Classification Of Microorganisms Research Articles

Application of 16S rDNA Sequencing Technology in the Analysis of Pathogenic Bacteria in Sputum of Severe Pneumonia

The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. Therefore, early diagnosis is of great significance to the prognosis of patients. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis.

Classification of Intestinal Microorganisms Cultured from the Feces of Pet Dogs Fed Commercial Feed

The purpose of this study was to investigate the microorganisms found in the intestines of dogs fed commercial feed though the aerobic culture of dog excrement. 16 specimens of pet dog feces were cultured employing BAP, MaC, and EMB medium. Strains of Escherichia coli were detected in all the cultured specimens, along with a few other bacteria of significance. All 16 samples were identified as containing multiple E. coli strains using a API20E kit. Two samples showed a swarming phenomenon in the BAP medium that was identified as a Proteus mirabilis strain. In 10 samples, only E. coli species were identified, while E. coli species and P. mirabilis species were identified in 2 samples. A small number of E. coli and gram-positive bacteria were detected in 3 specimens, and a small number of E. coli and gram-positive rods were detected in one specimen. It has been shown that E. coli is predominantly distributed in the feces of dogs fed with commercial feed. The fact that E. coli is distributed in the feces of dogs is of concern as it can cause serious problems such as water pollution and food poisoning.

Rapid Proteomic Profiling by MALDI-TOF Mass Spectrometry for Better Brain Tumor Classification.

Glioblastoma is one of the most aggressive primary brain cancers. The precise grading of tumors is important to adopt the best follow-up treatment but complementary methods to histopathological diagnosis still lack in achieving an unbiased and reliable classification. To progress in the field, a rapid Matrix Assisted Laser Desorption Ionization - Time of Flight Mass spectrometry (MALDI-TOF MS) protocole, devised for the identification and taxonomic classification of microorganisms and based on the analysis of whole cell extracts, was applied to glioma cell lines. The analysis of different human glioblastoma cell lines permitted to identify distinct proteomic profiles thus demonstrating the ability of MALDI-TOF to distinguish different malignant cell types. In the study, the authors showed the ability of MALDI-TOF profiling to discriminate glioblastoma cell lines, demonstrating that this technique could be used in complement to histological tumor classification. The proposed procedure is rapid and inexpensive and could be used to improve brain tumors classification and help propose a personalized and more efficient treatment.

Metagenomic Investigation of Bacterial and Archaeal Diversity of Hammam Essalihine Hot Spring from Khenchela, Algeria

Hot springs are natural environments where hot groundwater comes out from the earth. Exploring the microbial diversity present in hot springs is important first to determine the microorganisms able to proliferate there and to understand their role in biogeochemical cycles. In Algeria, research concerning microbial populations in those ecosystems is limited. This study describes bacterial and archaeal diversity of the ‘Hammam Essalihine’ hot spring in Khenchela province in north-east Algeria using a culture-independent approach. This is the first microbial diversity investigation in the ‘Hammam Essalihine’ hot spring using next-generation sequencing techniques to assess the species classification of thermophilic microorganisms. Genomic DNA was extracted from water samples and the V4–V5 region of 16S rRNA gene were amplified, sequenced, and analyzed. The average temperature of water varies from 68 to 70 °C. High-throughput sequencing analysis revealed the presence of 21 bacterial phyla, including an unknown phylum and distributed across 42 families and 39 genera. The majority of the sequences were observed to belong to the kingdom Bacteria. The bacterial community from this hot spring is dominated by Proteobacteria (41.52%), Chloroflexi (7.62%), and Bacteroidetes (7.62%), whereas the community of Archaea is scarcely present in the study site and the two identified operational taxonomic units (OTUs) are far from what is known in the GenBank database. The study shows several uncharacterized sequences, indicating that the water of ‘Hammam Essalihine’ hot spring contains undescribed microorganisms. This study is thought to add to the understanding of thermophile diversity and ecology of ‘Hammam Essalihine’ hot spring.

