New biochemical pathways for forming short-chain fatty acids during fermentation in rumen bacteria

Short-chain fatty acids (SCFA) are essential to cattle as a source of energy and for other roles in metabolism. These molecules are formed during fermentation by microbes in the rumen, but even after decades of study, the biochemical pathways responsible for forming them are not always clear. Here we review recent advances in this area and their importance for improving animal productivity. Studies of bacterial genomes have pointed to unusual biochemical pathways in rumen organisms. One study found that 8% of rumen organisms forming acetate, a major SCFA, had genes for a pathway previously unknown in bacteria. The existence of this pathway was subsequently confirmed biochemically in propionibacteria. The pathway was shown to involve 2 enzymes that convert acetyl-coenzyme A to acetate. Similar studies have revealed new enzymatic steps for forming propionate and butyrate, other major SCFA. These new steps and pathways are significant for controlling fermentation. With more precise control over SCFA, cows can be fed more precisely and potentially reach higher productivity.

The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella

Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.

The phenotype and genotype of fermentative prokaryotes

Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.

Redefining the coenzyme A transferase superfamily with a large set of manually-annotated proteins

The coenzyme A (CoA) transferases are a superfamily of proteins central to the metabolism of acetyl-CoA and other CoA thioesters. They are diverse group, catalyzing over a hundred biochemical reactions and spanning all three domains of life. A deeply rooted idea, proposed two decades ago, is these enzymes fall into three families (I, II, III). Here we find they fall into different families, which we achieve by analyzing all CoA transferases characterized to date. We manually annotated 94 CoA transferases with functional information (including rates of catalysis for 208 reactions) from 97 publications. This represents all enzymes we could find in the primary literature, and it is double the number annotated in four protein databases (BRENDA, KEGG, MetaCyc, UniProt). We found family I transferases are not closely related to each other in terms of sequence, structure, and reactions catalyzed. This family is not even monophyletic. These problems are solved by regrouping the three families into six, including one family with many non-CoA transferases. The problem (and solution) became apparent only by analyzing our large set of manually-annotated proteins. It would have been missed if we had used the small number of proteins annotated in UniProt and other databases. Our work is important to understanding the biology of CoA transferases. It also warns investigators doing phylogenetic analyses of proteins to go beyond information in databases. This article is protected by copyright. All rights reserved.

A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria

Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. IMPORTANCE Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.

Using neural networks to mine text and predict metabolic traits for thousands of microbes

Microbes can metabolize more chemical compounds than any other group of organisms. As a result, their metabolism is of interest to investigators across biology. Despite the interest, information on metabolism of specific microbes is hard to access. Information is buried in text of books and journals, and investigators have no easy way to extract it out. Here we investigate if neural networks can extract out this information and predict metabolic traits. For proof of concept, we predicted two traits: whether microbes carry one type of metabolism (fermentation) or produce one metabolite (acetate). We collected written descriptions of 7,021 species of bacteria and archaea from Bergey's Manual. We read the descriptions and manually identified (labeled) which species were fermentative or produced acetate. We then trained neural networks to predict these labels. In total, we identified 2,364 species as fermentative, and 1,009 species as also producing acetate. Neural networks could predict which species were fermentative with 97.3% accuracy. Accuracy was even higher (98.6%) when predicting species also producing acetate. Phylogenetic trees of species and their traits confirmed that predictions were accurate. Our approach with neural networks can extract information efficiently and accurately. It paves the way for putting more metabolic traits into databases, providing easy access of information to investigators.

PSXII-6 Supplementation of Angus crossbred steers with avian-derived polyclonal antibody preparations against the ruminal methanogen Methanobrevibacter ruminantium M1 does not alter in vivo methane emissions

