More monensin-sensitive, ammonia-producing bacteria from the rumen

Equine fecal microbiota response to short term antibiotic administration

Though generally safe, research continues to demonstrate negative side effects of antibiotic administration on the gastrointestinal (GIT) microbiota across species. In horses, antibiotic associated diarrhea (AAD) is a life-threatening condition linked to the GIT microbiota. This study tested the hypothesis that short term antibiotic administration to healthy horses would negatively impact the fecal microbiota as measured by their ability to digest nutrients and through fecal shedding of disease-associated-bacteria. Twenty-four horses were assigned to one of four treatment groups: control (CO); potassium penicillin/gentamicin sulfate (KPG); ceftiofur crystalline free acid (EX); trimethoprim/sulfamethoxazole (SMZ); and treated for 4 days. Fecal samples were collected before treatment began (S0), the day after treatment conclusion (S5), and at 10, 14, 21, and 28 days after initiating treatment. Horses had highly individualized responses to antibiotic administration. All horses receiving antibiotics experienced significantly softer stool compared to controls. Lactobacillus spp. were dramatically reduced in all antibiotic treated S5 samples. Horses receiving antibiotics were significantly more likely to test positive for C. difficile or C. perfringens on fecal qPCR. In conclusion, response to antibiotic administration displays high inter-individual variability, but shows changes to the functions of fecal microbiota that may depend on the antibiotic used.

Polyether ionophore resistance in a one health perspective

Antimicrobial resistance is a major threat to human health and must be approached from a One Health perspective. Use of antimicrobials in animal husbandry can lead to dissemination and persistence of resistance in human pathogens. Polyether ionophores (PIs) have antimicrobial activities and are among the most extensively used feed additives for major production animals. Recent discoveries of genetically encoded PI resistance mechanisms and co-localization of resistance mechanisms against PIs and antimicrobials used in human medicine on transferrable plasmids, have raised concerns that use of PIs as feed additives bear potential risks for human health. This review summarizes the current knowledge on PI resistance and discusses the potential consequences of PI-usage as feed additives in a One Health perspective.

Impact of nicotine and cotinine on macrophage inflammatory plasticity via vesicular modifications in gastrointestinal bacteria

OBJECTIVES

This study aimed to elucidate mechanistic explanation(s) for compositional changes to enteric microbiota by determining the impacts of continuous nicotine/cotinine exposure on representative gastrointestinal bacteria and how these alterations impact innate immune cell plasticity.

METHODS

In vitro cultures of the gastrointestinal bacteria (Bacteroides fragilis 25285, Prevotella bryantii B14, and Acetoanaerobium sticklandii SR) were continuously exposed to nicotine or cotinine. Supernatant samples were collected for fermentation acid analysis. Vesicles were collected and analyzed for physiological changes in number, size, and total protein cargo. Cultured macrophages were stimulated to a tolerogenic phenotype, exposed to control or altered (nicotine or cotinine - exposed) vesicles, and inflammatory plasticity assessed via inflammatory cytokine production.

RESULTS

Nicotine/cotinine exposure differentially affected metabolism of all bacteria tested in a Gram (nicotine) and concentration-dependent (cotinine) manner. Physiological studies demonstrated changes in vesiculation number and protein cargo following nicotine/cotinine exposures. Continuous exposure to 1 μM nicotine and 10 μM cotinine concentrations reduced total protein cargo of Gram (-) - 25285 and B14 vesicles, while cotinine generally increased total protein in Gram (+) - SR vesicles. We found that theses physiological changes to the vesicles of 25285 and SR formed under nicotine and cotinine, respectively, challenged the plasticity of tolerogenic macrophages. Tolerogenic macrophages exposed to vesicles from 1 μM nicotine, and 5 or 10 μΜ cotinine cultures produced significantly less IL-12p70, TNFα, or KC/GRO, regardless of macrophage exposure to nicotine/cotinine.

CONCLUSIONS

Nicotine/cotinine exposure differentially alters bacterial metabolism and vesicle physiology, ultimately impacting the inflammatory response of tolerogenic macrophages.

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.

Trends in Biological Ammonia Production

Food production heavily depends on ammonia-containing fertilizers to improve crop yield and profitability. However, ammonia production is challenged by huge energy demands and the release of ~2% of global CO₂. To mitigate this challenge, many research efforts have been made to develop bioprocessing technologies to make biological ammonia. This review presents three different biological approaches that drive the biochemical mechanisms to convert nitrogen gas, bioresources, or waste to bio-ammonia. The use of advanced technologies-enzyme immobilization and microbial bioengineering-enhanced bio-ammonia production. This review also highlighted some challenges and research gaps that require researchers' attention for bio-ammonia to be industrially pragmatic.

Oral administration of Pinus koraiensis cone essential oil reduces rumen methane emission by altering the rumen microbial composition and functions in Korean native goat (Capra hircus coreanae)

This study aimed to investigate Pinus koraiensis cone essential oil (PEO) as a methane (CH₄) inhibitor and determine its impact on the taxonomic and functional characteristics of the rumen microbiota in goats. A total of 10 growing Korean native goats (Capra hircus coreanae, 29.9 ± 1.58 kg, male) were assigned to different dietary treatments: control (CON; basal diet without additive) and PEO (basal diet +1 g/d of PEO) by a 2 × 2 crossover design. Methane measurements were conducted every 4 consecutive days for 17-20 days using a laser CH₄ detector. Samples of rumen fluid and feces were collected during each experimental period to evaluate the biological effects and dry matter (DM) digestibility after PEO oral administration. The rumen microbiota was analyzed via 16S rRNA gene amplicon sequencing. The PEO oral administration resulted in reduced CH₄ emission (eructation CH₄/body weight^0.75, p = 0.079) without affecting DM intake; however, it lowered the total volatile fatty acids (p = 0.041), molar proportion of propionate (p = 0.075), and ammonia nitrogen (p = 0.087) in the rumen. Blood metabolites (i.e., albumin, alanine transaminase/serum glutamic pyruvate transaminase, creatinine, and triglyceride) were significantly affected (p < 0.05) by PEO oral administration. The absolute fungal abundance (p = 0.009) was reduced by PEO oral administration, whereas ciliate protozoa, total bacteria, and methanogen abundance were not affected. The composition of rumen prokaryotic microbiota was altered by PEO oral administration with lower evenness (p = 0.054) observed for the PEO group than the CON group. Moreover, PICRUSt2 analysis revealed that the metabolic pathways of prokaryotic bacteria, such as pyruvate metabolism, were enriched in the PEO group. We also identified the Rikenellaceae RC9 gut group as the taxa potentially contributing to the enriched KEGG modules for histidine biosynthesis and pyruvate oxidation in the rumen of the PEO group using the FishTaco analysis. The entire co-occurrence networks showed that more nodes and edges were detected in the PEO group. Overall, these findings provide an understanding of how PEO oral administration affects CH₄ emission and rumen prokaryotic microbiota composition and function. This study may help develop potential manipulation strategies to find new essential oils to mitigate enteric CH₄ emissions from ruminants.