Microbial characteristics of culturable fungi and bacteria in aerosol particles of a coastal region

In this study, atmospheric bioaerosol particles were collected from March to December 2015 in the coastal region of Qingdao. The dominant fungi were identified, and the concentrations and size distributions of bacteria, total fungi and dominant fungi were measured. The most dominant fungal taxon was Cladosporium, followed by Alternaria, Penicillium and Aspergillus. The concentrations of fungi showed significant seasonal variation (p 7.0 μm. The size patterns of the four dominant fungi were distinct due to their respective properties. With correlation analysis, we found PM10, CO and NO2 were positively associated with the bacterial concentration. The factors correlated with fungal concentrations included temperature, relative humidity, CO, NO2, SO2 and O3. The results of RDA showed that the most important meteorological factors affecting the microorganism species composition were temperature and relative humidity, and the dominant air pollutants were SO2, CO and O3. We selected related parameters to conduct multiple linear regression analysis to explore the synergistic effects on a given microorganism. The contribution to the rate of changes in bacterial and fungal concentrations caused by related factors was less than 30%, indicating that the sources and community changes had a great influence on bioaerosol concentrations. The more detailed the classification of microorganisms is, the more specific correlation information may be obtained through our analysis method.

Penile Implant Infection: Experience With Expanded Salvage Criteria and a Shortened Course of Postoperative Antibiotics.

IntroductionThe preferred treatment for inflatable penile prosthesis (IPP) infection includes antibiotic therapy, device removal, and immediate replacement. While this is an accepted procedure, the delivery and length of postoperative antibiotics are not standardized. Furthermore, historical salvage criteria may be overly restrictive given the new salvage techniques.AimOur aim is to determine if an expanded salvage criteria and shorter course of antibiotics demonstrate acceptable IPP infection rates.MethodsWe retrospectively reviewed 466 consecutive IPP cases from a single surgeon between March 2014 and March 2019. Salvage and reinfection were determined by current procedural terminology codes, and the final cohort was individually reviewed for integrity. Demographic, operative, and culture data from each patient were obtained. All patients were discharged on oral antibiotics after initial salvage. Patients were not excluded for exposed hardware, immunosuppression, tissue necrosis, severe diabetes, or corporal purulence. Owing to the small sample size, only descriptive statistics were used to describe the final cohort.Main Outcome MeasuresThe main outcome measures were classification of microorganisms cultured at the time of salvage and salvage failure rate.ResultsA total of 26 cases of IPP infections (6%) were identified. The median (interquartile ratio) age and body mass index were 62 (58–66) and 32 (28–34), respectively. During initial salvage, gross purulence was noted in 9 patients (35%), and 22 patients (84%) had a malleable prosthesis placed. The most prescribed postoperative antibiotic was Bactrim/Augmentin with a median (interquartile ratio) antibiotic duration of 14 days (11–14). After IPP salvage, 2 patients (8%) developed a reinfection while on oral antibiotics. One of those patients was immunosuppressed, and the other was infected with Candida glabrata.ConclusionExpanded salvage criteria and postoperative oral antibiotic duration of at least 14 days demonstrated an acceptable infection rate. This suggests that a longer antibiotic therapy may not be necessary.Chandrapal J, Harper S, Davis LG, et al. Penile Implant Infection: Experience With Expanded Salvage Criteria and a Shortened Course of Postoperative Antibiotics. Sex Med 2020;8:383–387.

Forensic Microbiology, an Important Tool in Crime Investigation

Forensic science is the application of science to civil and criminal laws, also called as “criminalistics”. Its branches are rooted in every branch of science and many other aspects of modern society. Forensic scientists are responsible to analyze scientific evidence during the course of investigation either by travelling to the scene of the crime or by performing analysis on objects in the laboratory. Forensic microbiology is the science by which microorganisms ‘behaviors are used to determine the origin of a particular microbial strain, the path of an outbreak or the identity of a criminal. Recently there has been a significant development in forensic microbiology as a result of the significant development in molecular biology, microbiology and biochemistry sciences. It was found that the rapid identification and classification of infectious microorganisms are of great importance in the case of biological and microbial threat, and the analysis of the microbial genome sequence, whose cost has decreased significantly in recent years, greatly helps in this area.

General principles of antibiotic resistance evolution in bacteria (review of literature).

