A review of simulation and modeling approaches in microbiology
Bacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic ...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2016-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/493 |
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| author | A. I. Klimenko Z. S. Mustafin A. D. Chekantsev R. K. Zudin Yu. G. Matushkin S. A. Lashin |
| author_facet | A. I. Klimenko Z. S. Mustafin A. D. Chekantsev R. K. Zudin Yu. G. Matushkin S. A. Lashin |
| author_sort | A. I. Klimenko |
| collection | DOAJ |
| description | Bacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic data challenges not only biostatisticians but also biomodelers, since these data are essential to improve the modeling quality while simulation methods are useful to understand the evolution of microbial communities and their function in the ecosystem. An outlook on the existing modeling and simulation approaches based on different types of experimental data in the field of microbial ecology and environmental microbiology is presented. A number of approaches focusing on a description of such microbial community aspects as its trophic structure, metabolic and population dynamics, genetic diversity as well as spatial heterogeneity and expansion dynamics is considered. We also propose a classification of the existing software designed for simulation of microbial communities. It is shown that although the trend for using multiscale/hybrid models prevails, the integration between models concerning different levels of biological organization of communities still remains a problem to be solved. The multiaspect nature of integration approaches used to model microbial communities is based on the need to take into account heterogeneous data obtained from various sources by applying high-throughput genome investigation methods. |
| format | Article |
| id | doaj-art-b13abab9e4554a76b50a286c10caa2d6 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-b13abab9e4554a76b50a286c10caa2d62025-02-01T09:58:02ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592016-01-0119674575210.18699/VJ15.095436A review of simulation and modeling approaches in microbiologyA. I. Klimenko0Z. S. Mustafin1A. D. Chekantsev2R. K. Zudin3Yu. G. Matushkin4S. A. Lashin5Institute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaBacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic data challenges not only biostatisticians but also biomodelers, since these data are essential to improve the modeling quality while simulation methods are useful to understand the evolution of microbial communities and their function in the ecosystem. An outlook on the existing modeling and simulation approaches based on different types of experimental data in the field of microbial ecology and environmental microbiology is presented. A number of approaches focusing on a description of such microbial community aspects as its trophic structure, metabolic and population dynamics, genetic diversity as well as spatial heterogeneity and expansion dynamics is considered. We also propose a classification of the existing software designed for simulation of microbial communities. It is shown that although the trend for using multiscale/hybrid models prevails, the integration between models concerning different levels of biological organization of communities still remains a problem to be solved. The multiaspect nature of integration approaches used to model microbial communities is based on the need to take into account heterogeneous data obtained from various sources by applying high-throughput genome investigation methods.https://vavilov.elpub.ru/jour/article/view/493microbial communitiesecological simulationevolutionary modelingprokaryotes |
| spellingShingle | A. I. Klimenko Z. S. Mustafin A. D. Chekantsev R. K. Zudin Yu. G. Matushkin S. A. Lashin A review of simulation and modeling approaches in microbiology Вавиловский журнал генетики и селекции microbial communities ecological simulation evolutionary modeling prokaryotes |
| title | A review of simulation and modeling approaches in microbiology |
| title_full | A review of simulation and modeling approaches in microbiology |
| title_fullStr | A review of simulation and modeling approaches in microbiology |
| title_full_unstemmed | A review of simulation and modeling approaches in microbiology |
| title_short | A review of simulation and modeling approaches in microbiology |
| title_sort | review of simulation and modeling approaches in microbiology |
| topic | microbial communities ecological simulation evolutionary modeling prokaryotes |
| url | https://vavilov.elpub.ru/jour/article/view/493 |
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