scholarly journals Analysis of the Metatranscriptome of Microbial Communities by Comparison of Different Assembly Tools Reveals Improved Functional Annotation

2017 ◽  
Vol 3 (4) ◽  
Author(s):  
Chandan Badapanda
Keyword(s):  
Microbial Communities ◽  
Functional Annotation

scholarly journals OrtSuite – from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Author(s):  
João Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

Abstract The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96 % of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

scholarly journals OrtSuite – from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Author(s):  
Joao Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Vinicios Fleming Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96 % of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. Identification of putative synergistic species interactions was evaluated using the sequenced genomes of an independent study which had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy to use workflow that allows for rapid functional annotation based on a user curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

scholarly journals OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes

2021 ◽  
Vol 4 (12) ◽  
pp. e202101167
Author(s):  
João Pedro Saraiva ◽  
Alexandre Bartholomäus ◽  
René Kallies ◽  
Marta Gomes ◽  
Marcos Bicalho ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source Software ◽  
Species Interactions ◽  
Functional Annotation ◽  
Ecosystem Processes ◽  
Independent Study ◽  
Microbial Interactions ◽  
High Complexity ◽  
Benzoate Degradation ◽  
User Friendly

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

T-RFLP – a representative tool to study pulmonary microbial communities

Pneumologie ◽  
2009 ◽  
Vol 63 (S 01) ◽  
Author(s):  
T Zakharkina ◽  
C Herr ◽  
A Yildirim ◽  
M Friedrich ◽  
R Bals
Keyword(s):  
Microbial Communities

Screening bioactive secondary metabolites from Costa Rican enviromental microbial communities

Planta Medica ◽  
2015 ◽  
Vol 81 (11) ◽  
Author(s):  
JJ Araya ◽  
M Chavarría ◽  
A Pinto-Tomás ◽  
C Murillo ◽  
L Uribe ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Microbial Communities ◽  
Costa Rican ◽  
Bioactive Secondary Metabolites

Enhanced CO2 concentrations change the structure of Antarctic marine microbial communities

2016 ◽  
Vol 552 ◽  
pp. 93-113 ◽  
Author(s):  
AT Davidson ◽  
J McKinlay ◽  
K Westwood ◽  
PG Thomson ◽  
R van den Enden ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Co2 Concentrations ◽  
Antarctic Marine ◽  
Marine Microbial Communities

1642 Effect of Enterococcus fecalis SROD5 supplementation on microbial communities and quantities of in vitro rumen fermentation

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 800-800
Author(s):  
L. L. Mamuad ◽  
S. S. Lee ◽  
A. A. Biswas ◽  
C. D. Jeong
Keyword(s):  
Microbial Communities ◽  
Rumen Fermentation ◽  
In Vitro Rumen Fermentation
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