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Journal articles on the topic 'Database of microorganisms'
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Brovarnyk, V. V., and T. M. Golovach. "Database for Depositary Department of Microorganisms." Mikrobiolohichnyi Zhurnal 77, no. 5 (September 30, 2015): 81–86. http://dx.doi.org/10.15407/microbiolj77.05.081.
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Nakano, Y., Y. Shibata, M. Kawada, M. Kojima, H. Fukamachi, Y. Shibata, S. Okano, K. Matsushima, Y. Abiko, and Y. Yamashita. "A searchable database for proteomes of oral microorganisms." Oral Microbiology and Immunology 20, no. 6 (December 2005): 344–48. http://dx.doi.org/10.1111/j.1399-302x.2005.00235.x.
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Prabha, Ratna, Dhananjaya P. Singh, and Anil Rai. "StressMicrobesInfo: Database of Microorganisms Responsive to Stress Conditions." Interdisciplinary Sciences: Computational Life Sciences 8, no. 3 (August 12, 2015): 203–8. http://dx.doi.org/10.1007/s12539-015-0102-2.
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Jenkins, T. M., T. M. Scott, J. R. Cole, S. A. Hashsham, and J. B. Rose. "Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases." Water Science and Technology 50, no. 1 (July 1, 2004): 309–14. http://dx.doi.org/10.2166/wst.2004.0072.
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Virulence-factor activity relationship (VFAR) is a concept that was developed as a way to relate the architectural and biochemical components of a microorganism to its potential to cause human disease. Development of these relationships requires specialised bioinformatics databases that do not exist at present. A pilot-scale VFAR database was designed for three different waterborne organisms: Escherichia coli, Norovirus and Cryptosporidium, to evaluate VFAR relationships. For the web-based database, each organism has separate pages containing virulence genes, occurrence genes, primer sets and probes, taxonomy, outbreaks, and serotype/species/genogroup/genotype. As the database continues to grow, it will be possible to relate the occurrence and prevalence of certain genes in various microorganisms to outbreak data and, subsequently, to establish the utility of using a combination of specific genes as markers of virulence and in establishing virulence-factor activity relationships (VFARs). The database and the VFARs established will be of use to the regulatory community as a way to assist with prioritising those organisms, which need to be regulated.
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Medvedeva, S. E., A. N. Boyandin, Yu P. Lankin, D. A. Kotov, T. V. Kargatova, E. K. Rodicheva, and L. Yu Popova. "A database on natural and transgenic luminous microorganisms: BiolumBase." Microbiology 74, no. 2 (March 2005): 236–43. http://dx.doi.org/10.1007/s11021-005-0057-0.
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HIRAISHI, Akira, Hironori IWANO, Kazuyo SATO, Takeshi MATSUMURA, and Tadashi KOISHIZAWA. "Improved Database Management System for Surveillance of Drug-Resistant Microorganisms." JOURNAL OF THE JAPANESE ASSOCIATION OF RURAL MEDICINE 58, no. 1 (2009): 34–38. http://dx.doi.org/10.2185/jjrm.58.34.
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Steindel, Steven J., and Marianne K. Simon. "Characterization of Microorganism Identification in the United States in 1996." Archives of Pathology & Laboratory Medicine 125, no. 7 (July 1, 2001): 913–20. http://dx.doi.org/10.5858/2001-125-0913-comiit.
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Abstract Context.—The National Inventory of Clinical Laboratory Testing Services (NICLTS) was designed to give an unbiased estimate of all patient testing performed by laboratories registered under the Clinical Laboratory Improvement Amendments in 1996. Objective.—Survey data were used to develop a profile of laboratory testing primarily intended to identify microorganisms or antibodies to these microorganisms. Design.—Estimates of the extent of microorganism identification were derived from the NICLTS database by identifying associated tests and methods. The volumes for tests performed at locations that primarily prepared blood components for distribution were excluded. Organisms of public health importance were identified from the National Notifiable Disease list maintained by the Centers for Disease Control and Prevention. Participants.—Laboratories that were enrolled in the 1996 Online Certification Survey and Reporting System, maintained by the US Health Care Finance Administration, and that performed laboratory testing in 1996. Outcome Measure.—Estimated volumes and associated confidence limits by test, method, specimen type, public health importance, and testing location. Results.—Excluding testing of the blood supply, 315 million tests (95% confidence limits, 280–354 million tests) were performed in the United States for microorganism identification. Those tests for which public health consensus requires national reporting represented 38% of this total. Although hospitals performed 46% of all microorganism identification, they only performed 33% of the testing for microorganisms of public health importance. Independent and specialty laboratories performed 38% of all testing but 65% of the testing for microorganisms of public health importance. Direct methods (methods not involving culture) were used in 77% of the tests for microorganisms of public health importance and in 42% of all identification tests. Conclusions.—The distribution of microorganism identification testing found using NICLTS data is consistent with plans to modernize the public health surveillance system in the United States.
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Hernández-Rosas, Francisco, Katia A. Figueroa-Rodríguez, Luis A. García-Pacheco, Joel Velasco-Velasco, and Dora M. Sangerman-Jarquín. "Microorganisms and Biological Pest Control: An Analysis Based on a Bibliometric Review." Agronomy 10, no. 11 (November 17, 2020): 1808. http://dx.doi.org/10.3390/agronomy10111808.
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The use of microorganisms for biological pest control as biological control agents (BCAs) and biopesticides was developed worldwide in the 1960s. Despite the abundance of reviews published on this topic, no meta-analysis using bibliometric tools has been published. The objective of this study was to determine patterns of research on microorganisms for the biological control of pests, based on publications available in the SCOPUS® database. The data were obtained from the Elsevier® Scopus meta-database using the search terms “biological pest control” and “microorganism” (title, abstract, and keywords). The main publications were identified, along with the journals, countries, and institutions that have published on the subject. The data were analyzed with VOSviewer to determine the co-occurrence of terms, and four maps were generated. The results show two phases in the scientific research on the subject: The first is the characterization of biological control agents, and the second is focused on the commercial development of biopesticides and biological control agents. The most recent research emphasizes the discovery of new species and strains that have commercial potential, with an emphasis on genetic engineering and biotechnology.
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Ellis, L. B. M. "The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction." Nucleic Acids Research 28, no. 1 (January 1, 2000): 377–79. http://dx.doi.org/10.1093/nar/28.1.377.
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Hari, Kumar L., Alan T. Goates, Ravi Jain, Aaron Towers, Vanessa S. Harpin, James M. Robertson, Mark R. Wilson, et al. "The Microbial Rosetta Stone: a database system for tracking infectious microorganisms." International Journal of Legal Medicine 123, no. 1 (July 8, 2008): 65–69. http://dx.doi.org/10.1007/s00414-008-0247-1.
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ZWIETERING, MARCEL H., TACO WIJTZES, JACORA C. DE WIT, and KLAAS VAN'T RIET. "A Decision Support System for Prediction of the Microbial Spoilage in Foods." Journal of Food Protection 55, no. 12 (December 1, 1992): 973–79. http://dx.doi.org/10.4315/0362-028x-55.12.973.