Currently, the impact of antibiotic resistance on human health is a worldwide problem and its study is of great interest from a molecular genetic, environmental and clinical view-point. This review summarizes the latest data about antibiotic resistance, the classification of microorganisms as sensitive and resistant to the action of antibiotics, reveals the concept of minimum inhibitory concentration from modern positions. The resistance of microorganisms to antibacterial agents can be intrinsic and acquired, as well as being one of the examples of evolution that are currently available for study. Modern methods of whole-genome sequencing and complex databases of nucleotide-tagged libraries give an idea of the multifaceted nature of the mechanisms of intrinsic resistance to antibiotics and are able to provide information on genes encoding metabolic enzymes and proteins that regulate the basic processes of the physiology of bacteria. The article describes the main ways of spreading the resistance of microorganisms, reflects the concepts of "founder effect" and the fitness cost of bacteria, which underlie the emergence and evolution of antibiotic resistance. It is shown that the origin of antibiotic resistance genes that human pathogens currently possess can be traced by studying the surrounding not only clinical, but also non-clinical (ecological) habitats. As well as microorganisms of the surrounding ecosystems are the donors of resistance genes in horizontal gene transfer.

Correction to: Microbial synergy and stoichiometry in heap biooxidation of low-grade porphyry arsenic-bearing gold ore.

In the original publication the section heading "Classification of microorganisms" appearing above the sub-section "Air and liquid circulation in the heap" in page four is incorrect. The correct section heading should be read as "Results and discussion".

A Rapid and Simple Method for Screening Microorganisms with a Potential for Catechol Biodegradation

Catechol is a highly toxic compound that is also a key intermediate in biodegradation pathways of various aromatic compounds. In this paper, a new screening method for isolation of microorganisms with the potential for catechol biodegradation is reported. The method described is based on the ability of catechol to form a color complex with Fe3+ ions. For this purpose, basal medium that is widely used for classification of microorganisms by carbon requirements was used. Specifically, minimal Bushnell Haas medium plates supplemented with catechol at 500 mg l−1 concentration were used for both yeast and bacteria cultivation. After appearance of microorganism colonies on the growth medium, each plate was flooded with 7.0 ml of 5% (w/v) of FeCl3 and incubated for a period of 5 min at room temperature. Flooding with this solution led to the formation of a green color from Fe3+-catechol complexes in the growth medium and an appearance of clear zones around colonies of microorganisms that utilize catechol as a sole source of carbon. Based on this, the presented method could be useful as a screening step for microorganisms with a potential for catechol biodegradation.

Improved MALDI-MS method for the highly sensitive and reproducible detection of biomarker peaks for the proteotyping of Salmonella serotypes.

The rapid identification and classification of pathogenic microorganisms, including Salmonella enterica, is important for the surveillance and prevention of foodborne diseases. Matrix-assisted laser desorption\ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been shown to be an effective tool for the rapid identification of microorganisms. In a previous report, a mass database consisting of 12 biomarker proteins, S8, L15, L17, L21, L25, S7, superoxide dismutase (SodA), peptidylprolyl cis-trans isomerase C, Gns, YibT, YaiA, and YciF, was introduced for the serotyping of S. enterica via MALDI-MS (Applied Microbiology and Biotechnology, 2017, 101, 8557-8569). However, the reproducibility of peak detection of biomarkers such as SodA at m\z 23 000 was poor. We report here an optimized MALDI-MS method for detecting these biomarkers with high sensitivity and reproducibility. The issue was solved by controlling the bacterial concentration at 1 × 10 to 1 × 102 MFU (3 × 106 to 3 × 107 CFU\μL, as calculated from the MFU), using the colony suspension supernatant obtained by centrifugation, and using matrix additives such as methylenediphosphonic acid and N-decyl-β-D-maltopyranoside. We propose that the method including the above steps is one of the best for detecting biomarkers with high sensitivity and reproducibility.

Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry.

