Joseph H. Skarlupka

Despite microorganisms being primarily responsible for landfill material decomposition, limited characterization has been performed across both landfill depth and age. Here, we investigated the microbial communities and physicochemical parameters in two active and two closed landfill wells from surface to bottom, as well as fill dirt and leachate at a sanitary landfill near Madison, Wisconsin, USA. Amplicon community sequencing fungi, bacteria and archaea revealed distinct microbial community structures across landfill sites. The observed patterns of microbial community succession by depth and age mirror the known phases of the landfill life cycle. Younger surface samples were dominated by aerobic fungi, which transitioned to fermentative bacteria and methanogenic archaea in older, deeper, layers. Simultaneously, high species richness was preserved across landfill ages, while reduced evenness at specific depths support spatial niche differentiation. In conjunction with the lack of trends found for physicochemical parameters by depth, this supports niche differentiation driven by the highly heterogenous waste inputs. This study provides the first comprehensive vertical profile of bacterial, fungal, and archaeal communities across landfill depths and ages, highlighting the influence of these parameters on physicochemical factors and microbial distribution within landfills. These results have implications for improving landfill management, including renewable gas energy production, minimizing emissions, and increasing degradation rates.

Mapping genome-wide selective sweeps is of high relevance in cattle population genomics, having successfully identified thousands of genomic regions and candidate genes, with potential to reveal links to agriculturally important traits such as those related to production and adaptation to extreme environments. However, pinpointing the underlying causal variants remains a key priority in understanding molecular mechanisms controlling these traits. The lack of an integrative resource for selective sweeps has impeded meta-analysis and candidate variant prioritization. In the current update of the Bovine Genome Database (BGD; https://bovinegenome.elsiklab.missouri.edu), we address this gap by incorporating a curated dataset consolidating 92 519 selective sweeps identified through 340 genome-wide analyses across 213 cattle populations worldwide. Incorporating this new dataset into BovineMine enables meta-analysis across studies and populations to identify consensus signals, and the exploration of selective sweeps in the context of genes, gene functions, genomic variations, and quantitative trait loci. Furthermore, the BGD JBrowse genome browser enables visualization of sweep regions alongside other genomic features and functional annotations such as histone marks, open chromatin regions, and chromatin states. This BGD update facilitates the prioritization of candidate causal variants and helps identify unanswered questions in disentangling the molecular basis of adaptive and economically important traits in cattle.

Oral swabs of dairy cows have been suggested as a proxy for direct ruminal sampling, and this approach can identify the presence of up to 70% of the rumen microbial community. Here, we further extend the utility of this approach by correlating the bacterial community of swabs collected from 226 dairy cows on a research farm in Wisconsin, USA, with average milk yield and days in milk, two phenotypes previously associated with differences in the ruminal microbiome. We then obtained milk production efficiency data for a subset of these animals (gross feed efficiency [GFE] and residual feed intake [RFI]) and correlated these metrics against their associated microbial data. We found that when using the oral swabs, we could identify correlations between bacterial genera and days in milk ( P < 0.05). We further show that the ruminal microbiota was associated with average milk yield and days in milk for animals in their first lactation. Differential abundance testing identified amplicon sequence variants (ASVs) associated with these metrics ( P < 0.05). Our comparison of bacterial communities between high and low efficiency groups, as determined by GFE and RFI, identified a significant difference in Shannon’s diversity in second lactation cows ( P < 0.05). We also found that RFI was significantly correlated with the bacterial community in second lactation animals ( P < 0.05). Differential abundance analysis identified multiple oral- and rumen-associated ASVs correlated with GFE and RFI ( P < 0.05). This study further establishes the utility of oral swabs as a ruminal proxy. IMPORTANCE: Improving milk production efficiency is a key goal in the dairy industry and is traditionally pursued through genetic selection, diet optimization, and herd management practices. The ruminal microbiome, essential for digesting feed, has been linked to milk production efficiency, suggesting that microbiome modulation could improve efficiency. However, the integration of rumen microbiology into current management practices is hampered by the difficulty of large-scale rumen sampling, as proxies like fecal samples do not accurately reflect the ruminal microbiota. Traditional methods, like cannulation and stomach tubing, are labor-intensive and impractical for extensive sampling. Our research demonstrates the potential use of oral swabs as a scalable, effective method for characterizing the microbiome and its associations with milk production metrics, recapitulating established associations obtained through traditional ruminal sampling methods.