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A method was developed to combine qualitative and quantitative information to predict possible growth of microorganisms in foods. The pH, water activity, temperature, and oxygen availability of foods are coupled to the growth characteristics of microorganisms. Therefore, a database with characteristics of foods and a database of kinetic parameters of microorganisms were built. In the first database, a tree structure based on physical similarity was built, for the case that information about the characteristics of a particular food is unknown. By comparing with similar products at the same level of the tree or the level above, the product information can be estimated. A method is developed to make an estimation of the microbial growth kinetics on the basis of models. This is done by introducing a growth factor, which can be calculated on the basis of readily available data from literature. Since all the information can be altered, the system can give better predictions when more and more accurate information is added.
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Shi, Wenyu, Qinglan Sun, Guomei Fan, Sugawara Hideaki, Ohkuma Moriya, Takashi Itoh, Yuguang Zhou, et al. "gcType: a high-quality type strain genome database for microbial phylogenetic and functional research." Nucleic Acids Research 49, no. D1 (October 29, 2020): D694—D705. http://dx.doi.org/10.1093/nar/gkaa957.
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Abstract Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
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Alizadeh, Maryam, Leila Yousefi, Farzaneh Pakdel, Reza Ghotaslou, Mohammad Ahangarzadeh Rezaee, Ehsaneh Khodadadi, Mahin Ahangar Oskouei, Mohammad Hossein Soroush Barhaghi, and Hossein Samadi Kafil. "MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology." Advances in Pharmacological and Pharmaceutical Sciences 2021 (May 7, 2021): 1–8. http://dx.doi.org/10.1155/2021/9928238.
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There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS’s crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.
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Kazantsev, F. V., A. A. Smirnova, A. S. Rozanov, Yu E. Uvarova, D. A. Afonnikov, S. E. Peltek, and S. A. Lashin. "Information system on microbial collections as a part of bioresource collections portal for Russia’s FASO organizations: a working protocol." Vavilov Journal of Genetics and Breeding 22, no. 2 (April 8, 2018): 279–84. http://dx.doi.org/10.18699/vj18.361.
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Nowadays, many scientific organizations of Russia own collections of microorganisms on which large volumes of information have been generated. These data represent the descriptions of objects of diverse nature (bacteria, archaea, fungi, protists) and their properties, which have been carefully collected and cataloged by generations of researchers. Not every organization that has such collections has an open access electronic catalog, which not only complicates work with these unique materials, but also even hides the fact of the existence of such collections. This state of affairs requires the development of electronic resources for presenting these materials to the scientific community. To put together the information on microorganism collections, we have developed an internet portal (http://www.biores.cytogen.ru/microbes/) of microbial bioresource collections of FASO organizations in the Russian Federation. The portal was created under the project developing the information system for bioresource collections of FASO institutes. It is a platform where collection organizations can place information about the storage units of their collections, as well as other information on collections, including links to their own catalogs. In this paper, we describe the principles of working with the portal. The portal’s graphical interface allows users, both registered and unregistered, to receive the following information about collections of microorganisms: a list of collections represented in the database, contact details of the organization and information about the curator of the collection, summary statistics for each collection, as well as information on storage units. Registered users – owners of collections – have the opportunity to create and modify records about the storage units of their collections, and to update their description. To automate work with the portal, software access to the database through the REST API has been implemented (http://api.biores.cytogen.ru/ microbes/). At present, the portal is still being filled, but it already contains a description of more than 13,000 items of storage (of which 3500 are in the microorganisms’ part) of 65 bioresource collections in Russia’s FASO organizations. Of these collections, 12 with microorganisms have a total diversity of funds of about 50,000 strains).
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Gunasekera, Aravinda S., Karen S. Sfanos, Dedra K. Harmody, Shirley A. Pomponi, Peter J. McCarthy, and Jose V. Lopez. "HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates." Applied Microbiology and Biotechnology 66, no. 4 (November 16, 2004): 373–76. http://dx.doi.org/10.1007/s00253-004-1763-7.
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González-Toril, E., R. Amils, R. J. Delmas, J. R. Petit, J. Komárek, and J. Elster. "Diversity of bacteria producing pigmented colonies in aerosol, snow and soil samples from remote glacial areas (Antarctica, Alps and Andes)." Biogeosciences Discussions 5, no. 2 (April 15, 2008): 1607–30. http://dx.doi.org/10.5194/bgd-5-1607-2008.
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Abstract. Four different communities and one culture of pigmented microbial assemblages were obtained by incubation in mineral medium of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas). Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. The phylogenetic comparison with the currently available rDNA database allowed the identification of sequences belonging to Proteobacteria (Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the maritime Antarctic soil the poorest (only one). Snow samples from Col du midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteria clone). The only microorganism identified in the maritime Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. The two snow samples from the Alps only shared one common microorganism. Most of the identified microorganisms have been detected previously in cold environments (Dietzia kujamenisi, Pseudonocardia Antarctica, Hydrogenophaga palleronii and Brebundimonas sp.), marine sediments (Aquiflexus balticus, Pseudomonas pseudoalkaligenes, Pseudomonas sp. and one uncultured Alphaproteobacteria), and soils and rocks (Pseudonocardia sp., Agrobactrium sp., Limnobacter sp. and two uncultured Alphaproteobacetria clones). Air current dispersal is the best model to explain the presence of very specific microorganisms, like those used in this work, in very distant environments. In addition these microorganisms have to be resistant to extreme conditions and able to grow in oligotrophic environments. Considering the habitats in which they have been identified, the presence of pigments must be related with their ability to resist high doses of radiation.
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González-Toril, E., R. Amils, R. J. Delmas, J. R. Petit, J. Komárek, and J. Elster. "Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples." Biogeosciences 6, no. 1 (January 8, 2009): 33–44. http://dx.doi.org/10.5194/bg-6-33-2009.
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Abstract. Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.
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Chalita, Mauricio, Sung-min Ha, Yeong Ouk Kim, Hyun-Seok Oh, Seok-Hwan Yoon, and Jongsik Chun. "Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus." Pathogens 9, no. 3 (March 10, 2020): 204. http://dx.doi.org/10.3390/pathogens9030204.
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Shotgun metagenomics is of great importance in order to understand the composition of the microbial community associated with a sample and the potential impact it may exert on its host. For clinical metagenomics, one of the initial challenges is the accurate identification of a pathogen of interest and ability to single out that pathogen within a complex community of microorganisms. However, in absence of an accurate identification of those microorganisms, any kind of conclusion or diagnosis based on misidentification may lead to erroneous conclusions, especially when comparing distinct groups of individuals. When comparing a shotgun metagenomic sample against a reference genome sequence database, the classification itself is dependent on the contents of the database. Focusing on the genus Streptococcus, we built four synthetic metagenomic samples and demonstrated that shotgun taxonomic profiling using the bacterial core genes as the reference database performed better in both taxonomic profiling and relative abundance prediction than that based on the marker gene reference database included in MetaPhlAn2. Additionally, by classifying sputum samples of patients suffering from chronic obstructive pulmonary disease, we showed that adding genomes of genomospecies to a reference database offers higher taxonomic resolution for taxonomic profiling. Finally, we show how our genomospecies database is able to identify correctly a clinical stool sample from a patient with a streptococcal infection, proving that genomospecies provide better taxonomic coverage for metagenomic analyses.
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BARANYI, JÓZSEF, and MARK L. TAMPLIN. "ComBase: A Common Database on Microbial Responses to Food Environments†." Journal of Food Protection 67, no. 9 (September 1, 2004): 1967–71. http://dx.doi.org/10.4315/0362-028x-67.9.1967.
