About

Jeffrey Firkins is a Distinguished Professor in the College of Food, Agricultural, and Environmental Sciences at The Ohio State University. His research focuses on animal sciences, with particular emphasis on food, agricultural, and environmental aspects. As a distinguished faculty member, he has contributed significantly to the department and the university's research initiatives.

Research topics

• Biology
• Biochemistry
• Food science
• Organic chemistry
• Genetics
• Chromatography
• Chemistry
• Ecology
• Animal science
• Agronomy
• Computational biology
• Botany
• Biotechnology

Selected publications

• Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota

  Microbiome · 2026-04-15

  articleOpen access

  BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem. RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways. CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.

  PublisherDOI

• Effects of isobutyrate and 2-methylbutyrate at different levels of rumen degraded protein on ruminal nutrient digestibility, microbial protein synthesis, and milk production in lactating cows

  Journal of Dairy Science · 2025-07-16 · 2 citations

  articleOpen access

  Effects of isobutyrate and 2-methylbutyrate (IB-2MB) supplementation and its interaction with 2 levels of dietary RDP were investigated in a replicated 4 × 4 Latin square design with 2 × 2 factorial arrangement: 9% or 11% RDP (% of dietary DM) with or without IB-2MB supplementation (0.09% IB and 0.06% 2MB in dietary DM). The level of dietary RDP was mainly adjusted with soybean meal products, and the concentration of RUP was constant (6% of dietary DM) based on National Academies of Sciences, Engineering, and Medicine 2021 requirements. Eight ruminally cannulated Holstein cows in the second lactation (192 DIM ± 41.3 SD; milk yield, 42.6 kg/d ± 4.67 SD) were fed the treatment diets for 4 wk in each period. The triple marker system and reticular sampling technique were used to determine ruminal digestibility of nutrients and microbial protein synthesis. Total collection of feces and urine were collected for 3 d in the last week of each period. Data were analyzed using the PROC MIXED of SAS with treatment and period as fixed effects, and square and cow within square as random effects. The model for rumen fermentation data included time (repeated measure) and its interaction with RDP and IB-2MB as fixed effects (0, 3, 6 h after feeding). Milk yield and DMI were not affected by treatments. The high RDP treatments increased ruminal ammonia, plasma urea concentration, and increased urinary N and urea excretion compared with low RDP. Ruminal digestibility of NDF was lower (23.4% vs. 27.3%) for high RDP compared with low RDP. Milk fat yield was increased for IB-2MB when high RDP was supplied (1.20 kg/d vs. 1.43 kg/d) and was not affected under low RDP. The IB-2MB supplementation increased ruminal concentration of IB and did not affect 2MB concentration. An interaction between RDP and IB-2MB supplementation was observed in which milk fat yield and ECM were greater for IB-2MB supplementation under high RDP, whereas no difference was detected under low RDP. Similar interactions were observed for the concentrations of 18:1 trans-10 and UFA in milk fatty acids, which was decreased for IB-2MB supplementation under high RDP. The IB-2MB supplementation decreased ruminal true digestibility of nonammonia N and ruminal apparent digestibility of NDF and tended to decrease ruminal true digestibility of DM, and OM, although the efficiency of microbial protein synthesis (nonammonia bacterial N per unit of OM digested; efficiency of microbial protein synthesis [EMPS]) increased for IB-2MB supplementation. No effect of RDP levels, IB-2MB supplementation, or their interaction on total-tract DM, OM, NDF, N, and starch digestibility was observed. In conclusion, the IB-2MB supplementation increased milk fat yield only when RDP was sufficient and was likely due to changes in ruminal fatty acid metabolism. Although EMPS was increased, IB-2MB supplementation decreased ruminal apparent NDF digestibility in this experimental condition without affecting total-tract digestibility of NDF.

  PublisherOA PDFDOI

• New Insights into Microbial Nitrogen Utilization in the Rumen Enabled by Genome-Resolved Multi-Omics

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-23

  preprintOpen access

  Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, cannot fully capture the diverse and complex N metabolic dynamics within the rumen ecosystem. To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that canonical mechanism of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and its regulatory proteins, are absent in the genomes of many key and predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes that perform N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) concentrations had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, shifts in concentrate levels triggered alterations in N assimilation, including increased expression of amino acid biosynthesis pathways. These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.

