About
Paul Weimer is an Associate Professor of Bacteriology at the University of Wisconsin-Madison, now holding the status of Emeritus. He is affiliated with the Department of Bacteriology within the College of Agricultural & Life Sciences. His office is located in the Microbial Sciences Building at 1550 Linden Dr., Madison, WI. His research focus, background, and key contributions are not detailed on the page, which primarily provides contact information, departmental links, and administrative details.
Research topics
- Biology
- Chemistry
- Biochemistry
- Agronomy
- Food science
- Engineering
- Environmental science
- Pulp and paper industry
- Organic chemistry
- Environmental chemistry
- Waste management
Selected publications
The ISME Journal · 2025-01-01 · 7 citations
articleOpen accessLactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.
UDP-glucuronic acid decarboxylase in alfalfa: a target to improve ruminal digestibility of stems
Journal of Experimental Botany · 2025-12-17 · 1 citations
articleAlfalfa (Medicago sativa) has a high nutritional value, but poor digestibility of the stems limits its value as an energy source in ruminant diets. Xylan and lignin negatively impact cell wall digestibility, whereas pectins have high digestibility in the rumen. In plants, UDP-xylose synthase (UXS) catalyzes the decarboxylation of UDP-glucuronic acid to form UDP-xylose in an irreversible step that is key for xylan synthesis. We functionally characterized two UXS genes in alfalfa (MsaUXS2 and MsaUXS4) and investigated their impact on ruminal digestibility. Both genes are more highly expressed in stems than leaves, and the enzymes have UDP-glucuronic acid decarboxylase activity in vitro. Silencing MsaUXS2/MsaUXS4 via RNAi altered plant growth and resulted in a 40% decrease in xylose, a 115% increase in arabinose, and a 60% increase in galacturonic acid in the polysaccharide matrix as well as a 20% decrease in lignin in the cell wall. Together, our data show a major role for MsaUXS2 and MsaUXS4 in xylan synthesis and secondary cell wall deposition in alfalfa. Additionally, silenced lines had on average 30% increased gas production at 24 h in in vitro rumen digestibility assays, demonstrating the potential of targeting UXS genes to increase stem digestibility.
2024-02-05
peer-review1st authorCorrespondingMicroorganisms · 2024-01-21 · 48 citations
reviewOpen accessSenior authorCorrespondingThe Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2–C7 carboxylic acids—potential precursors for industrial fuel and chemical production—is examined.
Preprints.org · 2023-12-29 · 1 citations
preprintOpen accessSenior authorThe Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy source for growth has been well documented, although it can also ferment amino acids to ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at low ruminal pH (&amp;lt; 5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium, and its role of in ruminal community function and in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids – potential precursors for industrial fuel and chemical production, is examined.
Frontiers in Microbiomes · 2023-08-15 · 3 citations
articleOpen accessWe evaluated the influence of diets differing in non-fiber carbohydrates and rumen-degradable protein (RDP) levels on changes in the ruminal bacterial populations in lactating Holstein cows. In all, 12 ruminally cannulated cows were assigned to diets with high or low RDP levels. Within each RDP level, molasses was substituted for corn grain at a concentration of 0%, 5.25%, or 10.5% of diet dry matter in a replicated 3 × 3 Latin square design with 28-day periods. Liquid and solid rumen digesta fractions collected at the end of each period underwent 16S rRNA gene sequencing to identify operational taxonomic units and were analyzed for short-chain fatty acids. Protein degradability affected 6 bacterial genera, whereas carbohydrate alteration impacted 13 genera ( p &lt; 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction ( p &lt; 0.05), with Bacteroidetes genera showing a greater abundance in solids and Firmicutes genera demonstrating a greater prevalence in liquids. Regarding relative abundances, with increasing molasses, Succiniclasticum decreased in liquid ( p &lt; 0.05), and CF231 , YRC22 , Clostridium , Desulfovibrio , BF311 , and Oscillospira increased in solids ( p &lt; 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids ( p &lt; 0.05). Genera with abundances found to be correlated with fermentation products in the liquid included Shuttleworthia , Treponema , Lachnospira , and Schwartzia , which typically have lower relative abundances, showing strong positive correlations with molar proportions (mol%) of propionate, butyrate, and valerate ( p &lt; 0.05), and negative correlations with pH and acetate mol% ( p &lt; 0.05). Fibrobacter was positively correlated with lactate mol% ( p &lt; 0.05). Butyrate mol% exhibited a quadratic increase as molasses increased ( p = 0.017), and lactate mol% rose with increased RDP levels ( p = 0.042). No treatment effects were detected for pH propionate and valerate mol%; however, we observed a tendency ( p = 0.075) for a quadratic effect of molasses treatment on the mol% of acetate. These findings substantiate the pivotal role of diet in shaping rumen microbiota and metabolism, elucidating a nuanced relationship between dietary components, bacterial community structure, and metabolic output. This offers a more detailed understanding of rumen function and the potential for high-precision dietary management in lactating cows.
