Fig. S1. Schematic of experimental set-up of the combined approach to recover diversity from magnetic collections and genomic analysis of single cells. After a magnetic enrichment from an environmental sample (A) a selective enriched collection of MTB was obtained (B). Using universal eubacterial primers almost full-length 16S rRNA genes were amplified and subcloned for sequencing (C). Every MTB morphotype was selected by single cell sorting applying micromanipulation under microscopic control (D). Genomic DNA of selected cells were amplified using the viral Φ29 DNA-polymerase by multiple displacement amplification (MDA). Amplified DNA served as template for 16S rRNA PCR allowing phylogenetic analysis of selected morphotypes (E). For genetic analysis of microsorted CS-05 cells genomic DNA was amplified a second time by the MDA, enzymatically debranched, checked for contaminations and subcloned for analysis (F).

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