Roles of structural and non-structural carbohydrates and proteins in the reticulo-rumen

It is well recognised that the reticulo-rumen needs to be buffered to prevent undesirable increases in its acidity due to the production of organic acids during fermentation (Van Soest, Reference Van Soest1994; Mertens, Reference Mertens1997; Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008). It is also well established that the dietary physically effective NDF (peNDF), that is, a fibre that stimulates chewing, saliva production and rumen buffering, is required for this (Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008; Zebeli et al., Reference Zebeli, Aschenbach, Tafaj, Boguhn, Ametaj and Drochner2012a; Lean et al., Reference Lean, Golder and Hall2014). The relationship between peNDF and rumen buffering is not yet well understood and defined, and not linear (Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008; Zebeli et al., Reference Zebeli, Aschenbach, Tafaj, Boguhn, Ametaj and Drochner2012a; Lean et al., Reference Lean, Golder and Hall2014). In addition, peNDF is required for the maintenance of the fibre mat in the reticulo-rumen (Zebeli et al., Reference Zebeli, Aschenbach, Tafaj, Boguhn, Ametaj and Drochner2012a). This mat serves to retain small feed particles, that may otherwise escape the reticulo-rumen undegraded (Bhatti and Firkins, Reference Bhatti and Firkins1995; Tafaj et al., Reference Tafaj, Junck, Maulbetsch, Steingass, Piepho and Drochner2004). Increasing this escape alters the site and extent of degradation of nutrient in the digestive tract, and can have implications for the nutrient utilisation and health of the cow, such as hind gut acidosis (see the ‘Hindgut fermentation’ section). This shows that dairy cows diets need to contain sufficient peNDF. Zebeli et al. (Reference Zebeli, Aschenbach, Tafaj, Boguhn, Ametaj and Drochner2012a) concluded that the proportion of feed particles longer than 8 mm needed to be >18.5% to prevent a rumen pH depression below 5.8 for more than 6 h/day.

Tafaj et al. (Reference Tafaj, Junck, Maulbetsch, Steingass, Piepho and Drochner2004) investigated the composition and metabolism of different fractions of digesta in the reticulo-rumen of dairy cows and coined the term ‘particle-associated rumen liquid’ (PARL) for the proportion of rumen fluid attached to digesta particles found in the dorsal sac of the rumen. In contrast, the contents of the ventral sac were shown to mainly consist of extensively digested, small-sized, potentially escapable particles, suspended in the free rumen liquid (FRL; Tafaj et al., Reference Tafaj, Junck, Maulbetsch, Steingass, Piepho and Drochner2004). Numerous studies (Tafaj et al., Reference Tafaj, Junck, Maulbetsch, Steingass, Piepho and Drochner2004; Li et al., Reference Li, Penner, Hernandez-Sanabria, Oba and Guan2009) reported differences in the concentrations and metabolisms of microorganism between PARL and FRL in the ventral rumen sac. The FRL had a different microbial composition, as well as lower concentrations of volatile fatty acids (VFA) and a higher pH than PARL. Despite this, the FRL is the most investigated phase of the reticulo-rumen, and the effects of high-grain diets on the characteristics of PARL are not yet well understood.

Next, to the dietary contents of non-fibre carbohydrates (NFC) and starch, the dietary contents of non-starch NFC also affect gastrointestinal health and nutrient utilisation. Hall and Weimer (Reference Hall and Weimer2016) observed that the in vitro utilisation was highest for glucose, followed by fructans and inulin and that the microbial protein yield was 20% greater for fructans and inulin compared with glucose. Mojtahedi and Danesh Mesgaran (Reference Mojtahedi and Danesh Mesgaran2011) partially substituted dietary starch with pectin by replacing barley grain with sugar beet pulp and concluded that this increased chewing, rumen pH and nutrient digestibility. Another mechanism through which replacing starch with sugars may enhance rumen health and nutrient utilisation, is that this stimulates butyrate production, and, thereby, the energy supply to and functionality of the rumen epithelium (Dionissopoulos et al., Reference Dionissopoulos, Laarman, AlZahal, Greenwood, Steele, Plaizier, Matthews and McBride2013; Malhi et al., Reference Malhi, Gui, Yao, Aschenbach, Gabel and Shen2013). Golder et al. (Reference Golder, Celi, Rabiee and Lean2014b and Reference Golder, Denman, McSweeney, Wales, Auldist, Wright, Marett, Greenwood, Hannah, Celi, Bramley and Lean2014c) also observed that sugars differ in their effect on reticulo-rumen function, including the production of lactic acid.

Most experimental inductions of SARA used a combination of feed restriction, increased grain feeding and reduced feeding of peNDF (Supplementary Material S2, Kleen et al., Reference Kleen, Hooijer, Rehage and Noordhuizen2003; Krause and Oetzel, Reference Krause and Oetzel2005; Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008). The amount and rumen degradability of the grain, the abruptness and duration of the increased grain feeding, and the reduction of the dietary peNDF varied greatly among studies, which challenges comparisons among these studies. The starch content of the SARA-inducing diets were around the top end of what has been observed on commercial dairy farms with high yielding cows (Plaizier et al., Reference Plaizier, Garner, Droppo and Whiting2004; Dann, Reference Dann2010; Senaratne et al., Reference Senaratne, McGeough, Ominski and Plaizier2016). As on farms, SARA is likely caused by a combination of high grain and low peNDF feeding (Kleen et al., Reference Kleen, Hooijer, Rehage and Noordhuizen2003 and Reference Kleen, Upgang and Rehage2013). The effects of inducing SARA by high grain feeding are more severe than that induced by a low peNDF feeding (see ‘Diagnosis and prevalence of poor gastrointestinal health on dairy farms’ section, Khafipour et al., Reference Khafipour, Krause and Plaizier2009a and Reference Khafipour, Krause and Plaizier2009b; Kleen et al, Reference Kleen, Upgang and Rehage2013). Hence, the effects of most experimentally-induced SARA may be more severe than those of on-farm SARA. Thus, experimental methods that more closely represent SARA on dairy farms are needed. These methods will need to adopt a combination of feed restriction, and low, respectively, high, dietary contents of coarse fibre and starch.

Differences in ruminal responses to different grain species and cultivars, as well as to different processing techniques are evident (Lean et al., Reference Lean, Golder, Black, King and Rabiee2013). This includes differences among grains in rumen pH response over time, in propionate, valerate and ammonia concentrations in the rumen and differs in acidosis risk. Sensible approaches to controlling the risk include testing for quality, rumen degradability and/or risk of acidosis (a near IR reflectance test has been developed for this purpose); establishing a regular supply from a consistent source; and careful and consistent processing of grain. Use of by-products of human food production including flour and maize manufacturing processes and distilling wastes and fats to maintain the energy density of the diet and to control starch and sugar intakes are strategies employed to reduce the risk of acidosis and potentially increase the profitability of production (Lean et al., Reference Lean, Golder, Black, King and Rabiee2013; Golder et al., Reference Golder, Celi, Rabiee and Lean2014b and Reference Golder, Denman, McSweeney, Wales, Auldist, Wright, Marett, Greenwood, Hannah, Celi, Bramley and Lean2014c).

Guidelines for the dietary structural and non-structural carbohydrates contents that optimise productivity and animal well-being while reducing the risk of rumen acidosis are provided in the Supplementary Material S3. Of these, the guidelines for dietary starch and peNDF are considered the most critical, but they are not generally agreed upon, likely to general and in need of urgent updating. Also, other techniques for the measurement of peNDF are needed, as factors other than feed particle size, including the fragility of feed particles, also affect the ability of a feed to stimulate chewing and rumen buffering (Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008; Zebeli et al., Reference Zebeli, Aschenbach, Tafaj, Boguhn, Ametaj and Drochner2012a).