Dairy cows rely on their complex rumen microbial community to convert host-indigestible feed into nutrients usable for host growth, maintenance, and milk production. Previous work by our group found that the rumen bacterial community is dynamic over the course of two lactations and that cows with high and low milk production efficiency (MPE) have different taxa associated with either phenotype. Here, we characterized the ruminal fungal and archaeal communities to determine if these microbial populations exhibit properties similar to that of the rumen bacteria with respect to MPE over time. Our results show a decrease in fungal diversity over the course of both lactation cycles with an increase during the transition period. The fungal community had only a few taxa associated with efficiency. For the ruminal archaea, we found no change in diversity across both lactation cycles and only taxa in the genus Methanospera were found to be more abundant in high-MPE cows. Given that our previous study used 454 pyrosequencing, we also sought to determine if a resequencing of these communities using Illumina-based technology would alter our previous findings. We found that resequencing showed no significant deviation from our original broad conclusions, with the exception of some minor taxonomic associations.

A major goal in dairy research is to improve milk production efficiency (MPE). With the advent of next-generation sequencing, efforts are underway to improve MPE by manipulating the rumen microbiota. MPE correlates to ruminal bacterial community composition (BCC), but the adult rumen microbiota is highly stable and returns to a baseline BCC after heavy perturbation. We seek to influence rumen BCC by early intervention in pre-weaning calves. Two cannulated Holstein donors of disparate MPE were selected. Three cohorts of 6 bull calves were established and dosed by gavage with a rumen inoculum sourced from the high-efficiency donor (HE), the low-efficiency donor (LE), or an autoclaved 50:50 mix as a microbe-free control (C). Dosing occurred at birth, then biweekly through 6 weeks. Feces were collected at each dosing. Daily preweaning intake of calf starter, which correlates to downstream feed efficiency, was greatest in HE calves and lowest in C calves (P < 0.05), though preweaning average daily gain did not differ between cohorts (P = 0.210). Calves were sacrificed at 8 weeks to access rumen contents and rumen wall sections were collected to assess papillation. Fecal and rumen samples were subjected to 16S rRNA amplicon sequencing. BCC differed by cohort in fecal and rumen samples (P < 0.05), with HE calf samples most similar to adult rumen samples and C calves least similar. Additionally, HE calves tended to have elongated papillae (P =0.062), the development of which is dependent on byproducts of microbial metabolism in the rumen and which points to differences in potential absorptive capacity of the epithelium. These data demonstrate that the rumen BCC can be influenced by early intervention. Future work includes expansion of this dosing protocol to a cohort of 60 female calves, following rumen BCC development and the impact on MPE in through the first lactation.

The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.

Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large-scale is required. Here, we further optimized the analysis of buccal swab samples as a proxy for direct microbial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the Simpson’s diversity, Shannon’s evenness and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding (P 60%) taxa in buccal and rumen samples had significant variance in absolute abundance between sampling methods, but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants, but further validates and refines buccal swabbing as a method to assess the rumen microbiota in large herds. IMPORTANCE: The gastrointestinal tract of ruminants harbors a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health and performance. While the influence of environmental factors on rumen microbes is well-documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of non-invasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.

Impaired thermoregulation and lowered average daily gains (ADG) result when livestock graze toxic endophyte (Epichloë coenophialum)-infected tall fescue (E+) and are hallmark signs of fescue toxicosis (FT), a disease exacerbated by increased temperature and humidity (+temperature-humidity index; +THI). We previously reported FT is associated with metabolic and microbiota perturbations under thermoneutral conditions; here, we assessed the influence of E+ grazing and +THI on the microbiota:metabolome interactions. Using high-resolution metabolomics and 16S rRNA gene sequencing, plasma/urine metabolomes and the fecal microbiota of Angus steers grazing non-toxic or E+ tall fescue were evaluated in the context of +THI. E+ grazing affected the fecal microbiota profile; +THI conditions modulated the microbiota only in E+ steers. E+ also perturbed many metabolic pathways, namely amino acid and inflammation-related metabolism; +THI affected these pathways only in E+ steers. Integrative analyses revealed the E+ microbiota correlated and co-varied with the metabolomes in a THI-dependent manner. Operational taxonomic units in the families Peptococcaceae, Clostridiaceae, and Ruminococcaceae correlated with production parameters (e.g., ADG) and with multiple plasma/urine metabolic features, providing putative FT biomarkers and/or targets for the development of FT therapeutics. Overall, this study suggests that E+ grazing increases Angus steer susceptibility to +THI, and offers possible targets for FT interventions.