Developing rumen mimicry process for biological ammonia synthesis

The ruminant rumen houses hyper-ammonia-producing bacteria (HAB) that produce ammonia with minimal energy use. Here we developed a mimicry process to produce bio-ammonia, a solution of ammonia and ammonium. The rumen microbes were used to ferment soybean (SYB), soybean protein isolate (SPI), and pepsin-hydrolysate (HP) for bio-ammonia production. The maximum bio-ammonia produced from SYB, SPI, and HP were 0.65, 1.2_, and 1.1 g/L, respectively. The presence of non-protein in SYB hindered bio-ammonia production and the processing of SYB to SPI and HP significantly (p < 0.05) increased bio-ammonia production. HP was converted to bio-ammonia quicker than SPI suggesting that enzymatic hydrolysis increases bioprocessing efficiency. Metagenomic analysis of a sample culture revealed that the HAB population is predominantly Klebsiella quasivariicola (73%), Escherichia coli (6%), and Enterobacter cloacae (6%). The bioprocessing steps developed would enable industrial ammonia production to achieve a low CO₂ footprint.

Effects of Hops Treatment on Nitrogen Retention, Volatile Fatty Acid Accumulations, and Select Microbial Populations of Composting Poultry Litter Intended for Use as a Ruminant Feedstuff

Poultry litter is a valuable crude protein feedstuff for ruminants, but it must be treated to kill pathogens before feeding. Composting effectively kills pathogens, but it risks losing ammonia to volatilization or leaching during degradation of uric acid and urea. Hops bitter acids also exert antimicrobial activity against certain pathogenic and nitrogen-degrading microbes. Consequently, the present studies were conducted to test if adding bitter acid-rich hop preparations to simulated poultry litter composts may improve nitrogen retention while simultaneously improving pathogen killing. Results from an initial study, testing doses of Chinook or Galena hops preparations designed to each deliver 79 ppm hops β-acid, revealed that, after nine days simulated composting of wood chip litter, ammonia concentrations were 14% lower (p < 0.05) in Chinook-treated composts than untreated composts (13.4 ± 1.06 µmol/g). Conversely, urea concentrations were 55% lower (p < 0.05) in Galena-treated than untreated composts (6.2 ± 1.72 µmol/g). Uric acid accumulations were unaffected by hops treatments in this study but were higher (p < 0.05) after three days than after zero, six, or nine days of composting. In follow-up studies, Chinook or Galena hops treatments (delivering 2042 or 6126 ppm of β-acid, respectively) for simulated composts (14 days) of wood chip litter alone or mixed 3:1 with ground Bluestem hay (Andropogon gerardii) revealed that these higher dosages had little effect on ammonia, urea, or uric acid accumulations when compared to untreated composts. Volatile fatty acid accumulations measured in these later studies were affected by the hops treatments, with butyrate accumulations being lower after 14 days in hops-treated composts than in untreated compost. In all studies, beneficial effects of Galena or Chinook hops treatments were not observed on the antimicrobial activity of the simulated composts, with composting by itself decreasing (p < 0.05) counts of select microbial populations by more than 2.5 log10 colony forming units/g compost dry matter. Thus, while hops treatments had little effect on pathogen control or nitrogen retention within the composted litter, they did lessen accumulations of butyrate, which may prevent adverse effects of this fatty acid on palatability of litter fed to ruminants.

Ruminal fermentation pattern of acidosis-induced cows fed either monensin or polyclonal antibodies preparation against several ruminal bacteria

This study was designed to evaluate a spray-dried multivalent polyclonal antibody preparation (PAP) against lactate-producing bacteria as an alternative to monensin (MON) to control ruminal acidification. Holstein cows (677 ± 98 kg) fitted with ruminal cannulas were allocated in an incomplete Latin square design with two 20 days period. Cows were randomly assigned to control (CTL), PAP, or MON treatments. For each period, cows were fed a forage diet in the first 5 days (d−5 to d−1), composed of sugarcane, urea and a mineral supplement, followed by a 74% concentrate diet for 15 days (d 0 to d 14). There were no treatment main effects (P &gt; 0.05) on dry matter intake (DMI) and microbial protein synthesis. However, there was a large peak (P &lt; 0.01) of intake on d 0 (18.29 kg), followed by a large decline on d 1 (3.67 kg). From d2, DMI showed an increasing pattern (8.34 kg) and stabilized around d 8 (12.96 kg). Higher mean pH was measured (P &lt; 0.01) in cattle-fed MON (6.06 vs. PAP = 5.89 and CTL = 5.91). The ruminal NH3-N concentration of CTL-fed cows was lower (P &lt; 0.01) compared to those fed MON or PAP. The molar concentration of acetate and lactate was not affected (P &gt; 0.23) by treatments, but feeding MON increased (P = 0.01) propionate during the first 4 days after the challenge. Feeding MON and PAP reduced (P = 0.01) the molar proportion of butyrate. MON was effective in controlling pH and improved ruminal fermentation of acidosis-induced cows. However, PAP was not effective in controlling acidosis. The acidosis induced by the challenge was caused by the accumulation of SCFAs. Therefore, the real conditions for evaluation of this feed additive were not reached in this experiment, since this PAP was proposed to work against lactate-producing bacteria.

Red clover supplementation modifies rumen fermentation and promotes feed efficiency in ram lambs

Red clover produces isoflavones, including biochanin A, which have been shown to have microbiological effects on the rumen while also promoting growth in beef cattle. The objective was to determine if supplementation of biochanin A via red clover hay would produce similar effects on the rumen microbiota and improve growth performance of lambs. Twenty-four individually-housed Polypay ram lambs (initial age: 114 ± 1 d; initial weight: 38.1 ± 0.59 kg) were randomly assigned to one of three experimental diets (85:15 concentrate:roughage ratio; N = 8 rams/treatment): CON-control diet in which the roughage component (15.0%, w/w, of the total diet) consisted of orchardgrass hay; 7.5-RC-red clover hay substituted for half (7.5%, w/w, of the total diet) of the roughage component; and 15-RC-the entire roughage component (15.0%, w/w, of the total diet) consisted of red clover hay. Feed intake and weight gain were measured at 14-d intervals for the duration of the 56-d trial, and rumen microbiological measures were assessed on days 0, 28, and 56. Red clover supplementation impacted growth performance of ram lambs. Average daily gains (ADG) were greater in ram lambs supplemented with red clover hay (7.5-RC and 15-RC) than for those fed the CON diet (P < 0.05). Conversely, dry matter intake (DMI) was lower in 7.5-RC and 15-RC than for CON lambs (P = 0.03). Differences in ADG and DMI resulted in greater feed efficiency in ram lambs supplemented with red clover hay (both 7.5-RC and 15-RC) compared to CON (P < 0.01). Rumen microbiota were also altered by red clover supplementation. The total viable number of hyper-ammonia-producing bacteria in 7.5-RC and 15-RC decreased over the course of the experiment and were lower than CON by day 28 (P ≤ 0.04). Amylolytic bacteria were also lower in 15-RC than in CON (P = 0.03), with a trend for lower amylolytic bacteria in 7.5-RC (P = 0.08). In contrast, there was tendency for greater cellulolytic bacteria in red clover supplemented lambs than in CON (P = 0.06). Red clover supplementation also increased fiber utilization, with greater ex vivo dry matter digestibility of hay for both 7.5-RC and 15-RC compared to CON by day 28 (P < 0.03). Results of this study indicate that low levels of red clover hay can elicit production benefits in high-concentrate lamb finishing systems through alteration of the rumen microbiota.

Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture

This study investigated the effects of active dry yeast (ADY) and yeast culture (YC) supplementation on rumen bacteria and metabolites in finishing bulls fed high-concentrate diets using the full-length 16S rDNA gene sequencing and liquid chromatography-mass spectrometry. Supplementation with ADY improved the alpha diversity and relative abundance of rumen bacteria, while YC only affected relative abundance of rumen bacteria at the genus level. Sixty-three differential metabolites were identified in rumen fluid after ADY supplementation, and 17 after YC. PICRUSt2 functional prediction showed that ADY supplementation improved the capacity of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of terpenoids and polyketides, and energy metabolism in rumen bacteria (all P < 0.05). Correlation analysis showed that the rumen differential metabolites following ADY supplementation were mainly related to Oligosphaera, Verruc, Mycoplasma, and Anaeroplasma. Supplementation with ADY was more effective than YC in remodeling the rumen bacterial flora structure and metabolite composition under high-concentrate diets.

Implication and challenges of direct-fed microbial supplementation to improve ruminant production and health

Direct-fed microbials (DFMs) are feed additives containing live naturally existing microbes that can benefit animals' health and production performance. Due to the banned or strictly limited prophylactic and growth promoting usage of antibiotics, DFMs have been considered as one of antimicrobial alternatives in livestock industry. Microorganisms used as DFMs for ruminants usually consist of bacteria including lactic acid producing bacteria, lactic acid utilizing bacteria and other bacterial groups, and fungi containing Saccharomyces and Aspergillus. To date, the available DFMs for ruminants have been largely based on their effects on improving the feed efficiency and ruminant productivity through enhancing the rumen function such as stabilizing ruminal pH, promoting ruminal fermentation and feed digestion. Recent research has shown emerging evidence that the DFMs may improve performance and health in young ruminants, however, these positive outcomes were not consistent among studies and the modes of action have not been clearly defined. This review summarizes the DFM studies conducted in ruminants in the last decade, aiming to provide the new knowledge on DFM supplementation strategies for various ruminant production stages, and to identify what are the potential barriers and challenges for current ruminant industry to adopt the DFMs. Overall literature research indicates that DFMs have the potential to mitigate ruminal acidosis, improve immune response and gut health, increase productivity (growth and milk production), and reduce methane emissions or fecal shedding of pathogens. More research is needed to explore the mode of action of specific DFMs in the gut of ruminants, and the optimal supplementation strategies to promote the development and efficiency of DFM products for ruminants.

Spent Craft Brewer's Yeast Reduces Production of Methane and Ammonia by Bovine Rumen Microbes

Methane and ammonia are byproducts of rumen fermentation that do not promote animal growth, and methane is a key contributor to anthropogenic climate disruption. Cows eructate every few breaths and typically emit 250–500 L of methane gas daily. Significant research is focused on finding diets and additives that lower the production of methane and ammonia. Emerging research has shown that humulones and lupulones, molecules that are found in the cones of hops (Humulus lupulus), have potential in this regard. These molecules, which are also key flavor components in beer, are biologically active: they are known inhibitors of Gram-positive bacteria. Ruminants' sophisticated digestive systems host billions of microorganisms, and these systems' outputs will likely be affected in the presence of brewer's yeast (Saccharomyces cerevisiae). So-called spent yeast is produced during the beer-brewing process and contains humulones and lupulones in concentrations that vary by beer style, but it is generally discarded as waste. Our research suggests that adding spent craft brewer's yeast to rumen microbes by single time-point 24-h in vitro incubations suppresses production of methane and ammonia. This project examines the correlation between the quantities of hop acids in spent yeast and the production of methane and ammonia by bovine rumen microbes in vitro. We determined, by HPLC, the hop acid concentrations in spent yeast obtained from six beer styles produced at a local brewery. We performed anaerobic incubation studies on bovine rumen microbes, comparing the effects of these materials to a baker's yeast control and to the industry-standard antibiotic monensin. Results include promising decreases in both methane (measured by GC–FID) and ammonia (measured by colorimetric assay) in the presence of craft brewer's yeast, and a strong correlation between the quantities of hop acids in the spent yeast and the reduction of methane and ammonia. Notably, two of the yeast samples inhibited methane production to a greater degree than the industry-standard antibiotic monensin. Our results suggest that spent brewer's yeast has potential to improve ruminant growth while reducing anthropogenic methane emission.

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge

Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d^-1), or BCA (6 g d^-1). The basal diet consisted of corn silage and dried distiller’s grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1–4: 40% corn; d 5–8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.

The effect of biofloc produced from a fish farming system on nutrients digestibility, rumen fermentation, feeding behavior, and blood parameters of Najdi goats

The aim of this study was to evaluate the effect of biofloc produced from a fish pond on digestibility, rumen fermentation, rumination activity, and blood parameters of Najdi goats. At the first, 200 common carp fish (1.00 g) in two water tanks were used for producing biofloc. Then, 12 goats (average body weight of 32.00 ± 1.50 kg aging eight months) were assigned through a completely randomized design to two treatments (six replicates) and fed for one month. The treatments were comprised of a control diet and a trial diet containing 1.50% biofloc. At the end of the experiment, digestibility of nutrients, rumen fermentation, blood metabolites, and rumination activity were measured. The results showed that the digestibility of dry matter (DM), crude protein, neutral detergent fiber (NDF), and acid detergent fiber (ADF) significantly increased in goats fed with 1.50% biofloc. Also, the rumen protozoa population, plasma glucose, average time of eating, rumination, and chewing per NDF and ADF intakes, total rumination time, and chewing activity were significantly increased. There was no significant difference between treatments for DM intake, ruminal ammonia nitrogen, blood urea nitrogen, cholesterol, and triglyceride. The pH of rumen fluid significantly decreased in treatment containing biofloc. The results of the current study confessed that the use of biofloc (1.50% DM) as a supplement in Najdi goat’s diet can improve the digestibility of the diet. It is recommended further and detailed trials with different levels of biofloc in sheep or different livestock species to know more about this untapped supplement source.