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The advancement of predictive microbiology relies on available data that describe the behavior of microorganisms in different environmental matrices. For such information to be useful to the predictive microbiology research community, data must be organized in a manner that permits efficient access and data retrieval. Here, we describe a database protocol that encompasses observations of bacterial responses to food environments, resulting in a database (ComBase) for predictive microbiology purposes. The data included in ComBase were obtained from cooperating research institutes and from the literature and are publicly available via the Internet.
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Nesterova, D. D., A. N. Neshataev, N. V. Lukyanenko, A. A. Petrova, V. V. Prokopyev, and T. S. Sergeev. "Results of studying disinfectant-resistance of bacteria, excreted from patients in microbiological provision of epidemiological surveillance of hcai at multitype medical institution." Perm Medical Journal 35, no. 5 (December 15, 2018): 42–50. http://dx.doi.org/10.17816/pmj35542-50.
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Aim. To improve microbiological monitoring of disinfectant-resistance of microorganisms, excreted from clinical material in epidemiological surveillance of HCAI.
Materials and methods. Over the period from 2012 to 2016, while conducting resistance monitoring, 3320 investigations of clinical material were performed. The number of studied microorganisms was 1557. The number of excreted disinfectant-resistant microorganism strains was 337. The studies of microorganisms from clinical material for resistance were realized to 48 disinfectants of 15 groups with different reactants.
Results. During the present study it was established that microbiological monitoring, oriented for continuous monitoring of microorganisms circulation will permit to increase the number of studies in 2016 by 2.6 times, to reduce the total number of disinfectant-resistant flora in 2016 by 62 %. The greatest weight of excreted cultures was in the units of surgical profile – 48.8 %, resuscitation profile – 30 %, therapeutic one – 21.2 %. Clinical material, from which positive results were obtained, was determined by scourage (from 43.5 % in the surgical unit to 74.8 % in therapeutic), blood sterility (from 2.7 % in therapeutic units to 31.4 % in resuscitation units). Microflora, excreted from clinical material is presented predominantly by P. aeruginosa – 24.0 %, Kl. pneumoniae – 30.0 %, E. coli – from 12.9 to 22.1 %, St. aureus – from 3.0 to 7.6 %. The studies regarding disinfectant-resistance to 48 items from 15 groups of chemical compounds are the evidence of growing resistance to QAC, including QAC + amines – 24.7 %, QAC + aldehyde-containing – 6.8 %, chlorine-containing – 21.9 %. The highest resistance to disinfectants used was in Acinetobacter spp., Kl. pneumoniae, P. aeruginosa, E. coli.
Conclusions. The developed algorithm of microbiological study, based on software, permitted to form the database, to monitor epidemiologically significant microorganisms and correct choice of disinfectants and disinfection tactics.
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Zhang, Xiaojing, L. Y. Zhou, and H. G. Zheng. "Trends on rapid detection technology of food microorganisms based on web of science database." IOP Conference Series: Materials Science and Engineering 439 (November 6, 2018): 032125. http://dx.doi.org/10.1088/1757-899x/439/3/032125.
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Skoufos, Giorgos, Filippos S. Kardaras, Athanasios Alexiou, Ioannis Kavakiotis, Anastasia Lambropoulou, Vasiliki Kotsira, Spyros Tastsoglou, and Artemis G. Hatzigeorgiou. "Peryton: a manual collection of experimentally supported microbe-disease associations." Nucleic Acids Research 49, no. D1 (October 20, 2020): D1328—D1333. http://dx.doi.org/10.1093/nar/gkaa902.
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Abstract We present Peryton (https://dianalab.e-ce.uth.gr/peryton/), a database of experimentally supported microbe-disease associations. Its first version constitutes a novel resource hosting more than 7900 entries linking 43 diseases with 1396 microorganisms. Peryton's content is exclusively sustained by manual curation of biomedical articles. Diseases and microorganisms are provided in a systematic, standardized manner using reference resources to create database dictionaries. Information about the experimental design, study cohorts and the applied high- or low-throughput techniques is meticulously annotated and catered to users. Several functionalities are provided to enhance user experience and enable ingenious use of Peryton. One or more microorganisms and/or diseases can be queried at the same time. Advanced filtering options and direct text-based filtering of results enable refinement of returned information and the conducting of tailored queries suitable to different research questions. Peryton also provides interactive visualizations to effectively capture different aspects of its content and results can be directly downloaded for local storage and downstream analyses. Peryton will serve as a valuable source, enabling scientists of microbe-related disease fields to form novel hypotheses but, equally importantly, to assist in cross-validation of findings.
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Shulipa, Ye O., Ye Yu Chernysh, L. D. Plyatsuk, and M. Fukui. "Ontological Tools in Anaerobic Fermentation Technologies: Bioinformation Database Applications." Journal of Engineering Sciences 7, no. 1 (2020): H1—H8. http://dx.doi.org/10.21272/jes.2020.7(1).h1.
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An important direction of forming an effective system for recycling waste of various genesis is to optimize the processes of their treatment using the latest information resources. The paper deals with theoretical studies of directions for the systematization and optimization of anaerobic waste processing technologies using ontological tools based on information resources. Significant scientific support to biochemical research is provided by electronic bioinformatics databases such as KEGG, BacDive, and EAWAG-BBD, etc., which provide access to a collection of graphical representations and text descriptions of metabolic or signal pathways, schemes of regulation of biological processes, information about the organism. They cover various aspects of bacterial and archaic biodiversity, information on microbial biocatalytic reactions and biodegradation pathways of mainly xenobiotic chemical compounds. Also, in the course of work based on analytical data of electronic databases of bioinformatics, in particular, the interaction of necessary ecological and trophic groups of microorganisms, biochemical simulation of anaerobic waste processing with biofuel production was carried out. Keywords: waste disposal, bioinformatics database, anaerobic fermentation, biofuel.
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Selvakumar, Ariamalar, and Michael Borst. "Variation of microorganism concentrations in urban stormwater runoff with land use and seasons." Journal of Water and Health 4, no. 1 (March 1, 2006): 109–24. http://dx.doi.org/10.2166/wh.2006.0009.
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Stormwater runoff samples were collected from outfalls draining small municipal separate storm sewer systems. The samples were collected from three different land use areas based on local designation (high-density residential, low-density residential and landscaped commercial). The concentrations of microorganisms in the stormwater runoff were found to be similar in magnitude to, but less variable than, those reported in the stormwater National Pollutant Discharge Elimination System (NPDES) database. Microorganism concentrations from high-density residential areas were higher than those associated with low-density residential and landscaped commercial areas. Since the outfalls were free of sanitary wastewater cross-connections, the major sources of microorganisms to the stormwater runoff were most likely from the feces of domestic animals and wildlife. Concentrations of microorganisms were significantly affected by the season during which the samples were collected. The lowest concentrations were observed during winter except for Staphylococcus aureus. The Pearson correlation coefficients among different indicators showed weak linear relationships and the relationships were statistically significant. However, the relationships between indicators and pathogens were poorly correlated and were not statistically significant, suggesting the use of indicators as evidence of the presence of pathogens is not appropriate. Further, the correlation between the concentration of the traditionally monitored indicators (total coliforms and fecal coliforms) and the suggested substitutes (enterococci and E. coli) is weak, but statistically significant, suggesting that historical time series will be only a qualitative indicator of impaired waters under the revised criteria for recreational water quality by the US EPA.