  PublisherOA PDFDOI

• Culture techniques for ciliate protozoa from the rumen: Recent advances and persistent challenges

  Anaerobe · 2024-05-22 · 6 citations

  articleOpen accessSenior author

  Ciliate protozoa are key members of the microbial community of the rumen. Their study is important to the health and productivity of cattle, which are their hosts. However, there have been persistent challenges in culturing this microbial group in the laboratory. This review will sum up recent advances along with these persistent challenges. Protozoa have been maintained in three types of cultures (ex vivo, in vitro batch, in vitro continuous). Ex vivo cultures are prepared readily from rumen contents by washing away contaminating cells (e.g., bacteria). They have been useful in making basic observations of metabolism, such as which types of fermentation products protozoa form. However, these cultures can be maintained for only short periods (minutes or hours). In vitro batch and in vitro continuous cultures can be used in longer experiments (weeks or longer). However, it is not currently possible to maintain protozoa in these cultures unless bacteria are also present. We conclude the review with a protocol for preparing ex vivo cultures of protozoa. Our protocol has been standardized and used successfully across animal diets, users, and institutions. We anticipate this review will prepare others to culture rumen ciliate protozoa and reach new insights into this important microbial group.

  PublisherDOI

• Ability of three dairy feed evaluation systems to predict postruminal outflows of amino acids in dairy cows: A meta-analysis

  Journal of Dairy Science · 2024-01-11 · 6 citations

  articleOpen access

  Adequate prediction of postruminal outflows of essential AA (EAA) is the starting point of balancing rations for EAA in dairy cows. The objective of this meta-analysis was to compare the performance of 3 dairy feed evaluation systems (National Research Council [NRC], Cornell Net Protein and Carbohydrate System version 6.5.5 [CNCPS], and National Academies of Sciences, Engineering and Medicine [NASEM]) to predict EAA outflows (Trp was not tested). The data set included a total of 354 treatment means from 70 duodenal and 24 omasal studies. To avoid Type I error, mean and linear biases were considered of concern if statistically significant and representing > 5.0% of the observed mean. Analyses were conducted on raw observed values and on observations adjusted for the random effect of study. The analysis on raw data indicates the ability of the feed evaluation system to predict absolute values whereas the analysis on adjusted values indicates its ability to predict responses of EAA outflows to dietary changes. For the prediction of absolute values (based on raw data), NRC underpredicted outflows of all EAA, from 5.3 to 8.6% of the observed mean (%obs.mean) except for Leu, Lys, and Val; NASEM overpredicted Lys (10.8%obs.mean); and CNCPS overpredicted Arg, His, Lys, Met, and Val (5.2 to 26.0%obs.mean). No EAA had a linear bias of concern with NASEM, followed by NRC for His (6.8%obs.mean), and CNCPS for all EAA (5.6 to 12.2%obs.mean) except Leu, Phe, and Thr. On the other hand, for the prediction of responses to dietary changes (based on adjusted data), NRC had 2 EAA presenting a linear bias of concern, followed by NASEM and CNCPS with 4 and 6 EAA, respectively. Predictions of His showed a linear bias of concern (5.3 to 9.6%obs.mean) with the 3 feed evaluation systems. Measured chemistry of crude protein and EAA were reported for 1 or more feed ingredients of the ration in 36% of the studies, and resulted in decreased linear biases in the 3 feed evaluation systems. The difference in mean biases of Met outflows was systematically positive when comparing omasal versus duodenal studies. Predictions of Met outflows with NRC had a higher concordance correlation coefficient in duodenal (used to develop NRC equations) versus omasal studies, whereas the opposite was observed with CNCPS, the latter showing the lowest mean bias for Met in omasal sampling studies. The 30% difference in Met mean biases between sampling sites appeared related to a similar difference found for observed Met versus NAN outflows between duodenal and omasal studies, which is independent of predictions. In conclusion, NRC and NASEM yielded accurate predictions of EAA outflows, with a small superiority of NASEM to predict absolute values, and slight superiority of NRC to predict the responses to dietary changes. In comparison, CNCPS may present mean and linear biases of concern for many EAA. Moreover, it remains to determine which sampling site is more representative of the true supply of EAA to the cows.

  PublisherOA PDFDOI

• International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility

  Journal of Dairy Science · 2024-12-18 · 10 citations

  reviewOpen access1st authorCorresponding

  Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding to the array of enzymes needed for depolymerization and resulting fermentation of sugars. Carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi and emphasize the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic acid), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.

