Weimer research programs, beginning with the pioneering studies of the research groups of Robert Hungate and Marvin Bryant in the 1940s. In fact, despite the difficulties inherent in studying a habitat of limited accessibility and the requirements for experimental work under strictly anaerobic conditions, the rumen has come to be regarded as one of the best-understood of all microbial habitats Most studies of ruminal microbes have been conducted in batch culture usually at fairly high substrate concentrations. This growth mode has been useful for examining the products and kinetics of digestion by mixed ruminal microflora (so-called in vitro digestion experiments); for isolating and characterizing pure cultures; and for examining interactions among microorganisms at different tro- phic levels(e.g, interspecies H, transfer reactions; see Sec. IV.C. 4). Studies have also been carried out in continuous culture in which substrates are fed either continuously or at defined(e. g, hourly) intervals. This mode of growth is more useful for some types of studies, because under proper conditions it can simulate the feeding schedule of the animal. One type of continuous culture, the chemostat, has been widely used in growth studies. In this mode of culture, one substrate in the feed medium is present at a concentration that limits microbial growth. Feeding of the culture vessel at different volumetric flow rates results in the achievement of a stead state in which the rate of microbial growth is equal to the dilution rate [that is (volumetric flow rate)/(working volume of the culture vessel)). The chemostat allows the experimenter to examine the microbial response to growth at subopt mal rates; an important consideration because microbes in nature normally grow at rates well below their maxima(Slater 1988). Appropriate fitting of data to theoretically derived equations permits determination of fundamental growth pa- rameters such as affinity constants, true growth yields, and maintenance coeffi cients(see Sec. IV.C.5. b). Until recently, chemostat studies were limited to using soluble substrates, but several new configurations have permitted growth in continuous mode on insoluble substrates such as cellulose( Kistner and Kornelius 1990: Weimer et al., 1991). Culture systems have also been constructed that allow differential fow rates for solids and liquids, further approximating the conditions in the rumen(Hoover et al., 1983). However, no laboratory culture method can fully simulate the complexities of digestion within the rumen itself, because in vivo digestion involves not only microbial activity but also rumination and masti ation, salivary secretions, and recycling of some nutrients. B. The Ruminal Environment Much of our understanding of the physiology and microbiology of the rumen has come from in vitro studies of rumen contents. Early studies with rumen con- tents used samples recovered from animals at the slaughterhouse, but the microbi- ology of the rumen under such conditions does not represent that of the living
10 Weimer research programs, beginning with the pioneering studies of the research groups of Robert Hungate and Marvin Bryant in the 1940s. In fact, despite the difficulties inherent in studying a habitat of limited accessibility and the requirements for experimental work under strictly anaerobic conditions, the rumen has come to be regarded as one of the best-understood of all microbial habitats. Most studies of ruminal microbes have been conducted in batch culture, usually at fairly high substrate concentrations. This growth mode has been useful for examining the products and kinetics of digestion by mixed ruminal microflora (so-called in vitro digestion experiments); for isolating and characterizing pure cultures; and for examining interactions among microorganisms at different trophic levels (e.g., interspecies H2 transfer reactions; see Sec. IV.C.4). Studies have also been carried out in continuous culture in which substrates are fed either continuously or at defined (e.g., hourly) intervals. This mode of growth is more useful for some types of studies, because under proper conditions it can simulate the feeding schedule of the animal. One type of continuous culture, the chemostat, has been widely used in growth studies. In this mode of culture, one substrate in the feed medium is present at a concentration that limits microbial growth. Feeding of the culture vessel at different volumetric flow rates results in the