Rumen metabolomic alterations and implications for cattle health

Metabolomics technology has become an important part of livestock science to better understand health and disease (Goldansaz et al., Reference Goldansaz, Guo, Sajed, Steele, Plastow and Wishart2017). Compared with classical one-metabolite one-biochemical reaction studies, high-throughput metabolomic technologies provide broader information of metabolic pathways in (microbial) cells, allowing the establishment of metabolic patterns in a complex system, such as the gastrointestinal ecosystem. Ametaj et al. (Reference Ametaj, Zebeli, Saleem, Psychogios, Lewis, Dunn, Xia and Wishart2010) and Saleem et al. (Reference Saleem, Ametaj, Bouatra, Mandal, Zebeli, Dunn and Wishart2012) performed comprehensive studies characterising the bovine ruminal fluid metabolome combining several technologies, such as ¹Proton nuclear magnetic resonance (1H-NMR), Gas chromatography–mass spectrometry, direct flow injection-mass spectrometry, inductively coupled plasma mass spectrometry, with computer-aided literature mining. These studies quantified a large spectrum of metabolites in the bovine ruminal fluid. In addition, they reported potentially toxic biomarkers in the rumen fluid of dairy cows that experienced SARA after being fed barley grain-rich diets. Feeding such diets is, therefore, accompanied with the release of various metabolic compounds, including methylated amines as well as bacterial cell wall components, such as endotoxins, that may be toxic to the host, and may have implications on the overall health of dairy cows. More specifically, these data indicated that cows fed 45% barley grain (60% concentrate in dry matter) had higher concentrations of methylamine, endotoxin, ethanol, xanthine, N-nitrosodimethylamine, 3-phenylpropionate in their rumen fluid. A similar conclusion was reported in a recent study with dairy cows (Zhang et al., Reference Zhang, Zhu, Jiang and Mao2017).

There are indications that the toxins associated with high grain diets, including endotoxins, secondary metabolites and microbial-associated molecular patterns, can interact with the epithelia and translocate into systemic and lymphatic circulation (Aschenbach et al., Reference Aschenbach, Seidler, Ahrens, Schrodl, Buchholz, Garz, Kruger and Gabel2003; Khafipour et al., Reference Khafipour, Krause and Plaizier2009a). In the Ussing chamber system, Emmanuel et al. (Reference Emmanuel, Madsen, Churchill, Dunn and Ametaj2007) demonstrated that endotoxins translocate across the rumen wall at a greater rate than across the colon wall. Alternately, it was observed that at acidic pH values on the mucosal side increased the permeability of ³H-mannitol more than fivefold to sixfold through colon and rumen tissues, respectively (Emmanuel et al., Reference Emmanuel, Madsen, Churchill, Dunn and Ametaj2007). Research by Aschenbach et al. (Reference Aschenbach, Oswald and Gabel2000) demonstrated that the permeability of rumen epithelia to histamine, another polyamine linked to high grain feeding and bovine laminitis (Nocek, Reference Nocek1997), increased when pH declined. Thus, SARA conditions can lead not only to the generation of multiple toxic compounds in the rumen but also predisposes translocation of these compounds across the gastrointestinal tract epithelia (see the ‘The role of the rumen and hindgut epithelia in gastrointestinal health’ section).

Hindgut fermentation

Hindgut fermentation has been associated with high intake of starches and other fermentable substrates that are not fully digested in the upper gastrointestinal tract (Gressley et al., Reference Gressley, Hall and Armentano2011). Feeding of large amounts of grain, and conditions when the rumen mat does not function properly, such as during SARA conditions, inevitably lead to larger amounts of fermentable substrates that by-pass rumen fermentation. Cattle have limited amylolytic activity in the small intestine (Matthé et al., Reference Matthé, Lebzien, Hric, Flachowsky and Sommer2001), and incompletely degraded substrates, most importantly starches, are fermented in the hindgut, increasing the risk of hindgut acidosis. Emerging evidence suggests that hindgut diseases may afflict the health status of cattle the same way as rumen diseases (Gressley et al., Reference Gressley, Hall and Armentano2011; Steele et al., Reference Steele, Penner, Chaucheyras-Durand and Guan2016).

The mechanisms of pH regulation in the hindgut are unexplored. The ability of the hindgut to self-regulate pH is limited, mainly due to a lack of salivary buffering and the protozoa (Gressley et al., Reference Gressley, Hall and Armentano2011). However, similar to the reticulo-rumen, an anion exchange (AE) resulting in the release of bicarbonate exists. In the reticulo-rumen, protozoa modulate bacterial metabolism and are able to remove starch from the milieu and, therefore, stabilise the pH. Hence, the absence of protozoa in the hindgut increases the percentage of the total available substrate for bacterial fermentation, and, potentially, the variation in pH (Van Soest, Reference Van Soest1994). Comparisons of the nutrient absorption pathways of the reticulo-rumen and the hindgut have also shown that, while there are functional similarities in metabolic signatures, the complements of host genes which are involved are not highly similar (Metzler-Zebeli et al., Reference Metzler-Zebeli, Schmitz-Esser, Klevenhusen, Podstatzky-Lichtenstein, Wagner and Zebeli2013). Also, the values of pH viewed as thresholds of SARA in the rumen (pH at 5.6 in Gozho et al., Reference Gozho, Krause and Plaizier2007; or 5.8 in Zebeli et al., Reference Zebeli, Dijkstra, Tafaj, Steingass, Ametaj and Drochner2008) are much lower than those of acidosis in the hindgut (typically at a range of 6.0 to 6.6; Metzler-Zebeli et al., Reference Metzler-Zebeli, Schmitz-Esser, Klevenhusen, Podstatzky-Lichtenstein, Wagner and Zebeli2013), indicating different mechanisms and development bases of ruminal acidosis compared hindgut acidosis.

The intestinal mucosa is comprised a monolayer rather than of a stratified epithelium, as in the rumen. The simpler histological structure makes the hindgut epithelium more susceptible to the acidic damage, barrier damage and translocations of toxins than the rumen (Li et al., Reference Li, Khafipour, Krause, Kroeker, Rodriguez-Lecompte, Gozho and Plaizier2012a; Tao et al., Reference Tao, Duanmu, Dong, Ni, Chen, Shen and Zhao2014). However, this susceptibility may be attenuated by the mucous secretion that protects the epithelia that exists in the large intestine, but not in the reticulo-rumen (Van Soest, Reference Van Soest1994). Nevertheless, Emmanuel et al. (Reference Emmanuel, Madsen, Churchill, Dunn and Ametaj2007) reported a higher translocation of endotoxin across colon epithelia compared with rumen epithelia. The concentration of endotoxin in the large intestine can exceed values recorded from the same subjects in the reticulo-rumen (Li et al., Reference Li, Khafipour, Krause, Kroeker, Rodriguez-Lecompte, Gozho and Plaizier2012; Metzler-Zebeli et al., Reference Metzler-Zebeli, Schmitz-Esser, Klevenhusen, Podstatzky-Lichtenstein, Wagner and Zebeli2013). Thus, microbial dysbiosis and epithelial damage in the hindgut can lead to systemic translocation of bacteria and toxins resulting in similar symptoms than SARA (Plaizier et al., Reference Plaizier, Krause, Gozho and McBride2008; Plaizier et al., Reference Plaizier, Khafipour, Li, Gozho and Krause2012b; Zebeli and Metzler-Zebeli, 2012). Hence, several symptoms that are attributed to adverse conditions in the rumen may be the result of adverse conditions in the hindgut.

