The Bowel Microbiota and Inflammatory Bowel Diseases

Table 1

Common terms used in bowel microbial ecology.

Phylogeny	The history of organismal lineages as they change through time. It implies that different species arise from previous forms via descent, linking all forms of life.
Dysbiosis	A term generally used in relation to the bowel biome indicating an imbalance in the composition of the microbiota.
Firmicutes	A phylum of bacteria, most of which have gram-positive cell wall structure. The principal genera detected in human faeces are Clostridium, Eubacterium, Anaerostipes, Coprococcus, Dorea, Lachnospira, Roseburia, Faecalibacterium, Ruminococcus, Subdoligranulum, and Coprobacillus.
Bacteroidetes	A phylum of bacteria that have gram-negative cell wall structure. The principal genera detected in human faeces are Bacteroides, Parabacteroides, and Alistipes.
Actinobacteria	A phylum of gram-positive bacteria that includes, amongst others, the genera Bifidobacterium and Collinsella that are often detected as members of the bowel microbiota of humans.
Proteobacteria	A phylum of bacteria that includes Escherichia coli, a common facultatively anaerobic species in the bowel.
Bacteroides-Prevotella cluster	A broad phylogenetic classification comprising gram-negative, anaerobic species forming a major portion of the bowel microbiota.
Clostridial cluster XIVa.	A broad phylogenetic classification comprised of several genera and species of gram-positive bacteria, not exclusively clostridia.
Clostridial cluster IV	A broad phylogenetic classification comprised of several genera and species of gram-positive bacteria, not exclusively clostridia.
Enrichment culture	An understanding of the environmental conditions favored by an organism, together with genetic clues about the microbe’s abilities is used to guide the design of culture media and conditions.
Probiotic	Live microorganisms which when administered in adequate amounts confer a health benefit on the host.
Prebiotic	A dietary supplement of nondigestible carbohydrate (inulin and fructo-oligosaccharides are the best known) that can be metabolized by particular bacteria in the human colon.