Latest estimates based on comparisons of 16S rRNA-encoding gene sequences from gut microbial ecosystems reveal a daunting genetic diversity, with at least 341 distinct phylotypes evident in the ruminal bacteria (Edwards et al. 2004) and 395 in the human intestine (Eckburg et al. 2005). Some metabolic functions are fairly widespread throughout the genetic spectrum, such as glucose utilization, for example. Others, however, are not. In spite of so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, which has so many health implications in terms of the fatty acid composition of ruminant-derived foods, is effectively carried out only by the Butyrivibrio group. Furthermore, the final step of biohydrogenation of C18 fatty acids, stearate formation, can be achieved only by a tiny sub-group of the butyrivibrios. Single bacterial species can also have very distinctive effects on the health of the host animal or human. Oxalobacter formigenes is a member of the ruminal and human intestinal microflora. It converts oxalic acid to formic acid, thus removing the potentially toxic oxalic acid, which is present at high concentrations in some foods such as rhubarb and spinach. In some individuals, however, O. formigenes cannot be detected, perhaps having been eliminated by antibiotic therapy. The resulting inability of the intestine to metabolise oxalic acid can cause kidney stones composed of calcium oxalate. Re-inoculation of these individuals with O. formigenes results in relief from disease. In ruminants, the conversion of tryptophan to indoleacetic acid and then to 3-methylindole causes bovine pulmonory disease. Elimination of the Lactobacillus species responsible for the indoleacetic acid to 3-methylindole conversion corrects the problem. Finally, perhaps the most celebrated example of the difference a single species can make is the ‘mimosine story’ in ruminants. Mimosine is an amino acid that is found in some plants, including Leucaena leucocephala. Leucaena had been identified as a potentially useful protein-rich feedstuff for Australian livestock. However, the mimosine caused thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were not toxic to ruminants in other continents led to the discovery of Synergistes jonesii, which, when inoculated into Australian cattle, metabolised 3-hydroxy-4(1H)-pyridone and protected the animals from toxicity. Thus, in the almost overwhelming flood of information that emanates from molecular microbial ecology and genomics of gut bacteria, it should never be forgotten that this vast community consists of many important metabolic niches inhabited by species each with specific metabolic capability.