Rapid and accurate identification of microorganisms and estimation of their biomasses are of extreme importance to public health. Mass spectrometry has become an important technique for these purposes. Previously we published a workflow named Microorganism Classification and Identification (MiCId v.12.26.2017) that was shown to perform no worse than other workflows. This manuscript presents MiCId v.12.13.2018 that, in comparison with the earlier version v.12.26.2017, allows for biomass estimates, provides more accurate microorganism identifications (better controls the number of false positives), and is robust against database size increase. This significant advance is made possible by several new ingredients introduced: first, we apply a modified expectation-maximization method to compute for each taxon considered a prior probability, which can be used for biomass estimate; second, we introduce a new concept called ownership, through which the participation ratio is computed and use it as the number of taxa to be kept within a cluster of closely related taxa; third, based on confidently identified peptides, we calculate for each taxon its degree of independence from the rest of taxa considered to determine whether or not to split this taxon off the cluster. Using 270 data files, each containing a large number of MS/MS spectra, we show that, in comparison with v.12.26.2017, version v.12.13.2018 yields superior retrieval results. We also show that MiCId v.12.13.2018 can estimate species biomass reasonably well. The new MiCId v.12.13.2018, designed to run in Linux environment, is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Microscopic Characterization of Biological and Inert Particles Associated with Spacecraft Assembly Cleanroom

NASA cleanrooms are certified by particle counts and are humidity-controlled, temperature-regulated, and oligotrophic in nature for assembling spacecraft subsystems. Microorganisms, which are not part of the cleanroom certification metrics, should not be overlooked when assessing the cleanliness of the facility since they can enter through soil or air, shed from humans, adapt to the oligotrophic conditions, and subsequently could contaminate spacecraft. These biogenic particles need to be identified to extend our knowledge of biological contamination for future NASA mission use. This study collected particles from the cleanroom and estimated the distribution of fallout microbial cell and inert dust particles using microscopy and molecular techniques. Aluminum coupon-based polycarbonate filter assemblies were deployed in the spacecraft assembly cleanroom facility to collect fallout particles. Epifluorescence and electron microscopy showed that particles varied in size and structure, and displayed live/dead biological and inert particle signatures from sources that include spores and fungal hyphae. Additionally, correlative epifluorescence and field emission scanning electron microscopy, combined with energy-dispersive X-ray analysis (for elemental compositions) methods, differentiated whether microbes adhering to particles were live/dead cells or inert particles. This visualization approach allowed for the classification of microorganisms as being standalone (free-living) or associated with a particle, as well as its characteristic size. Furthermore, time-course microscopy was used to determine the microbial cell growth and confirm the biological/molecular identification. Routine investigation of cleanroom biological and inert fallout particles will help to determine the biological load of spacecraft components and will also have direct relevance to the pharmaceutical and medical industries. One of the main objectives for NASA’s current and future missions is to prevent forward and back contamination of exploring planets. The goal of this study is to determine the association of microorganisms with the inert, natural cleanroom fallout particles and to ascertain whether microorganisms prefer to adhere to a particle size. A novel microscopy technique was developed, and by utilizing various molecular techniques, particles and associated microbial phylogeny were characterized. An accurate assessment of the microbes associated with cleanroom particles is necessary to protect the health of the people who occupy the room for long duration for aeronautical, medical, and pharmaceutical industries.

Assessing alignment-based taxonomic classification of ancient microbial DNA.

The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.

Аспекти використання особливостей лазерного випромінювання для оптимізації діагностичних методів при курації пацієнтів з генералізованими захворюваннями пародонта