Despite the importance of the hindgut in nutrition and health of cattle, the effects of diet composition on hindgut fermentation have been largely overlooked. Also, comparatively little is known about the mucosal adaptation of the hindgut in cattle in response to an energy-enhanced nutritional plane. This lack of knowledge hampers the development of efficient and sustainable strategies to modulate metabolism and health of the hindgut, which are needed to improve overall health and productivity of cattle. The difficulty of obtaining samples from the hindgut and the lack of models to simulate hindgut fermentation are also reasons why only limited research has been conducted in the hindgut, especially regarding influences of nutrition on the epithelial function and host–microbiota interaction. By understanding the underlying mechanisms of pH regulation, cellular communication and hindgut microbiome and host interaction in the hindgut, it will be possible to understand and better manage complex digestive diseases in cattle.

Overview and biotic perturbants of gut microbiota

Ruminants, including cattle, rely on symbiotic microbial communities within the digestive tract for the utilisations of their dietary nutrients (Flint and Bayer, Reference Flint and Bayer2008). These symbionts are comprised of anaerobic fungi, archaea, bacteria and viruses. The stability of the reticulo-rumen and hindgut ecosystems rely on the ecological properties of its resident microbiota (Khafipour et al., Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016). Both reticulo-rumen and hindgut harbour an immense species- and strain-level diversity with overlapping metabolic capabilities (Khafipour et al., Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016; Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). However, the number of substrate degradation points that are essential to fundamental reticulo-rumen fermentation processes are modest, resulting in the presence of between tens and hundreds of bacterial species with the potential enzymatic activity required for each degradation point (Weimer, Reference Weimer2015). Hence, despite of high inter-animal differences in the composition of rumen microbiota, the presence of a ‘core microbiome’ ensures that the reticulo-rumen ecosystem is functionally redundant and capable to carryout main metabolic activities that are essential for the survival of the ruminant host (Khafipour et al., Reference Khafipour, Li, Plaizier and Krause2009c; Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). Another important characteristic of the reticulo-rumen and hindgut ecosystems is the resilience of its microbial symbionts against perturbations by biotic (e.g. exogenous microbes) and abiotic (e.g. changes in the nutrient profile, pH) stresses. From an ecological perspective, resilience is the amount of stress or perturbation that a system can tolerate before it changes from one stable equilibrium state to another (Folke et al., Reference Folke, Carpenter, Walker, Scheffer, Elmqvist, Gunderson and Holling2004). Overall, the reticulo-rumen and hindgut microbiomes, owing to their complex composition and functional redundancy, are robust against these perturbations (Weimer, Reference Weimer2015). However, the type of microbial response depends on the intensity and nature of the perturbants (Golder et al., Reference Golder, Celi, Rabiee and Lean2014b and Reference Golder, Denman, McSweeney, Wales, Auldist, Wright, Marett, Greenwood, Hannah, Celi, Bramley and Lean2014c; Khafipour et al., Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016).

Changes in diet composition and exposure to exogenous (allochthonous) microbes originating from the diet and environment are important factors that can expose the reticulo-rumen and hindgut microbiota to perturbations (Khafipour et al., Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016). The ability of exogenous microbes to integrate into and colonise the reticulo-rumen niche is limited by competing resident (autochthonous) members that are adapted to the environment of the rumen (Weimer, Reference Weimer2015). Food-born microbes may integrate into the gastrointestinal microbiomes and constitute a ‘transient microbiome’ that has the ability to affect the functionality of the microbial community (Derrien and van Hylckama Vlieg, Reference Derrien and van Hylckama Vlieg2015). These changes are usually temporary. However, the presence of open niches where an exogenous strain is capable to metabolise biomolecules that are non-degradable by, or even toxic to, other reticulo-rumen microbes can be an exception to this, and result in the successful integration and establishment of this strain in the reticulo-rumen ecosystem (Weimer, Reference Weimer2015).

Effects of high-grain feeding on gut microbiota

Apart from biotic perturbants, abiotic stresses, including those induced by high-grain feeding, have the ability to temporarily or permanently change the composition and functionality of reticulo-rumen and hindgut microbiota (Khafipour et al., Reference Khafipour, Li, Plaizier and Krause2009c; Derakhshani et al., Reference Derakhshani, De Buck, Mortier, Barkema, Krause and Khafipour2016; Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). Abrupt changes in the nutrient, and especially the carbohydrate, composition of the diet can rapidly affect the reticulo-rumen microbiota. This, in turn, may alter biochemical parameters of the reticulo-rumen and hindgut ecosystems (Fernando et al., Reference Fernando, Purvis, Najar, Sukharnikov, Krehbiel and Nagaraja2010; Li et al., Reference Li, Khafipour, Krause, Kroeker, Rodriguez-Lecompte, Gozho and Plaizier2012; Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). Studies have shown that excessive grain feeding and the resulting ruminal acidosis reduce the richness, evenness and diversity of microbiota, and the abundances of many beneficial microbial taxa in the reticulo-rumen (Khafipour et al., Reference Khafipour, Li, Plaizier and Krause2009c and Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016; Mao et al., Reference Mao, Zhang, Wang and Zhu2013) and in the hindgut (Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). Members of gut microbiota differ in their functionality and ability to utilise different groups of substrates (Henderson et al., Reference Henderson, Cox, Ganesh, Jonker, Young and Janssen2015). Hence, a higher richness and diversity of these microbiota enable a more efficient use of nutrient resources, and enhance their stability, and are, therefore, most often beneficial (Russell and Rychlik, Reference Russell and Rychlik2001; Ley et al., Reference Ley, Turnbaugh, Klein and Gordon2006). Thus, the reductions in richness and diversity of gastrointestinal microbiota that occur during high-grain feeding and SARA suggest that these microbiotas are transformed into less functional and desirable state (Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). There may, however, be exceptions to this as functionality is shared by a variety of microbial taxa (Russell and Rychlik, Reference Russell and Rychlik2001; Weimer, Reference Weimer2015)., Hence, these changes do not have to be reflective of changes in the functionality of these microbiota. (The compositions of microbiota vary within the reticulo-rumen. In the lumen of a healthy reticulo-rumen, bacteria belonging to the Firmicutes and Bacteroidetes phyla dominate. Particle-associated microbes, such as Ruminococcus spp. and Fibrobacter succinogenes, play a central role in biofilm formation and sequential breakdown of cellulosic biomass, especially in the fibre mat (Leng, Reference Leng2014). The microbiome of the liquid fraction is dominated by amylolytic and proteolytic bacteria of the Bacteroidetes phylum, including Prevotella spp. (McCann et al., Reference McCann, Wickersham and Loor2014). The rumen tissue-associated/epimural microbiota, similar to the mucosa-associated microbiota in other compartments of the gastrointestinal tract, contain a high proportion of bacteria belonging to Proteobacteria (Derakhshani et al., Reference Derakhshani, De Buck, Mortier, Barkema, Krause and Khafipour2016). This may be due to the presence of aerotolerant bacterial lineages among the members of this phyla that play a role in reducing the oxygen that diffuses from the blood to the epithelium, and, thereby, maintain the anaerobic ecosystem of the reticulo-rumen (Albenberg et al., Reference Albenberg, Esipova, Judge, Bittinger, Chen, Laughlin, Grunberg, Baldassano, Lewis and Li2014).

High grain feeding and a resulting grain-induced SARA decrease the relative abundance of Bacteroidetes and increase that of Firmicutes in the luminal content of the reticulo-rumen, resulting in a dysbiotic community and a potential loss of community function (Khafipour et al., Reference Khafipour, Li, Plaizier and Krause2009c; Mao et al., Reference Mao, Zhang, Wang and Zhu2013; Petri et al., Reference Petri, Schwaiger, Penner, Beauchemin, Forster, McKinnon and McAllister2013). White et al. (Reference White, Lamed, Bayer and Flint2014) concluded that Firmicutes differ from Bacteroidetes in how they degrade plant biomass in the reticulo-rumen. Firmicutes degrade cell surfaces, whereas the degradation by Bacteroidetes is mainly periplasmic and intracellular. El Kaoutari et al. (Reference El Kaoutari, Armougom, Gordon, Raoult and Henrissat2013) reported that, on average, Firmicutes encode fewer glycan-cleaving enzymes than Bacteroidetes, and that, therefore, Bacteroidetes have higher efficiency in the degradability of fibre than Firmicutes. This implies that an increase in the Firmicutes to Bacteroidetes ratio in the luminal content resulting from high-grain feeding is undesirable.

High grain feeding and grain-induced SARA also affect the abundances of many members of the microbial community in the lumen content of the reticulo-rumen at the lower taxonomical levels. These effects include increasing the relative abundances of amylolytic and lactic acid utilising species, and reducing the relative abundances of fibrolytic species, with the magnitudes of these effects varying among studies and among cows within experiments (Khafipour et al., Reference Khafipour, Krause and Plaizier2009b; Petri et al., Reference Petri, Schwaiger, Penner, Beauchemin, Forster, McKinnon and McAllister2013; Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). These variations are, in part, due to host–microbiota coevolution throughout the course of life that results in co-differentiation or co-diversification of host–microbiota in an individualised manner (Zaneveld et al., Reference Zaneveld, Turnbaugh, Lozupone, Ley, Hamady, Gordon and Knight2008). These variations contribute to variability in the resilience of the microbiota and their hosts to changes in diet composition among cows. Nevertheless, some of the contradicting and inconsistent effects of dietary changes on gastrointestinal microbiota among studies may be also due to a large number of factors, such as variations in the inclusion rate and the type of grain, differences between experimental approaches, including those used for microbiota characterisation, such as DNA extraction methodology, standardisation of amount of DNA for sequencing, and the choice of primers used (universal bacterial primers v. target-specific primers, or different choices of hypervariable regions of 16S ribosomal RNA gene), and the sample sizes among these studies (Khafipour et al., Reference Khafipour, Li, Tun, Derakhshani, Moossavi and Plaizier2016).

Differences between microbiota in the reticulo-rumen and the hind gut

The presence of mucus in the hindgut and differences in the profile of dietary and mucosa-associated glycans between the hindgut and the rumen may contribute to differences in the abundances of bacteria taxa between these sites (Koropatkin et al., Reference Koropatkin, Cameron and Martens2012). In the reticulo-rumen, most dietary glycans are exposed to fermentation and converted into VFA. Thus, the contribution of dietary glycans in shaping the microbiota composition of the hindgut is minor (Koropatkin et al., Reference Koropatkin, Cameron and Martens2012). However, some members of the hindgut microbiota have the ability to degrade the glycans found in host mucous secretions or shed epithelial cells (Koropatkin et al., Reference Koropatkin, Cameron and Martens2012). Hindgut microbiota vary widely in their glycan preferences as well as the number of different glycans that they are capable to degrade (Koropatkin et al., Reference Koropatkin, Cameron and Martens2012). As such, species that are adapted to using these endogenous glycans, such as Bacteroides spp. that can degrade dozen different types of glycans (Johansson et al., Reference Johansson, Ambort, Pelaseyed, Schütte, Gustafsson, Ermund, Subramani, Holmén-Larsson, Thomsson and Bergström2011), can more effectively colonise hindgut mucosa, and thus, exert a disproportionate effect on the hindgut homoeostasis. As described in the ‘Hindgut fermentation’ section, high-grain feeding also affects the environmental conditions and the composition of the digesta in the hindgut, including increased starch fermentation and, as a result, the composition and functionality of the hindgut microbiota, similarly to what is observed in the rumen. This may contribute to the relatively high abundance of Firmicutes and the relatively low abundance of Bacteroidetes in the hindgut compared with the reticulo-rumen (Plaizier et al., Reference Plaizier, Li, Danscher, Derakshani, Andersen and Khafipour2017). These shifts can also pave the way for the enrichment of facultative pathogens that are a threat for food borne diseases in humans (Steele et al., Reference Steele, Penner, Chaucheyras-Durand and Guan2016).

Functional organisation of the gastrointestinal tract and its contribution to gastrointestinal health

The gastrointestinal tract must facilitate digesta passage, nutrient digestion, nutrient absorption, barrier function, luminal nutrient sensing and host–microbial communication. The regulation of these functions is complex, but all these functions are essential for balanced gastrointestinal tract function. In order to maintain homoeostasis in the presence of dense microbial biomasses in its lumen, the digestive tract has adopted strategies to physically limit the direct contact of microbiota in the digesta with the intestinal epithelium via mucosal layers. The rumen is an exception to this, as its epithelium does not contain a mucosal layer. Nevertheless, rumen epithelium has developed a multilayer structure with tight junctions to overcome this problem (Graham and Simmons, Reference Graham and Simmons2005). The epithelium of the hindgut does not have a multilayer structure, but it is covered by mucus, the inner layer of which is firmly attached to the epithelial cells and usually resistant to bacterial colonisation. These, and other differences in volume, retention time, mechanisms facilitating nutrient digestion (microbial fermentation v. mammalian enzymes), nutrient absorption, morphology and histology, and immune responsiveness among regions of the gastrointestinal tract are essential to understand when considering gastrointestinal health.

Volatile fatty acid absorption is critical as it supplies the vast majority of metabolisable energy and glucose to ruminants. Absorption of VFA also contributes to the stabilisation of ruminal pH (Penner et al., Reference Penner, Aschenbach, Gäbel, Rackwitz and Oba2009; Aschenbach et al., Reference Aschenbach, Penner, Stumpff and Gabel2011). The primary pathways allowing for improved stabilisation of ruminal pH is suspected to be the AE pathway, where VFA in the dissociated state are absorbed in exchange for the secretion of bicarbonate (Aschenbach et al., Reference Aschenbach, Bilk, Tadesse, Stumpff and Gabel2009). Subsequently, it has been shown that increasing the bicarbonate gradient increases the rate of VFA transport through the AE pathway (Dengler et al., Reference Dengler, Rackwitz, Benesch, Pfannkuche and Gäbel2013). The contribution of VFA absorption towards stabilisation of ruminal pH suggests that increasing fermentation should result in a corresponding increase in VFA absorption. However, inducing SARA has been shown to reduce VFA absorption across the reticulo-rumen, while simultaneously increasing saliva production (Schwaiger et al., Reference Schwaiger, Beauchemin and Penner2013a and Reference Schwaiger, Beauchemin and Penner2013b). The reduction in VFA absorption as a consequence of SARA is likely a mechanism to prevent intracellular acidification and tissue damage associated with excessive absorption of VFA while partitioning bicarbonate through saliva to buffer ruminal pH. The mechanisms regulating VFA absorption and partitioning arterial bicarbonate supply have not yet been elucidated. Other models to induce SARA, such as a rapid but moderate grain adaptation, have shown that the epithelium responds rapidly to increasing VFA concentrations. Mechanisms for how the ruminal epithelium responds have previously been discussed, but it is notable to indicate that much of the adaptive response occurs within 1 week of an abrupt diet change (Schurmann et al., Reference Schurmann, Walpole, Gorka, Ching, Loewen and Penner2014). The increase in absorption, however, does also coincide with a ‘leaky’ epithelium. In fact, Schurmann et al. (Reference Schurmann, Walpole, Gorka, Ching, Loewen and Penner2014) reported increased rates of ³H-mannitol flux across the rumen epithelium with advancing days on a diet containing 50% concentrate. This increased permeability of the tissue may suggest that rapid dietary changes that should stimulate proliferation may also lead to increased permeability of the rumen epithelium. The same study also demonstrated that along with changes for ruminal fermentation and ruminal epithelial function, dramatic changes were observed in terms of digesta mass and tissue mass along the gastrointestinal tract (Gorka et al., Reference Gorka, Schurmann, Walpole, Blonska, Li, Plaizier, Kowalski and Penner2017). Thus, studies evaluating the functionality of the gastrointestinal tract need to consider regions beyond the reticulo-rumen.

