Food Science and Technology Department


First Advisor

Samodha C. Fernando

Date of this Version



A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Food Science and Technology, Under the Supervision of Professor Samodha C. Fernando. Lincoln, Nebraska: May, 2022

Copyright © 2022 Nirosh D. Aluthge


Research conducted in the past couple of decades has showcased the importance of the gut microbiota in human health and well-being. While many studies have reported on the differences in community membership between a disease state and a healthy state, few have investigated the mechanisms through which an aberrant microbiota contributes to a disease phenotype. One of the primary reasons for this are the many technical and ethical barriers to conducting the necessary studies directly in human individuals. Human microbiota-associated (HMA) porcine models have the potential to become important research tools which can enable the testing of hypotheses regarding host-microbiota interactions in human health and disease without directly involving humans. However, relatively few microbiome studies have utilized porcine models in this capacity. Through multiple studies, we evaluated HMA porcine models in terms of their suitability for use in gut microbiota studies. Results demonstrated that (1) compared to an HMA C3H/HeN mouse model, a higher percentage of donor taxa from donors of different age groups were able to persistently colonize HMA piglets, (2) while a majority of donor taxa in infant donors were able to colonize HMA piglets, rare/low-abundance taxa found in the infant donors enriched once engrafted into the piglets, and (3) the potential for using HMA piglets for studying host-microbiota interactions related to obesity. We believe that further improvements to address some of the shortcoming and challenges associated with HMA piglets will facilitate more wide-spread use of this animal model in the field of gut microbiome research.

Advisor: Samodha C. Fernando

Fig.2.6. - Phylogenetic tree depicting the overall distribution of core donor ASVs classified as Firmicutes among the two HMA animal models.pdf (70 kB)
Supplementary Data 1 - Core ASV distribution for each donor in the two HMA animal models including the respective relative abundances and taxonomic classifications.xlsx (37 kB)
Supplementary Data 2 - Phylum, family, and genus level groupings of colonizers and persistent colonizers in the two HMA animal models and their distribution in the human donors.xlsx (25 kB)
Supplementary Data 3 - Mean relative abundances and taxonomic classifications for the persistent colonizers identified for each animal model within each donor.xlsx (27 kB)
Supplementary Data 4 - Taxonomic classifications for core ASVs from each human donor that failed to colonize either of the two animal models.xlsx (14 kB)
Supplementary Data 5 - Taxonomic classifications for 27 common core ASVs found across the 4 donors.xlsx (9 kB)
Supplementary Data 6 - Colonization success of the 27-common core ASVs among the two HMA animal models.xlsx (9 kB)
Supplementary Data 7 - Phylum, family, and genus level taxonomy assignments and relative abundances for the core ASVs from each donor that established in each animal model.xlsx (36 kB)
Supplementary Data 8 - Relative abundance comparisons at each sampling time point for the persistent colonizers of each animal model for each donor.xlsx (114 kB)
Supplementary Data 9 - Taxonomic classifications of persistent colonizers with donor-like abundances for each animal model.xlsx (14 kB)
Supplementary Data 10 - Phylum, family, genus level taxonomy assignments for core ASVs from donors of subsequent study which colonized the two HMA animal models.xlsx (30 kB)