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Kreuzer-Martin, Helen W., and Kristin H. Jarman. "Stable Isotope Ratios and Forensic Analysis of Microorganisms." Applied and Environmental Microbiology 73, no. 12 (April 27, 2007): 3896–908. http://dx.doi.org/10.1128/aem.02906-06.
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ABSTRACT In the aftermath of the anthrax letters of 2001, researchers have been exploring various analytical signatures for the purpose of characterizing the production environment of microorganisms. One such signature is stable isotope ratios, which in heterotrophs, are a function of nutrient and water sources. Here we discuss the use of stable isotope ratios in microbial forensics, using as a database the carbon, nitrogen, oxygen, and hydrogen stable isotope ratios of 247 separate cultures of Bacillus subtilis 6051 spores produced on a total of 32 different culture media. In the context of using stable isotope ratios as a signature for sample matching, we present an analysis of variations between individual samples, between cultures produced in tandem, and between cultures produced in the same medium but at different times. Additionally, we correlate the stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen for growth medium nutrients or water with those of spores and show examples of how these relationships can be used to exclude nutrient or water samples as possible growth substrates for specific cultures.
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Xing, Zhikai, Yunting Zhang, Meng Li, Chongye Guo, and Shuangli Mi. "RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing." Microorganisms 8, no. 10 (October 10, 2020): 1563. http://dx.doi.org/10.3390/microorganisms8101563.
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Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.
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Paściak, Mariola, Władysław Dacko, Joanna Sikora, Danuta Gurlaga, Krzysztof Pawlik, Grzegorz Miękisiak, and Andrzej Gamian. "Creation of an In-House Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Corynebacterineae Database Overcomes Difficulties in Identification of Nocardia farcinica Clinical Isolates." Journal of Clinical Microbiology 53, no. 8 (June 3, 2015): 2611–21. http://dx.doi.org/10.1128/jcm.00268-15.
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Nocardiosis is a rare disease that is caused by Gram-positive actinobacteria of theNocardiagenus and affects predominantly immunocompromised patients. In its disseminated form, it has a predilection for the central nervous system and is associated with high mortality rates. Therefore, prompt identification of the pathogen is critical. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry is a relatively novel technique used for identification of microorganisms. In this work, an upgraded MALDI-TOF Biotyper database containingCorynebacterineaerepresentatives of strains deposited in the Polish Collection of Microorganisms was created and used for identification of the strain isolated from a nocardial brain abscess, mimicking a brain tumor, in an immunocompetent patient. Testing with the API Coryne system initially incorrectly identifiedRhodococcussp., while chemotaxonomic tests, especially mycolic acid analysis, enabled correctNocardiaidentification only at the genus level. Subsequent sequence analysis of 16S rRNA andsecA1genes confirmed the identification. To improve the accuracy of the results, an in-house database was constructed using optimized parameters; with the use of the database, the strain was eventually identified asNocardia farcinica. Clinical laboratories processing various clinical strains can upgrade a commercial database to improve and to accelerate the results obtained. This is especially important in the case ofNocardia, for which valid microbial diagnosis remains challenging; reference laboratories are often required to identify and to survey these rare actinobacteria.
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Xie, Le, Wei Wei, Lanlan Cai, Xiaowei Chen, Yuhong Huang, Nianzhi Jiao, Rui Zhang, and Ya-Wei Luo. "A global viral oceanography database (gVOD)." Earth System Science Data 13, no. 3 (March 24, 2021): 1251–71. http://dx.doi.org/10.5194/essd-13-1251-2021.
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Abstract. Virioplankton are a key component of the marine biosphere in maintaining diversity of microorganisms and stabilizing ecosystems. They also contribute greatly to nutrient cycles/cycling by releasing organic matter after lysis of hosts. In this study, we constructed the first global viral oceanography database (gVOD) by collecting 10 931 viral abundance (VA) data and 727 viral production (VP) data, along with host and relevant oceanographic parameters when available. Most VA data were obtained in the North Atlantic (32 %) and North Pacific (29 %) oceans, while the southeast Pacific and Indian oceans were quite undersampled. The VA in the global ocean was 1.17(±3.31)×107 particles mL−1. The lytic and lysogenic VP in the global ocean was 9.87(±24.16)×105 and 2.53(±8.64)×105 particlesmL-1h-1, respectively. Average VA in coastal oceans was higher than that in surface open oceans (3.61(±6.30)×107 versus 0.73(±1.24)×107 particles mL−1), while average VP in coastal and surface open oceans was close. Vertically, VA, lytic VP and lysogenic VP deceased from surface to deep oceans by about 1 order of magnitude. The total number of viruses in the global ocean estimated by bin-averaging and the random forest method was 1.56×1030 and 1.49×1030 particles, leading to an estimate of global ocean viral biomass at 35.9 and 34.4 Tg C, respectively. We expect that the gVOD will be a fundamental and very useful database for laboratory, field and modeling studies in marine ecology and biogeochemistry. The full gVOD database (Xie et al., 2020) is stored in PANGAEA (https://doi.org/10.1594/PANGAEA.915758).
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Ossandón, F. J., G. Rivera, F. Lazo, and David S. Holmes. "Predicting the Function of Hypothetical Genes in Genomes of Bioleaching Microorganisms." Advanced Materials Research 71-73 (May 2009): 203–6. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.203.
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A particularly challenging problem in genome annotation is to attribute function to genes annotated as “hypothetical, no known function”. These typically account for about 40% of all genes regardless of the genome. Some of these are “orphan” genes and are not found in any other genome. Some of these could encode species specific proteins and so are particularly interesting for evaluating novel metabolic potential and for understanding the evolution of genes and genomes. Several similarity and non-similarity bioinformatics tools exist that help predict function of hypotheticals, but none are able to suggest function for more than a few percent and the annotation of the others remains a formidable task. We have developed a bioinformatics tool called AlterORF (www.AlterORF.cl) that is able to identify alternate open reading frames (ORFs) embedded within annotated genes. Analysis of over 2 million genes in over 700 completely sequenced genomes reveals that alternate ORFs of substantial length (potentially encoding 70 amino acids or more) are surprisingly common, especially in G+C rich genomes. During our examination of these alternate ORFs, we uncovered hundreds of examples where the alternate ORF has a significant hit with databases of motifs and domains (e.g. CDD, Pfam) and where the actual annotated gene is described as hypothetical and has no database match. This strongly suggests that the annotated gene has been incorrectly identified and that the alternate ORF is the real gene. We describe the evaluation of the following genomes of bioleaching microorganisms and others that reside in similar ecological niches using AlterORF: Acidithiobacillus ferrooxidans (2 strains), Leptospirillum type II, Methylacidiphilum infernorum, Picrophilus torridus, Sulfolobus acidocaldarius, S. solfataricus, S. tokodaii, Thermodesulfovibrio yellowstonii, Thermoplasma acidophilum and T. volcanium. Examples of novel genes from these microorganisms and their suggested roles in metabolism will be described.
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Pleißner, Klaus-Peter, Peter Schmelzer, Wolfgang Wehrl, and Peter R. Jungblut. "Short Communication– Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms." PROTEOMICS 4, no. 10 (October 2004): 2987–90. http://dx.doi.org/10.1002/pmic.200400927.