An experiment was conducted to evaluate the effect of supplementing twenty Angus crossbred steers with avian-derived polyclonal antibody preparations (PAP) against the ruminal methanogen Methanobrevibacter ruminantium M1 on in vivo methane production, using the sulfur hexafluoride (SF6) tracer technique (Johnson et al., 1994). Steers were fed chopped bermudagrass hay (BGH) ad libitum and 0.7 kg d-1 of corn gluten feed. The experiment followed a change-over design. Treatments were 1) supplementation of 3 mL d-1 of PAP against M. ruminantium M1 (PAP-M1), and 2) supplementation of 3 mL d-1 of a non-immunized egg product (CON). Individual BGH intake was recorded using an electronic radio-frequency monitoring system (GrowSafe System Ltd., Airdrie, Alberta, Canada). There was a 14-d adaptation period to the feeding regime, with no PAP supplementation, followed by an 18-d treatment period. Steers were dosed with brass permeation tubes with a known release rate of SF6 on d 7 of treatment period. Enteric methane emissions were sampled from d 13 to 18 of the treatment period, into N-rinsed pre-evacuated U-shaped polyvinyl chloride canisters (2 L) through a capillary tube. Methane emissions were averaged per animal within period. Data were analyzed as a change-over design using a model with fixed effects of order, period, and treatment and random effect of steer within order. Dry matter intake (DMI) was not different (P = 0.44) between treatments. Methane emissions, expressed as grams per day (P = 0.86), as grams per kilogram of DMI (P = 0.78), or in terms of methane emission factors (Ym, P = 0.78) were not different between PAP-M1 and CON treatments. Supplementation of steers with PAP against M. ruminantium M1 did not decrease enteric methane emissions. Based on preliminary ex situ trials, evaluation of different doses and combinations of PAP against other methanogenic species warrant further investigation.

184 President Oral Presentation Pick: Supplementation of Angus crossbred steers with avian-derived polyclonal antibody preparations against ruminal methanogenic Archaea alters ruminal fermentation and decreases ex situ methane production

An experiment was conducted to evaluate the effect of supplementing fourteen ruminally cannulated Angus crossbred steers with polyclonal antibody preparations (PAP) from avian origin against ruminal methanogens Methanobrevibacter gottschalkii Ho (PAP-Ho) and M. ruminantium M1 (PAP-M1). Steers were fed bermudagrass hay ad libitum and 2 kg d-1 of corn gluten feed. A randomized block design was used, with a 3 × 2 + 1 factorial arrangement, replicated in three periods. Factors were proportions of PAP against Ho and M1 in the mixture (100:0, 50:50, and 0:100 Ho:M1) and level of supplementation of each mixture (3 or 6 mL d-1). Control steers had no PAP supplementation. Steers were adapted to the feeding regimen for 14 d, with no PAP supplementation, followed by a 21-d treatment period. Ruminal fluid (RF) from each steer (experimental unit) was collected before PAP supplementation (h 0) and every 4 h (for a 24-h period) on d 0, 14, and 21 of treatment period for the determination of ruminal fermentation profile. In addition, RF collected at h 0 was individually mixed with McDougall’s Buffer (1:3 ratio) to inoculate serum bottles and polycarbonate tubes for the determination of methane production and in vitro fermentation profile. Treatment means were evaluated by preplanned, non-orthogonal, single-degree-of-freedom contrasts. There was no effect (P ≥ 0.48) of level of inclusion on ex situ methane production (ESMP). When PAP-M1 was used either alone or in combination with PAP-Ho, ESMP decreased (P ≤ 0.05) compared to control. Ex situ ruminal fermentation profile was not different (P ≥ 0.12) across treatments. In vivo molar proportion of propionate tended to be greater (P = 0.10) with supplementation of PAP-M1, alone or combined, compared with control. Polyclonal antibody preparations against ruminal methanogens have the potential to decrease enteric methane emissions.

Accurate estimation of microbial sequence diversity with Distanced

MOTIVATION

Microbes are the most diverse organisms on the planet. Deep sequencing of ribosomal DNA (rDNA) suggests thousands of different microbes may be present in a single sample. However, errors in sequencing have made any estimate of within-sample (alpha) diversity uncertain.

RESULTS

We developed a tool to estimate alpha diversity of rDNA sequences from microbes (and other sequences). Our tool, Distanced, calculates how different (distant) sequences would be without sequencing errors. It does this using a Bayesian approach. Using this approach, Distanced accurately estimated alpha diversity of rDNA sequences from bacteria and fungi. It had lower root mean square prediction error (RMSPE) than when using no tool (leaving sequencing errors uncorrected). It was also accurate with non-microbial sequences (antibody mRNA). State-of-the-art tools (DADA2 and Deblur) were far less accurate. They often had higher RMSPE than when using no tool. Distanced thus represents an improvement over existing tools. Distanced will be useful to several disciplines, given microbial diversity affects everything from human health to ecosystem function.