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures

Biochanin A, an isoflavone present in the pasture legume red clover (Trifloium pratense L.), alters fermentation in the rumen of cattle and other ruminants. Biochanin A inhibits hyper-ammonia-producing bacteria and promotes cellulolytic bacteria and fiber catalysis in vitro and ex vivo. Consequently, biochanin A supplementation improves weight gain in grazing steers. Red clover contains biologically active isoflavones that may act synergistically. Therefore, the objective was to evaluate the effect of two levels of red clover hay on growth performance and the microbial community in growing steers grazing mixed grass pastures. A grazing experiment was conducted over 2 early growing seasons (2016 and 2017) with 36 cross-bred steers and twelve rumen-fistulated, growing Holstein steers for evaluation of average daily gain and rumen microbiota, respectively. Steers were blocked by body weight and assigned to pastures with one of four treatments: 1) pasture only, 2) pasture + dry distillers’ grains (DDG), 3) pasture + DDG + low level of red clover hay (~15% red clover diet), or 4) pasture + DDG + high level of red clover hay (~30% red clover diet). DDG were added to treatments to meet protein requirements and to balance total protein supplementation between treatments. All supplementation strategies (DDG ± red clover hay) increased average daily gains in comparison to pasture-only controls (P < 0.05), with a low level of red clover supplementation being the most effective (+0.17 kg d^-1 > DDG only controls; P < 0.05). Similarly, hyper-ammonia-producing bacteria inhibition (10–100-fold; P < 0.05), fiber catalysis (+10–25%; P < 0.05) and short chain fatty acid concentrations were greatest with the low red clover supplement (+~25%; P < 0.05). These results provide evidence that lower levels or red clover supplementation may be optimal for maximizing overall microbial community function and animal performance in grazing steers.

Effects of narasin supplementation on dry matter intake and rumen fermentation characteristics of Bos indicus steers fed a high-forage diet

This study evaluated the effects of narasin on intake and rumen fermentation characteristics of Bos indicus steers offered a high-forage diet for 140 d. On day 0 of the study, 30 rumen-fistulated Nellore steers [initial body weight (BW) = 281 ± 21 kg] were assigned to 30 individual pens in a randomized complete block design according to their initial BW. Animals were randomly assigned to 1 of the 3 treatments: 1) forage-based diet without narasin (CONT; n = 10), 2) CONT diet plus 13 ppm of narasin (13NAR; n = 10), and 3) CONT diet plus 20 ppm of narasin (20NAR; n = 10). The forage used was Tifton-85 (Cynodon dactylon spp.), whereas the carrier for narasin was a 50:50 mixture of soybean hull:corn. The experimental period was divided into 5 periods of 28 d each. Throughout the experimental period, total dry matter intake (DMI) was recorded daily, whereas mineral salt intake was recorded weekly. Blood and ruminal fluid samples were collected on day 0 (prior to treatment feeding), 28, 56, 84, 112, and 140 of the study. Moreover, total tract apparent nutrient digestibility was performed for a 5-d period every 28 d. No treatment effects were observed on forage, mineral, concentrate, or total DMI (P ≥ 0.22). Nonetheless, 13NAR tended to have a greater mineral intake vs. 20NAR cohorts (P = 0.08) Narasin-supplemented animals had reduced rumen acetate, Ac:Pr ratio, as well as greater (P ≤ 0.02) rumen propionate concentrations vs. CONT cohorts. Moreover, 13NAR increased rumen propionate and decreased butyrate, Ac:Pr vs. 20NAR cohorts (P ≤ 0.01). Throughout the experimental period, narasin-supplemented animals had reduced ammonia concentrations vs. CONT cohorts (P < 0.01), whereas no differences were observed between 13NAR and 20NAR (P = 0.80). No treatment or dose effects were observed (P ≥ 0.23) on DM, organic matter (OM), protein, neutral detergent fiber (NDF), acid detergent fiber (ADF), and mineral digestibility. Animals fed 13NAR had a reduced mean plasma urea concentration vs. CONT cohorts (P = 0.03), whereas no further differences were observed (P ≥ 0.12). In summary, narasin supplementation to beef steers offered a high-forage diet did not impact forage, mineral, and total DMI, as well as nutrient digestibility, whereas rumen fermentation characteristics, rumen ammonia, and plasma urea concentrations were positively impacted and lasted throughout the experimental period. Additionally, 13 ppm of narasin resulted in a reduced Ac:Pr ratio and rumen ammonia when compared to animals supplemented with 20 ppm.

Inhibition of Bacteroidetes and Firmicutes by select phytochemicals

Current research indicates that changes in gut microbiota can impact the host, but it is not always clear how dietary and environmental factors alter gut microbiota. One potential factor is antimicrobial activity of compounds ingested by the host. The goal of this study was to determine the antimicrobial activity of common plant secondary metabolites against pure cultures of paired, structurally and phylogenetically distinct gastrointestinal bacteria of human or bovine origin: Prevotella bryantii B₁4, Bacteroides fragilis 25285, Acetoanaerobium (Clostridium) sticklandii SR and Clostridioides difficile 9689. When growth media were amended with individual phytochemicals (the alkaloids: berberine, capsaicin, nicotine, piperine and quinine and the phenolic: curcumin), growth of each species was inhibited to varying degrees at the three greatest concentrations tested (0.10-10.00 mg mL^-1). The viable cell numbers of all the cultures were reduced, ≥4-logs, by berberine at concentrations ≥1.00 mg mL^-1. Quinine performed similarly to berberine for B₁4, 25285, and SR at the same concentrations. The other phytochemicals were inhibitory, but not as much as quinine or berberine. Nicotine had activity against all four species (≥2-log reduction in viable cell number at 10.00 mg mL^-1), but had stronger activity against the Gram-positive bacteria, SR and 9689, (≥4-log reductions at 10.00 mg mL^-1). In conclusion, the phytochemicals had varying spectra of antimicrobial activity. These results are consistent with the hypothesis that ingested phytochemicals have the ability to differentially impact gut microbiota through antimicrobial activity.

Functional prediction, characterization, and categorization of operome from Acetoanaerobium sticklandii DSM 519

Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia producing anaerobic bacterium that can be able utilizes amino acids as sole carbon and energy sources for its growth and energetic metabolism. A lack of knowledge on its molecular machinery and 30.5% conserved hypothetical proteins (HPs; operome) hinders the successful utility in biofuel applications. In this study, we have predicted, characterized and categorized its operome whose functions are still not determined accurately using a combined bioinformatics approach. The functions of 64 of the 359 predicted HPs are involved in diverse metabolic subsystems. A. sticklandii operome has consisted of 16% Rossmann fold and 46% miscellaneous folds. Subsystems-based technology has classified 51 HPs contributing to the small-molecular reactions, 26 in macromolecular reactions and 12 in the biosynthesis of cofactors, prosthetic groups and electron carriers. A generality of functions predicted from its operome contributed to the cell cycle, amino acid metabolism, membrane transport, and regulatory processes. Many of them have duplicated functions as paralogs in this genome. A. sticklandii has the ability to compete with invading microorganisms and tolerate abiotic stresses, which can be overwhelmed by the predicted functions of its operome. Results of this study revealed that it has specialized systems for amino acid catabolism-directed solventogenesis and acidogenesis but the level of gene expression may determine the metabolic function in amino acid fermenting niches in the rumina of cattle. As shown by our analysis, the predicted functions of its operome allow us for a better understanding of the growth and physiology at systems-scale.