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Krylov, Pavel, Artem Isakov, Elena Nesmeyanova, Natalia Borozdina, Margarita Postnova, and Valery Novochadov. "The Analysis Proteome Dominant Species of Microorganisms in Agrobiocenosis the Volgograd Region for the Presence of Nickel and Cobalt-Dependent Proteins." Natural Systems and Resources, no. 4 (December 2018): 21–28. http://dx.doi.org/10.15688/nsr.jvolsu.2018.4.3.
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The use of modern bioinformatic approaches for the solution of environmentally oriented tasks provides new data that can be used for spot control anthropogenic ecosystems and ecosystem rebuilding of their violation obtained from adverse factors of natural and antropogenical genesis. This work aims at demonstrating and identifying nickel and cobalt binding proteins in dominant species of microorganisms of agrocenosis that allows you to create an information database for accumulating and processing information about the regularities of the functioning of agro-ecosystem in arid conditions, leading to the growth of economic efficiency of the farming system and increase the success of environmental management. The main purpose of the work was to study the presence of nickel and cobalt binding proteins included in the proteome, the dominant species of microorganisms from three typical agrocenoses of the Volgograd region. Nickel and cobalt binding proteins were distributed not only in their functional features, participation in metabolism, proteolytic activity, transport and regulation of gene expression and proteins, The results of virtual screening proteome the dominant microorganisms of the genus Bacillus and Actinomyces in the Uniprot database showed that the soil microbiota of the considered agrocenosis is also characterized by a sufficiently large number of metal – dependent proteins: 264 – for representatives of the Genus Actinomyces and 564 – for Bacillus subtilis, of of which about 35–40 % are annotated. According to the results, the concentration of metals in the soil of agrocenosis, namely in the arid zone, has a very strong impact on the livelihoods of crops and microorganisms in the soil. The use of the obtained results can be used as a basis for the implementation of targeted high-precision management of biocenoses in order to improve the sustainability of natural communities and the economic efficiency of agrocenoses.
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Piarroux, Raphael, Frédéric Gabriel, Frédéric Grenouillet, Patrick Collombon, Philippe Louasse, Martine Piarroux, and Anne-Cécile Normand. "Using MALDI-ToF mass spectrometry to identify mushroom species: Proof of concept analysis of Amanita genus specimens." Medical Mycology 59, no. 9 (April 23, 2021): 890–900. http://dx.doi.org/10.1093/mmy/myab018.
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Abstract Food poisoning caused by toxic mushrooms, such as species in the Amanita genus, occurs frequently around the world. To properly treat these patients, it is important to rapidly and accurately identify the causal species. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry is a rapid technique that has been used in medical laboratories for the past three decades to identify bacteria, yeasts, and filamentous fungi. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-Tof MS) is a rapid method used for the past three decades to identify microorganisms. In this study, we created and internally validated a MALDI-Tof MS reference database comprising 15 Amanita species frequently encountered in France, and we challenged this database with 38 Amanita specimens from four French locations, using a free online application for MALDI-ToF spectra identifications. Assessment of the database showed that mass spectra can be obtained by analyzing any portion of a carpophore and that all portions enabled identification of the carpophore at the species level. Most carpophores were correctly identified using our database, with the exception of specimens from the Vaginatae section. Decay tests also demonstrated that decayed portions (like those found in the kitchen garbage can) of Amanita phalloides mushrooms could be properly identified using MALDI-ToF MS. Our findings provide important insight for toxicology laboratories that often rely on DNA sequencing to identify meal leftovers implicated in food poisoning. In future developments, this technique could also be used to detect counterfeit mushrooms by including other genera in the reference database. Lay Summary MALDI-ToF MS is a powerful identification tool for microorganisms. We demonstrate that the technique can be applied to Amanita specimens. This will prevent food intoxications as a rapid and definite identification can be obtained, and it can also be used for food remnants.
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Senthilraj, Rajapandi, Ganduri Sathyanarayana Prasad, and Kunchithapatham Janakiraman. "Sequence-based identification of microbial contaminants in non-parenteral products." Brazilian Journal of Pharmaceutical Sciences 52, no. 2 (June 2016): 329–36. http://dx.doi.org/10.1590/s1984-82502016000200011.
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ABSTRACT Phenotypic profiles for microbial identification are unusual for rare, slow-growing and fastidious microorganisms. In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rRNA sequencing has played a pivotal role in the accurate identification of microorganisms and the discovery of novel isolates in microbiology laboratories. The 16S rRNA region is universally distributed among microorganisms and is species-specific. Accordingly, the aim of our study was the genotypic identification of microorganisms isolated from non-parenteral pharmaceutical formulations. DNA was separated from five isolates obtained from the formulations. The target regions of the rRNA genes were amplified by PCR and sequenced using suitable primers. The sequence data were analyzed and aligned in the order of increasing genetic distance to relevant sequences against a library database to achieve an identity match. The DNA sequences of the phylogenetic tree results confirmed the identity of the isolates as Bacillus tequilensis, B. subtilis, Staphylococcus haemolyticus and B. amyloliqueficians. It can be concluded that 16S rRNA sequence-based identification reduces the time by circumventing biochemical tests and also increases specificity and accuracy.
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Kubátová, A. "Collection of food relevant microscopic fungi under the Czech national programme of protection of genetic resources of economically significant microorganisms – a short report." Czech Journal of Food Sciences 28, No. 1 (February 18, 2010): 79–82. http://dx.doi.org/10.17221/235/2009-cjfs.
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A unique project exists in the Czech Republic, namely the Czech National Programme of Protection of Genetic Resources of Economically Significant Microorganisms and Tiny Animals (NPPGR), which includes nineteen Czech collections of microorganisms (bacteria, fungi), viruses, and tiny animals. It is fully financed by the Ministry of Agriculture of the Czech Republic. Under this Programme, the Culture Collection of Fungi (CCF) in Prague maintains 293 fungal strains, 225 of which are food and feed relevant fungi (e.g. toxigenic <I>Aspergillus flavus, Penicillium verrucosum</I>, and <I>Fusarium sporotrichioides</I>). The main aims of the Programme are to provide adequate protection of the microbial genetic resources that are of importance to the agriculture and food industries, to provide strains (free of charge) for the research and educational purposes, and to support the cooperation between Czech and foreign institutions. A database of all microorganisms is accessible online.
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Choo-Smith, L. P., K. Maquelin, T. van Vreeswijk, H. A. Bruining, G. J. Puppels, N. A. Ngo Thi, C. Kirschner, et al. "Investigating Microbial (Micro)colony Heterogeneity by Vibrational Spectroscopy." Applied and Environmental Microbiology 67, no. 4 (April 1, 2001): 1461–69. http://dx.doi.org/10.1128/aem.67.4.1461-1469.2001.
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ABSTRACT Fourier transform infrared and Raman microspectroscopy are currently being developed as new methods for the rapid identification of clinically relevant microorganisms. These methods involve measuring spectra from microcolonies which have been cultured for as little as 6 h, followed by the nonsubjective identification of microorganisms through the use of multivariate statistical analyses. To examine the biological heterogeneity of microorganism growth which is reflected in the spectra, measurements were acquired from various positions within (micro)colonies cultured for 6, 12, and 24 h. The studies reveal that there is little spectral variance in 6-h microcolonies. In contrast, the 12- and 24-h cultures exhibited a significant amount of heterogeneity. Hierarchical cluster analysis of the spectra from the various positions and depths reveals the presence of different layers in the colonies. Further analysis indicates that spectra acquired from the surface of the colonies exhibit higher levels of glycogen than do the deeper layers of the colony. Additionally, the spectra from the deeper layers present with higher RNA levels than the surface layers. Therefore, the 6-h colonies with their limited heterogeneity are more suitable for inclusion in a spectral database to be used for classification purposes. These results also demonstrate that vibrational spectroscopic techniques can be useful tools for studying the nature of colony development and biofilm formation.
