Effects of feed intake on composition of sheep rumen contents and their microbial population size

Cross-reactivity of antibodies to different rumen methanogens demonstrated using immunomagnetic capture technology

Methane is produced in the rumen of ruminant livestock by methanogens, accounting for approximately 14.5% of anthropogenic greenhouse gas emissions in terms of global warming potential. The rumen contains a diversity of methanogens species, and only a few of these have been cultured. Immunomagnetic capture technology (ICT) is a simple and effective method to capture and concentrate target organisms in samples containing complex microflora. We hypothesized that antibody-coated magnetic beads could be used to demonstrate antibody specificity and cross-reactivity to methanogens in rumen samples. Sheep polyclonal antibodies raised against four isolates of rumen dwelling methanogens, Methanobrevibacter ruminantium strain M1, Methanobrevibacter sp. AbM4, Methanobrevibacter sp. D5, and Methanobrevibacter sp. SM9 or an equal mix of all four isolates, were used to coat paramagnetic beads. ICT was used together with flow cytometry and qPCR to optimize key parameters: the ratio of antibody to beads, coupling time between antibody and paramagnetic beads to produce immunomagnetic beads (IMBs), and optimal incubation time for the capture of methanogen cells by IMBs. Under optimized conditions, IMBs bound strongly to their respective isolates and showed a degree of cross-reactivity with isolates of other Methanobrevibacter spp. in buffer and in rumen fluid, and with resident methanogens in rumen content samples. The evidence provided here indicates that this method can be used to study the interaction of antibodies with antigens of rumen methanogens, to understand antigen cross-reactivity and antibody binding efficiency for the evaluation of antigens used for the development of a broad-spectrum anti-methanogen vaccine for the abatement of methane production.

Heat stress impacts the multi-domain ruminal microbiota and some of the functional features independent of its effect on feed intake in lactating dairy cows

Background

Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime).

Results

The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relative abundance of Bacteroidetes (primarily Gram-negative bacteria) while decreasing that of Firmicutes (primarily Gram-positive bacteria) and the Firmicutes-to-Bacteroidetes ratio. Some genera were exclusively found in the heat-stressed cows and thermal control cows. Some co-occurrence and mutual exclusion between some genera were also found exclusively for each thermal condition. Heat stress did not significantly affect the overall functional features predicted using the 16S rRNA gene sequences and ITS1 sequences, but some enzyme-coding genes altered their relative abundance in response to HS.

Conclusions

Overall, HS affected the prokaryotes, fungi, and protozoa of the ruminal microbiota in lactating Holstein cows to a different extent, but the effect on the structure of ruminal microbiota and functional profiles was limited when not confounded by the effect on feed intake. However, some genera and co-occurrence were exclusively found in the rumen of heat-stressed cows. These effects should be attributed to the direct effect of heat stress on the host metabolism, physiology, and behavior. Some of the “heat-stress resistant” microbes may be useful as potential probiotics for cows under heat stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00717-z.

Ruminal use of undegraded-feed soluble protein and accuracy of the estimations of the nutrient content in ruminal bacteria

BACKGROUND

The possible escape from the rumen of undegraded-feed soluble proteins (SP) was investigated using nitrogen-15 (¹⁵ N) infusions (25 mg) in three rumen and duodenum cannulated wethers. Animals were fed three isoproteic diets differing in SP content and including protein concentrates either untreated (control) or treated with solutions of either malic acid (MHT) or orthophosphoric acid (OHT) and heat.

RESULTS

Compared with control, MHT and OHT diets reduced ruminal concentrations of ammonia-nitrogen (NH₃ -N) by 35.9% (P = 0.007), non-ammonia nitrogen (NAN) by 36.8% (P = 0.007), and SP-nitrogen (SP-N) by 45.2% (P = 0.072) over the post-feeding period. Both NAN and SP-N were lower (P ≤ 0.040) for OHT than for MHT diet. The ¹⁵ N enrichment of NAN and SP-N did not vary either among diets or with time, and both values were closely related (R² = 0.965; P < 0.001). Estimations, either using solid-associated bacteria (SAB) or liquid-associated bacteria (LAB) as a reference, indicated that 0.983 and 0.894 of SP-N (values averaged across diets) was of microbial origin, respectively, which would indicate a practically negligible ruminal escape of feed SP-N. Values of ¹⁵ N-enrichment in SAB and LAB fitted well to previously published SAB-LAB relationships, indicating a 22% underevaluation of the N supply from SAB when only LAB is used as a reference.

