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

Palmer, D.; Adkins, P. R. F.; Isensee, P.; Dorfmeyer, R. A.; Su, E.; Turner, G.; Davis, D. J.; Bivens, N. J.; McAdams, Z. L.; Ericsson, A. C.

doi:10.64898/2026.10.08.757609

bioRxiv · 10.64898/2026.10.08.757609

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

Palmer, D.·Adkins, P. R. F.·Isensee, P.·Dorfmeyer, R. A.·Su, E.·Turner, G.·Davis, D. J.·Bivens, N. J.·McAdams, Z. L.·Ericsson, A. C.

View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

systems biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Palmer, D., Adkins, P. R. F., Isensee, P., Dorfmeyer, R. A., Su, E., Turner, G., Davis, D. J., Bivens, N. J., McAdams, Z. L., Ericsson, A. C.. 2026-10-09. 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. https://doi.org/10.64898/2026.10.08.757609

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Dietary fibre responses emerge through host-dietary regime interplay: Apple pectin modulates immune reactivity in adult zebrafish

Dietary fibres are rarely consumed independently. Instead, they form part of an overall diet that includes dietary fibres from different sources, in varying amounts and consumed under different feeding patterns. Here, we tested how dietary regimes containing apple pectin, oat {beta}-glucan, or cellulose shaped the host. We analysed gut microbiome composition by 16S rRNA sequencing, measured brain and intestinal SCFA profiles by targeted metabolomics, and assessed immunomodulation by measuring gene expression systemically in the blood and locally in the spleen, as well as intestinal enzyme activity. The dietary intervention was conducted for 12 weeks on adult female and male zebrafish (Danio rerio). Our results show that the gut microbial composition can be relatively stable across different dietary fibre exposure patterns yet still vary significantly between the sexes. Additionally, the effect of sex on the gut microbiome may become more evident when dietary fibres are administered at high dosages, but intermittently. Dietary fibre regimes can alter intestinal short-chain fatty acid profiles more readily than brain profiles, which show a stronger sexually dimorphic response. Interestingly, apple pectin modulated the zebrafish immune response through interactions dependent on the overall regime, tissue, sex, and host immune status. Notably, tissue il1b gene expression differed depending on how apple pectin was administered and the host's physiological state. Collectively, our study emphasises the highly context-specific effects of dietary fibres, shaped by the dynamic interplay between the overall dietary regime and intertwined host factors.

systems biology↗

bioRxiv2026

Co-transcriptomic network analysis of host-parasite interactions reveals genes underpinning parasite fitness

Interactions between parasites and their host organisms generate continuous variation in infection outcomes. Although dual transcriptome studies have demonstrated extensive molecular dialogues between interacting species, it is still unclear how natural variation in host and parasite gene regulatory networks and coordination between them contribute to diverse disease phenotypes. Here, we re-contextualized co-transcriptomes from recombinant inbred lines of the plant-parasitic root-knot nematode Meloidogyne hapla infecting Medicago truncatula host plants with relative measures of infection intensity as a proxy for parasite load. We used infection intensity to estimate interaction gradients on gene expression by calculating its covariance with transcript levels. Quantitative analyses of interaction gradients for host and parasite transcriptomes identified major differences in development-related transcriptional programs along the infection continuum. In addition, integrated network analyses connected host cell wall remodeling with parasite protein production and secretion. Silencing of candidate root-knot nematode genes reduced host galling and parasite reproductive fitness, providing experimental support for our network-derived predictions. Together, our findings present an integrated systems genetics framework connecting naturally occurring genetic variation to quantitative disease phenotypes.

systems biology↗

bioRxiv2026

Targeted proteomics informed by long-read RNA-sequencing reveals protein isoform expression associated with bone mineral density

The expanding catalog of sQTLs from projects like GTEx has established that genetic risk for complex traits is frequently mediated through RNA splicing. Yet it is generally unknown whether disease-associated splice events produce stable, distinct protein isoforms and whether they are functionally consequent. Even the deepest shotgun proteomics efforts only capture a minority of annotated splice events; isoform-specific peptides are systematically under-sampled by nature of being lower abundance and intrinsically harder to detect. Here, we implement a genetics-guided targeted mass spectrometry (MS) strategy to detect splice-derived protein isoforms prioritized by sQTL colocalization. Using internal standard parallel reaction monitoring (IS-PRM), we targeted 288 peptides corresponding to 166 putative BMD-associated isoforms in differentiating osteoprogenitor cells and patient-derived primary mesenchymal stem cells (MSCs). Targeted acquisition increased recovery of isoform-informative peptides relative to conventional DDA, rescued splice events that were undetected or sparsely sampled under global acquisition, and confirmed protein-level expression of genetically prioritized isoforms in clinical material. Together, this work establishes that targeted MS is a useful approach to support validation of protein expression in studies of the genetics of splicing.

systems biology↗