The mechanism(s) of translocation for toxic compounds may be favoured by impairment of the barrier function of the rumen epithelium (Emmanuel et al., Reference Emmanuel, Madsen, Churchill, Dunn and Ametaj2007), depletion of protective factors (Hollmann et al., Reference Hollmann, Miller, Hummel, Sabitzer, Metzler-Zebeli, Razzazi-Fazeli and Zebeli2013) and increased luminal osmolality (Owens et al., Reference Owens, Secrist, Hill and Gill1998). Also, the chronic exposure to ethanol can increase the epithelial permeability and portal vein translocation of endotoxin (Enomoto et al., Reference Enomoto, Ikejima, Yamashina, Hirose, Shimizu, Kitamura, Takei, Sato and Thurman2001). Interestingly, both concentrations of both endotoxin and ethanol in the reticulo-rumen fluid increased when amounts of grain in the diet of cows also increased (Ametaj et al., Reference Ametaj, Zebeli, Saleem, Psychogios, Lewis, Dunn, Xia and Wishart2010). This indicates potential interactions of the generated compounds, that is, ethanol, biogenic amines and endotoxin, that potentiate the epithelial permeability of the endotoxin.

Although the reticulo-rumen has been the focus when investigating SARA, it is clear that outcomes arising from SARA affect multiple regions of the gastrointestinal tract. The organisation of the gastrointestinal tract also differs markedly with the reticulo-rumen and omasum consisting of a stratified squamous epithelium and the more distal regions containing simple epithelia. For the reticulo-rumen and the omasum, the stratified nature is thought to provide physical protection from abrasive feeds (Greenwood et al., Reference Greenwood, Morrill, Titgemeyer and Kennedy1997), while also supporting barrier function properties.

Past research has reported that the induction of acute ruminal acidosis decreases the barrier function of the total gastrointestinal tract (Minuti et al., Reference Minuti, Ahmed, Trevisi, Piccioli-Cappelli, Bertoni, Jahan and Bani2014). However, that research was unable to determine regional effects and confirm whether the reticulo-rumen, hindgut regions, or other regions are likely to lead ruminants to greater risk for antigen or pathogen translocation. Although regional effects are rarely provided, Penner et al. (Reference Penner, Aschenbach, Wood, Walpole, Kanafany-Guzman, Hendrick and Campbell2014) has characterised the permeability of the gastrointestinal tract epithelia to small (³H-mannitol) and large (¹⁴C-inulin) molecules using the Ussing chamber approach. In this study, epithelia from the rumen, omasum, duodenum, jejunum, ileum, caecum, proximal colon and distal colon were collected from Holstein steers fed a forage-based diet. They reported that potentials for inulin to cross the epithelia of the rumen and omasum were high, despite having low permeability to mannitol. The jejunum was also noted as a region with a high permeability. Although these calves were not exposed to a nutritional challenge and therefore, the results should represent a ‘healthy’ gastrointestinal tract, they do suggest that the rumen may be implicated in the transepithelial flux of large molecules. Pederzolli et al. (Reference Pederzolli, Van Kessel, Campbell, Hendrick, Wood and Penner2018) followed a similar model but induced ruminal acidosis to assess regional effects on epithelial barrier function resulting from ruminal acidosis. Surprisingly, they were not able to detect major changes in barrier function among regions of the gastrointestinal tract when compared with calves that were not challenged. Thus, the impact of ruminal acidosis on regional differences in epithelial barrier function remains not fully understood. However, from the literature reviewed here, it is evident that the translocation of large molecules such as lipopolysaccharide (LPS) can occur across the digestive tract and that high grain feeding increases this translocation. It cannot be assumed that this translocation occurs only in the rumen.

Although SARA has been a major focus as a causative factor negatively affecting gastro-intestinal health, it should be acknowledged that other factors such as low feed intake or rapid dietary transitions can also compromise the absorptive and barrier function of the gastrointestinal tract. For example, Zhang et al. (Reference Zhang, Albornoz, Aschenbach, Barreda and Penner2013a and 2013b) restricted heifers to 75%, 50% or 25% of their ad libitum dry matter intake and observed a dose-dependent reduction in absorption of VFA across the reticulo-rumen along with an increase in permeability of the total gastrointestinal tract when restricted to 25% of their ad libitum feed intake. Although the magnitude of low feed intake may seem extreme, transition dairy cattle, particularly those experiencing transition diseases (hypocalcaemia, ketosis) or infectious diseases (metritis, mastitis), may have dry matter intake reductions of a similar extent. In another study, evaluating milk-fed Holstein calves, Wood et al. (Reference Wood, Palmer, Steele, Metcalf and Penner2015) reported an age-dependent decrease in the permeability of the total gastrointestinal tract. However, this age-dependent reduction was disrupted by weaning with weaned calves having markedly greater permeability than calves that were not weaned. Thus, in addition to ruminal acidosis, factors that reduce or dramatic change nutrient supply, including nutrient supply to the gastrointestinal tract, can also compromise the functionality of this tract.

Genomic alterations and implications on health: rumen epithelium and beyond

The advent of high-throughput gene expression tools, such as microarrays, for use in cattle (Everts et al., Reference Everts, Band, Liu, Kumar, Liu, Loor, Oliveira and Lewin2005) have been instrumental for the study of gastrointestinal health as it relates to ruminal acidosis and its peripheral tissue responses. Steele et al. (Reference Steele, Croom, Kahler, AlZahal, Hook, Plaizier and McBride2011a) reported a comprehensive analysis of the rumen epithelium transcriptome in cows afflicted by ruminal acidosis upon feeding a 65% grain diet. The study identified several genes associated with cholesterol synthesis as being markedly downregulated after a 3-week induction of ruminal acidosis. This data indicated that, besides the well-described damage of the epithelial morphology during acidosis, an alteration in cholesterol metabolism contributes to malfunction of these cells, for example, through an aberrant cell membrane lipid composition. This malfunction could have a negative impact on transport mechanisms (Christon et al., Reference Christon, Meslin, Thevenoux, Linard, Leger and Delpal1991). In non-ruminant models, the metabolism of cholesterol to isoprenoid intermediates also induces changes in cellular proliferation, migration and oxidative stress, all of which are associated with grain feeding (Gabel et al., Reference Gabel, Aschenbach and Muller2002).

Steele et al. (Reference Steele, Croom, Kahler, AlZahal, Hook, Plaizier and McBride2011a) also recognised that IGF binding proteins (IGFBP3, 5 and 6) and the cadherin-like transmembrane glycoprotein desmoglein 1 (DSG1), all with a potential role in rumen papillae proliferation (Shen et al., Reference Shen, Seyfert, Lohrke, Schneider, Zitnan, Chudy, Kuhla, Hammon, Blum, Martens, Hagemeister and Voigt2004), were altered during rumen acidosis. For instance, downregulation of DSG1 was associated with increased permeability or paracellular transport, thereby providing the means for microbes, LPS and other toxic compounds (e.g. bioactive amines) to translocate and elicit detrimental health effects (Steele et al., Reference Steele, Vandervoort, AlZahal, Hook, Matthews and McBride2011b and Reference Steele, Dionissopoulos, AlZahal, Doelman and McBride2012). The gradual upregulation of IGFBP5 coupled with a gradual downregulation of IGFBP3 during adaptation to a high-grain diet have been consistent in studies of ruminal acidosis. These effects provide a link between IGF-1 and ruminal cell proliferation (Shen et al., Reference Shen, Seyfert, Lohrke, Schneider, Zitnan, Chudy, Kuhla, Hammon, Blum, Martens, Hagemeister and Voigt2004), that is, an upregulation of IGFBP5 potentiates the effect of IGF-1 on cell proliferation, whereas downregulation of IGFBP3 encourages cell growth (Steele et al., Reference Steele, Dionissopoulos, AlZahal, Doelman and McBride2012). It is noteworthy that the changes in DSG1, IGFBP5 and IGFBP3 expression in response to chronic acidosis also have been detected in rumen epithelium tissue postpartum compared with prepartum (Steele et al., Reference Steele, Schiestel, AlZahal, Dionissopoulos, Laarman, Matthews and McBride2015). This leads to the suggestion that the IGF-axis may be involved in the adaptation of the rumen epithelium to the higher fermentable diets typical of the postpartum period.