achievement of a steady state in which the rate of microbial growth is equal to the dilution rate [that is, (volumetric flow rate)/(working volume of the culture vessel)]. The chemostat allows the experimenter to examine the microbial response to growth at suboptimal rates; an important consideration because microbes in nature normally grow at rates well below their maxima (Slater 1988). Appropriate fitting of data to theoretically derived equations permits determination of fundamental growth parameters such as affinity constants, true growth yields, and maintenance coeffi- cients (see Sec. IV.C.5.b). Until recently, chemostat studies were limited to using soluble substrates, but several new configurations have permitted growth in a continuous mode on insoluble substrates such as cellulose (Kistner and Kornelius, 1990; Weimer et al., 1991). Culture systems have also been constructed that allow differential flow rates for solids and liquids, further approximating the conditions in the rumen (Hoover et al., 1983). However, no laboratory culture method can fully simulate the complexities of digestion within the rumen itself, because in vivo digestion involves not only microbial activity but also rumination and mastication, salivary secretions, and recycling of some nutrients. B. The Ruminal Environment Much of our understanding of the physiology and microbiology of the rumen has come from in vitro studies of rumen contents. Early studies with rumen contents used samples recovered from animals at the slaughterhouse, but the microbiology of the rumen under such conditions does not represent that of the living
Microbiology of the Dairy Animal ruminant owing to the practice of withholding food from the animal for at least 24 h before slaughter. More realistic studies of rumen microbiology were facili tated by development of procedures to sample the rumen via a stomach tube or a surgically implanted fistula(Fig. 4). The latter allows recovery of a more representative grab sample containing both solids and liquor, and it provides a port for periodic insertion or removal of test materials(.g, feedstuffs placed in nylon-mesh bags) for measurement of digestion in situ Ruminal studies have revealed that the physical and chemical conditions within the rumen are fairly constant Rumen temperature remains within a few degrees of 39C as a result of heat production by both animal tissues and the microflora of the digestive tract. Despite the continuous influx of O, into the rumen through swallowing of feed and water and through diffusion from the bloodstream via the capillaries feeding the gut epithelial cells, the rumen remains highly anaerobic, with O2 concentrations ranging from 0.25 to 3.0 HM(Ellis et al., 1989). Maintenance of these low concentrations of oxygen appears to result from the combined effects of facultative anaerobes and strict anaerobes(protozoa nd bacteria). The strict anaerobes can apparently consume substantial amounts of O, in reactions involving h, oxidation as long as concentrations of O, remain below 7 uM(Ellis et al., 1989). The rumen is not only anaerobic but also highly educing, with an oxidation-reduction potential near -400 mV Figure 4 A researcher removing a sample of digesta from a ruminally fistulated cow
Microbiology of the Dairy Animal 11 ruminant owing to the practice of withholding food from the animal for at least 24 h before slaughter. More realistic studies of rumen microbiology were facilitated by development of procedures to sample the rumen via a stomach tube or a surgically implanted fistula (Fig. 4). The latter allows recovery of a more representative grab sample containing both solids and liquor, and it provides a port for periodic insertion or removal of test materials (e.g., feedstuffs placed in nylon-mesh bags) for measurement of digestion in situ. Ruminal studies have revealed that the physical and chemical conditions within the rumen are fairly constant. Rumen temperature remains within a few degrees of 39°C as a result of heat production by both animal tissues and the microflora of the digestive tract. Despite the continuous influx of O2 into the rumen through swallowing of feed and water and through diffusion from the bloodstream via the capillaries feeding the gut epithelial cells, the rumen remains highly anaerobic, with O2 concentrations ranging from 0.25 to 3.0 µM (Ellis et al., 1989). Maintenance of these low concentrations of oxygen appears to result from the combined effects of facultative anaerobes and strict anaerobes (protozoa and bacteria). The strict anaerobes can apparently consume substantial amounts of O2 in reactions involving H2 oxidation as long as concentrations of O2 remain below 7 µM (Ellis et al., 1989). The rumen is not only anaerobic but also highly reducing, with an oxidation-reduction potential near 400 mV. Figure 4 A researcher removing a sample of digesta from a ruminally fistulated cow
