Corbin, Kendall

Research Activities

The Corbin research program is working to create bridges between the areas of agriculture and human health by studying and exploiting microorganisms.

One of the central pillars of my research program is to understand the relationship between diet, health, and the human microbiome using microcosm in vitro models. The use of in vitro digestion and colon models provides a unique opportunity to model the behavior of substrates throughout the digestive tract and probe their effect on the microbiota, in controlled non-invasive experiments. Since starting at UK, I have established a state-of-the-art colon model facility equipped with cutting edge technology, including the acquisition of a SHIME (Simulator of Human Intestinal Microbial Ecosystem) platform. The SHIME in my program is only the second unit in the United States. At this time, I have two active international research projects related to digestion and gut health. The first project is the international INFOGEST Ring Trial. The goal of this project isto develop a harmonized method for measuring alpha-amylase activity, the key enzyme in starch digestion. The second funded project is investigating the association between chronic fatigue and gut dysbiosis in children with neurodevelopmental disorders and is a collaboration with University of Calgary and Arizona State University. Another focus of our research is investigating the role of extracellular RNA in intercellular ad interkingdom communication (NSF funded), with particular focus on understanding if/how exRNAs modulate microbiomes (gut and plant-associated).

Another key area of our work to development tools for harnessing microbial cellulose production. To achieve this, in collaboration with the Pacific Northwest National Laboratory, we are integrating multi-omic data with biochemical and structural data to elucidate mechanics controlling cellulose production in species from the genus Komagataeibacter. This work has the potential to advance the efficiency of bacterial cellulose production and its utilization as a biomaterial in medical and biotechnology applications. Specific applications of interest include the use of bacterial cellulose for delivery of drugs/prebiotics/probiotics and as a degradable biomaterial for face masks

Projects

The Role of Extracellular RNA in Intercellular and Interkingdom Communication

Emerging evidence identifies intercellular communication as a key function of extracellular RNA (exRNA), including communication between organisms. RNA has many characteristics that make it a good signal: it is ephemeral, information-dense, and common to all forms of life. Understanding how to manipulate exRNA communication can advance both agriculture and medicine through the development of new environmentally friendly pesticides, treatments of dysbiosis in both plants and animals (converting unhealthy microbiomes to healthy ones), and a host of new diagnostic and therapeutic tools for earlier detection and/or treatment of disease.

Individuals working on project: Hanna Lefevers, Kevin Gonzalez Morelo, Lakshay Anand , Kendall Corbin

Investigating how storage conditions affect the microbial safety of soft winter wheat

Preventing foodborne illnesses is challenging due to the complex nature of linking individual illnesses to an ingredient or food. It is rarely possible to make this association unless an outbreak occurs. Historically, wheat flour has been considered a low-risk food ingredient. However, in the last two decades foodborne outbreaks and recalls associated to contaminated wheat flour has exposed the potential health risks associated to consuming raw, uncooked wheat products. The aim of this project is to investigate how variety selection, storage time and storage conditions affect the microbial safety and microbial diversity of soft winter wheat.

Individuals working on project: Lakshay Anand and Kendall Corbin

Embracing Complexity: Exploring the connections between chronic fatigue, behaviour, and gut microbiome dysbiosis in children with neurodevelopmental disorders

Neurodevelopmental disorders (NDDs), represent the largest identifiable subpopulation of children with disabilities in North America. Up to 80% of children with NDDs exhibit behaviours of concern. Despite their prevalence and significant impact on pediatric patients and their families, the underlying cause of behaviours of concern can be difficult to elucidate and treatments are limited. This is due in part to the neurodevelopmental complexity of these patients. Both chronic fatigue and gut microbiome dysbiosis are promising emerging, cutting-edge modifiable risk factors for behaviours of concern. For this project, we will investigate correlations between chronic fatigue and degree of gut microbiome dysbiosis in children with NDDs who have behaviours of concern.

Individuals working on project: Kendall Corbin

Developing a Genomic Toolkit to Harness Bacterial Cellulose Production

The overarching goal of this proposal is to unravel the metabolic pathways controlling the physicochemical properties of cellulose generated by bacteria in the genus Komagataeibacter. For this project, the responsiveness of six cellulose producing strains of will be evaluated when grown in the presence of different carbon sources. It is anticipated that information generated from this study will provide novel insights on how cellulose production can be improved through the manipulation of metabolic pathways.

