Biology subjects

Adkins, P. R. F.

Publications and source records attributed to Adkins, P. R. F..

2 recordsLinked to original sources

bioRxiv2026

Multi-domain analysis of the fecal microbiome of dairy heifers, beef heifers, bred beef heifers, and adult beef cows in the central United States using paired 16S rRNA and 18S rRNA metabarcoding

The growth and performance of cattle is dependent on efficient feed conversion, facilitated by the gut microbiome, including both prokaryotic and eukaryotic organisms. Extrinsic factors such as management practices and intrinsic factors like age and genetics can shape these communities. To characterize the relative effects of such factors on the prokaryotic and eukaryotic microbiomes, fresh fecal samples from dairy heifers (n = 8), beef heifers (n = 8), bred beef heifers (n = 8), and adult beef cows (n = 8) were subjected to paired 16S rRNA (V4) and a novel 18S rRNA (V4-V5) metabarcoding assay, and 18S rRNA amplicons were annotated using two databases in parallel. Taxonomic resolution of 18S rRNA amplicons was excellent, with SILVA and EUKARYOME databases each providing better resolution of different groups of organisms. While no differences in eukaryotic richness or alpha diversity were detected, beta diversity differed in all pairwise comparisons except between beef heifers and bred beef heifers. Prokaryotic richness was lower in adult beef cows than the other groups, and beta diversity differed in all pairwise comparisons. Adult beef cows were the most distinct, characterized by replacement of fungal organisms with protozoa and loss of thermophilic bacteria in the eukaryotic and prokaryotic compartments, respectively. Among numerous differentially abundant features, dairy heifers harbored greater abundance of Cooperia oncophora while beef heifers contained greater abundance of Buxtonella sulcata and Mucor. Correlation network analysis revealed multiple significant positive and negative associations between bacterial, fungal, and protozoal features during maturation of the fecal microbiome. Collectively, these data highlight the richness and diversity of both the prokaryotic and eukaryotic compartments of the bovine fecal microbiome, and the influence of management practices and age on both communities. From a technical standpoint, these data demonstrate the ability to resolve fungal, protozoal, and metazoan organisms, including potential parasites and pathogens, with a single metabarcoding assay. They also highlight the nuanced differences between databases and the value of parallel analyses using more than one database.

systems biology↗

bioRxiv2020

Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens

S. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species that have been isolated from the bone and blood of lame broilers. We were the first to report that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers. Further, we showed that a particular isolate of S. agnetis, chicken isolate 908, can induce lameness in over 50% of exposed chickens, far exceeding normal BCO incidences in broiler operations. We have previously reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S. agnetis isolates, including an additional chicken BCO strain, and ten isolates from milk, mammary gland secretions or udder skin, from the collection at the University of Missouri. To trace phylogenetic relationships, we constructed phylogenetic trees based on multi-locus sequence typing, and Genome-to-Genome Distance Comparisons. Chicken isolate 908 clustered with two of the cattle isolates along with three isolates from chickens in Denmark and an isolate of S. agnetis we isolated from a BCO lesion on a commercial broiler farm in Arkansas. We used a number of BLAST tools to compare the chicken isolates to those from cattle and identified 98 coding sequences distinguishing isolate 908 from the cattle isolates. None of the identified genes explain the differences in host or tissue tropism. These analyses are critical to understanding how Staphylococci colonize and infect different hosts and potentially how they can transition to alternative niches (bone vs dermis). ImportanceStaphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with different disease manifestations. The data show the chicken and cattle isolates are very closely related but the chicken isolates all cluster together suggesting a single jump from cattle to chickens.

microbiology↗