AAPG Bulletin · 2022-06-25 · 4 citations
articleABSTRACT The Red Wing Creek field in the Williston Basin is one of a few well-known petroleum fields in the world to produce from a structure associated with a meteorite impact. Interpretation of a three-dimensional seismic data set 56 mi2 (145 km2) in area shows the crater is 5.6 mi (9.1 km) in diameter and has three unique structural zones. First, the central uplift complex has a maximum diameter of 3.8 mi (5.1 km), and consists of an uplifted central core, composed entirely of strata of the Mississippian Madison Group, and a flanking inner rim. The seismic reflectivity within the central core is poor, but well log data indicate extensive stratigraphic repetition. The central core is surrounded by an annular rim (1.1 mi [1.7 km] wide), which is structurally thickened by imbricate thrusts that dip toward the central core. This rim comprises eight distinct radial sectors, segmented by nine high-angle, reverse faults. The second part of the crater is a depressed annular trough with a maximum diameter of 0.9 mi (1.5 km); its inner limit is bounded by antithetic normal faults and its outer limit by concentrically linked normal faults that dip toward the central part of the crater. This group of faults marks the edge of the third zone, the outer rim. The outer rim is slightly uplifted, relatively undisturbed, and its strata dip at a maximum angle of 8° away from the central crater. The results of this study were applied to further field development. Four horizontal wells were drilled in new Madison Group targets, resulting in three new producing wells.
Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms
Microorganisms · 2022 · 189 citations
1st authorCorresponding- Biology
- Food science
- Chemistry
As major structural components of plant cell walls, cellulose and hemicellulose are degraded and fermented by anaerobic microbes in the rumen to produce volatile fatty acids, the main nutrient source for the host. Cellulose degradation is carried out primarily by specialist bacteria, with additional contributions from protists and fungi, via a variety of mechanisms. Hemicelluloses are hydrolyzed by cellulolytic bacteria and by generalist, non-cellulolytic microbes, largely via extracellular enzymes. Cellulose hydrolysis follows first-order kinetics and its rate is limited by available substrate surface area. Nevertheless, its rate is at least an order of magnitude more rapid than in anaerobic digesters, due to near-obligatory adherence of microbial cells to the cellulose surface, and a lack of downstream inhibitory effects; in the host animal, fiber degradation rate is also enhanced by the unique process of rumination. Cellulolytic and hemicellulolytic microbes exhibit intense competition and amensalism, but they also display mutualistic interactions with microbes at other trophic levels. Collectively, the fiber-degrading community of the rumen displays functional redundancy, partial niche overlap, and convergence of catabolic pathways that all contribute to stability of the ruminal fermentation. The superior hydrolytic and fermentative capabilities of ruminal fiber degraders make them promising candidates for several fermentation technologies.
