long term, waste is disposed of directly into the environment which can damage aquatic ecosystems and harm human health. Textile wastewater has a complementary picture and has a deep color. One of the most dangerous heavy metals contained in textile waste is hexavalent chromium (Cr(VI)). Several ways can be done to reduce hexavalent chromium (Cr(VI)) by bioremediation. Based on the results of the literature review, it shows that the bioremediation agents from single isolate microorganisms that are most effective in degrading chromium with high efficiency are Bacillus subtilis and Pseudomonas aeruginosa. The most effective consortium servers with constant reduction rates are the consortium of bacteria genus Mesophilobacter, Methylococcus, Agrobacterium, Neisseria, Xanthobacter, Deinococcus, Sporosarcina, and Bacillus by reducing BOD levels by 85.71%. The hexavalent chromium-degrading microorganisms are characterized by the presence of chromate reductase enzymes, mostly gram-negative bacteria, and a high growth rate.

Association of Oral Microbial Community Dysbiosis and Dental Disorders Among pregnant woman Attending Gatenga Health Center, Kigali, Rwanda

Objective: This study aimed to evaluate the association with the oral microbial community derangement and dental disorders during pregnant. Materials and Methods : A total of 60 pregnant women were selected, of the 60 women, 30 pregnant women had dental disorders, and the remaining 30 did not have dental disorders (control group). The oral swab samples were collected from the women during a routine clinic visit. Samples were transported to INES Ruhengeri Clinical Microbiology Laboratory for microbial identification analysis. Chi-square test (x2) was used to test association with oral microbial community imbalance and dental disorders. Data were analyzed by SPSS version 22. Results Yeast was the most isolated microorganism among both groups of women and stood at 100% and 80%, respectively. The oral microbial community derangement was statistically significant (x2 =52.93, P &lt; 0.00001) to contribute to dental disorders among pregnant women. For single microorganism derangement, Staphylococcus aureus (x2 = 5, P = 0.025347), Enterobacter spp. (x2 =7.4, P = 0.006522), and Staphylococcus spp. (x2 = 30, P &lt; 0.00001) were statistically significant to contribute to dental disorders. Conclusions: Pregnancy leads to oral microbiota dysbiosis which is a risk factor for dental disorders among pregnant women. Women should seek dental consultation during pregnancy for early detection and management of dental disorders.

A novel relationship for the maximum specific growth rate of a microbial guild

One of the major parameters that characterizes the kinetics of microbial processes is the maximum specific growth rate. The maximum specific growth rate for a single microorganism (${\mu _{max}}$) is fairly constant. However, a certain microbial process is typically catalyzed by a group of microorganisms (guild) that have various ${\mu _{max}}$ values. In many occasions, it is not feasible to breakdown a guild into its constituent microorganisms. Therefore, it is a common practice to assume a constant maximum specific growth rate for the guild ($\acute{\mu}_{max}$) and determine its value by fitting experimental data. This assumption is valid for natural environments, where microbial guilds are stabilized and dominated by microorganisms that grow optimally in those environments' conditions. However, a change in an environment's conditions will trigger a community shift by favoring some of the microorganisms. This shift leads to a variable ${\acute{\mu}_{max}}$ as long as substrate availability is significantly higher than substrate affinity constant. In this work, it is illustrated that the assumption of constant ${\acute{\mu}_{max}}$ may underestimate or overestimate microbial growth. To circumvent this, a novel relationship that characterizes changes in ${\acute{\mu}_{max}}$ under abundant nutrient availability is proposed. The proposed relationship is evaluated for various random microbial guilds in batch experiments.

Necrotizing Enterocolitis and Intestinal Microbiota: The Timing of Disease and Combined Effects of Multiple Species

Background: The purpose of this study was to investigate the relationship between intestinal microbiota and necrotizing enterocolitis (NEC).Methods: 16S rRNA gene sequencing was used to compare the microbial composition of feces. The first sample was collected within 48 h after birth, then once per week until the NEC diagnosis, and finally 1–2 weeks after treatment or 28 days after birth.Results: The alpha diversity of the microbiota in the NEC group was higher than that in the control group. Beta diversity analysis showed that the control group had a higher similarity at the onset of NEC, while the NEC group was distributed in subgroups. Linear discriminant analysis effect size and taxonomic composition analyses indicated that the abundance of Bacteroides and Actinobacteria in NEC infants at birth was much higher than that in the control group, and this trend continued until NEC occurred. At this time, Rhizobiales, Dysgonomonas, Ochrobactrum, Ralstonia, Pelomonas, Acinetobacter, etc., were also more abundant in NEC infants. The upregulated different metabolic pathways in the NEC group were mainly concentrated on degradation/utilization/assimilation, biosynthesis, and generation of precursor metabolites and energy.Conclusions:1. The microbial community differs according to the time of NEC diagnosis (bounded by 20 days).2. No single microorganism is related to NEC, and the combined effect of multiple species is of great significance in the occurrence of NEC. Premature infants are easily affected by bacteria living in the environment, and compared with ordinary premature infants, NEC infants have a higher abundance of waterborne bacteria. Therefore, attention should be paid to the contamination of water sources and various ventilator pipelines for premature infants hospitalized in the neonatal intensive care unit.3. An in-depth study of the mode of microbial colonization in premature infants combined with the different functions of various metabolic pathways involved in different microorganisms may be able to identify the cause of NEC.