In search of an uncultured human-associated TM7 bacterium in the environment

Abstract

We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed microbial communities.

Figure 1. Neighbor-joining phylogenetic tree of Candidate Division TM7 with 255 TM7 phylotypes, where 160 are identified as being environmental, 42 as animal-associated, and 53 as human-associated, with a total of 208 unique OTUs.

The bar chart above the outer ring represents the clone counts for each of the 16 phylotypes in our study. Subdivisions 1 and 2 are marked with a gray banner on the inner border of ring. Bootstrap values of major branches are indicated according to legend. An interactive version of this tree (http://www.phylotouch.com/tm7), developed with jsPhyloSVG , includes meta-analysis data such as distance matrices and links to sequences and publications.

Figure 2. Quantification of Bacteria, TM7, and TM7a-like phylotypes by (A) qPCR and (B) FISH.

Average number of (A1 and B1) Bacteria cells mL⁻¹, (A2 and B2) Candidate Division TM7 cells mL⁻¹, and (A3 and B3) TM7a-like cells mL⁻¹. Closed circles indicate undetermined quantification values. Error bars represent standard error of the mean.

Figure 3. Micrographs depicting TM7 (red) and TM7a-like (blue) in the total microbial community (green) of activated sludge samples through (A–B) FISH and STARFISH (C1–C2).

(A) TM7a-like short filamentous cells with three segments labeled with both TM7 and TM7a probes. (B) TM7 and TM7a-like cells (latter marked with arrows) as coccobacilli and cocci; two insets show TM7a diplo-bacillus morphologies commonly found in sludge. (C) TM7 long filamentous cells (C1, red-orange) taking up a mixture of dissolved tritiated amino acids (C2, bright field) through micro-autoradiography (STARFISH) assay, suggesting TM7 are metabolic active in wastewater. Scale bars = 5 µm.