Phylogenetic Placement of Community Members of Human Colonic Biota

Abstract

The human colonic biota is a natural community of bacteria that are not only symbiotic but constitute an important host defense. Extensive work done two decades ago led to the conclusion that the colonic ecosystem consists of phylogenetically diverse taxa including both gram-positive and gram-negative elements. However, it has been possible only recently to accurately determine the phylogeny of these organisms and to study them without using culture-based methods. In a recent study of the human colonic biota in which standard nonselective culture methods were compared with amplification and cloning of rDNA [1], both methods were found to be biased, but both detected organisms with similar phylogenetic distributions. Most of the organisms fell into only four clusters. Two of those clusters were the genera Bacteroides and Bifidobacterium. The other two clusters fell into two separate branches of the phylogenetic tree containing organisms that have been classified in several different genera including Clostridium, Eubacterium, Fusobacterium, Peptostreptococcus, and Ruminococcus. Studies of other bacterial communities have also generally shown limited phylogenetic diversity within an ecosystem. Herein, we more precisely map the organisms found in the above-mentioned rDNA-based study of one healthy volunteer and compare the results with the placement of organisms found in earlier investigations involving the nonselective isolation and identification of human colonic biota. In earlier studies, Moore and Holdeman [2] and Holdeman et al. [3] described the numerically predominant biota of 20 Japanese Hawaiians and three astronauts. The standard for placement of all organisms in the present study was their location in the phylogenetic tree generated in the May 1995 release of the Ribosomal Database Project (RDP) data base [4]. The placement of organisms that belonged to named taxa available in the RDP was established by determining their phylogenetic location in that reference. Organisms not present in the RDP but with available sequences were placed by using the Genetic Data Environment software package on a Sun Sparcstation 2 data base (Sun Microsystems, Mountain View, CA) to align their sequences with those of known organisms. Aligned sequences were analyzed phylogenetically in the same software package running a parsimony analysis. As shown in table 1, all the studies cited gave similar results in that most of the biomass found in the human colon fell into just four phylogenetic clusters. Cluster 1 consisted of the genus Bacteroides, well known as accounting for more than one-quarter of all isolates [2, 3, 5]; this genus falls on two contiguous branches of the RDP tree. The genus Bifidobacterium was designated as cluster 2. Bifidobacterium falls into one RDP group of gram-positive bacteria with a high guanine plus cytosine (G + C) content,