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Didovich, S. V. "Database of biological indicators of control of legume agrocenoses productivity." TAURIDA HERALD OF THE AGRARIAN SCIENCES 1 (25) (2021): 85–97. http://dx.doi.org/10.33952/2542-0720-2021-1-25-85-97.
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Experimental data gained through research requires systematization and interpretation of the effectiveness of applicable objects, methods and agricultural technologies. This data is of scientific and practical value for proper decision-making in agricultural practice. The purpose of the research is twofold: 1) to develop a structured database based on the results of long-term field experiments using various plant-microbial symbioses in legumes agrocenoses under soil and climatic conditions of the Crimea; 2) to generalize information to search for the possibility of biological control of plant productivity. The database has the minimum software requirements: Microsoft Office suite for Microsoft Windows operating systems (XP or higher OS) and software package for statistical analysis Statistica_10. Data collection, sorting and systematization, as well as matrix writing was carried out in Microsoft Excel; database structure development and design – using Microsoft Visual Basic for Application (VBA); data analysis and processing, as well as agrocenosis productivity modelling, were carried out with the help of Statistica (StatSoft) version 10. The database size is 8 MB. It has three structured VBA blocks: 1) biological activity of the soil, 2) physiological and biochemical status, productivity of plants and 3) matrices of indicators of biological activity of the soil and plant biology. Information on the structural and functional organization of the soil microbiocenosis, enzymatic activity and soil respiration, symbiotic efficiency, intensity and direction of microbiological and biochemical processes in the rhizosphere of legumes, as well as their physiological status, productivity and seed quality included sequentially. The Database is implemented on 23 electronic sheets in Microsoft Excel, integrates and interacts with the Statistica_10. The Database allows searching for interactive links in the system “microorganisms–plants–soil”, modelling the productivity of agrocenoses, identifying plant-microbial systems with the active interface when using polyfunctional microbial preparations in the technology of growing legumes under soil and climatic conditions of the Crimea. With the help of the database, we found that the use of polyfunctional microbial preparations causes different potential in the system “microorganisms–plants–soil”. Bacterization of plants with microbial preparations has 1.8 times factorial effect more on the physiology and productivity of legumes (76 %) compared to a factorial effect on the biological activity of the soil in the agrocenosis (42 %). The potential of the interaction of the cyanorhizobial consortium with legumes was revealed. It had a minimal total factor difference (29 %) between the physiological and biochemical state, productivity of legumes and indicators of biological activity of soil compared to ‘Rhizobofit’ (36 %), ‘Rhizobofit’, ‘Phosphoenterin’, ‘Biopolycid’ (33 %), ‘Rhizobofit’ and arbuscular mycorrhizal fungi (39 %).
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Silva, Rafael Souza, and Adriana Cristina Oliveira. "Epidemiology and nosocomial infection control in a pediatric unit." Revista de Enfermagem UFPE on line 2, no. 2 (April 1, 2008): 187. http://dx.doi.org/10.5205/reuol.422-11319-1-le.0202200808.
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ABSTRACTThis research aimed at determining the pediatric patients profile at a School- Hospital, according to the variables sex, age, patients lenght-of stay, colonizing/infecting microorganisms, nosocomial infections (NI) and patiens outcomes. This was a prospective and descriptive epidemiological study developed in 2006 to which a database was developed in the SPSS program so as to type datas and analysed them afterwards. It was identified 668 patients, from whom, 53,7% were male, global avarage age was 5,1 years old and lenght-of-stay avarage was 10,1 days. It was colonized by resistant microorganisms 4,2% of the patients and 7,5% developed NI, being sepsis them most recurrent and Staphylococcus epidermides and Cândida albicans the most evident microorganisms. There were 98,5% of discharge and 1,5% of deaths. This study reinforces the needing for continuous/active NI surveillance programes and the identification of (re) emergence of resistant bacterias so as to direct NI prevention and controle measures by those microorganisms. Descriptors: nosocomial infections; pediatrics; resistance; drug; children.RESUMOObjetivou-se com este estudo determinar o perfil dos pacientes pediátricos de um Hospital Universitário, conforme o sexo, idade, tempo de internação, microrganismos colonizantes/infectantes, infecções hospitalares (IH) e desfecho dos mesmos. Tratou-se de um estudo epidemiológico descritivo, realizado em 2006, para o qual foi elaborado um banco de dados no programa SPSS para a digitação dos dados e posterior análise estatística descritiva. Identificaram-se 668 pacientes, sendo 53,7% do sexo masculino, a média de idade global de 5,1 anos e o tempo médio de internação de 10,1 dias. Foram colonizados por microrganismos resistentes 4,2% dos pacientes e 7,5% desenvolveram IH, sendo as sepses mais recorrentes e o Staphylococcus epidermides e Cândida albicans os microrganismos mais prevalentes. Houve 98,5% de altas e 1,5% de óbitos. Reforça-se a necessidade de programas de vigilância contínua/ativa de IH e a identificação da (re) emergência de bactérias resistentes a fim de direcionar medidas de prevenção e controle de IH por estes microrganismos. Descritores: infecção hospitalar; pediatria; resistência; drogas; criança.RESUMENEl presente estudio determinó el perfil de los pacientes pediátricos de un Hospital Universitario, según las variables sexo, edad, tiempo de internación, microorganismos colonizadores/infectantes, infecciones hospitalarias (IH) y finalización de los mismos. Se trata de un estudio epidemiológico realizado en 2006. Se realizó una análisis estadística descriptiva utilizando el programa SPSS. Se identificaron 668 pacientes, siendo 53,7% del sexo masculino, con una media de edad global de 5,1 años y tiempo de internación de 10,1 días. Fueron colonizados por microorganismos resistentes 4,2% de los pacientes y 7,5% desarrollaron IH, siendo as sepses más frecuentes y el Staphylococcus epidermides y Candida albicans los microorganismos más prevalecientes. Hubo 98,5% de altas y 1,5% de fallecimientos. Se refuerza la necesidad de programas de vigilancia continua/activa de IH y la identificación de la (re) emergencia de bacterias resistentes con el objetivo de orientar medidas de prevención y control de IH por estos microorganismos. Descriptores: infección hospitalaria; pediatría; resistencia; drogas; niños.
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Blin, Kai, Simon Shaw, Satria A. Kautsar, Marnix H. Medema, and Tilmann Weber. "The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes." Nucleic Acids Research 49, no. D1 (November 5, 2020): D639—D643. http://dx.doi.org/10.1093/nar/gkaa978.
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Abstract Microorganisms produce natural products that are frequently used in the development of antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent years, genome mining has evolved into a prominent method to access this potential. antiSMASH is one of the most popular tools for this task. Here, we present version 3 of the antiSMASH database, providing a means to access and query precomputed antiSMASH-5.2-detected biosynthetic gene clusters from representative, publicly available, high-quality microbial genomes via an interactive graphical user interface. In version 3, the database contains 147 517 high quality BGC regions from 388 archaeal, 25 236 bacterial and 177 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.