Isolation and identification of hyper-ammonia-producing bacteria from commercial fermented skates (Raja kenojei)

Ammonia-producing bacteria were isolated and identified from five commercial fermented skates (A1, A2, A3, A4, and A5). In addition, the pH, ammonia nitrogen, total volatile nitrogen (TVBN), trimethylamine nitrogen (TMAN), and amino nitrogen contents of skate samples were also determined. A total of 88 strains of ammonia-producing bacteria was isolated and seven hyper-ammonia-producing bacteria isolates (A2-2, A2-3, A2-12, A2-18, A2-20, A3-6 and A3-14) were selected based on ammonia nitrogen producing ability. Those isolates were identified as Proteus hauseri (three strains), Providencia rustigianii (three strains), and Kurthia gibsonii. The pH and ammonia nitrogen content in skate samples were ranged from 8.63 to 9.03, and 4.86 to 7.31 g/kg, respectively. No significant difference of pH values was observed in skate samples A2, A3, A4 and A5. While, skate samples A3, A4 and A5 showed similar level of TVBN and TMAN content. Skate sample A2 showed the highest amino nitrogen content among all samples, which indicated the highest degree of protein degradation of skate muscle during fermentation. Bivariate cluster analysis showed that skate samples A3, A4, and A5 clustered together at a relatively high level, implying a similar microbial environment during fermentation. The cluster analysis allowed different commercial fermented skates to be clearly differentiated based on the characteristics determined in this study. This study can provide important information for investigating the mechanisms underlying ammonia flavor formation in skate muscle during fermentation.

Effects of red clover isoflavones on tall fescue seed fermentation and microbial populations in vitro

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo.

Effect of calcium lignosulfonate supplementation on metabolic profiles of confined lambs

This study aimed to evaluate the effect of calcium lignosulfonate associated with whole cottonseed in high-concentrate diets for sheep. Eight Dorper crossbred sheep with an average live weight of 42.5 ± 1.70 kg were assigned to two 4 × 4 Latin squares. The following experimental diets were evaluated: control diet (without calcium lignosulfonate) and diets with inclusion of 50, 100, and 150 g of calcium lignosulfonate/kg fresh matter. Diets were composed of soybean meal, ground corn, and whole cottonseed. Feed intake, digestibility, metabolic characteristics, and feeding behavior were evaluated. The intake of nutritional components did not show significant differences as a function of the lignosulfonate levels in the diet; however, the increase in calcium lignosulfonate levels linearly decreased the dry matter digestibility. Rumen ammonia nitrogen concentrations decreased linearly as the lignosulfonate levels in the diets were increased. There was no effect of lignosulfonate levels on blood parameters or feeding behavior of the animals. The use of lignosulfonate associated with cottonseed decreases the digestibility of dry matter and the concentration of rumen ammonia nitrogen, but does not change the intake of nutritional components, the blood parameters, or the feeding behavior of sheep.

Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows

Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.

Effects of rotating antibiotic and ionophore feed additives on volatile fatty acid production, potential for methane production, and microbial populations of steers consuming a moderate-forage diet

Ionophores and antibiotics have been shown to decrease ruminal methanogenesis both in vitro and in vivo but have shown little evidence toward a sustainable means of mitigation. Feed additive rotation was proposed and investigated for methane, VFA, and microbial population response. In the present study, cannulated steers ( = 12) were fed a moderate-forage basal diet in a Calan gate facility for 13 wk. In addition to the basal diet, steers were randomly assigned to 1 of 6 treatments: 1) control, no additive; 2) bambermycin, 20 mg bambermycin/d; 3) monensin, 200 mg monensin/d; 4) the basal diet + weekly rotation of bambermycin and monensin treatments (B7M); 5) the basal diet + rotation of bambermycin and monensin treatments every 14 d (B14M); and 6) the basal diet + rotation of bambermycin and monensin treatments every 21 d (B21M). Steers were blocked by weight in a randomized complete block design where the week was the repeated measure. Rumen fluid was collected weekly for analysis ( = 13), and results were normalized according to individual OM intake (OMI; kg/d). Potential activity of methane production was not significantly different among treatments ( > 0.05). However, treatment tended to affect the CH-to-propionate ratio ( = 0.0565), which was highest in the control and lowest in the monensin, B21M, and B14M treatments (0.42 vs. 0.36, 0.36, and 0.33, respectively). The CH:propionate ratio was lowest in wk 2 and 3 ( < 0.05) but the ratio in wk 4 to 12 was not different from the ratio in wk 0. Week also affected total VFA, with total VFA peaking at wk 3 and plummeting at wk 4 (4.02 vs. 2.86 m/kg OMI; < 0.05). A significant treatment × week interaction was observed for the acetate-to-propionate (A:P) ratio, where bambermycin- and rotationally fed steers did not have a reduced A:P ratio compared with monensin-fed steers throughout the feeding period ( < 0.0001). Microbial analysis revealed significant shifts, but several predominant classes showed adaptation between 4 and 6 wk after additive initiation. There was no significant evidence to suggest that rotations of monensin and bambermycin provided additional benefits to steers consuming a moderate-forage diet at the microbial/animal and environmental level versus those continuously fed.

Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation

Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds (NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Hops (Humulus lupulus L.) Bitter Acids: Modulation of Rumen Fermentation and Potential As an Alternative Growth Promoter

Antibiotics can improve ruminant growth and efficiency by altering rumen fermentation via selective inhibition of microorganisms. However, antibiotic use is increasingly restricted due to concerns about the spread of antibiotic-resistance. Plant-based antimicrobials are alternatives to antibiotics in animal production. The hops plant (Humulus lupulus L.) produces a range of bioactive secondary metabolites, including antimicrobial prenylated phloroglucinols, which are commonly called alpha- and beta-acids. These latter compounds can be considered phyto-ionophores, phytochemicals with a similar antimicrobial mechanism of action to ionophore antibiotics (e.g., monensin, lasalocid). Like ionophores, the hop beta-acids inhibit rumen bacteria possessing a classical Gram-positive cell envelope. This selective inhibition causes several effects on rumen fermentation that are beneficial to finishing cattle, such as decreased proteolysis, ammonia production, acetate: propionate ratio, and methane production. This article reviews the effects of hops and hop secondary metabolites on rumen fermentation, including the physiological mechanisms on specific rumen microorganisms, and consequences for the ruminant host and ruminant production. Further, we propose that hop beta-acids are useful model natural products for ruminants because of (1) the ionophore-like mechanism of action and spectrum of activity and (2) the literature available on the plant due to its use in brewing.

Ruminal tryptophan-utilizing bacteria degrade ergovaline from tall fescue seed extract

The objectives of this study were to evaluate degradation of ergovaline in a tall fescue [ (Schreb.) Darbysh.] seed extract by rumen microbiota ex vivo and to identify specific bacteria capable of ergovaline degradation in vitro. Rumen cell suspensions were prepared by harvesting rumen fluid from fistulated wether goats ( = 3), straining, and differential centrifugation. Suspensions were dispensed into anaerobic tubes with added Trypticase with or without extract (∼10 μg kg ergovaline). Suspensions were incubated for 48 h at 39°C. Samples were collected at 0, 24, and 48 h for ergovaline analysis and enumeration of hyper-ammonia producing (HAB) and tryptophan-utilizing bacteria. Ergovaline values were analyzed by repeated measures using the mixed procedure of SAS. Enumeration data were log transformed for statistical analysis. When suspensions were incubated with extract, 11 to 15% of ergovaline disappearance was observed over 48 h ( = 0.02). After 24 h, suspensions with added extract had 10-fold less HAB than controls ( = 0.04), but treatments were similar by 48 h ( = 1.00). However, after 24 h and 48 h, suspensions with extract had 10-fold more tryptophan-utilizing bacteria ( < 0.01) that were later isolated and identified by their 16S RNA gene sequence as . The isolates and other known rumen pure cultures ( JB1, B159, HD4, B, F, MD1, SR) were evaluated for the ability to degrade ergovaline in vitro. Pure culture cell suspensions were incubated as described above and samples were taken at 0 and 48 h for ergovaline analysis. Data were analyzed using the ANOVA procedure of SAS. All HAB, including the isolates, tested degraded ergovaline (54 to 75%; < 0.05). B14 was also able to degrade ergovaline but to a lesser capacity (12%; < 0.05), but all other bacteria tested did not degrade ergovaline. The results of this study indicate which rumen bacteria may play an important role in ergovaline degradation and that microbiological strategies for controlling their activity could have ramifications for fescue toxicosis and other forms of ergotism in ruminants.

High levels of whole raw soya beans in dairy cow diets: digestibility and animal performance

The aim of this study was to evaluate the effects of high levels of whole raw soya beans in the diets of lactating cows. Twelve Holstein dairy cows were used, randomized in three 4 ×  4 balanced and contemporary Latin squares and fed the following diets: (i) control (C), without including whole raw soya beans; (ii) 80 g/kg in DM of whole raw soya beans (G80); (iii) 160 g/kg in DM of whole raw soya beans (G160); and (iv) 240 g/kg in DM of whole raw soya beans (G240). There was significant reduction (p < 0.05) in dry matter intake (kg/day) in cows supplemented with G240 compared with C (23.8 vs. 25.3 respectively). G240 diets presented lower crude protein digestibility (g/kg) (p < 0.05) in comparison with C diet (683 vs. 757 respectively). There was significant effect of experimental rations in nitrogen balance (p < 0.05), G240 diet presenting significant reduction in comparison with the other diets, and faecal excretion of nitrogen was higher for G240 diet. The concentration of ruminal ammoniacal nitrogen was significantly higher (p < 0.05) for cows receiving control diet, compared to other diets. G240 diet resulted in significantly lower milk and protein yield (p < 0.05) in comparison with C diet. Significant C18:2 cis fatty acids were observed in milk concentrations (p < 0.05) for G240 diet. The use of high level of whole raw soya beans in dairy cow diets improves the unsaturated fatty acid profile in milk, and the diets (G80 and G160) led to minor alterations in the digestive processes and animal metabolism.

Gut microbiota Modulated by Probiotics and Garcinia cambogia Extract Correlate with Weight Gain and Adipocyte Sizes in High Fat-Fed Mice

Results of recent studies on gut microbiota have suggested that obesogenic bacteria exacerbate obesity and metabolic dysfunction in the host when fed a high fat diet (HFD). In order to explore obesity-associated bacterial candidates and their response to diet, the composition of faecal bacterial communities was investigated by analyzing 16S rRNA gene sequences in mice. Dietary intervention with probiotics and Garcinia cambogia extract attenuated weight gain and adipocyte size in HFD-fed mice. To identify obesity-causative microbiota, two statistical analyses were performed. Forty-eight bacterial species were found to overlap between the two analyses, indicating the commonly identified species as diet-driven and obesity-associated, which would make them strong candidates for host-microbiome interaction on obesity. Finally, correlation based network analysis between diet, microbe, and host revealed that Clostridium aminophilum, a hyper-ammonia-producing bacterium, was highly correlated with obesity phenotypes and other associated bacteria, and shown to be suppressed by the combination of probiotics and Garcinia cambogia extract. Results of the present study suggest that probiotics and Garcinia cambogia extract alleviate weight gain and adiposity, in part via differentially modulating the composition of gut microbiota in HFD fed mice.

Effects of a specific blend of essential oils on apparent nutrient digestion, rumen fermentation and rumen microbial populations in sheep fed a 50:50 alfalfa hay:concentrate diet

Objective

An experiment was conducted to investigate the effects of a specific mixture of essential oils (MEO), containing thyme, clove and cinnamon EO, on rumen microbial fermentation, nutrient apparent digestibility and blood metabolites in fistulated sheep.

Methods

Six sheep fitted with ruminal fistulas were used in a repeated measurement design with two 24-d periods to investigate the effect of adding MEO at 0 (control), 0.8, and 1.6 mL/d on apparent nutrient digestibility, rumen fermentation characteristics, rumen microbial population and blood chemical metabolites. Animals were fed with a 50:50 alfalfa hay:concentrate diet.

Results

Ruminal pH, total volatile fatty acids (VFA) concentration, molar proportion of individual VFA, acetate: propionate ratio and methane production were not affected with MEO. Relative to the control, Small peptides plus amino acid nitrogen and large peptides nitrogen concentration in rumen fluid were not affected with MEO supplementation; while, rumen fluid ammonia nitrogen concentration at 0 and 6 h after morning feeding in sheep fed with 1.6 mL/d of MEO was lower (p<0.05) compared to the control and 0.8 mL/d of MEO. At 0 h after morning feeding, ammonia nitrogen concentration was higher (p<0.05) in sheep fed 0.8 mL/d of MEO relative to 1.6 mL/d and control diet. Ruminal protozoa and hyper ammonia producing (HAP) bacteria counts were not affected by addition of MEO in the diet. Relative to the control, no changes were observed in the red and white blood cells, hemoglobin, hematocrit, glucose, beta-hydroxybutyric acid, cholesterol, total protein, albumin, blood urea nitrogen and aspartate aminotransferase and alanine aminotransferase concentration. Apparent total tract digestibility of dry matter, crude proten, organic matter, and neutral detergent fiber were not influenced by MEO supplementation.

Conclusion

The results of the present study suggested that supplementation of MEO may have limited effects on apparent nutrient digestibility, ruminal fermentation and protozoa and HAP bacteria count, blood cells and metabolites.

Biochemical and genetic diversity of carbohydrate-fermenting and obligate amino acid-fermenting hyper-ammonia-producing bacteria from Nellore steers fed tropical forages and supplemented with casein

Background

Dietary protein plays a major role in ruminant nutrition, and protein supplementation is a widespread practice among farmers in the tropics. Ruminal bacteria are the main agents of dietary protein and amino acid degradation, yet few studies have focused on the isolation and characterization of hyper-ammonia-producing bacteria in animals fed tropical diets or supplemented with rumen-degradable proteins. This work investigated the bacterial community diversity of the rumen of Nellore steers fed tropical forages, with or without casein supplementation. We also isolated and characterized ruminal bacteria showing high levels of ammonia production.