CONCLUSION

Both the negligible ruminal escape of feed SP and the underevaluation of the bacterial nutrient supply as a consequence of the use of LAB as the only bacterial reference should be considered to improve ruminant protein feeding systems. © 2019 Society of Chemical Industry.

Feed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed Intake

The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Differences in chickens’ feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE). On day 30 posthatch, 28 low-RFI (good FE) and 29 high-RFI (poor FE) chickens across both feeding-level groups (n = 112) were selected. Supervised multigroup data integration and relevance network analyses showed that especially Lactobacillus (negative) in ileal digesta, Turicibacter (positive) in cecal digesta, and Enterobacteriaceae (positive) in both intestinal segments depended on chicken’s feed intake, whereas the level of Anaerotruncus in cecal digesta was most discriminative for high RFI. Moreover, shallower crypts and fewer goblet cells in ceca indicated host-related energy-saving mechanisms with low RFI, whereas greater tissue resistance suggested a stronger jejunal barrier function in low-RFI chickens. Values corresponding to feed intake level × RFI interactions indicated larger pancreas and lower levels of ileal and cecal short-chain fatty acids in restrictively fed high-RFI chickens than in the other 3 groups, suggesting host physiological adaptations to support greater energy and nutrient needs of high-RFI chickens compensating for the restricted feeding.

IMPORTANCE The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Feed Restriction Modulates the Fecal Microbiota Composition, Nutrient Retention, and Feed Efficiency in Chickens Divergent in Residual Feed Intake

There is a great interest to understand the impact of the gut microbiota on host's nutrient use and FE in chicken production. Both chicken's feed intake and gut bacterial microbiota differ between high and low-feed efficient chickens. To evaluate the impact of the feed intake level on the feed efficiency (FE)-associated variation in the chicken intestinal microbiota, differently feed efficient chickens need to eat the same amount of feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29 days posthatch (dph), FE and nutrient retention in chickens of low and high residual feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph. FE was determined for the period between 9 and 30 dph and feces for nutrient retention were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and 14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis dissimilarity matrices showed significant separation between time points, and feeding level groups at 29 dph for the fecal bacterial communities. Relevance networking indicated positive associations between Acinetobacter and feed intake at 16 dph, whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus negatively correlated to chicken's feed intake. Enterobacteriaceae was indicative for low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points. However, restrictive feeding-associated changes in the fecal microbiota were not similar in low and high RFI chickens, which may have been related to the higher nutrient retention and thus lower fecal nutrient availability in restrictively fed high RFI chickens. This may also explain the decreased RFI value in restrictively fed high RFI chickens indicating improved FE, with a stronger effect in females.

Unravelling methanogenesis in ruminants, horses and kangaroos: the links between gut anatomy, microbial biofilms and host immunity

