Gut microbiology – broad genetic diversity, yet specific metabolic niches

Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite 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, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the ‘mimosine story’ in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability.