High‐resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities

2021 ◽  
Author(s):  
Yen Ning Chai ◽  
Yufeng Ge ◽  
Vincent Stoerger ◽  
Daniel P. Schachtman
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Synthetic Microbial Communities ◽  
Low Nitrogen ◽  
Phenotypic Responses

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.

High-Resolution Dynamics of Microbial Communities during Dissimilatory Selenate Reduction in Anoxic Soil

2015 ◽  
Vol 49 (13) ◽  
pp. 7684-7691 ◽  
Author(s):  
Ronald R. Navarro ◽  
Tomo Aoyagi ◽  
Makoto Kimura ◽  
Hideomi Itoh ◽  
Yuya Sato ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities

High-resolution metagenomics targets specific functional types in complex microbial communities

2008 ◽  
Vol 26 (9) ◽  
pp. 1029-1034 ◽  
Author(s):  
Marina G Kalyuzhnaya ◽  
Alla Lapidus ◽  
Natalia Ivanova ◽  
Alex C Copeland ◽  
Alice C McHardy ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Functional Types

scholarly journals Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

2019 ◽  
Vol 218 ◽  
pp. 481-504 ◽  
Author(s):  
Caroline Gauchotte-Lindsay ◽  
Thomas J. Aspray ◽  
Mara Knapp ◽  
Umer Z. Ijaz
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Microbial Communities ◽  
Contaminated Soils ◽  
Rational Design ◽  
Data Driven ◽  
Molecular Tools ◽  
Complex Samples ◽  
Driven Systems

We present here a data-driven systems biology framework for the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils.

scholarly journals Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristal Zuñiga ◽  
Tingting Li ◽  
Michael T. Guarnieri ◽  
Jackson P. Jenkins ◽  
Chien-Ting Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sustainable Growth ◽  
Synthetic Microbial Communities

scholarly journals Massively parallel screening of synthetic microbial communities

2019 ◽  
Vol 116 (26) ◽  
pp. 12804-12809 ◽  
Author(s):  
Jared Kehe ◽  
Anthony Kulesa ◽  
Anthony Ortiz ◽  
Cheri M. Ackerman ◽  
Sri Gowtham Thakku ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Massively Parallel ◽  
Phenotypic Characterization ◽  
Interspecies Interactions ◽  
Additional Species ◽  
Plant Symbiont ◽  
Complementary Approach ◽  
Potential Applications ◽  
Synthetic Microbial Communities

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiontHerbaspirillum frisingensein a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.

scholarly journals Two-target quantitative PCR to predict library composition for shallow shotgun sequencing

2020 ◽  
Author(s):  
Matthew Y. Cho ◽  
Marc Oliva ◽  
Anna Spreafico ◽  
Bo Chen ◽  
Xu Wei ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Quantitative Pcr ◽  
Shotgun Sequencing ◽  
Accurate Prediction ◽  
Missing Information ◽  
Bacterial Genes

AbstractShotgun sequencing enables retrieving high resolution information 40 from complex microbial communities. However, the technique is limited by missing information about host-to-microbe ratios observed in different sample types. This makes it challenging to plan sequencing experiments, especially in the context of high sample multiplexing and/or limited sequencing output. We evaluated a qPCR-based assay to predict host-to microbe ratio prior to sequencing. Using a two-target assay aimed at conserved human and bacterial genes, we predicted human-to-microbe ratios in two sample types and validated it on independently collected samples. The assay enabled accurate prediction for a broad range of sample compositions.

scholarly journals Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Pengfan Zhang ◽  
Stjin Spaepen ◽  
Yang Bai ◽  
Stephane Hacquard ◽  
Ruben Garrido-Oter
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Polymorphic Variation ◽  
Sequencing Data ◽  
Sequencing Errors ◽  
Extensive Evaluation ◽  
Culture Independent ◽  
Reference Sequences ◽  
Synthetic Microbial Communities

AbstractSynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.

Sign in / Sign up

Export Citation Format

Share Document