The present essay aims to resolve the question as to why macropod marsupials (e.g. kangaroos and wallabies, hereinafter termed ‘macropods) and horses produce much less methane (CH4) than do ruminants when digesting the same feed. In herbivores, gases produced during fermentation of fibrous feeds do not pose a major problem in regions of the gut that have mechanisms to eliminate them (e.g. eructation in the rumen and flatus in the lower bowel). In contrast, gas pressure build-up in the tubiform forestomach of macropods or in the enlarged tubiform caecum of equids would be potentially damaging. It is hypothesised that, to prevent this problem, evolution has favoured development of controls over gut microbiota that enable enteric gas production (H2 and CH4) to be differently regulated in the forestomach of macropods and the caecum of all three species, from the forestomach of ruminants. The hypothesised regulation depends on interactions between their gut anatomy and host-tissue immune responses that have evolved to modify the species composition of their gut microbiota which, importantly, are mainly in biofilms. Obligatory H2 production during forage fermentation is, thus, captured in CH4 in the ruminant where ruminal gases are readily released by eructation, or in acetate in the macropod forestomach and equid caecum–colon where a build-up in gas pressure could potentially damage these organs. So as to maintain appropriate gut microbiota in different species, it is hypothesised that blind sacs at the cranial end of the haustral anatomy of the macropod forestomach and the equid caecum are sites of release of protobiofilm particles that develop in close association with the mucosal lymphoid tissues. These tissues release immune secretions such as antimicrobial peptides, immunoglobulins, innate lymphoid cells and mucin that eliminate or suppress methanogenic Archaea and support the growth of acetogenic microbiota. The present review draws on microbiological studies of the mammalian gut as well as other microbial environments. Hypotheses are advanced to account for published findings relating to the gut anatomy of herbivores and humans, the kinetics of digesta in ruminants, macropods and equids, and also the composition of biofilm microbiota in the human gut as well as aquatic and other environments where the microbiota exist in biofilms.

Interactions between microbial consortia in biofilms: a paradigm shift in rumen microbial ecology and enteric methane mitigation

Minimising enteric CH4 emissions from ruminants is a current research priority because CH4 contributes to global warming. The most effective mitigation strategy is to adjust the animal’s diet to complement locally available feed resources so that optimal production is gained from a minimum of animals. This essay concentrates on a second strategy – the use of feed additives that are toxic to methanogens or that redirect H2 (and electrons) to inhibit enteric CH4 emissions from individual animals. Much of the published research in this area is contradictory and may be explained when the microbial ecology of the rumen is considered. Rumen microbes mostly exist in organised consortia within biofilms composed of self-secreted extracellular polymeric substances attached to or within feed particles. In these biofilms, individual colonies are positioned to optimise their use of preferred intermediates from an overall process of organic matter fermentation that generates end-products the animal can utilise. Synthesis of CH4 within biofilms prevents a rise in the partial pressure of H2 (pH2) to levels that inhibit bacterial dehydrogenases, and so reduce fermentation rate, feed intake and digestibility. In this context, hypotheses are advanced to explain changes in hydrogen disposal from the biofilms in the rumen resulting from use of anti-methanogenic feed additives as follows. Nitrate acts as an alternative electron sink when it is reduced via NO2– to NH3 and CH4 synthesis is reduced. However, efficiency of CH4 mitigation is always lower than that predicted and decreases as NO3– ingestion increases. Suggested reasons include (1) variable levels of absorption of NO3–or NO2– from the rumen and (2) increases in H2 production. One suggestion is that NO3– reduction may lower pH2 at the surface of biofilms, thereby creating an ecological niche for growth of syntrophic bacteria that oxidise propionate and/or butyrate to acetate with release of H2. Chlorinated hydrocarbons also inhibit CH4 synthesis and increase H2 and formate production by some rumen methanogens. Formate diffuses from the biofilm and is converted to HCO3– and H2 in rumen fluid and is then excreted via the breath. Short-chain nitro-compounds inhibit both CH4 and formate synthesis when added to ruminal fluid but have little or no effect in redirecting H2 to other sinks, so the pH2 within biofilms may increase to levels that support reductive acetogenesis. Biochar or activated charcoal may also alter biofilm activity and reduce net CH4 synthesis; direct electron transfer between microbes within biofilms may also be involved. A final suggestion is that, during their sessile life stage, protozoa interact with biofilm communities and help maintain pH2 in the biofilm, supporting methanogenesis.