Functional genomics approaches, either utilising microarrays or Reverse transcription polymerase chain reaction (RT-PCR), have also verified differential expression of genes with roles in maintenance of intracellular pH (↓ solute carrier family 9 member A3 (SLC9A3); Schlau et al., Reference Schlau, Guan and Oba2012), cholesterol synthesis (↓ 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS) 1; ↓ lanosterol synthase; Gao and Oba, Reference Gao and Oba2016), or lack of change in ketogenic genes known to be controlled at the level of transcription (e.g. HMGCS2; 3-hydroxymethyl-3-methylglutaryl-CoA lyase; Steele et al., 2011; Schlau et al., Reference Schlau, Guan and Oba2012; Gao and Oba, Reference Gao and Oba2016). Some of these effects have been verified at the protein level (e.g. ↓ solute carrier family 16 member 1), whereas others have been opposite (e.g. ↑ SLC9A3) (Laarman et al., Reference Laarman, Pederzolli, Wood, Penner and McBride2016). Clearly, it cannot be assumed that transcription controls the activity of enzymes or transporters involved in the key function of the ruminal epithelium, and care should be taken when interpreting such findings. However, besides allowing for a holistic evaluation of physiologic responses, genome-enabled technologies provide the means to generate novel hypotheses than can be tested in a more discrete fashion. An example of this is a recent in vitro work in which isolated rumen epithelial cells were cultured in vitro with two levels of pH (7.4 or 5.5) and two concentrations of LPS (0 or 10 μg/ml) (Zhang et al., Reference Zhang, Chang, Xu, Xu, Guo, Jin and Shen2016). Results clearly underscored the positive association between LPS and pro-inflammatory markers in rumen epithelium (e.g. interleukin (IL)-1β, chemokines), and the negative association between pH and pro-inflammatory markers.

Beyond the well-established effects of ruminal acidosis on epithelial integrity and molecular responses, there has been interest in using genome-enabled technologies for evaluating the post-ruminal effect of acidosis. Examples include work with mRNA and/or protein expression in the liver (Chang et al., Reference Chang, Zhang, Xu, Jin, Guo, Zhuang and Shen2015; Xu et al., Reference Xu, Cardoso, Pineda, Trevisi, Shen, Rosa, Osorio and Loor2017), white blood cells (Stefanska et al., Reference Stefanska, Nowak, Komisarek, Taciak, Barszcz and Skomial2017) and mammary gland (Jin et al., Reference Jin, Chang, Zhang, Guo, Xu and Shen2016; Zhang et al., Reference Zhang, Chang, Xu, Xu, Guo, Jin and Shen2016). In regards to the liver, acute (1 day) or chronic (10 weeks) ruminal acidosis in Holstein cows induced by feeding a high-grain diet causes upregulation of inflammatory mediators (Chang et al., Reference Chang, Zhang, Xu, Jin, Guo, Zhuang and Shen2015; Xu et al., Reference Xu, Cardoso, Pineda, Trevisi, Shen, Rosa, Osorio and Loor2017). Hence, the pro-inflammatory response to acidosis is not unique to rumen epithelium and even extends to circulating white blood cells (Stefanska et al., Reference Stefanska, Nowak, Komisarek, Taciak, Barszcz and Skomial2017) and the mammary gland (Zhang et al., Reference Zhang, Chang, Xu, Xu, Guo, Jin and Shen2016). These molecular responses across studies are often accompanied by reductions in rumen pH and increases in concentrations of rumen LPS, along with classical decreases in the ratio of rumen fluid acetate to propionate.

Recent efforts to better understand the response of the liver to grain challenges have gone beyond the inflammatory response. For instance, an acute grain challenge after a 1 day of feed restriction downregulated genes encoding metabolic enzymes associated with elongation (ELOVL fatty acid elongase 6) and desaturation (stearoyl-CoA desaturase) of long-chain fatty acids but upregulated gluconeogenic genes (pyruvate dehydrogenase kinase 4; phosphoenolpyruvate carboxykinase 1; Xu et al., Reference Xu, Cardoso, Pineda, Trevisi, Shen, Rosa, Osorio and Loor2017). From a mechanistic standpoint, blocking elongation and desaturation could lead to ceramide production and trigger inflammation (Kasumov et al., Reference Kasumov, Li, Li, Gulshan, Kirwan, Liu, Previs, Willard, Smith and McCullough2015). Upregulation of fatty acid oxidation and gluconeogenic genes coincided with an increase in plasma free fatty acids, suggesting transient adaptations in energy metabolism. At least in non-ruminants, these enzymes are known to be regulated at the transcriptional level (Nakamura et al., Reference Nakamura, Yudell and Loor2014) suggesting that changes observed could have functional relevance in terms of liver function. It is uncertain if these metabolic responses occur during long-term ruminal acidosis.

Although research to date has clearly linked ruminal events to molecular alterations in various tissues, the actual mechanisms behind the changes in transcription and translation during ruminal acidosis are not well known. As demonstrated by a recent study evaluating epigenetic mechanisms associated with ruminal acidosis (Chang et al., Reference Chang, Zhang, Xu, Jin, Guo, Zhuang and Shen2015), this represents a fertile area for future research. The focus on epigenetic regulation during ruminal acidosis arose from data in model organisms demonstrating that excessive activation of inflammatory pathways induces endotoxin tolerance and cross-tolerance towards other pathogen-associated molecular patterns (Foster et al., Reference Foster, Hargreaves and Medzhitov2007; Saturnino et al., Reference Saturnino, Prado, Cunha-Melo and Andrade2010). Chang et al. (Reference Chang, Zhang, Xu, Jin, Guo, Zhuang and Shen2015) demonstrated that high-grain induced ruminal acidosis for 10 weeks not only upregulated expression of Toll-like receptor 4 (TLR4) mRNA and protein, but that this effect was associated with TLR4 promoter hypomethylation and lower chromatin compaction, all of which suggested a functional link between LPS translocation from rumen to liver causing inhibition of DNA methylation rendering the DNA of inflammatory genes more accessible to the action of transcription factors such as NF-κB (Chang et al., Reference Chang, Zhang, Xu, Jin, Guo, Zhuang and Shen2015).

Buffers

Buffers are commonly included in dairy cow diets to stabilise the rumen pH (Golder, Reference Golder2014). Sodium bicarbonate and magnesium oxide are commonly used rumen buffers (Staples and Lough, Reference Staples and Lough1989; Hu and Murphy, Reference Hu and Murphy2005; Golder, Reference Golder2014). In addition to buffering, sodium bicarbonate also stabilises the rumen acidity by increasing the water intake and reducing ruminal starch digestion (Russell and Chow, Reference Russell and Chow1993). Erdman (Reference Erdman1988) observed that adding a combination of magnesium oxide and bicarbonate to dairy cow diets increased butter fat by 0.3% to 0.4%. Also, Golder et al. (Reference Golder, Celi, Rabiee and Lean2014b) observed that adding both sodium bicarbonate and magnesium oxide to the diet reduced the variability in feed intake during a carbohydrate challenge study. Hence, the effects of these buffers appears to be additive. Other buffers that have been added to cattle diets include potassium carbonate, potassium bicarbonate, and sodium sesquicarbonate and the skeletal remains of the seaweed Lithothamnium calcareum (Erdman, Reference Erdman1988; Golder, Reference Golder2014; Lean et al., Reference Lean, Golder and Hall2014). In addition to buffering, supplementing with sodium bicarbonate, potassium carbonate, potassium bicarbonate and sodium sesquicarbonate affects the dietary cation–anion difference.