AVAILABILITY AND IMPLEMENTATION

Distanced is freely available at https://github.com/thackmann/Distanced.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Postprandial Blood Glucose and Insulin Responses of Horses to Feeds Differing in Soluble Fiber Concentration

In humans, the consumption of soluble fibers reduces glycemic response after a meal. We hypothesized high soluble fiber diets would reduce and delay postprandial glucose and insulin responses in horses. In a 4 × 4 Latin square design experiment, four Quarter Horse geldings were adapted to diets containing orchardgrass hay (ORCH) or ORCH with 1 of 3 treatment ingredients: molassed sugar beet pulp (BEET), almond hulls (HULL), or steam-crimped oats (OATS). Blood was serially sampled for 6 hours after feeding 0.15% body weight (BW) of the treatment ingredient (meal test) or 1.1 g starch/kg BW from oats plus the treatment ingredient (starch test) to evaluate glycemic and insulinemic responses. Glycemic response during the meal test peaked between 60 and 90 min after feeding (P < .05) and tended to be altered by diet (P = .071) and diet × time (P = .076). Serum insulin was affected by diet (P = .008), time (P < .001), and diet × time (P < .001) during the meal test, with concentrations lower in ORCH compared with BEET and OATS (P < .05). In the starch test, glucose was lower (P < .05) in ORCH and HULL compared with BEET and insulin was lower (P = .046) in ORCH compared with BEET. In both tests, horses took longer (P < .05) to consume HULL, likely influencing postprandial responses. Future research integrating the functional properties of feeds with physiological responses will be necessary to elucidate how soluble fiber affects postprandial glucose metabolism in horses.

Exogenous fibrolytic enzymes and recombinant bacterial expansins synergistically improve hydrolysis and in vitro digestibility of bermudagrass haylage

Four experiments were conducted to examine the effects of a recombinant bacterial expansin-like protein (BsEXLX1) from Bacillus subtilis and a commercial exogenous fibrolytic enzyme (EFE) preparation for ruminants on hydrolysis of pure substrates (cellulose and xylan) and in vitro digestibility of bermudagrass haylage (BMH). Recombinant Escherichia coli BL21 strain was used to express BsEXLX1; the protein was purified using an affinity column. In experiment 1, carboxymethylcellulose, Whatman #1 filter paper (General Electric, Boston, MA) and oat-spelt xylan substrates were subjected to 4 treatments (1) sodium citrate buffer (control), (2) BsEXLX1 (162 µg/g of substrate), (3) EFE (2.3 mg/g of substrate), and (4) EFE + BsELX1 in 3 independent runs. Samples were incubated at optimal conditions for both additives (pH 5 and 50°C) or at ruminal (pH 6 and 39°C) or ambient (pH 6 and 25°C) conditions for 24 h and sugar release was measured. In experiment 2, digestibility in vitro of BMH was examined after treatment with the following: (1) control (buffer only), (2) BsEXLX1 (162 µg/g of dry matter), (3) EFE (2.2 mg/g of dry matter), and (4) EFE + BsEXLX1 in 3 independent runs at 39°C for 24 h. Experiment 3 examined effects of EFE and BsEXLX1 on simulated preingestive hydrolysis and profile of released sugars from BMH after samples were suspended in deionized water with sodium azide at 25°C for 24 h in 2 independent runs. In experiment 4, the sequence of the BsEXLX1 purified protein was compared with 447 ruminal bacterial genomes to identify similar proteins from the rumen. In experiment 1, compared with EFE alone, EFE and BsEXLX1 synergistically increased sugar release from carboxymethylcellulose and Whatman #1 filter paper under all simulated conditions; however, hydrolysis of xylan was not improved. In experiment 2, compared with EFE alone, treatment with EFE and BsEXLX1 increased neutral detergent fiber and acid detergent fiber digestibility of bermudagrass haylage (by 5.5 and 15%, respectively) and total volatile fatty acid concentrations, and decreased acetate-propionate ratio. In experiment 3, compared with EFE alone. The EFE and BsEXLX1 synergistically reduced concentrations of neutral detergent fiber and acid detergent fiber and increased release of sugars by 9.3%, particularly cellobiose (72.5%). In experiment 4, a similar sequence to that of BsEXLX1 was identified in Bacillus licheniformis, and similar hypothetical protein sequences were identified in Ruminococcus flavefaciens strains along with different protein structures in E. xylanophilum and Lachnospiraceae. This study showed that an expansin-like protein synergistically increased the hydrolysis of pure cellulose substrates and the hydrolysis and digestibility in vitro of BMH.

Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids

Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well-recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden-Meyerhof-Parnas pathway. This study shows that reconstruction of metabolic pathways - a common goal of omics studies - could be incorrect if well-recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically.

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage, "Candidatus Epulopiscium" and related giant bacteria. These symbionts lack cellulases but encode a distinctive and lineage-specific array of mostly intracellular carbohydrases concurrent with the unique and tractable dietary resources of their hosts. Importantly, enzymes initiating the breakdown of the abundant and complex algal polysaccharides also originate from these symbionts. These are also highly transcribed and peak according to the diel lifestyle of their host, further supporting their importance and host-symbiont cospeciation. Because of their distinctive genomic blueprint, we propose the classification of these giant bacteria into three candidate genera. Collectively, our findings show that the acquisition of metabolically distinct "Epulopiscium" symbionts in hosts feeding on compositionally varied algal diets is a key niche-partitioning driver in the nutritional ecology of herbivorous surgeonfishes.

Comparing the responses of rumen ciliate protozoa and bacteria to excess carbohydrate

When given excess carbohydrate, certain microbial species respond by storing energy (synthesizing reserve carbohydrate), but other species respond by dissipating the energy as heat (spilling energy). To determine the importance of these responses in the rumen microbial community, this study quantified the responses of mixed ciliate protozoa vs bacteria to glucose. We hypothesized that ciliates would direct more glucose to synthesis of reserve carbohydrate (and less to energy spilling) than would bacteria. Ciliates and bacteria were isolated from rumen fluid using filtration and centrifugation, resuspended in nitrogen-free buffer to limit growth, and dosed with 5 mM glucose. Compared with bacteria, ciliates consumed glucose >3-fold faster and synthesized reserve carbohydrate 4-fold faster. They incorporated 53% of glucose carbon into reserve carbohydrate-nearly double the value (27%) for bacteria. Energy spilling was not detected for ciliates, as all heat production (104%) was accounted by synthesis of reserve carbohydrate and endogenous metabolism. For bacteria, reserve carbohydrate and endogenous metabolism accounted for only 68% of heat production, and spilling was detected within 11 min of dosing glucose. These results suggest that ciliates alter the course of ruminal carbohydrate metabolism by outcompeting bacteria for excess carbohydrate, maximizing reserve carbohydrate synthesis, and minimizing energy spilling.

Transport of a Fluorescent Analogue of Glucose (2-NBDG) versus Radiolabeled Sugars by Rumen Bacteria and Escherichia coli

Fluorescent tracers have been used to measure solute transport, but transport kinetics have not been evaluated by comparison of radiolabeled tracers. Using Streptococcus equinus JB1 and other bacteria, the objective of this study was to determine if a fluorescent analogue of glucose (2-NBDG) would be transported with the same kinetics and transporters as [(14)C]glucose. We uniquely modified a technique for measuring transport of radiolabeled tracers so that transport of a fluorescent tracer (2-NBDG) could also be measured. Deploying this technique for S. equinus JB1, we could detect 2-NDBG transport quantitatively and within 2 s. We found the Vmax of 2-NBDG transport was 2.9-fold lower than that for [(14)C]glucose, and the Km was 9.9-fold lower. Experiments with transport mutants suggested a mannose phosphotransferase system (PTS) was responsible for 2-NBDG transport in S. equinus JB1 as well as Escherichia coli. Upon examination of strains from 12 species of rumen bacteria, only the five that possessed a mannose PTS were shown to transport 2-NBDG. Those five uniformly transported [(14)C]mannose and [(14)C]deoxyglucose (other glucose analogues at the C-2 position) at high velocities. Species that did not transport 2-NBDG at detectable velocities did not possess a mannose PTS, though they collectively possessed several other glucose transporters. These results, along with retrospective genomic analyses of previous 2-NBDG studies, suggest that only a few bacterial transporters may display high activity toward 2-NBDG. Fluorescent tracers have the potential to measure solute transport qualitatively, but their bulky fluorescent groups may restrict (i) activity of many transporters and (ii) use for quantitative measurement.