Journal of Dairy Science · 2021-10-22
erratumOpen access1st authorCorrespondingAn error has been noted in values for DMI in Table 3 (page 270). The corrected table is shown below, with corrected values shown in bold. The authors regret the error. Table 3Production and ruminal chemistry data for cows in the different milk fat response groups1Response groups: cows with milk fat percentage affected by starch fermentability (S-responsive), monensin (M-responsive; Rumensin 80, Elanco Animal Health, Greenfield, IN), or starch fermentability and monensin (SM-responsive), and cows not affected by either starch fermentability or monensin (nonresponsive).MeasurementS-responsiveM-responsiveSM-responsiveNonresponsiveCow 1664Cow 2464Cow 1272Cow 2088Cow 1884Cow 2082Cow 1692Cow 2470Production data,2Production data from last 5 d (10 milkings) of each 28-d period, averaged across all 4 treatment periods. kg/d DMI25.024.226.622.025.224.126.624.2 Milk yield48.035.938.432.734.922.142.636.8 3.5% FCM40.234.442.832.738.427.642.237.6 Protein1.251.161.230.971.180.861.221.06 Lactose2.181.892.341.982.241.482.251.82Ruminal chemistry3Ruminal chemistry from samples collected 6 h postfeeding on last 3 d of each 28-d period, averaged across all 4 treatment periods. pH5.725.945.876.096.056.125.885.96 Total VFA, mM159156149135136145151129 Acetate, mol %57.658.758.862.764.364.363.063.7 Propionate, mol %22.923.723.217.519.217.720.219.6 Butyrate, mol %13.212.111.614.312.413.312.612.3 Acetate:propionate ratio2.722.562.693.643.413.683.173.30Total number of ARISA peaks,4ARISA = automated ribosomal intergenic spacer analysis; AL = amplicon length. Includes total number of unique AL identified in full set of 24 samples (3 daily samples × 4 experimental periods × 2 phases) for each cow. AL1761751881731761821711681 Response groups: cows with milk fat percentage affected by starch fermentability (S-responsive), monensin (M-responsive; Rumensin 80, Elanco Animal Health, Greenfield, IN), or starch fermentability and monensin (SM-responsive), and cows not affected by either starch fermentability or monensin (nonresponsive).2 Production data from last 5 d (10 milkings) of each 28-d period, averaged across all 4 treatment periods.3 Ruminal chemistry from samples collected 6 h postfeeding on last 3 d of each 28-d period, averaged across all 4 treatment periods.4 ARISA = automated ribosomal intergenic spacer analysis; AL = amplicon length. Includes total number of unique AL identified in full set of 24 samples (3 daily samples × 4 experimental periods × 2 phases) for each cow. Open table in a new tab Shifts in bacterial community composition in the rumen of lactating dairy cows under milk fat-depressing conditionsJournal of Dairy ScienceVol. 93Issue 1PreviewEighteen ruminally cannulated dairy cattle were fed a series of diets (in 28-d periods) designed to elicit different degrees of milk fat depression (MFD) for the purpose of relating MFD to ruminal bacterial populations. Cows were fed a TMR containing 25% starch (DM basis) supplied as corn silage, a slowly fermented starch (SFS treatment, period 1), then switched to a TMR containing 27% starch, much of it supplied as ground high-moisture corn, a rapidly fermented starch (RFS treatment, period 2). Full-Text PDF Open Archive
Bioresource Technology · 2021 · 103 citations
- Chemistry
- Waste management
- Pulp and paper industry
Frequent coauthors
- 61 shared
Garret Suen
University of Wisconsin–Madison
- 42 shared
Ronald D. Hatfield
U.S. Dairy Forage Research Center
- 42 shared
Hans‐Joachim G Jung
Agricultural Research Service
- 40 shared
David M. Stevenson
University of Wisconsin–Madison
- 38 shared
John Ralph
University of Wisconsin–Madison
- 36 shared
R. E. Muck
U.S. Dairy Forage Research Center
- 33 shared
D.R. Mertens
- 29 shared
Alfred D. French
Education
- 2005
Ph.D., Bacteriology
University of Wisconsin-Madison
- 2002
M.S., Bacteriology
University of Wisconsin-Madison
- 2000
B.S., Bacteriology
University of Wisconsin-Madison
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