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Dat, Ton That Huu, Pham Viet Cuong, Tran Thi Dung Dung, Vu Thi Thu Huyen, and Nguyen Thi Kim Cuc. "BIODIVERSITY ASSESSMENT OF MICROORGANISMS ASSOCIATED WITH TWO MARINE SPONGES (Haliclona oculata AND Amphius huxleyi) COLLECTED AT THE LANG CO BAY OF VIETNAM." Tạp chí Khoa học và Công nghệ Biển 18, no. 3 (November 3, 2018): 286–95. http://dx.doi.org/10.15625/1859-3097/18/3/10642.
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Sponges (Phylum Porifera) are ancient sedentary and filter-feeding animals which harbour very diverse and abundant associated microbial community in their tissues with density up to 40–50% of sponge tissue volume. In this study, the diversity of associated microorganisms with two marine sponges Haliclona oculata and Amphius huxleyi collected at the Lang Co bay of Vietnam was assessed by analysis of hypervariable V3 and V4 regions of the 16S rRNA gene using Illumina MiSeq system. The taxonomic diversity of sponge-associated microorganisms was classified to different taxonomic levels (kingdom, phylum, class, order, family, and genus). Based on Bayesian classification method and reference sequences derived from Greengenes database, the associated microorganisms in studied sponges were assigned to 17 phyla (H. oculata) and 13 phyla (A. huxleyi). Many microbial taxa were detected in two sponge species, however, they were distinctive by the abundance. Proteobacteria was the most dominant phylum in both sponge species, and all of 4 classes Epsilonproteobacteria, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were found in H. oculata and A. huxleyi.
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Gomes de Oliveira, Geilson, Renata Mirian Nunes Eleutério, Ana Katherine Silveira Gonçalves, Paulo César Giraldo, and José Eleutério Jr. "Atypical Squamous Cells in Liquid-Based Cervical Cytology: Microbiology, Inflammatory Infiltrate, and Human Papillomavirus-DNA Testing." Acta Cytologica 62, no. 1 (November 8, 2017): 28–33. http://dx.doi.org/10.1159/000481654.
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Objective: The aim of this study was to assess the correlation between atypical squamous cells (ASC) and inflammatory infiltrate and vaginal microbiota using cervical liquid-based cytological (SurePath®) and high-risk human papillomavirus (HR-HPV) tests. Study Design: A cross-sectional study was conducted using a 6-year database from a laboratory in Fortaleza (Brazil). Files from 1,346 ASC cases were divided into subgroups and results concerning inflammation and vaginal microorganisms diagnosed by cytology were compared with HR-HPV test results. Results: An absence of specific microorganisms (ASM) was the most frequent finding (ASC of undetermined significance, ASC-US = 74%; ASC - cannot exclude high-grade squamous intraepithelial lesion, ASC-H = 68%), followed by bacterial vaginosis (ASC-US = 20%; ASC- H = 25%) and Candida spp. (ASC-US = 6%; ASC-H = 5%). Leukocyte infiltrate was present in 71% of ASC-US and 85% of ASC-H (p = 0.0040), and in these specific cases HR-HPV tests were positive for 65 and 64%, respectively. A positive HR-HPV test was relatively more frequent when a specific microorganism was present, and Candida spp. was associated with HR-HPV-positive results (p = 0.0156), while an ASM was associated with negative HR-HPV results (p = 0.0370). Conclusion: ASC-US is associated with an absence of inflammation or vaginosis, while ASC-H smears are associated with Trichomonas vaginalis and inflammatory infiltrate. A positive HR-HPV is associated with Candida spp. in ASC cytology.
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Lasch, Peter, Andy Schneider, Christian Blumenscheit, and Joerg Doellinger. "Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries." Molecular & Cellular Proteomics 19, no. 12 (September 30, 2020): 2125–38. http://dx.doi.org/10.1074/mcp.tir120.002061.
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Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS2 data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC–MS measurements. Peptide masses are then extracted from MS1 data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient – less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS1 peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.
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Garczarek, Laurence, Ulysse Guyet, Hugo Doré, Gregory K. Farrant, Mark Hoebeke, Loraine Brillet-Guéguen, Antoine Bisch, et al. "Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes." Nucleic Acids Research 49, no. D1 (October 30, 2020): D667—D676. http://dx.doi.org/10.1093/nar/gkaa958.
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Abstract Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
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Lyu, Chuanyu, Tong Chen, Bo Qiang, Ningfeng Liu, Heyu Wang, Liangren Zhang, and Zhenming Liu. "CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean." Nucleic Acids Research 49, no. D1 (September 28, 2020): D509—D515. http://dx.doi.org/10.1093/nar/gkaa763.
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Abstract Marine organisms are expected to be an important source of inspiration for drug discovery after terrestrial plants and microorganisms. Despite the remarkable progress in the field of marine natural products (MNPs) chemistry, there are only a few open access databases dedicated to MNPs research. To meet the growing demand for mining and sharing for MNPs-related data resources, we developed CMNPD, a comprehensive marine natural products database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various physicochemical and pharmacokinetic properties, standardized biological activity data, systematic taxonomy and geographical distribution of source organisms, and detailed literature citations. It is an integrated platform for structure dereplication (assessment of novelty) of (marine) natural products, discovery of lead compounds, data mining of structure-activity relationships and investigation of chemical ecology. Access is available through a user-friendly web interface at https://www.cmnpd.org. We are committed to providing a free data sharing platform for not only professional MNPs researchers but also the broader scientific community to facilitate drug discovery from the ocean.
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Santos, Mónica, Armando Almeida, Catarina Lopes, and Tiago Oliveira. "Os Telemóveis implicam risco biológico?" Revista Portuguesa de Saúde Ocupacional 9 (June 30, 2020): S29—S39. http://dx.doi.org/10.31252/rpso.11.04.2020.
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Introduction / background / objectives Mobile phones are used more frequently, both in a personal and professional context. Several researchers have presented evidence that they are objects that generally contain several microorganisms, some of which are possibly pathogenic. There will be some professional sectors where this issue may become problematic, namely between hospital health institutions (not only due to the type of microorganisms that exist, but also due to the immunosuppression and/ or general bad medical conditions of the individuals present). The aim of this review is to understand what is described in terms of biological risk for workers who handle mobile phones, although almost all published studies convert to the Health sector and the emphasis is given to patients (and secondarily to the community) and not to the workers themselves. Methodology It is a Scoping Review, initiated through a survey conducted in April 2019 in the databases “CINALH plus with full text, Medline with full text, Database of Abstracts of Reviews of Effects, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Cochrane Methodology Register, Nursing and Allied Health Collection: comprehensive, MedicLatina and RCAAP”. Content The temperature of the mobile phone can create good conditions for the development of some microorganisms. From here they can pass to the user’s face, eyes and mouth. In addition, some of the mobile phones used at work are not just for one person, but are passed between shifts; in some countries they are shared by several members of the family and/ or lent to children, to play. In addition, many use this object during meals/ in the kitchen and even when they are in the bathroom, which enhances the microbiological load. Smartphones appear to be more contaminated, due to being generally larger and providing more interaction and handling; simultaneously, those with a touch screen have less colonization than keyboards (possibly due to the homogeneity of the surface). Some researchers have hypothesized that there is a relationship between the colonization of some mobile phones and that which exists inside women’s bags, where they are usually transported. Conclusions Although the studies were very dispar in relation to looking for any type of microorganisms or just bacteria or viruses and in addition to the real microbiological diversity between countries, the different cultivation techniques certainly made it possible for some strains to grow and others not to be viable. Although these biases can justified some significant percentage differences, it was also clear that all cell phones contain numerous microorganisms, although most of these are not relevant for immunocompetent individuals, bet all articles were written before the Pandemic by Covid-19 . Thus, in the context of Occupational Health, there seems to be no significant risk for workers who are not immunosuppressed. However, the exceptions, simultaneously, can become relevant: for Employees with changes in the functioning of the immune system, for microorganisms with multidrug resistance to conventionally used drugs and, obviously, at this stage (april 2020 ) for new strains, for which there is still no natural immunity (by previous infection) or provided by an effective vaccine and, therefore, capable of causing very extensive disease in populations and, although the number of serious cases is small, given the contagion dimension, this acquires a very relevant amplitude, for all its human, emotional, technical, labor and economic implications. For this reason, it is recommended to use the phone very carefully (especially in circumstances where biological contamination is more likely and/ or intense), both at work and in a personal context; as well as the proper and regular disinfection of these objects, by 70% alcohol.