Individuals working on project: Bashir Akhoon, Carlos Rodriguez Lopez, and Kendall Corbin

Exploring the Microbiota of Brassica oleracea vegetables and the closest wild relative Brassica cretica

The process of crop domestication has led to significant alterations in crop phenotypes, enhancing traits beneficial to human needs. However, the consequences of domestication on the holobiont, encompassing the plant and its associated microbiota, have often been overlooked. To date, significant efforts have been made to understand plant-microbe interactions in domesticated agronomic crops. This lack of information hinders our ability to understand how domestication has altered the edible microbiota of economically important horticultural crops that are consumed raw. This study aims to investigate the effect of domestication on the microbial communities of Brassica oleracea at key developmental stages of each variety, focusing on the soil microbiota and microbiota associated with the edible plant parts. By comparing domesticated Brassica oleracea varieties, such as Kale, Collards, and Broccoli, with its wild relative, Brassica cretica, we seek to elucidate how domestication has influenced microbial assemblages in nutritionally valuable horticultural crops.

Individuals working on project: Easton Sarver and Kendall Corbin

Computational Methods

Microbial data analysis utilizes a diverse range of computational methods. A standard pipeline for metagenome data analysis consists of several steps including quality control of raw sequencing data, denoising, filtering of low-quality and chimeric sequences (Callahan et al., 2016), taxonomic classification of the sequences with machine-learning build classifiers trained using databases such as GreenGenes(DeSantis et al., 2006) for bacterial and UNITE(Abarenkov et al., 2024) for fungal sequences, determining alpha and beta diversity, and conducting statistical analysis for differential abundance. Quantitative Insights Into Microbial Ecology (QIIME) (Bolyen et al., 2019) is a tool that provides several modules to handle each aspect of microbial data analysis. It also allows for the installation of third-party tools to enhance its functionality, such as contamination removal. QIIME is a freely available command-line scientific tool that is also available through UKY's HPC.

The research projects involved in this group will utilize computational methods primarily implemented as freely available open-source bioinformatics tools. These tools may already be available through the HPC or can be easily installed on HPC using package installation managers such as Miniconda (Anaconda Inc., 2018) or by requesting them from the administration. A large-scale dataset will be used in a project that encompasses publicly available datasets from around the world that necessitates the use of memory and computational resources available through UKY’s HPC.

List of Software

The Role of Extracellular RNA in Intercellular and Interkingdom Communication

Dataset download (command-line): NCBI SRA-toolkit and NCBI datasets (Sayers et al., 2022)

Quality Control tools: fastqc (Andrews. ,2010) , multiqc (Ewels et al., 2016), trimmomatic (Bolger et al., 2014), trim Galore (Krueger , 2016), PEAR (Zhang et al., 2014)

Microbiome data analysis: QIIME2 (Bolyen et al., 2019), tools for alignment such as bowtie2 (Langmead & Salzberg, 2012)

Microbial Genome assembly and characterization: Flye (Kolmogorov et al., 2019), canu (Koren et al., 2017), phylophlan (Asnicar et al., 2020), checkM (Parks et al., 2015)

R (R Core Team, 2013) and R-Bioconductor (Gentleman et al., 2004): this will facilitate installation of several R packages that will useful for analysis.

Python: Python provides great libraries especially machine learning (Ayodele, 2010) libraries such as scikit-learn (Pedregosa et al., 2011) and TensorFlow (Abadi et al., 2016).

Anaconda/Miniconda package manager (Anaconda Inc.,2018): this will facilitate installation of other scientific packaged needed for the project.

Investigating how storage conditions affect the microbial safety of soft winter wheat

Quality Control tools: fastqc (Andrews. ,2010) , multiqc (Ewels et al., 2016), trimmomatic (Bolger et al., 2014), trim Galore (Krueger , 2016), PEAR (Zhang et al., 2014)

Microbiome data analysis: QIIME2 (Bolyen et al., 2019), tools for alignment such as bowtie2 (Langmead & Salzberg, 2012)

R (R Core Team, 2013) and R-Bioconductor (Gentleman et al., 2004): this will facilitate installation of several R packages that will useful for analysis.

Anaconda/Miniconda package manager (Anaconda Inc.,2018)