  PublisherOA PDFDOI

• Invited Review: Role for isoacids in dairy nutrition*

  Applied Animal Science · 2024-07-30 · 12 citations

  articleOpen access1st authorCorresponding

  This literature review explains current understanding of the mechanisms by which branched-chain volatile fatty acids (BCVFA), historically termed isoacids, can improve fiber digestibility, microbial protein production, and either milk production or production efficiency. Peer-reviewed literature and ADSA abstracts were the primary course of information reviewed. Although traditionally included in isoacid supplements with the 3 BCVFA, the straight-chain valerate does not warrant being included. Because of the high concentration of its precursor leucine in corn protein, isovalerate is less likely to be needed than 2-methylbutyrate and isobutyrate. If conditions are not amenable for BCVFA assimilation into microbes, particularly if ruminal ammonia is deficient, more supplemental BCVFA are available for postruminal metabolism. Isovalerate is likely metabolized primarily in the rumen epithelium, whereas isobutyrate and 2-methylbutyrate are likely metabolized in the liver or peripheral tissues. If BCVFA improve fiber degradability, typically by 3 to 5 percentage units, a more balanced consortium of ruminal microbes should improve efficiency of microbial protein production so long as ruminal nitrogenous precursors are adequate. Increased acetate production from improved fiber digestibility is thought to increase milk fat production, particularly in multiparous cows. In primiparous cows, the acetate from improved fiber degradability might be diverted to body weight gain. Milk production efficiency responses of 5% to 10% have been recorded with optimum doses of BCVFA and adequate rumen-degraded protein supply.

  PublisherDOI

• Supplementing branched-chain volatile fatty acids in dual-flow cultures varying in dietary forage and corn oil concentrations. III: Protein metabolism and incorporation into bacterial protein

  Journal of Dairy Science · 2023-08-23 · 10 citations

  articleOpen accessSenior author

  Some cellulolytic bacteria cannot transport branched-chain AA (BCAA) and do not express complete synthesis pathways, thus depending on cross-feeding for branched-chain volatile fatty acid (BCVFA) precursors for membrane lipids or for reductive carboxylation to BCAA. Our objective was to assess BCVFA uptake for BCAA synthesis in continuous cultures administered high forage (HF) and low forage (LF) diets without or with corn oil (CO). We hypothesized that BCVFA would be used for BCAA synthesis more in the HF than in LF diets. To help overcome bacterial inhibition by polyunsaturated fatty acids in CO, BCVFA usage for bacterial BCAA synthesis was hypothesized to decrease when CO was added to HF diets. The study was an incomplete block design with 8 dual-flow fermenters used in 4 periods with 8 treatments (n = 4) arranged as a 2 × 2 × 2 factorial. The factors were: HF or LF (67 or 33% forage, 33:67 alfalfa:orchardgrass pellets), without or with supplemental CO (3% of dry matter), and without or with 2.15 mmol/d (5 mg/d 13C) each of isovalerate, isobutyrate, and 2-methylbutyrate for one combined BCVFA treatment. The flow of bacterial BCAA increased by 10.7% by supplementing BCVFA and 9.14% with LF versus HF; similarly, dosing BCVFA versus without BCVFA increased BCAA by 1.98% in total bacterial AA, whereas LF increased BCAA by 1.92% versus HF. Additionally, BCVFA supplementation increased bacterial AA flow by 16.6% when supplemented in HF − CO and 12.4% in LF + CO diets, but not in the HF + CO (−1.5%) or LF − CO (+6.7%) diets (Diet × CO × BCVFA interaction). The recovery of 13C in bacterial AA flow was 31% lower with LF than with HF. Of the total 13C recovered in bacteria, 13.8, 17.3, and 30.2% were recovered in Val, Ile, and Leu, respectively; negligible 13C was recovered in other AA. When fermenters were dosed with BCVFA, nonbacterial and total effluent flows of AA, particularly of alanine and proline, suggest decreased peptidolysis. Increased ruminal outflow of bacterial AA, especially BCAA, but also nonbacterial AA could potentially support postabsorptive responses from BCVFA supplementation to dairy cattle.

  PublisherOA PDFDOI

• Invited review: Rumen modifiers in today's dairy rations

  Journal of Dairy Science · 2023-03-18 · 43 citations

  reviewOpen access1st authorCorresponding

  Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.