Antimicrobials

Countries differ greatly in the availability of antimicrobial agents for use in acidosis control, and it is likely that less of these antibiotics will be available in the future due to concerns related to antibiotic resistance. Also, it should not be assumed that other products used to control bacterial populations will not be associated with antimicrobial resistance (Nagaraja and Taylor, Reference Nagaraja and Taylor1987). Antibiotics that are used in the cattle industries include tylosin and virginiamycin (VM). Feeding combinations of feed additives may have synergistic effects (Nagaraja et al., Reference Nagaraja, Taylor, Harmon and Boyer1987; Lean et al., Reference Lean, Wade, Curtis and Porter2000; Golder et al., Reference Golder, Celi, Rabiee and Lean2014b), but literature is limited, and further research is required in this field. The latter statement extends beyond the interactions between ionophores and antibiotics to the vast combination of rumen modifying agents that are used in dairy herds and feed lots. These combinations include buffering agents, ionophores, bambermycin, yeasts, yeast products and direct fed microbials (DFM).

Tylosin is a macrolide antibiotic that inhibits protein biosynthesis in Gram-positive bacteria. Its main use is to reduce the incidence of the liver abscess in feedlot cattle that are associated with rumen acidosis (Amachawadi and Nagaraja, Reference Amachawadi and Nagaraja2016). Tylosin increased total VFA and butyrate concentrations and tended to decrease plasma lactate concentrations in the reticulo-rumen of lactating dairy cattle during a ruminal acidosis challenge (Lean et al., Reference Lean, Wade, Curtis and Porter2000). However, tylosin did not affect VFA and lactate in the rumen in steers (Horton and Nicholson, Reference Horton and Nicholson1980; Nagaraja et al., Reference Nagaraja, Sun, Wallace, Kemp and Parrott1999). Despite the more than 45 years of use, Amachawadi and Nagaraja (Reference Amachawadi and Nagaraja2016) found no evidence of resistance to tylosin in Fusobacterium necrophorum and Trueperella pyogenes isolates from liver abscesses of cattle.

Virginiamycin is another antibiotic that is effective against gram-positive bacteria that are associated with lactic acid production. It has been used successfully in feedlots to reduce the risk of lactic acidosis (Rowe and Pethick, Reference Rowe and Pethick1994; Rogers et al., Reference Rogers, Branine, Miller, Wray, Bartle, Preston, Gill, Pritchard, Stilborn and Bechtol1995). It has also been observed that VM stabilises rumen pH and increases the digestibility of and energy utilisation from grain (Godfrey et al., Reference Godfrey, Rowe, Thorniley, Boyce and Speijers1995). Another effect of VM is that can increase propionate production in the reticulo-rumen (Nagaraja et al., Reference Nagaraja, Godfrey, Winslow and Rowe1995a and Reference Nagaraja, Godfrey, Winslow, Rowe and Kemp1995b; Clayton et al., Reference Clayton, Hansch, Huijnen and Rowe1996).

Classes of antibiotics that are not used in human medicine, and, therefore, may have more potential for use in livestock include the ionophores and bambermycin. Monensin is a carboxylic polyether ionophore produced by a naturally occurring strain of Streptomyces cinnamonensis (Haney and Hoehn, Reference Haney and Hoehn1967). It is approved for use in lactating cattle in several countries including: Australia, the United Kingdom, Argentina, Brazil, New Zealand, South Africa, Canada, and the United States. Sodium monensin use increases ruminal propionate production, reflecting an increase in propionate producing bacteria compared with those producing formate, acetate, lactate and butyrate (Lean et al., Reference Lean, Golder and Hall2014). Methane production from the reticulo-rumen is decreased and dietary proteins are less digested in the reticulo-rumen (Richardson et al., Reference Richardson, Raun, Potter, Cooley and Rathmacher1976; Russell and Houlihan, Reference Russell and Houlihan2003). Monensin selectively inhibits gram-positive bacteria, in particular lactate producing bacteria in the rumen without affecting most lactate utilising bacteria (Dennis et al., Reference Dennis, Nagaraja and Bartley1981; Weimer et al., Reference Weimer, Stevenson, Mertens and Thomas2008). Consequently, monensin has been proposed as an agent for the control of rumen lactic acidosis. There are very few in vivo studies that provide information on ruminal lactate production or concentrations following monensin. Burrin and Britton (Reference Burrin and Britton1986) found that ruminal lactate concentrations in feedlot steers were not affected by monensin. Nagaraja et al. (Reference Nagaraja, Avery, Bartley, Galitzer and Dayton1981) found both increased and decreased lactate concentrations in the reticulo-rumen due to monensin treatment in three acidosis challenge studies. Nagaraja et al. (Reference Nagaraja, Avery, Bartley, Roof and Dayton1982) observed that monensin decreased ruminal lactate in a subsequent glucose challenge study, but Golder (Reference Golder2014) did not find that monensin affected ruminal lactate in cattle. Fairfield et al. (Reference Fairfield, Plaizier, Duffield, Lindinger, Bagg, Dick and McBride2007) found that a monensin controlled release capsule did not affect rumen pH and lactate in dairy cows during the transition period and early lactation in which rumen acidosis was not common.

Bacteria, such as Streptococcus bovis may outgrow the amount of monensin administered to control microbial growth due to their high binding capacity for monensin (Chow and Russell, Reference Chow and Russell1990). Hence, monensin may not stabilise the reticulo-rumen when it is subjected to conditions conducive to acute acidosis and the growth of S. bovis, such as feeding highly fermentable diets. As a result, in vitro studies on monensin that were conducted at near-neutral pH and at lower cell densities than in vivo may not be representative for the role of this ionophore in grain-fed cattle.

Guan et al. (Reference Guan, Wittenberg, Ominski and Krause2006) observed that monensin had a transitory effect on protozoal numbers and methane emissions, suggesting that the microbiota can adapt to ionophores and their effects may be reduced over time. Notwithstanding this, there is evidence of increased production of propionate from lactate, which is a ruminal adaptation that sequesters hydrogen ions in safer ruminal pools, when monensin is fed in diets that may cause rumen acidosis (Lunn et al., Reference Lunn, Mutsvangwa, Odongo, Duffield, Bagg, Dick, Vessie and McBride2005). Hence, it is possible that monensin increases ruminal stability under conditions of moderate substrate loads. Monensin also appears to be effective in controlling acidosis risks when fed with tylosin or VM (Nagaraja et al., Reference Nagaraja, Taylor, Harmon and Boyer1987; Lean et al., Reference Lean, Wade, Curtis and Porter2000; Golder et al., Reference Golder, Celi, Rabiee and Lean2014b).