Results

Polymerase chain reaction–denaturing gradient gel electrophoresis analysis indicated no differences in the ruminal bacterial community composition between the control and supplemented animals. Amino acid-fermenting bacteria (n = 250) were isolated from crossbred Nellore steers fed Tifton 85 (Cynodon sp.) using trypticase as the sole carbon and organic nitrogen source in the enrichment and isolation media. The deamination rates in isolates obtained from steers supplemented with casein showed a higher incidence of deamination rates >350 nmol NH₃ mg protein⁻¹ min⁻¹ (P < 0.05), whereas isolates obtained from steers without supplementation showed deamination rates <200 nmol NH₃ mg protein⁻¹ min⁻¹. Although most isolates (84%) could ferment carbohydrates, none could hydrolyze proteins or use urea to sustain growth. All isolates were sensitive to lasalocid and monensin (1 μmol l⁻¹), and similarity analysis of the 16S rRNA sequences indicated a predominance of bacteria from the order Clostridiales, with variable homology (73–99%) to known bacterial species.

Conclusions

These results expand what is known about the biochemical and genetic diversity of hyper-ammonia-producing bacteria, and emphasize the role of carbohydrate-fermenting bacteria in ammonia production in the rumen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0369-9) contains supplementary material, which is available to authorized users.

Substrates enriched by the fungus Cunninghamella echinulata: an in vitro study of nutrient composition, sheep rumen fermentation and lipid metabolism

AIMS

Enrichment of wheat bran (WB), corn meal (CM) and barley flakes (BF) with the oleaginous fungus Cunninghamella echinulata (CE) might lead to effective use of these by-products in ruminant nutrition. We examined their effects on rumen fermentation and lipid metabolism.

METHODS AND RESULTS

WB, CM and BF substrates without or with brewer's grains (WBG, CMG, BFG) and enriched with CE were incubated with meadow hay (MH, 500 : 500, w/w) in rumen fluid in vitro for 24 h. The dry matter of the CE-enriched substrates increased (by 2-4%); however, digestibility decreased (P < 0·01). Adverse effects of CE-enriched substrates on the rumen ciliate population were observed. Little effect on the rumen eubacterial population was detected by the 16S-polymerase chain reaction/denaturizing gradient gel electrophoresis method. The increase in γ-linolenic acid output in the MH + BFGCE diet (800 : 200, w/w) was accompanied by an increase in rumen biohydrogenation of polyunsaturated fatty acids.

CONCLUSION

The diet substrates enriched with the fungus CE were less digestible than the untreated cereal substrates; no appreciable positive effect was observed on rumen fermentation patterns or the eubacterial and ciliate populations.

SIGNIFICANCE AND IMPACT OF THE STUDY

The in vitro study showed that adding CE-enriched substrates to ruminant diets is not effective for improving rumen fermentation.

Ruminal bacterial community shifts in grain-, sugar-, and histidine-challenged dairy heifers

Ruminal bacterial community composition (BCC) and its associations with ruminal fermentation measures were studied in dairy heifers challenged with combinations of grain, fructose, and histidine in a partial factorial study. Holstein-Friesian heifers (n=30) were randomly allocated to 5 triticale grain-based treatment groups: (1) control (no grain), (2) grain [fed at a dry matter intake (DMI) of 1.2% of body weight (BW)], (3) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI), (4) grain (1.2% of BW DMI) + histidine (6g/head), and (5) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI) + histidine (6g/head). Ruminal fluid was collected using a stomach tube 5, 115, and 215min after consumption of the rations and bacterial 16S ribosomal DNA sequence data was analyzed to characterize bacteria. Large variation among heifers and distinct BCC were evident in a between-group constrained principal components analysis. Bacterial composition in the fructose-fed heifers was positively related to total lactate and butyrate concentrations. Bacterial composition was positively associated with ruminal ammonia, valerate, and histamine concentrations in the grain-fed heifers. The predominant phyla were the Firmicutes (57.6% of total recovered sequences), Bacteroidetes (32.0%), and candidate phylum TM7 (4.0%). Prevotella was the dominant genus. In general, grain or histidine or their interactions with time had minimal effects on the relative abundance of bacterial phyla and families. Fructose increased and decreased the relative abundance of the Firmicutes and Proteobacteria phyla over time, respectively, and decreased the abundance of the Prevotellaceae family over time. The relative abundance of the Streptococcaceae and Veillonellaceae families was increased in the fructose-fed heifers and these heifers over time. A total of 31 operational taxonomic units differed among treatment groups in the 3.6h sampling period, Streptococcus bovis was observed in fructose fed animals. The TM7 candidate phylum had an increased abundance of sequence reads by over 2.5 fold due to the introduction of histidine into the diet. Rapid changes in BCC can occur in a short period after a single substrate challenge and the nature of these changes may influence ruminal acidosis risk and differ from those in cattle exposed to substrate challenges over a longer time period.

The effect of essential oils of Zataria multiflora and Mentha spicata on the in vitro rumen fermentation, and growth and deaminative activity of amino acid-fermenting bacteria isolated from Mehraban sheep

Gas (CO2 and CH4) and ammonia production in the rumen represent major sources of lost carbon and nitrogen, respectively. The essential oils of some plants have been shown to decrease gas and ammonia production by selectively inhibiting rumen microbes. Particularly, those of Zataria multiflora (ZEO; thymol 21%, carvacrol 32%) and Mentha spicata (SEO; carvone 55%) were evaluated in vitro as ruminant-feed additives. The experiments employed mixed rumen microbes and a hyper-ammonia-producing bacterium (HAP) isolated from the rumen of a Mehraban sheep. Both ZEO and SEO decreased in vitro fibre digestibility and also gas production by mixed rumen microbes that were fermenting a typical growing-lamb diet. ZEO decreased ammonia concentration in mixed culture of rumen microbes, but SEO exerted the opposite effect. A bacterial isolate (MT8) was obtained from the rumen of a Mehraban sheep, and the 16S rRNA gene sequence indicated that it was most closely related to Clostridium bifermentans. Isolate MT8 exhibited rapid ammonia production when peptides were the growth substrate, which indicated that MT8 was a HAP. Both oils inhibited the growth and ammonia production of isolate MT8. However, ZEO decreased ammonia production at lower doses, and to a greater degree, than did SEO. These results indicated that both essential oils could potentially be used to modulate rumen fermentation. The detrimental effects on fibre digestion could be problematic in high-forage diets, and this requires further investigation. Isolate MT8 is the first described HAP from the Mehraban sheep rumen. Results on ammonia production by isolate MT8 and mixed rumen microbes indicate differential mode of action of each oil on this parameter.

Board-invited review: Rumen microbiology: leading the way in microbial ecology

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.

