Increases in Enterobacteriaceae have been observed in human IBD and murine colitis as well as after antibiotic treatment and infection by enteric pathogens (Lupp et al., 2007; Hill et al., 2010; Stecher et al., 2010). Because the relative abundance of Enterobacteriaceae Sorafenib B-Raf increases under a variety of treatments, this group seems to be a general indicator of a disrupted intestinal microbiota, though not necessarily a trigger of colitis (Bloom et al., 2011). Differences between DSS-treated wt and STAT1?/? mice most likely reflect the differences observed in the degree of inflammation. Dramatic dynamics within the abundant Lachnospiraceae Molecular surveys of intestinal microbiota commonly classify sequences to higher-level taxonomic groups (for example, phylum, order and family) to characterize community composition and dynamics (Ley et al.

, 2005; Frank et al., 2007; Lupp et al., 2007). This approach assumes that all organisms belonging to the same taxon fill the same, or similar, ecological niche and display weak intra-taxon competition. A recent study of the mouse gut microbiota provided partial support for this assumption by demonstrating a relationship between phylogenetic similarity and co-occurrence, which has been succinctly captured by the maxim ��like will to like’ (Stecher et al., 2010). There is, however, no clear threshold for the level of genetic relatedness necessary for cohesive or repulsive ecological forces to act upon organisms (Achtman and Wagner, 2008), and it is therefore impossible to predict a priori if all members of a phylogenetic group have similar functional properties.

To examine this at the level of phylogenetic resolution currently attainable with 454 sequencing reads of 16S rRNA genes, we used a similar approach as Stecher et al. (2010) to compare the correlation Cilengitide of phylotype relative abundances across mouse gut microbiota samples with their 16S rRNA sequence dissimilarity for all phylotype pairs. Relationships between most phylotype pairs at all levels of genetic distance seemed to be neutral in these mouse gut communities (Figure 2a). Positive and negative correlations were nevertheless evident at all levels of genetic distance, but strong negative correlations, indicating antagonistic interactions, were hardly apparent for very similar phylotypes (>95%). One example of antagonism between distantly related organisms in the human intestines is how Bacillus thuringiensis produces a narrow-spectrum bacteriocin, thuricin CD, which specifically targets Clostridium difficile (Rea et al., 2010).