  PublisherOA PDFDOI

• Effects of corn silage and grain expressing α-amylase on ruminal nutrient digestibility, microbial protein synthesis, and enteric methane emissions in lactating cows

  Journal of Dairy Science · 2023-05-22 · 11 citations

  articleOpen access

  Increasing ruminal starch digestibility has the potential to improve microbial protein synthesis (MPS), milk production, and feed efficiency. Enogen corn (Syngenta Seeds LLC) expresses high α-amylase activity, and we evaluated effects of Enogen corn silage (CS) and grain (CG) on ruminal starch digestibility, MPS, and milk production in lactating dairy cows. Fifteen Holstein cows (6 ruminally cannulated and 9 noncannulated; average ± standard deviation at the beginning of the trial: 170 ± 40 d in milk; milk yield, 37.2 ± 7.73 kg/d; body weight, 714 ± 37 kg) were used in a replicated 3 × 3 Latin square design (28 d per period) with 3 treatments: a diet containing isoline CS and CG (control, CON); a diet with Enogen CS and isoline CG (ECS); and a diet with Enogen CS and CG (ECSCG). Dry matter (DM; 30%), starch (35% of DM), and particle size distribution of the isoline and Enogen CS were similar. However, the mean particle size of Enogen CG was larger (1.05 vs. 0.65 mm) than that of the isoline CG. Cannulated cows were used for digestibility and nutrient flow measurements, noncannulated cows were used for enteric CH4 measurements, and all cows were used for production evaluation. Dry matter intake (DMI) and milk yield were greater for ECS and ECSCG compared with CON (26.7 and 26.6 vs. 25.1 kg/d and 36.5 and 34.1 vs. 33.1 kg/d, respectively) without a difference between ECS and ECSCG. Milk protein yield was greater (1.27 vs. 1.14 and 1.17 kg/d) for ECS compared with CON and ECSCG. Milk fat content was greater (3.79 vs. 3.32%) for ECSCG compared with ECS. Milk fat yield and energy-corrected milk did not differ among treatments. Ruminal digestibilities of DM, organic matter, starch, and neutral detergent fiber were not different among treatments. However, ruminal digestibility of nonammonia, nonmicrobial N was greater (85 vs. 75%) for ECS compared with ECSCG. Total-tract apparent starch digestibility was lower (97.6 and 97.1 vs. 98.3%) for ECS and ECSCG compared with CON, respectively, and tended to be lower (97.1 vs. 98.3%) for ECSCG compared with ECS. Ruminal outflows of bacterial OM and nonammonia N tended to be greater for ECS than for ECSCG. Efficiency of MPS tended to be greater (34.1 vs. 30.6 g of N/kg of organic matter truly digested) for ECS versus ECSCG. Ruminal pH and total and individual short-chain fatty acid concentrations did not differ among treatments. Concentration of ruminal NH3 for ECS and ECSCG was lower (10.4 and 12.4 vs. 13.4 mmol/L, respectively) compared with CON. Methane per unit of DMI decreased for ECS and ECSCG compared with CON (11.4 and 12.2 vs. 13.5 g/kg of DMI, respectively) without a difference between ECS and ECSCG. In conclusion, ECS and ECSCG did not increase ruminal or total-tract starch digestibility. However, the positive effects of ECS and ECSCG on milk protein yield, milk yield, and CH4 per unit of DMI may show potential benefits of feeding Enogen corn. Effects of ECSCG were not apparent when compared with ECS, partly due to larger particle size of Enogen CG compared with its isoline counterpart.

  PublisherOA PDFDOI

Frequent coauthors

• J.H. Clark

  Urbana University

  99 shared

• R.M. Cleale

  66 shared

• D.L. Palmquist

  The Ohio State University

  56 shared

• M.D. Stern

  51 shared

• B.O. Brodie

  50 shared

• G.A. Varga

  50 shared

• M. L. Eastridge

  The Ohio State University

  49 shared

• John Huber

  Natural Resources Canada

  49 shared

Education

• Ph.D., Animal Sciences

  The Ohio State University

  1995

• M.S., Animal Sciences

  The Ohio State University

  1991

• B.S., Animal Sciences

  The Ohio State University

  1989

Awards & honors

• CFAES Distinguished Professor recipient, 2023-2024
• CFAES Distinguished Senior Faculty Research Award recipient,…
• Fellow of the American Dairy Science Association (ADSA), 202…
• American Feed Industry Association Dairy Nutrition Research…
• Gamma Sigma Delta Research Award of Merit, 2006