Weimer Ruminal ph varies within the range of approximately 5-7 because of op posing forces of microbial fermentation to produce acids on the one hand and their absorptive removal on the other (Table 4). Buffering is provided by the secretion of bicarbonate-rich saliva, which in high-producing dairy cows may approximate 150 L/day(Church, 1988). Normally, pH is highest immediately before feeding; pH values below 5 are usually associated with certain undesirable conditions(e.g, lactic acidosis; see Sect. V.E. 1) Total concentrations of ruminal VFAs and their molar proportions vary with diet, but total VFAs are generally near 100 mM, with the molar proportions of acetate, propionate, and butyrate approximately 68, 20, and 10%0, respectively (Mackie and Bryant, 1994): small amounts of isobutyrate, isovalerate, valerate, and caproate are also usually present C. The Ruminal Microbial Population The microbial population in the rumen includes numerous species of bacteria, protozoa, and fungi. There appear to be few differences among cattle, goats, and sheep with regard to either the digestibility of feeds or the species of microbe inhabiting the rumen(Baumgardt et al., 1964; Jones et al., 1972). In terms of sheer numbers of cells, the bacteria far outstrip the eukaryotes, but the latter group-because of their large cell size--contribute considerably to ruminal mi- crobial biomass 1. Bacteria More than 200 different bacterial species have been isolated from rumen contents and their properties determined, but only about 24 species are thought to be of Table 4 Factors Controlling Ruminal ph Determinants and remarks pH of feed Near neutrality for fresh herbage, hay and grains Acid(pH 5) for silage Acid production Diet composition(maximum rate and extent of digestion) eeding schedule(pH highest just before feeding) Microbial populations(species composition and fermentation Acid absorption across Fermentation product ratios (VFAs absorbed faster than lac- ruminal wall Amount of saliva Buffer capacity of saliva(concentrations of bicarbonate and
12 Weimer Ruminal pH varies within the range of approximately 5–7 because of opposing forces of microbial fermentation to produce acids on the one hand and their absorptive removal on the other (Table 4). Buffering is provided by the secretion of bicarbonate-rich saliva, which in high-producing dairy cows may approximate 150 L/day (Church, 1988). Normally, pH is highest immediately before feeding; pH values below 5 are usually associated with certain undesirable conditions (e.g., lactic acidosis; see Sect. V.E.1). Total concentrations of ruminal VFAs and their molar proportions vary with diet, but total VFAs are generally near 100 mM, with the molar proportions of acetate, propionate, and butyrate approximately 68, 20, and 10%, respectively (Mackie and Bryant, 1994); small amounts of isobutyrate, isovalerate, valerate, and caproate are also usually present. C. The Ruminal Microbial Population The microbial population in the rumen includes numerous species of bacteria, protozoa, and fungi. There appear to be few differences among cattle, goats, and sheep with regard to either the digestibility of feeds or the species of microbes inhabiting the rumen (Baumgardt et al., 1964; Jones et al., 1972). In terms of sheer numbers of cells, the bacteria far outstrip the eukaryotes, but the latter group—because of their large cell size—contribute considerably to ruminal microbial biomass. 1. Bacteria More than 200 different bacterial species have been isolated from rumen contents and their properties determined, but only about 24 species are thought to be of Table 4 Factors Controlling Ruminal pH Factor Determinants and remarks pH of feed Near neutrality for fresh herbage, hay and grains Acid (pH 5) for silages Acid production Diet composition (maximum rate and extent of digestion) Feeding schedule (pH highest just before feeding) Microbial populations (species composition and fermentation pathways) Acid absorption across Fermentation product ratios (VFAs absorbed faster than lacruminal wall tate) Salivation Amount of saliva Buffer capacity of saliva (concentrations of bicarbonate and phosphate)
