Biology subjects

McAdams, Z. L.

Publications and source records attributed to McAdams, Z. L..

11 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↗

bioRxiv2026

Alamandine/MrgD Pathway Modulates Gut-Bone Marrow Axis in Aging

Aging is associated with colon epithelial barrier integrity and upregulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in aging via modulating gut-BM axis. Mice of age 2-3 (Young) or 22-24 months (Old) were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated by using FITC-dextran. Lgr5+Olfm4+ intestinal stem cells (ISCs), Wnt3a and {beta}-catenin were evaluated by immunohistochemistry or western blotting. Fecal microbiome was analyzed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Cecal or serum bacterial metabolites were analyzed. The pro-myelopoietic potential of cecal supernatants (CS) was tested in the Young-BM cells. MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in aging was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels that were antagonized by the NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active {beta}-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and {beta}-diversity of the aging microbiome and decreased Bacillota/Bacteroidota. Ala decreased the CD80+ and increased CX3CR+ cells in the Old colons. Old-CS induced myelopoiesis in vitro in BM cells with higher number of monocytes and pro-inflammatory macrophages which was not observed in the CS derived from Ala-treated Old mice. Ala is a promising pharmacological agent for reversing the leaky gut of aging by restoring homeostasis in the gut-BM axis.

pharmacology and toxicology↗

bioRxiv2024

A novel dataset of 2,362 equine fecal microbiomes from eight veterinary teaching hospital on three continents reveals dominant effects of geography, breed, and disease

Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work largely employs single timepoint analyses, or horses selected based on limited health criteria. To address these issues and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.

microbiology↗

bioRxiv2024

Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis

To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.

microbiology↗

bioRxiv2024

Biological and technical variability in mouse microbiome analysis and implications for sample size determination

BackgroundThe gut microbiome (GM) affects host growth and development, behavior, and disease susceptibility. Biomedical research investigating the mechanisms by which the GM influences host phenotypes often involves collecting single fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice and while efforts are made to minimize these sources of variation, biological variation at the cage or individual mouse level and technical variation from 16S rRNA library preparation exist and may influence microbiome outcomes. Here we employed a hierarchical fecal sampling strategy to 1) quantify the effect size of biological and technical variation and 2) provide practical guidance for the development of microbiome studies involving laboratory mice. ResultsWe found that while biological and technical sources of variation contribute significant variability to microbiome alpha and beta diversity outcomes but their effect size is 3- to 30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying variability of alpha diversity metrics at the technical and biological levels, we then simulated whether sequencing multiple fecal samples from individual mice could improve effect size in a two-group experimental design. Collecting five fecal samples per mouse increased effect size achieving the maximum 5% reduction in the required number of animals per group. While reducing the number of animals required, sequencing costs were dramatically increased. ConclusionsOur data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. Additionally, repeated sampling improves statistical power however, its application is likely impractical given the increased sequencing costs.

microbiology↗

bioRxiv2024

Fetal programming by the maternal microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus

BackgroundThe microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects. ResultsHere we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase activity gene expression (bsh), abundance of certain bile acids, and hepatic expression of Slc10a1. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome- associated differences in methylation of 196 loci in total, 176 of which show conserved profiles between mother and offspring. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. ConclusionsCollectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

microbiology↗

bioRxiv2024

Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors

Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T+ Itpr3tf/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate naturally occurring diversity within the host GM as an experimental factor in biomedical research.

microbiology↗

bioRxiv2024

Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients

The gut microbiota (GM) influences multiple processes during host development and maintenance. To study these events, fecal microbiota transfer (FMT) to germ-free (GF) recipients is often performed. Mouse models of disease are also susceptible to GM-dependent effects, and cryo-repositories often store feces from donated mouse strains. Shipping live mice may affect the GM and result in an inaccurate representation of the baseline GM. We hypothesize that the use of such fecal samples for FMT would transfer shipping-induced changes in the donor GM to GF recipients. To test this, donor mice originating from two suppliers were shipped to the University of Missouri. Fecal samples collected pre- and post-shipping were used to inoculate GF mice. Pre- and post-shipping fecal samples from donors, and fecal and/or cecal contents were collected from recipients at one and two weeks post-FMT. 16S rRNA sequencing revealed supplier-dependent effects of shipping on the donor microbiome. FMT efficiency was independent of shipping timepoint or supplier, resulting in transmission of shipping-induced changes to recipient mice, however the effect of supplier-origin microbiome remained evident. While shipping may cause subtle changes in fecal samples collected for FMT, such effects are inconsistent among supplier-origin GMs and minor in comparison to other biological variables.

microbiology↗

bioRxiv2023

Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome relative to a standardized biological variable

BackgroundWhile murine fecal collection is central to microbiome research, there are a number of practical considerations that may vary during fecal sample collection, including time to sample storage, time of day the sample is collected, and position within the colon during terminal collections. While the need to control these factors is recognized, the relative effect on microbial community of duration at room temperature, time of day, and hindgut position, in the context of a known biological variable, is unclear. To answer these questions, and assess reproducibility of results across different microbiome compositions, parallel experiments were performed to investigate the effect of those factors on the microbiome of age- and sex-matched isogenic mice colonized with two different vendor-origin microbiomes. Results16S rRNA amplicon sequencing data from flash-frozen fecal samples showed no statistical difference in alpha or beta diversity compared to samples incubated for 1, 2, 3, 4, 6, and 9 hours at room temperature. Overall, samples collected in the AM period showed greater richness and alpha-diversity compared to samples collected in the PM period. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. When using two vendor-origin microbiomes as a biological variable, its effect size vastly outweighed the effect size of the time samples spent at room temperature, the time of day samples were collected, and the position within the colon from which samples were collected. ConclusionsThis study has highlighted multiple scenarios encountered in microbiome research that may affect outcome measures of microbial diversity and composition. Unexpectedly, delayed time to sample cold storage up to nine hours did not affect the alpha or global beta diversity of fecal sample. We then presented evidence of location- and time-dependent effects within the hindgut on microbial richness, diversity, and composition. We finally demonstrated a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.

microbiology↗

bioRxiv2023

Longitudinal characterization of the captive adult and tadpole Wyoming toad (Anaxyrus baxteri) microbiome

At one time thought to be extinct in the wild, the Wyoming toad (Anaxyrus baxteri) is one of the most critically endangered North American amphibian species. Despite approximately 20 years of ex situ breeding and reintroduction programs, these animals remain functionally extinct in the wild. There is concern among those working in these programs that individuals bred in captivity fail to develop the proper microbiome to withstand the stressors of their native habitat following release. In related species, the skin microbiome has been shown to have a defensive function against common pathogens affecting these animals. However, the early-life microbiome of developing tadpoles in this species remains unknown and therefore this defensive function is unexplored in the Wyoming toad. This study employed 16S rRNA amplicon sequencing to document the baseline microbiome of tadpoles bred for release and captive adult breeder populations. To characterize microbiome development, multiple rounds of skin mucosal and cloacal swabs were obtained concurrently from adult Wyoming toads bred at Omahas Henry Doorly Zoo and Aquarium. Our results revealed significant differences between tadpole and adult microbiomes, as well as significant sex-dependent differences within the adult Wyoming toads, in terms of richness and composition. Thus, these findings have identified the baseline microbiome of this endangered species, and variables significantly influencing its composition. Ongoing studies of the only extant wild population are expected to identify taxa not present in captive toads, and potentially help design husbandry modifications to maximize survivability following reintroduction to the wild.

microbiology↗

bioRxiv2022

Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes

Host genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiont Saccharimonadaceae. Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.

microbiology↗