Effect of feeding level on the composition of the intestinal microbiota in weaned piglets

In piglets, the development and composition of intestinal microbiota is influenced by dietary factors. A considerable reduction in feed intake during the transition from liquid to solid feed is often accompanied by postweaning diarrhea. Therefore, it is hypothesized that variations in feeding level during weaning may affect intestinal microbial composition. Forty-eight piglets fitted with simple ileal T-cannulas were used to examine the effects of a high (60 g/kg BW) and a low (30 g/kg BW) feeding level on the composition of the ileal and fecal microbiota. The assay diets contained graded inclusion levels of soybean (Glycine max) meal or casein. Bacterial cell numbers of total eubacteria, Lactobacillus spp., and the mainly proteolytic Clostridium leptum, Clostridium coccoides, Enterobacteriaceae, and Bacteroides-Prevotella-Porphyromonas group (Bacteroides group) of feces and ileal digesta were determined by use of real-time PCR. There were no interactions between feeding level and protein source except for the Bacteroides group in ileal digesta. Ileal cell numbers of lactobacilli were increased (P < 0.001) at the higher feeding level. In contrast, ileal cell numbers of Clostridium coccoides were lower (P < 0.001) at the higher feeding level. There were no differences of bacterial cell numbers in feces. Results indicate that feeding level affects microbial composition in the small intestine. Also, sufficient feed intake during weaning encourages proliferation of beneficial bacteria, thereby contributing to improved gut health.

The effect of medicated diets and level of feeding on caecal microbiota of lactating rabbit does

AIMS

To study the effect of the type of antibiotic used in medicated diets against pathogens and the feeding level on the microbial biodiversity in the rabbit caecum.

METHODS AND RESULTS

Three groups of eight does were given a diet unsupplemented (NAB) or with 100 ppm of bacitracin (BAC) or tiamulin (TIA). Litter sizes of four does in each group were adjusted to five (LS5) or to nine (LS9), to manipulate their levels of feed intake. The feeding level strongly affected caecal microbiota in does fed on NAB and BAC diet, whereas the effect of the antibiotic was higher in TIA-supplemented animals, even prevailing over the effect of feeding level. Daily food intake and milk yield (P<0.05) and caecum weight (P<0.10) were higher in feeding of LS9 does. The total volatile fatty acid concentration was lower with BAC (P<0.05).

CONCLUSIONS

The feeding level strongly affects caecal biodiversity in lactating does. The extent of the antibiotic effect depends on its nature, being significant with TIA but not with BAC.

SIGNIFICANCE AND IMPACT OF THE STUDY

Changes in the feeding level promote different profiles of caecal microbiota. Therapeutic doses of TIA may affect caecal microbiota, whereas BAC would not reduce diversity.

Validation of use of purine bases as a microbial marker by15N labelling in growing lambs given high-concentrate diets: effects of grain processing, animal age and digesta sampling site

The origin of post-ruminal purine bases (PB) was studied in 24 growing lambs that were given a pelleted concentrate plus barley straw (C) or whole barley grain plus protein supplement (WB). Six lambs from each treatment were slaughtered at 10 and 30 days post weaning after15N labelling of microbial nitrogen (N) and PB. Microbial contribution to digesta non-ammonia N (NAN) and PB was lower (P< 0·01) when estimated from duodenal rather than abomasal samples (0·36 v. 0·52 (s.e.d. 0·021) for NAN and 0·47 v. 0·77 (s.e.d. 0·029) for PB) as a result of endogenous contamination. In comparison with15N, total PB/N led to higher estimates (P< 0·01) of microbial contribution to abomasal NAN in WB treatment (0·62 v. 0·46 s.e.d. 0·049). The difference was removed after correcting for microbial PB, while this effect was not observed with < the C diet, resulting in a marker by diet interaction (P< 0·05). Abomasal PB flow increased (P< 0·1) from 10 to 30 days after weaning mainly due to the higher proportion of microbial PB (0·70 v. 0·81 (s.e.d. 0·047)). Rumen apparent PB degradation did not differ between diets in older lambs, but it was proportionally 0·39 lower for WB treatment (P< 0·05) in younger lambs. When the microbial PB flow was estimated indirectly from labelled microbial N and the PB/N ratio of bacterial extracts the estimates were in agreement with those derived from PB-15N in the WB treatment but resulted in unrealistic values in lambs on diet C. Results suggest that significant proportions of dietary PB can escape rumen degradation which may lead to overestimation of microbial contribution to abomasal NAN when the PB/N ratio is used as marker. The extent of the overestimation is affected by the lamb age and grain processing.

