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The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. We found two highly prevalent core phylogroups cores 1 and 2 , belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution.
Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health.
The interaction between the host and its gut microbiota is of fundamental importance for host health and disease. Recent research has shown that human intestinal microbiota can be linked to obesity Ley et al. It is hypothesized that the microbiota is composed of a variable part that differs between individuals and a stable part that is found in the vast majority of human beings Turnbaugh et al. Factors affecting the variable part of the microbiota are now rather well documented and depend on, among others, the environment we are exposed to, our genetic profile and our diet Alm et al.
Defining the stable part of the microbiota core microbiota has proven to be much more difficult Turnbaugh et al. Limitations with previous studies, however, are that they are based on either searching for phylogroups at predefined evolutionary depths or comparison of phylogenetic trees. Owing to the clonal growth of bacteria, that is, asexual reproduction, there is no real rationale for defining phylogroup depths Doolittle and Zhaxybayeva, The current discussion about the existence of operational taxonomic units OTUs or predefined taxonomic core phylogroups is therefore more or less semantic, that is, depending on defined phylogroup cutoff values.
The main problem with the phylogenetic tree-based comparative approaches, on the other hand, is the uncertainties in tree construction and the nearly infinite combinatorial possibilities of phylogenetic trees Liu et al. Thus, it is likely that the current approaches have failed to recognize important ancient co-evolution events between the core microbiota and the host Turnbaugh et al. The aim of this work was to search for a human core microbiota independent of both predefined phylogroup depths and phylogenetic trees.