Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome

Allen, Benjamin H.; Gupta, Nidhi; Edirisinghe, Janaka N.; Faria, José P.; Henry, Christopher S.

doi:10.1007/978-1-0716-1585-0_13

Cited by 6 publications

(6 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…in Eq. (9), a gLV equation describes specific growth of species i using a linear equation, i.e., where interaction coefficient a i,j denotes the effect of species population j on the specific growth of species i . For a binary community, Eq.…”

Section: Methodsmentioning

confidence: 99%

“…However, control and design of microbial community dynamics and function is a challenging task, primarily due to higher-order or emergent properties that are not observable from individual species in isolation but arise through nonlinear interspecies interactions (6,7). Therefore, rational design of microbial communities or consortia requires a fundamental knowledge of microbial interactions as a mechanistic linkage between the environment and the community compositions and function, necessitating the employment of predictive mathematical models as indispensable tools (8)(9)(10)(11)(12)(13)(14).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation

Song

Lee

Kessell

et al. 2022

Preprint

View full text Add to dashboard Cite

Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. However, we lack a fundamental understanding of how microbial interactions are driven by environmental factors due to the absence of generalizable theoretical foundations, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. This unique capability of our approach was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids), but competitively growing on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates, but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions such as asymmetry in interactions. Our approach can be extended to other related ecological systems to model their environment-dependent interspecies interactions from growth kinetics.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation

Song

Lee

Kessell

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…To address these issues, metabolic modeling studies and pipelines such as KBase have great promise to link assembled genomes to metabolic flux in a sample. 27 However, this analysis is currently limited to a few input genomes and not microbial communities in complex environments.…”

Section: A New Era Of Protein and Metabolite Analysismentioning

confidence: 99%

A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome

Sidebottom

2023

Clin Colon Rectal Surg

View full text Add to dashboard Cite

Over the past 20 years, the study of microbial communities has benefited from simultaneous advancements across several fields resulting in a high-resolution view of human consortia. Although the first bacterium was described in the mid-1600s, the interest in community membership and function has not been a focus or feasible until recent decades. With strategies such as shotgun sequencing, microbes can be taxonomically profiled without culturing and their unique variants defined and compared across phenotypes. Approaches such as metatranscriptomics, metaproteomics, and metabolomics can define the current functional state of a population through the identification of bioactive compounds and significant pathways. Prior to sample collection in microbiome-based studies it is critical to evaluate the requirements of downstream analyses to ensure accurate processing and storage for generation of high data quality. A common pipeline for the analysis of human samples includes approval of collection protocols and method finalization, patient sample collection, sample processing, data analysis, and visualization. Human-based microbiome studies are inherently challenging but with the application of complementary multi-omic strategies there is an unbounded potential for discovery.

show abstract

“…The raw reads were trimmed using Trimmomatic v0.32 to remove adaptors and improve the sequence quality ( 5 ). The trimmed reads were assembled using SPAdes v3.15.3 on the KBase online platform ( 6 , 7 ). The obtained contigs from the assembled reads were reduced to 27 contigs using the Medusa combo online genome scaffolder ( 8 ) with a single-contig Bacillus cereus isolate as a reference.…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of a Polyhydroxyalkanoate-Producing Bacillus cereus Strain Isolated from Nuevo Leon State, Mexico

Huerta-Alemán

Martínez-Herrera

Elufisan

et al. 2022

Microbiol Resour Announc

View full text Add to dashboard Cite

show abstract

Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome

Cited by 6 publications

References 27 publications

Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation

Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation

A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome

Draft Genome Sequence of a Polyhydroxyalkanoate-Producing Bacillus cereus Strain Isolated from Nuevo Leon State, Mexico

Contact Info

Product

Resources

About