α-Galactosylceramide protects swine against influenza infection when administered as a vaccine adjuvant

Natural killer T (NKT) -cells activated with the glycolipid ligand α-galactosylceramide (α-GalCer) stimulate a wide array of immune responses with many promising immunotherapeutic applications, including the enhancement of vaccines against infectious diseases and cancer. In the current study, we evaluated whether α-GalCer generates protective immunity against a swine influenza (SI) virus infection when applied as an intramuscular vaccine adjuvant. Immunization of newly weaned piglets with UV-killed pandemic H1N1 A/California/04/2009 (kCA04) SI virus and α-GalCer induced high titers of anti-hemagglutinin antibodies and generated virus-specific T cells that localized in intrapulmonary airways and in alveolar walls. Vaccination with α-GalCer resulted in a systemic increase in NKT-cell concentrations, including in the respiratory tract, which was associated with complete inhibition of viral replication in the upper and lower respiratory tract and much reduced viral shedding. These results indicate that NKT-cell agonists could be used to improve swine vaccine formulations in order to reduce the clinical signs of SI infection and limit the spread of influenza viruses amongst commercial pigs.

Electron transport phosphorylation in rumen butyrivibrios: unprecedented ATP yield for glucose fermentation to butyrate

From a genomic analysis of rumen butyrivibrios (Butyrivibrio and Pseudobutyrivibrio sp.), we have re-evaluated the contribution of electron transport phosphorylation (ETP) to ATP formation in this group. This group is unique in that most (76%) genomes were predicted to possess genes for both Ech and Rnf transmembrane ion pumps. These pumps act in concert with the NifJ and Bcd-Etf to form a electrochemical potential (ΔμH⁺ and ΔμNa⁺), which drives ATP synthesis by ETP. Of the 62 total butyrivibrio genomes currently available from the Hungate 1000 project, all 62 were predicted to possess NifJ, which reduces oxidized ferredoxin (Fd_ox) during pyruvate conversion to acetyl-CoA. All 62 possessed all subunits of Bcd-Etf, which reduces Fd_ox and oxidizes reduced NAD during crotonyl-CoA reduction. Additionally, 61 genomes possessed all subunits of the Rnf, which generates ΔμH⁺ or ΔμNa⁺ from oxidation of reduced Fd (Fd_red) and reduction of oxidized NAD. Further, 47 genomes possessed all six subunits of the Ech, which generates ΔμH⁺ from oxidation of Fd_red. For glucose fermentation to butyrate and H₂, the electrochemical potential established should drive synthesis of ∼1.5 ATP by the F₀F₁-ATP synthase (possessed by all 62 genomes). The total yield is ∼4.5 ATP/glucose after accounting for three ATP formed by classic substrate-level phosphorylation, and it is one the highest yields for any glucose fermentation. The yield was the same when unsaturated fatty acid bonds, not H⁺, served as the electron acceptor (as during biohydrogenation). Possession of both Ech and Rnf had been previously documented in only a few sulfate-reducers, was rare in other rumen prokaryotic genomes in our analysis, and may confer an energetic advantage to rumen butyrivibrios. This unique energy conservation system might enhance the butyrivibrios’ ability to overcome growth inhibition by unsaturated fatty acids, as postulated herein.

Maximizing efficiency of rumen microbial protein production

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen.

Targeted disruption of CD1d prevents NKT cell development in pigs

Studies in mice genetically lacking natural killer T (NKT) cells show that these lymphocytes make important contributions to both innate and adaptive immune responses. However, the usefulness of murine models to study human NKT cells is limited by the many differences between mice and humans, including that their NKT cell frequencies, subsets, and distribution are dissimilar. A more suitable model may be swine that share many metabolic, physiological, and growth characteristics with humans and are also similar for NKT cells. Thus, we analyzed genetically modified pigs made deficient for CD1d that is required for the development of Type I invariant NKT (iNKT) cells that express a semi-invariant T-cell receptor (TCR) and Type II NKT cells that use variable TCRs. Peripheral blood analyzed by flow cytometry and interferon-γ enzyme-linked immuno spot assays demonstrated that CD1d-knockout pigs completely lack iNKT cells, while other leukocyte populations remain intact. CD1d and NKT cells have been shown to be involved in shaping the composition of the commensal microbiota in mice. Therefore, we also compared the fecal microbiota profile between pigs expressing and lacking NKT cells. However, no differences were found between pigs lacking or expressing CD1d. Our results are the first to show that knocking-out CD1d prevents the development of NKT cells in a non-rodent species. CD1d-deficient pigs should offer a useful model to more accurately determine the contribution of NKT cells for human immune responses. They also have potential for understanding how NKT cells impact the health of commercial swine.