Microbiology of the Dairy Animal major importance in ruminal metabolism(Table 5). Like any natural environ ment, the rumen probably contains many other species that have to now resisted isolation. Moreover, the recent use of phylogenetic criteria (i.e, sequences of evolutionarily conserved macromolecules such as 16S ribosomal RNAs)in taxon- omy has altered microbiologists' concepts of what constitutes a microbial species As a result, new species will continue to be described, although the major func- tional groups of bacteria have probably been identified. The bacterial population can carry out essentially all of the enzymatic reactions that occur in the rumen with regard to digestion of feed materials, and bacteria are probably the main agents of ruminal digestion of carbohydrate and protein in feed. The pathways or conversion of carbohydrate(the ruminants major energy source) to different fermentation endproducts are shown in Figure 5 Total populations of bacteria in the rumen are hard to measure with accu racy, because a large fraction(perhaps up to 70%)of the cells are attached to solid surfaces [mostly to feed particles(Hobson and Wallace, 1982; Costerton et al., 1987), but to a certain degree to the rumen wall as well (Mead and Jones, 1981)). Thus, bacterial cell counts of 10-10 cells/mL, normally determined by counting unattached cells under the microscope or by plating onto nonselective culture media, must be regarded as considerable underestimates of the total popu- lation. The same must be said for the many studies on quantitating individual species or physiological groups by traditional culture methods. Recent use of nucleotide probes directed toward 16S rRNAs of specific phylogenetic units(e.g kingdom, species, or strain) has shown great promise for in situ studies of ruminal microbial ecology(Stahl et al., 1988), and it has been applied successfully to in vitro studies of ruminal contents(Krause and Russell, 1996)and defined cocul- tures of ruminal bacteria(Odenyo et al., 1994) In general, ruminal bacteria are adapted to grow within a fairly nar- row range of environmental conditions, which is hardly surprising given the relative constancy of environmental conditions in the rumen. Ruminal bacteria are mesophilic but are highly stenothermal (i. e, they grow within a narrow temperature range). Most have growth optima near the mean ruminal temper ature of 39C, and many exhibit poor or no growth at room temperature. Most ruminal bacteria also have some requirements for vitamins and amino acids that are present in low concentrations in the ruminal liquor(Bryant, 1970) Many species also require branched-chain VFAs for growth(Dehority, 1971). Because environmental conditions are fairly constant and organic growth substrates are continuously available, few ruminal bacteria have develope the capability to form resistant morphological forms, such as cysts or spore In fact, although various endospore-forming Clostridium species have been isolated from the rumen, they are rarely abundant, and in some instances may simply be transients that have little involvement in ruminal metabolism (Varel etal.1995)
Microbiology of the Dairy Animal 13 major importance in ruminal metabolism (Table 5). Like any natural environment, the rumen probably contains many other species that have to now resisted isolation. Moreover, the recent use of phylogenetic criteria (i.e., sequences of evolutionarily conserved macromolecules such as 16S ribosomal RNAs) in taxonomy has altered microbiologists’ concepts of what constitutes a microbial species. As a result, new species will continue to be described, although the major functional groups of bacteria have probably been identified. The bacterial population can carry out essentially all of the enzymatic reactions that occur in the rumen with regard to digestion of feed materials, and bacteria are probably the main agents of ruminal digestion of carbohydrate and protein in feed. The pathways for conversion of carbohydrate (the ruminant’s major energy source) to different fermentation endproducts are shown in Figure 5. Total populations of bacteria in the rumen are hard to measure with accuracy, because a large fraction (perhaps up to 70%) of the cells are attached to solid surfaces [mostly to feed particles (Hobson and Wallace, 1982; Costerton et al., 1987), but to a certain degree to the rumen wall as well (Mead