The aim of the research is to study the possibilities of using laser radiation (biofluorescence, elastic scattering) for diagnostic purposes to optimize and identify periodontopathogenic microorganisms. Materials and methods. For the biofluorescence fixation experiment, we used a 632.8 nm helium neon laser, 3mW; a 668 nm Lika surgeon M semiconductor laser, 30–250 mW; the Ocean Optics USB4000 miniature fiber optic spectrometer; quartz light guides, tripods; reference strains of microorganisms: Escherichia coli, Candida albicans, Klebsiella pneumoniae, Proteus mirabilis, Corynebacterium pseudodiphtheriae, Staphylococcus aureus, Staphylococcus epidermidis cultured on agar; a laptop with SpectraSuite software. The elastic scattering angular distribution was analyzed on the developed experimental platform. The excitation source was a 532 nm continuous-wave (CW) laser (TEM00 mode) with a power of &lt;50 mW. The elastic scattering angular distribution in the anterior and posterior hemispheres for aqueous suspensions of Staphylococcus aureus and Escherichia coli was investigated. Results. During the first part of the experiment, the colonies of the reference microorganisms were alternately irradiated by laser radiation beam first from neon laser helium, then from semiconductor laser. The reflection spectrum was recorded by the Ocean Optics USB4000 spectrometer and processed on a laptop using SpectraSuite software. The samples were irradiated at different angles (90 °, 45 °) in the dark, on a dark substrate. The radiation power of helium neon laser was stable – 3mW, and the radiation power of semiconductor varied in the range of 30-100mW. After irradiation of all the samples of cultures, as described above, and after the spectrograms processing, we did not get confirmation of the theory of biofluorescence: basically the spectrometer recorded only the spectrum of the reflected laser radiation. In the second part of the experiment, we investigated the elastic scattering angular distribution in the anterior and posterior hemispheres for aqueous suspensions of Staphylococcus aureus and Escherichia coli which have different spatial form factors. It was shown that complete integral extinction into the anterior hemisphere is linearly proportional to the bacterial concentration estimated by the McFarland standard on a certified device. A more detailed analysis of the elastic scattering angular distribution showed that the suspension of Staphylococcus aureus had a decrease in scattering in the anterior hemisphere and enhanced scattering in the posterior hemisphere compared with a suspension of bacteria Escherichia coli. The presented method can be applied to solve the problem of classification of microorganisms by the modelling of the elastic scattering angular distribution on the basis of models of elementary scatters with different form factors according to the Mie theory. Conclusion. The experiments on the study of biofluorescence of colonies of bacteria have not confirmed the possibility of recording specific spectra from each of the strains. However, the results of the study of elastic scattering in the suspensions of microorganisms indicated the possibility of determining the structural and concentration features of their content, namely to differentiate the rod shaped flora from the coccoid, and to estimate the relative number of particles in the suspension. The development of this technology can greatly simplify the diagnostics without the use of expensive and technologically difficult research methods in the future Key words: periodontal pathogen, biofluorescence, Mie theory, intensity of elastic optical scattering.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple “fingerprinting”; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.Graphical ᅟ

Potential Producers of Biogenic Magnetic Nanoparticles among Pathogenic and Opportunistic Microorganisms

Проблематика. Ускладнені форми інфекції при запальних процесах характеризуються зростанням резистентності мікрофлори до антибіотиків, що змушує шукати нові способи лікування, які б запобігали розвитку патогенних мікроорганізмів, підвищували місцевий імунітет і тим самим прискорювали регенеративні процеси. Мета. Метою роботи є класифікація патогенних та умовно-патогенних мікроорганізмів, які можуть бути потенційними продуцентами біогенних магнітних наночастинок (БМН), на предмет локалізації та властивостей БМН за допомогою методів порів­няльної геноміки з перспективою їх подальшого використання як магнітокерованих векторів для цільової доставки лікарських препаратів. Це дасть змогу використовувати методи гіпертермії для знешкодження патогенних та умовно-патогенних мікроорганізмів, які здатні до біомінералізації БМН, застосовуючи для нагріву клітин безпосередньо внутрішньоклітинні БМН цих мікроорганізмів. Методика реалізації. У роботі застосовано методи попарного та множинного вирівнювання з використанням вільної в доступі програми “BLAST” Національного центру біотехнологічної інформації. Результати. Виявлено, що такі штами, як E. coli (541-15), K. pneumoniae 342, C. perfringens str. 13 , P. fluorescens , є потенційними продуцентами саме кристалічного магнетиту, а мікроорганізми S. aureus RF122, S. suis BM407 , E. aerogenes KCTC 2190 , K. pneumoniae RYC492 , P. aeruginosa M18 можуть бути продуцентами внутрішньоклітинних аморфних БМН. Сила магнітодипольної взаємодії між БМН бактерій і БМН пухлин становить 10 - 7 –10 - 8 Н. Висновки. Пояснюється ефект знешкодження патогенних мікроорганізмів за допомогою методу магнітної гіпертермії за рахунок наявності БМН. Запропоновано використовувати для лікування гнійно-запальних процесів не тільки антибіотичні препарати, але й електромагнітні поля для тих мікроорганізмів, які є продуцентами БМН. Показано, що як вектори для цільової доставки лікарських препаратів доцільно використовувати мікроорганізми з природними магнітними властивостями, що зробить метод цільової доставки препаратів надійнішим та більш ефективним і зменшить його вартість.

New approaches in the systematics of rickettsiae.