In situ study of the relevance of bacterial adherence to feed particles for the contamination and accuracy of rumen degradability estimates for feeds of vegetable origin

An in situ study was conducted on four rumen-cannulated wethers to determine (using (15)N infusion techniques) the microbial contamination (mg bacterial DM or crude protein (CP)/100 mg DM or CP) and the associated error on the effective degradability of fourteen feeds: barley and maize grains, soyabean and sunflower meals, full-fat soyabean, maize gluten feed, soyabean hulls, brewers dried grains, sugarbeet pulp, wheat bran, lucerne and vetch-oat hays, and barley and lentil straws. The DM or CP contamination in residues (M) fitted to single exponential or sigmoid curves. A general model (M=m (1-e(-ft) ) (j)) was proposed to match this fit. Asymptotic values (m) varied from 2.84% to 13.3% and from 2.85% to 80.9% for DM and CP, respectively. Uncorrected results underestimated the effective degradability of both DM (P<0.05) and CP (P<0.01). For CP, this underestimation varied from 0.59 % to 13.1%, with a higher but unascertainable error for barley straw. Excluding maize grain, the microbial contamination of both DM and CP, and the associated underestimation of the effective degradability of CP, were positively related to the cellulose content of the feed. The error in the effective degradability of CP was also negatively related to the CP content and its apparent effective degradability (R(2) 0.867). This equation allows easier and more accurate estimates of effective degradability, needed to improve protein-rationing systems.

Ruminal fermentation and fill change with season in an arctic grazer: responses to hyperphagia and hypophagia in muskoxen (Ovibos moschatus)

We studied castrated adult muskoxen fed a standard diet of grass hay and supplement throughout the year to determine seasonal changes in digesta passage, fill, and fermentation without the confounding effects of reproductive demands or changes in food quality. Although food intake increased by 74% between spring and autumn, mean retention times of fluid and particulate digesta markers were maintained between seasons in both the rumen (9-13 h) and the intestines (27-37 h). The rumen contained 84.5% of digesta and accounted for 79% of dry matter digestion in the whole digestive tract. Ruminal fluid space and whole-gut digesta fill increased by 31%-34%, while ruminal rates of in situ degradation increased by more than 100% between spring and autumn for cellulose and hemicellulose. Hyperphagia in autumn was accompanied by increased bacterial counts in ruminal fluid (30%), declines in ruminal pH, and increases in the concentration of fermentation acids (16%) when compared with spring hypophagia. Consumption of fresh hay and supplement increased the concentrations of acids most markedly during winter and spring when bacterial counts were low. Low food intakes in winter and spring may limit the microbial population, whereas hyperphagia in autumn may foster a much more active microflora that requires consistent supplies of substrate. Plasticity of fill and fermentation in muskoxen minimizes winter costs and maximizes nutrients and energy gained from coarse forages in small home ranges throughout the year.

Integration of Ruminal Metabolism in Dairy Cattle

An important objective is to identify nutrients or dietary factors that are most critical for advancing our knowledge of, and improving our ability to predict, milk protein production. The Dairy NRC (2001) model is sensitive to prediction of microbial protein synthesis, which is among the most important component of models integrating requirement and corresponding supply of metabolizable protein or amino acids. There are a variety of important considerations when assessing appropriate use of microbial marker methodology. Statistical formulas and examples are included to document and explain limitations in using a calibration equation from a source publication to predict duodenal flow of purine bases from measured urinary purine derivatives in a future study, and an improved approach was derived. Sources of specific carbohydrate rumen-degraded protein components probably explain microbial interactions and differences among studies. Changes in microbial populations might explain the variation in ruminal outflow of biohydrogenation intermediates that modify milk fat secretion. Finally, microbial protein synthesis can be better integrated with the production of volatile fatty acids, which do not necessarily reflect volatile fatty acid molar proportions in the rumen. The gut and splanchnic tissues metabolize varying amounts of volatile fatty acids, and propionate has important hormonal responses influencing milk protein percentage. Integration of ruminal metabolism with that in the mammary and peripheral tissues can be improved to increase the efficiency of conversion of dietary nutrients into milk components for more efficient milk production with decreased environmental impact.