Effects of Dietary Supplementation with Hainanmycin on Protein Degradation and Populations of Ammonia-producing Bacteria In vitro

An in vitro fermentation was conducted to determine the effects of hainanmycin on protein degradation and populations of ammonia-producing bacteria. The substrates (DM basis) for in vitro fermentation consisted of alfalfa hay (31.7%), Chinese wild rye grass hay (28.3%), ground corn grain (24.5%), soybean meal (15.5%) with a forage: concentrate of 60:40. Treatments were the control (no additive) and hainanmycin supplemented at 0.1 (H0.1), 1 (H1), 10 (H10), and 100 mg/kg (H100) of the substrates. After 24 h of fermentation, the highest addition level of hainanmycin decreased total VFA concentration and increased the final pH. The high addition level of hainanmycin (H1, H10, and H100) reduced (p<0.05) branched-chain VFA concentration, the molar proportion of acetate and butyrate, and ratio of acetate to propionate; and increased the molar proportion of propionate, except that for H1 the in molar proportion of acetate and isobutyrate was not changed (p>0.05). After 24 h of fermentation, H10 and H100 increased (p<0.05) concentrations of peptide nitrogen and AA nitrogen and proteinase activity, and decreased (p<0.05) NH₃-N concentration and deaminase activity compared with control. Peptidase activitives were not affected by hainanmycin. Hainanmycin supplementation only inhibited the growth of Butyrivibrio fibrisolvens, which is one of the species of low deaminative activity. Hainanmycin supplementation also decreased (p<0.05) relative population sizes of hyper-ammonia-producing species, except for H0.1 on Clostridium aminophilum. It was concluded that dietary supplementation with hainanmycin could improve ruminal fermentation and modify protein degradation by changing population size of ammonia-producing bacteria in vitro; and the addition level of 10 mg/kg appeared to achieve the best results.

Ammonia production by human faecal bacteria, and the enumeration, isolation and characterization of bacteria capable of growth on peptides and amino acids

Background

The products of protein breakdown in the human colon are considered to be detrimental to gut health. Amino acid catabolism leads to the formation of sulfides, phenolic compounds and amines, which are inflammatory and/or precursors to the formation of carcinogens, including N-nitroso compounds. The aim of this study was to investigate the kinetics of protein breakdown and the bacterial species involved.

Results

Casein, pancreatic casein hydrolysate (mainly short-chain peptides) or amino acids were incubated in vitro with suspensions of faecal bacteria from 3 omnivorous and 3 vegetarian human donors. Results from the two donor groups were similar. Ammonia production was highest from peptides, followed by casein and amino acids, which were similar. The amino acids metabolized most extensively were Asp, Ser, Lys and Glu. Monensin inhibited the rate of ammonia production from amino acids by 60% (P = 0.001), indicating the involvement of Gram-positive bacteria. Enrichment cultures were carried out to investigate if, by analogy with the rumen, there was a significant population of asaccharolytic, obligately amino acid-fermenting bacteria (‘hyper-ammonia-producing’ bacteria; HAP) in the colon. Numbers of bacteria capable of growth on peptides or amino acids alone averaged 3.5% of the total viable count, somewhat higher than the rumen. None of these were HAP, however. The species enriched included Clostridium spp., one of which was C. perfringens, Enterococcus, Shigella and Escherichia coli.

Conclusions

Protein fermentation by human faecal bacteria in the absence of sugars not only leads to the formation of hazardous metabolic products, but also to the possible proliferation of harmful bacteria. The kinetics of protein metabolism were similar to the rumen, but HAP bacteria were not found.

Factors Affecting the Separation and Bioactivity of Red Clover (Trifoliumpratense) Extracts Assayed against Clostridium sticklandii, a Ruminal Hyper Ammonia-producing Bacterium

Red clover ( Trifolium pratense) is rich in phenolic compounds. Both the crude phenolic extract and biochanin A, an isoflavonoid component of the extract, suppress growth of Clostridium sticklandii, a bovine, Gram-positive, ruminal hyper-ammonia producing bacterium (HAB). The purpose of this study was to determine if other components of red clover extract contributed to its anti-HAB activity. Extracts of the Kenland cultivar of red clover, collected 0 h and 24 h after cutting, were separated by normal-phase thin-layer chromatography (TLC) in either ethyl acetate-hexanes (9:1, v/v) or ethyl acetate-methanol (4:1, v/v). Bands on TLC plates were assayed by either overlaying the plates with agar seeded with C. sticklandii, or setting the excised bands face-down onto plates of bacteria-seeded agar. Biochanin A inhibited C. sticklandii growth on TLC plates when as little as 8 nmol was present in the extract. An antimicrobial band, seen in a previous bioassay, was not found, suggesting that this second compound may be more labile than biochanin A.

Effects of hops (Humulus lupulus L.) extract on volatile fatty acid production by rumen bacteria

AIMS

To determine the effects of hops extract on in vitro volatile fatty acid (VFA) production by bovine rumen micro-organisms.

METHODS AND RESULTS

When mixed rumen microbes were suspended in media containing carbohydrates, the initial rates of VFA production were suppressed by β-acid-rich hops extract. The rates of VFA production increased over extended incubations (24 h), and hops extract caused an increase in the propionate to acetate ratio. Hops extract inhibited the growth and metabolism of Streptococcus bovis, but Selenomonas ruminantium and Megasphaera elsdenii were not affected. Likewise, the propionate production of M. elsdenii/S. bovis co-cultures, but not M. elsdenii/S. ruminantium co-cultures, was decreased in the presence of hops extract.

CONCLUSIONS

These results are consistent with the hypothesis that the hops inhibit Gram-positive lactic acid bacteria (S. bovis), and the rumen microbial community requires a period of adaptation before normal VFA production resumes. Selenomonas bovis and S. ruminantium both produce lactate, which is the substrate for propionate production by M. elsdenii. However, S. ruminantium has an outer membrane, while S. bovis does not.

SIGNIFICANCE AND IMPACT OF STUDY

The enhanced production of the gluconeogenesis precursor, propionic acid, provides further evidence that plant secondary metabolites from hops could be used to improve rumen fermentation.

Decreased competiveness of the foodborne pathogen Campylobacter jejuni during Co-culture with the hyper-ammonia producing anaerobe Clostridium aminophilum

Campylobacter spp. are a leading bacterial cause of human foodborne illness. When cocultured in anaerobic Bolton broth with the hyper-ammonia producing bacterium, Clostridium aminophilum, ammonia accumulation was greater and final growth of Campylobacter jejuni was reduced (CFU>or=1.4 log10/mL) compared to that obtained by pure culture controls. Co-culture with the less active ammonia-producing saccharolytic Prevotella albensis had no effect on final C. jejuni concentrations. When co-cultured similarly except with the addition of 10 micromol/L monensin, monensin-susceptible Cl. aminophilum was reduced by 2 to 4 log10 CFU/mL and concentrations of C. jejuni, which is insensitive to monensin, did not differ from its pure culture control. These results suggest that in the absence of added monensin, the hyper ammonia-producing Cl. aminophilum may be able to outcompete asaccharolytic C. jejuni for amino acid substrates and that this competitive ability was eliminated by addition on monensin.