To address the long-standing need for more precise descriptions of natural microbial ecosystems, 16S rRNAs were used to track certain species and phylogenetically coherent groups of microorganisms in their natural setting without culturing. Speciesand group-specific 16S rRNA-targeted oligonucleotide hybridization probes were developed to enumerate various strains of Bacteroides succinogenes and Lachnospira multiparus-like organisms in the bovine rumen before, during, and after perturbation of that ecosystem by the addition of the ionophore antibiotic monensin. Based on probe hybridization, relative numbers of L. multiparus-like organisms were depressed about 2-fold during monensin addition and demonstrated a transient 5to 10-fold increase immediately after removal of the antibiotic from the diet. The most pronounced population changes were observed among different strains of B. succinogenes, as evaluated by three hybridization probes. One probe hybridized to all strains, whereas the other two identified genetically distinct groups represented by strains isolated from the rumen and from the ceca of nonruminants. The rumen-type strains predominated on most days (ca. 0.2 to 0.8% of total ribosome numbers). Their proportion transiently increased about fivefold immediately after the addition of monensin to the feed and then transiently fell below the average premonensin level. During this time (ca. 2 weeks after monensin addition) the cecal type predominated (ca. 0.1 to 0.2%). Cultural enumeration of B. succinogenes on nonselective agar and by observing clearings in cellulose agar media were largely unsuccessful due to the low number of organisms present and the predominance of other cellulolytic species. The results demonstrate the utility of rRNA-targeted hybridization to monitor complex microbial communities and are most consistent with the hypothesis that altered microbial metabolism, rather than altered population composition, is primarily responsible for changes in ruminal fermentation patterns resulting from the feeding of monensin.

Four Holstein cows were used in a 4 x 4 Latin square design to investigate the effects of soybean hulls and lignosulfonate-treated soybean meal on ruminal fermentation and nutrient passage to the duodenum. Diets contained 32% corn silage, 19.8% alfalfa-grass hay, and 48.2% concentrate (DM basis). Treatments, arranged in a 2 x 2 factorial, were concentrate mixes based on 1) corn and soybean meal, 2) corn and treated soybean meal, 3) soybean hulls and soybean meal, and 4) soybean hulls and treated soybean meal. Individual protein supplements supplied 40% of dietary CP, and corn or soybean hulls constituted 28% of dietary DM. Intake of OM (mean 18.9 kg/d) was similar among treatments, but intake of NDF was 42% greater, and intake of nonstructural carbohydrate was 55% less, for cows fed soybean hulls. Passage of OM to the duodenum was similar among diets, but flow of NDF was 43% greater, and flow of nonstructural carbohydrate was 56% less, for cows fed soybean hulls. Ruminal pH was similar, but total concentrations of VFA increased 7% when soybean hulls replaced corn. Ruminal digestion of dietary CP was 15% less for cows fed treated soybean meal, but bacterial N flows were similar among treatments. Soybean hulls were digested to a similar extent as corn, but few interactions occurred between supplemental carbohydrate and protein sources.

The fibrolytic microbiota of the human large intestine was examined to determine the numbers and types of cellulolytic and hemicellulolytic bacteria present. Fecal samples from each of five individuals contained bacteria capable of degrading the hydrated cellulose in spinach and in wheat straw pretreated with alkaline hydrogen peroxide (AHP-WS), whereas degradation of the relatively crystalline cellulose in Whatman no. 1 filter paper (PMC) was detected for only one of the five samples. The mean concentration of cellulolytic bacteria, estimated with AHP-WS as a substrate, was 1.2 X 10(8)/ml of feces. Pure cultures of bacteria isolated on AHP-WS were able to degrade PMC, indicating that interactions with other microbes were primarily responsible for previous low success rates in detecting fecal cellulolytic bacteria with PMC as a substrate. The cellulolytic bacteria included Ruminococcus spp., Clostridium sp., and two unidentified strains. The mean concentration of hemicellulolytic bacteria, estimated with larchwood xylan as a substrate, was 1.8 X 10(10)/ml of feces. The hemicellulose-degrading bacteria included Butyrivibrio sp., Clostridium sp., Bacteroides sp., and two unidentified strains, as well as four of the five cellulolytic strains. This work demonstrates that many humans harbor intestinal cellulolytic bacteria and that a hydrated cellulose source such as AHP-WS is necessary for their consistent detection and isolation.

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