Lasalocid is a polyether antibiotic ionophore derived from strains of Streptomyces lasaliensis that has also been used to control lactic acidosis (Nagaraja et al., Reference Nagaraja, Avery, Bartley, Galitzer and Dayton1981). Lasalocid can translocate monovalent and divalent cations across bacterial cell membranes (Bergen and Bates, Reference Bergen and Bates1984), resulting in a modified reticulo-rumen environment through death or impaired growth of primarily Gram-positive rumen bacteria. The use of lasalocid equalled or exceeded the reduction in lactic acid production observed for monensin (Nagaraja et al., Reference Nagaraja, Avery, Bartley, Galitzer and Dayton1981), however, neither product influenced rumen pH. Both monensin and lasalocid prevented acute lactic acidosis in the study of Nagaraja et al. (Reference Nagaraja, Avery, Bartley, Galitzer and Dayton1981). Nagaraja et al. (Reference Nagaraja, Avery, Bartley, Roof and Dayton1982) found that lasalocid levels between 0.33 and 1.30 ppm reduced lactic acid concentrations and increased pH in the reticulo-rumen in cattle with glucose-induced lactic acidosis. Golder and Lean (Reference Golder and Lean2016) observed that lasalocid increased total VFA, propionate and ammonia and decreased acetate and butyrate molar percentage, without affecting the pH and the molar percentage of valerate in the reticulo-rumen.

Bambermycin is a phosphoglycolipid antibiotic that affects the functionality of rumen microbiota (Edwards et al., Reference Edwards, McEwan, McKain, Walker and Wallace2005). It is also referred to as flavomycin, flavophospholipol and moenomycin (Edwards et al., Reference Edwards, McEwan, McKain, Walker and Wallace2005; Golder, Reference Golder2014). This antibiotic reduces lactic acid production in vitro Meissner et al. (Reference Meissner, Henning, Leeuw, Hagg, Horn, Kettunen and Apajalahti2014), but does not appear to affect VFA production (Edwards et al., Reference Edwards, McEwan, McKain, Walker and Wallace2005). The effects of bambermycin on the production of dairy cows vary greatly among studies (Golder, Reference Golder2014). Also, in a small beef cow study, bambermycin did not affect production, and rumen fermentation (Golder, Reference Golder2014).

The effects of monensin and lasalocid on rumen VFA are not consistent among studies, not even among studies during which rumen acidosis was induced (Duffield et al., Reference Duffield, Rabiee and Lean2008; Golder, Reference Golder2014; Golder and Lean, Reference Golder and Lean2016). It is assumed that the variation in interactions between the host genome, ruminal meta-genome and the diet is partly responsible for the variation in response to antibiotics (Brulc et al., Reference Brulc, Antonopoulos, Berg Miller, Wilson, Yannarell, Dinsdale, Edwards, Frank, Emerson, Wacklin, Coutinho, Henrissat, Nelson and White2009; Jami and Mizrahi, Reference Jami and Mizrahi2012; Petri et al., Reference Petri, Schwaiger, Penner, Beauchemin, Forster, McKinnon and McAllister2013).

Microbials

A number of products of single or mixed bacterial cultures are used in cattle, including strains from Bifidobacterium, Enterococcus, Streptococcus, Prevotella, Bacillus, Lactobacillus, Megasphaera and Propionibacteria. Lactobacillus acidophilus and Propionibacterium freudenreichii are the primary bacterial DFM used in the dairy industry (Krehbiel et al., Reference Krehbiel, Rust, Zhang and Gilliland2003; McAllister et al., Reference McAllister, Beauchemin, Alazzeh, Baah, Teather and Stanford2011). Similar agents have been used in the beef industry.

Responses to DFM have been inconsistent, reflecting supplementation with many different organisms, strains of organisms, and combinations of organisms, differences in micro-organism inclusion level, diet, feeding management and animal factors (Krehbiel et al., Reference Krehbiel, Rust, Zhang and Gilliland2003; McAllister et al., Reference McAllister, Beauchemin, Alazzeh, Baah, Teather and Stanford2011). In general, there is evidence that DFM increased milk production in dairy cattle, improved health and performance in calves, and could reduce the risk of ruminal acidosis (Krehbiel et al., Reference Krehbiel, Rust, Zhang and Gilliland2003). These responses reflect use of bacteria that utilise lactate, for example, Megasphera elsdenii (Klieve et al., Reference Klieve, Hennessy, Ouwerkerk, Forster, Mackie and Attwood2003; Leeuw et al., Reference Leeuw, Siebrits, Henning and Meissner2009; Meissner et al., Reference Meissner, Henning, Leeuw, Hagg, Horn, Kettunen and Apajalahti2014) and Selenomonas ruminantium (Chiquette et al., Reference Chiquette, Lagrost, Girard, Talbot, Li, Plaizier and Hindrichsen2015), or increase propionate production (Kenney et al., Reference Kenney, Vanzant, Harmon and McLeod2015; Vyas et al., Reference Vyas, Beauchemin and Koenig2015). Responses to DFM in the rumen include a decrease in the area below a ruminal pH threshold defined for SARA, an increase in propionate concentrations, increased protozoa counts, and altered counts of lactate-utilising and lactate producing bacteria (Krehbiel et al., Reference Krehbiel, Rust, Zhang and Gilliland2003; McAllister et al., Reference McAllister, Beauchemin, Alazzeh, Baah, Teather and Stanford2011). Although there has been a very substantial amount of work on establishing mechanism and application of particular DFMs, including M. elsdenii, evidence of adoption is limited.

Yeasts are a non-homogenous group of rumen modifiers. Assumptions of equivalency of action in the reticulo-rumen or responses to supplementation within the group should, therefore, not be made. Most yeasts used in the livestock industry, contain, or are derived from Saccharomyces cerevisiae and Aspergillus oryzae strains, respectively (Yoon and Stern, Reference Yoon and Stern1995; Seo et al., Reference Seo, Kim, Kim, Upadhaya, Kam and Ha2010). There are two major types of yeast marketed; live yeast, sometimes termed ‘active dry yeast’, containing >15 billion live yeast cells/g; and yeast fermentation byproducts that do not contain live yeast but do include dead yeast, fermentation medium and various fermentation compounds. The action of the live yeast depends on the function of live yeast cells in the rerticulo-rumen, whereas the fermentation byproducts act through the supply of products of fermentation using yeasts.

Actions that have been identified with live yeasts include small increases in rumen pH, reductions in lactic acid, enhanced fibre digestion and small increases in VFA production (Erasmus et al., Reference Erasmus, Botha and Kistner1992; Chaucheyras-Durand et al., Reference Chaucheyras-Durand, Walker and Bach2008; Golder, Reference Golder2014). These actions, are modest in magnitude but may synergise with other strategies to control the risk of acidosis. Interestingly, feeding a yeast (S. cerevisiae CNCM I-1077; Levucell SC20; Lallemand Animal Nutrition, Montreal, QC, Canada) and monensin modified eating behaviour in dairy heifers by increasing the time taken to eat, reducing DMI at feeding in an acidosis challenge study using starch and fructose (Golder et al., Reference Golder, Celi, Rabiee and Lean2014b). Notwithstanding these changes, average daily gain (1.67 v. control 1.47 kg/day) and feed conversion ratio was high (6.44 v. 9.34 control kg of DMI/kg of gain), but not significantly, altered in this group. DeVries and Chevaux (Reference DeVries and Chevaux2014) found similar changes with the same yeast in lactating cows that increased meal frequency and decreased meal size and length of feeding bouts. Other actions of yeasts include increasing fibre digestion and increasing microbial protein production (Chaucheyras-Durand et al., Reference Chaucheyras-Durand, Walker and Bach2008) may be significant factors that could reduce the risk of acidosis. There appears to be relatively little evidence that yeast culture products increase the rumen pH (Erasmus et al., Reference Erasmus, Botha and Kistner1992; Robinson, Reference Robinson1997; Lehloenya et al., Reference Lehloenya, Krehbiel, Mertz, Rehberger and Spicer2008; Moya et al., Reference Moya, Calsamiglia, Ferret, Blanch, Fandiño, Castillejos and Yoon2009). However, Li et al. (Reference Li, Yoon, Scott, Khafipour and Plaizier2016) found that an S. cerevisiae fermentation product (Diamond V XPC; Diamond V Mills Inc., Cedar Rapids, IA, USA) stabilised rumen pH in dairy cows during moderate and high grain feeding.