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Wu, Linhuan, Qinglan Sun, Hideaki Sugawara, Song Yang, Yuguang Zhou, Kevin McCluskey, Alexander Vasilenko, et al. "Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources." BMC Genomics 14, no. 1 (2013): 933. http://dx.doi.org/10.1186/1471-2164-14-933.
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Chen, Xin-Fei, Xin Hou, Meng Xiao, Li Zhang, Jing-Wei Cheng, Meng-Lan Zhou, Jing-Jing Huang, Jing-Jia Zhang, Ying-Chun Xu, and Po-Ren Hsueh. "Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review." Microorganisms 9, no. 7 (July 19, 2021): 1536. http://dx.doi.org/10.3390/microorganisms9071536.
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Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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de los Santos-Villalobos, Sergio, Alondra María Díaz-Rodríguez, María Fernanda Ávila-Mascareño, Andrea Denisse Martínez-Vidales, and Fannie Isela Parra-Cota. "COLMENA: A Culture Collection of Native Microorganisms for Harnessing the Agro-Biotechnological Potential in Soils and Contributing to Food Security." Diversity 13, no. 8 (July 23, 2021): 337. http://dx.doi.org/10.3390/d13080337.
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COLMENA is a microbial culture collection dedicated to the characterization, classification, preservation, and transferal of native microorganisms isolated from various agro-systems and other ecosystems in Mexico. This collection aims to protect microbial diversity, reducing soil degradation, but also exploiting its agro-biotechnological potential. So far, COLMENA has isolated and cryopreserved soil microorganisms from different crops in two major agricultural regions in Mexico, the Yaqui Valley, Sonora, and the Fuerte Valley, Sinaloa. COLMENA has specialized in the identification and characterization of microbial strains with metabolic capacities related to the promotion of plant growth and the biocontrol of phytopathogens. Thus, COLMENA has identified several promising plant growth-promoting microbial (PGPM) strains due to their metabolic and genetic potentials and their beneficial effects in vivo and field trials. These findings demonstrate the biotechnological potential of these strains for their future use in profitable agricultural alternatives focused on enhancing global food security. To share the knowledge and results of the COLMENA team’s scientific research, a virtual platform was created, where the database of the studied and preserved microorganisms is available to professionals, researchers, agricultural workers, and anyone who is interested.
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Babaian, Caryn, and Sudhir Kumar. "Adventures in Evolution: The Narrative of Tardigrada, Trundlers in Time." American Biology Teacher 81, no. 8 (October 1, 2019): 543–52. http://dx.doi.org/10.1525/abt.2019.81.8.543.
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A lesson plan on the phylum Tardigrada is presented in a storytelling workbook that introduces the evolutionary concepts of adaptive radiation, speciation, divergence, and “tree-thinking” through narrative, transitional art, contemplative coloring, and data searches, which can be enhanced with microscopy wet labs. Students gain insight into the invertebrate world of the highly adaptable, ubiquitous microorganisms known colloquially as “water bears,” generating a microevolutionary and macroevolutionary perspective through a narrative that includes an introduction to the TimeTree database.
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Gonçalves, Brisa R. P., Bruna A. S. Machado, Samira A. Hanna, and Marcelo A. Umsza-Guez. "Prospective Study of Microbial Colorants under the Focus of Patent Documents." Recent Patents on Biotechnology 14, no. 3 (September 25, 2020): 184–93. http://dx.doi.org/10.2174/1872208313666191002125035.
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Background: Colorant-producing microorganisms are quite common in nature. These biomolecules present many biological activities such as antitumoral, antimicrobial and antioxidant, in addition to the various nuances of color, making them of special technological importance to the industrial sectors. Objective: This study aims to conduct a technological mapping in the patent, at European patent Office (EPO), in order to evaluate the global panorama of the use of microbial colorants. Methods: The experimental design was acquired by the keyword-driven approach through the advanced search in the Espacenet database European Patent Office (EPO). The keywords selected were bacteria or fungi* or yeast or algae or microorganism* but not plant* and pigment* or color* or colorant* or dye* and the International Patent Classification code, C09B61, for prospecting of interest. Results: There has been a linear increase in patents developed in the last 20 years, with Japan as the largest depositor in the area. The companies Dainippon Ink and Chemicals and Ajinomoto, both being Japanese, are the largest depositors with 20% of all patents. Among the microorganisms, the filamentous fungi appeared in the first place with 32% of documents and the fungi of the genus Monascus were the most frequently used. Conclusion: The use of microbial colorants has been growing among industries, mainly in food sectors, due to the growing demand for products of natural origin. Thus, the increase in research and technological development in the area of microbial colorants can become an economically viable and promising strategy for the various industrial sectors.
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Parra, Ángel, Carla Lossada, Aleivi Pérez, Johnny Navarrete, and Lenin González. "Characterization of CRISPR genetic sequences in microorganisms associated with infections in shrimp (Litopenaeus vannamei)." Revista de la Facultad de Agronomía, Universidad del Zulia 38, no. 2 (March 13, 2021): 360–81. http://dx.doi.org/10.47280/revfacagron(luz).v38.n2.08.
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In shrimp farming, the family of proteobacteria Vibrionaceae, especially the species of the genus Vibrio, represent one of the main responsible for infections in shrimp production (Litopenaeus vannamei), generating great losses to this industry. Phagotherapy emerges as a novel alternative for the control of said infections in substitution to the use of antibiotics, thanks to the specific inhibitory activity of these viruses. However, it is necessary to take into account the presence in prokaryotes of genetic sequences called clusters of regularly interspaced short palindromic repeats (CRISPR) that act as an immune system against invasion of external mobile genetic elements such as phage or plasmids. Due to its characteristics, the CRISPR/Cas system is used as a tool for gene editing. This study presents the comparative analysis of 7 CRISPR loci found in 5 sequences of complete genomes, available in the database of NCBI/GenBank, to determine the potential use of the phage strategy in shrimp farming. The CRISPR systems corresponded to types I-E, I-F and III-D. 53 % of the spacers (75/142) presented homology with plasmids, while the remaining 47 % (67/142) showed homology with bacteriophages, mostly non-typical Vibrio infective viruses. The use of phage therapy is proposed as a treatment for infections caused by members of the family Vibrionaceae in shrimp cultures, due to the low occurrence of CRISPR systems in the species studied and the low immunity to their phages, thus ensuring greater sensitivity.