A system for predicting energy and protein requirements of wild ruminants

Wild ruminants require energy and protein for the normal function. I developed a system for predicting these energy and protein requirements across ruminant species and life stages. This system defines requirements on the basis of net energy (NE), net protein (NP), and ruminally degraded protein (RDP). Total NE and NP requirements are calculated as the sum of NE and NP required for several functions (maintenance, activity, thermoregulation, gain, lactation, and gestation). To estimate the requirements for each function, I collected data predominantly for wild species and then formulated allometric and other equations that predict requirements across species. I estimated RDP requirements using an equation for cattle. I then related NE, NP, and RDP to quantities more practical for diet formulation (e.g. dry matter intake). I tabulated requirements over a range of body mass and life stages (neonate, juvenile, nonproductive adult, lactating adult, and gestating adult). Tabulated requirements suggest that adults at peak lactation require greatest quantities of energy and neonates generally require greatest quantities of protein, agreeing with suggestions that lactation is energetically expensive and protein is most limiting during growth. Equations used in this system were precise (allometric equations had R(2) generally ≥0.89 and coefficient of variation <31.1%) and expected to reliably predict requirements across species. Results showed that a system for beef cattle would overestimate NE and either over- or underestimate NP for gain when applied to wild ruminants, showing that systems for wild ruminants should not extrapolate from requirements for domestic ruminants. One prominent system for wild ruminants predicted at times vastly different protein requirements from those predicted by the proposed system. The proposed system should be further evaluated and expanded to include other nutrients.

Variability in in situ ruminal degradation parameters causes imprecision in estimated ruminal digestibility

The ruminal digestibility of dietary ingredients is frequently estimated with degradation parameters (e.g., rate and extent of degradation). Mean degradation parameters (e.g., those in a feed library) are often used, but limited data suggest considerable variation around these means, potentially leading to imprecise digestibility estimates. This experiment quantified degradation parameter variation for forage hays and determined the impact of this variation on the precision of ruminal digestibility estimates. Degradation data were those previously published by our laboratory and included degradation rate, lambda(d) (h(-1)), fraction instantly degraded, a (g x g(-1)), potential extent of degradation, (a + b) (g x g(-1)), and fraction not instantly degraded that is potentially degradable, b (g x g(-1)) of alfalfa, grass, and grass-legume hays. Ruminal digestibilities of chemical fractions (dry matter, neutral detergent fiber, acid detergent fiber, hemicellulose, crude protein) were estimated using these data. Ninety-five percent confidence limits of digestibility were determined using propagation of uncertainty with measured standard deviations of degradation parameters. Values for coefficients of variation of degradation parameters were large; averaged across chemical fractions, they were 24.8, 28.6, 20.7, and 12.6% for lambda(d), a, b, and (a + b). Ninety-five percent confidence limits of digestibility were large (80.5% of digestibility means) and often overlapped each other, even when digestibility means differed greatly numerically. Consequently, digestibility values computed with mean degradation parameters may have little biological and practical significance. When uncertainty in all parameters but lambda(d) was set to zero (lambda(d) alone had uncertainty), 95% confidence limits still encompassed 54.5% of digestibility means. Thus, uncertainty in lambda(d) alone caused considerable imprecision in estimated digestibility. These results caution against using mean degradation parameters to estimate digestibility.

A mechanistic model for predicting intake of forage diets by ruminants

Accurate voluntary feed intake (VFI) prediction is critical to the productivity and profitability of ruminant livestock production systems. Simple empirical models have been used to predict VFI for decades, but they are inflexible, restrictive, and poorly accommodate many feeding conditions, such as those of developing countries. We have developed a mechanistic model to predict VFI over a range of forage diets (low- and high-quality grasses and legumes) by wild and domestic ruminants of varying physiological states (growth, lactation, gestation, nonproductive). Based on chemical reactor theory, the model represents the reticulorumen, large intestine, and blood plasma as continuous stirred-tank reactors and the small intestine as a plug flow reactor. Predicted VFI is that which 1) fulfills an empirical relationship between chemostatic and distention feedback observed in the literature, and 2) leads to steady-state conditions. Agreement between observed and actual VFI was great (generally R(2) >0.9, root mean square prediction error <1.4 kg/d, CV <25%). Root mean square prediction error for our model was only 67% that of the Beef NRC (2000) model, the leading empirical prediction system for cattle. Together, these results demonstrate that our model can predict ruminant VFI more broadly and accurately than prior methods and, by consequence, serve as a crucial tool to ruminant livestock production systems.