The development of a formal order analysis (FOA) allowed constructing a classification of 49 genomes of Rickettsiaceae family representatives. Recently FOA has been extended with new tools—‘Map of genes,’ ‘Matrix of similarity’ and ‘Locality-sensitive hashing’—for a more in-depth study of the structure of rickettsial genomes. The new classification confirmed and supplemented the previously constructed one by determining the position of Rickettsia africae str. ESF-5, R. heilongjiangensis 054, R. monacensis str. IrR/Munich, R. montanensis str. OSU 85-930, R. raoultii str. Khabarovsk, R. rhipicephali str. 3-7-female6-CWPP and Rickettsiales bacterium str. Ac37b. The ‘Map of genes’ demonstrated the complete genomes and their components in a graphical form. The ‘Matrix of similarity’ was applied for an in-depth classification to a subtaxonomic category of the strain within the species R. rickettsii (11 strains) and R. prowazekii (ten strains). The ‘Matrix of similarity’ determines the degree of homology of complete genomes by pairwise comparison of their components and identification of those being identical and similar in the arrangement of nucleotides. A new genomosystematics approach is proposed for the study of complete genomes and their components through the development and application of FOA tools. Its applications include the development of principles for the classification of microorganisms, based on the analysis of complete genomes and their annotations. This approach may help in the taxonomic classification and characterization of some Candidatus Rickettsia spp. that are found in large numbers in arthropods worldwide.

Colmena: colección de microorganismos edáficos y endófitos nativos, para contribuir a la seguridad alimentaria nacional

Colmena (www.itson.mx/colmena), es una colección de microorganismos enfocada en la conservación, clasificación, caracterización, y transferencia de microorganismos nativos aislados de diversos agro-sistemas, y otros hábitats. El objetivo de esta colección es resguardar la diversidad microbiana asociada a los cambios de uso de suelo, disminuyendo la degradación de los suelos. Hasta el momento, microorganismos del suelo de dos importantes regiones agrícolas en México han sido aislados, el Valle del Yaqui, Sonora y el Valle del Fuerte, Sinaloa. Actualmente, colmena conserva aproximadamente 1 464 cepas de microorganismos edáficos asociadas a diversos cultivos agrícolas, tales como: trigo (448), maíz (313), alfalfa (54), brócoli (51), frijol (35), entre otros. Recientemente, la clasificación taxonómica de 353 cepas bacterianas y fúngicas -mediante la amplificación de los genes 16S RNAr y 5.8S RNAr- ha sido concluida, observando que los géneros bacterianos más abundantes son Bacillus (27%), Pseudomonas (8%) y Stenotrophomonas (6%), mientras que los géneros fúngicos más abundantes fueron Aspergillus (8%), Penicillium (3%) y Myrothecium (3%). Por otra parte, también se llevó a cabo la caracterización metabólica de una fracción de la colección, encontrando que 3% de la colección microbiana tiene la capacidad de producir de índoles (&gt; 5 mg/L), la solubilización de fósforo y producción de sideróforos fue observada en 36% y 61% de las cepas analizadas (396), respectivamente. Solo 3% de la colección microbiana total ha sido identificada como productora de celulasas y 11% de un total de 258 cepas analizadas presentaron β-hemolisis. Estos resultados muestran la versatilidad de estas cepas microbianas como alternativas potenciales costo-efectivas para prácticas agro-industriales, enfocadas a contribuir a la seguridad alimentaria global. &#x0D;

Environmental microorganism classification using conditional random fields and deep convolutional neural networks

The labeling of Environmental Microorganisms (EM) which help decomposing pollutants, plays a fundamental role for establishing sustainable ecosystem. We propose an environmental microorganism classification engine that can automatically analyze microscopic images using Conditional Random Fields (CRF) and Deep Convolutional Neural Networks (DCNN). First, to effectively represent scarce training images, a DCNN pre-trained for image classification using a large amount of data is re-purposed to our feature extractor that distils pixel-level features in microscopic images. In addition, pixel-level classification results by such features can be refined using global features that describe the whole image in toto. Finally, our CRF model localizes and classifies EMs by considering the spatial relations among DCNN-based features, and their relations to global features. The experimental results have shown 94.2% of overall segmentation accuracy and up to 91.4% mean average precision of the results.