and Jones, 1981)]. Thus, bacterial cell counts of 107–109 cells/mL, normally determined by counting unattached cells under the microscope or by plating onto nonselective culture media, must be regarded as considerable underestimates of the total population. The same must be said for the many studies on quantitating individual species or physiological groups by traditional culture methods. Recent use of nucleotide probes directed toward 16S rRNAs of specific phylogenetic units (e.g., kingdom, species, or strain) has shown great promise for in situ studies of ruminal microbial ecology (Stahl et al., 1988), and it has been applied successfully to in vitro studies of ruminal contents (Krause and Russell, 1996) and defined cocultures of ruminal bacteria (Odenyo et al., 1994). In general, ruminal bacteria are adapted to grow within a fairly narrow range of environmental conditions, which is hardly surprising given the relative constancy of environmental conditions in the rumen. Ruminal bacteria are mesophilic but are highly stenothermal (i.e., they grow within a narrow temperature range). Most have growth optima near the mean ruminal temperature of 39°C, and many exhibit poor or no growth at room temperature. Most ruminal bacteria also have some requirements for vitamins and amino acids that are present in low concentrations in the ruminal liquor (Bryant, 1970). Many species also require branched-chain VFAs for growth (Dehority, 1971). Because environmental conditions are fairly constant and organic growth substrates are continuously available, few ruminal bacteria have developed the capability to form resistant morphological forms, such as cysts or spores. In fact, although various endospore-forming Clostridium species have been isolated from the rumen, they are rarely abundant, and in some instances may simply be transients that have little involvement in ruminal metabolism (Varel et al. 1995)
Table 5 Physiological Properties of Ruminal Bacteria Nutritional typ Substrates utilized Products formed Additional characteristics Fibrolytic Butyrivibrio fibrisolvens -d C, Cd, Xn, Xd,P For. But. Ac Lac. EtOH Clostridium C G, Hx For, Ac, But, CO, Form endospores Fibrobacter succinogenes C. Cd Suc. Ac For For. Ac EtoH. Lac. H, C. Cd. Xn. Xd Ac EtOH, H,, For CO Ruminococcus flavefaciens C Cd, Xn, Xd P Ac. Suc. H, For CO, Succinivibrio dextrinosolvens P Hx Suc. Ac. For Starch and sugar digesters Actinobacillus succinogenes Hx, G, F, Mt,x, A Succ, Ac, Pyr, EtoH Facultative anaerobe Eubacterium ruminantium Hx G, F Meoh P xd For Megasphaera elsdeni S, Mt, Sc, Gol, Pep For. Ac Pro. But, H, CO, Converts Lac Pro Prevotella ruminicola G, HXFX For, But, Lac, CO2 Ruminobacter amylophilus Suc For. Ac Hydrolyzes pectin d S, Cd, Hx, X, A, Gol, P, Pro, Ac, But, For, Suc, Lac, A major agent of Suc> Prot. Xd. Suc Pro and lac→Pro Streptococcus bovis S. G,. Hx. Prol Lac, EtoH, Form, Ac, CO2 Hydrolyzes pectin Succinomonas amylolytic S.G. M Suc, Ac, Pro, H Treponema bryant Hx.X. A. G, L. Mt For. Ac Suc Proteolytic/amino acid fe Ac, But, BCVFAs, NH
Table 5 Physiological Properties of Ruminal Bacteria 14 Weimer Nutritional type Gram Substrates utilizeda Products formedb Additional characteristics Fibrolytic Butyrivibrio fibrisolvens d C, Cd, Xn, Xd, P For, But, Ac, Lac, EtOH, CO2 Clostridium spp.c C, G2, Hx For, Ac, But, CO2 Form endospores Fibrobacter succinogenes C, Cd Suc, Ac, For Lachnospira multiparus P, G2 For, Ac, EtOH, Lac, H2, CO2 Ruminococcus albus C, Cd, Xn, Xd Ac, EtOH, H2, For, CO2 Ruminococcus flavefaciens C, Cd, Xn, Xd, P Ac, Suc, H2, For, CO2 Succinivibrio dextrinosolvens P, Hx Suc, Ac, For Starch and sugar digesters Actinobacillus succinogenes Hx, G2, F, Mt, X, A Succ, Ac, Pyr, EtOH Facultative anaerobe Eubacterium ruminantium Hx, G2, F, MeOH, P, Xd For, Ac, But, Lac Megasphaera elsdenii S, Mt, Sc, Gol, Pep For, Ac, Pro, But, H2, CO2 Converts Lac → Pro Prevotella ruminicola S, Cd, Hx, Xd, L, F, P, For, Ac, Pro, Suc Prot Pseudobutyrvibrio fibrisolvens d G2, Hx, F, X For, But, Lac, CO2 Ruminobacter amylophilus S, Mt Suc, For, Ac Hydrolyzes pectin Selenomonas ruminantium d S, Cd, Hx, X, A, Gol, P, Pro, Ac, But, For, Suc, Lac, A major agent of Suc → Prot, Xd, Suc H2 Pro and Lac → Pro Streptococcus bovis S, G2, Hx, Prot Lac, EtOH, Form, Ac, CO2 Hydrolyzes pectin Succinomonas amylolytica S, G, Mt Suc, Ac, Pro, H2 Treponema bryantii Hx, X, A, G2, L, Mt For, Ac, Suc Proteolytic/amino acid fer- menting Clostridium aminophilum Pep, AA Ac, But, BCVFAs, NH3, CO2