In total, 467% (n=841) of all investigated

In total, 46.7% (n=841) of all investigated EPZ-6438 price Escherichia coli clones (n=1800) resulted in positive PCR products using the Com2xf/Ac1186r primer system and 48.8% (n=879) using the SC-Act-235aS20/SC-Act-878aA19 primer system. However, although 738 clone inserts (87.75%) were correctly assigned to actinobacterial sequences using primer system Com2xf/Ac1186r, 56 of the obtained PCR products (6.6%) could not be used for analyses because of the low quality of sequences and 26 clone inserts (3.0%) were most closely related to as yet uncultured bacteria. Altogether, just 23 clone

inserts (2.7%) were most closely related to non-Actinobacteria. Employing primer system SC-Act-235aS20/SC-Act-878aA19, PI3K inhibitor 689 (78.4%) of the clone sequences were correctly assigned, 61 (6.9%) were not usable for analyses, 32 (3.6%) were assigned to as yet uncultured bacteria and 97 clone inserts (11%) were most closely related to non-Actinobacteria. Both primer systems detected a large variety of Actinobacteria within water-damaged building material (Fig. 1). The majority of clone inserts were most closely related to Amycolatopsis and Pseudonocardia. Sequences of these genera were detected both most frequently and most abundantly in the investigated clone libraries of the different building material samples. Thirteen different genera were detected by only one clone insert. Investigations

concerning the differences in the actinobacterial community within water-damaged building material samples show the applicability of the new primer system for SSCP fingerprint analyses (Fig. 2). A high diversity in the actinobacterial community within the different samples was detected displayed by the different fingerprint pattern. The cluster analyses of the SSCP fingerprint analyses showed Cytidine deaminase no correlation between the population of Actinobacteria and the investigated material types – plaster, styrofoam or mineral material. The class Actinobacteria is one of the major phyla

within the domain Bacteria. At the time of writing, this class comprises 219 different genera, 48 families and 13 suborders (Zhi et al., 2009). Because of the high diversity, it is very difficult to develop a primer system that amplifies all actinobacterial 16S rRNA gene sequences. In silico testing of the developed primer resulted in a theoretical detection of around 50% of the actinobacterial species listed in the RDP database. But it is also quite possible that more sequences will be detected in the PCR detection system in spite of few mismatches. Allowing zero mismatches, only 0.6% of totally detected sequences were those of nontarget bacteria. Increasing the amount of detectable target (actinobacterial) sequences by modification of the primer system was always accompanied by an increase in detection of nontarget sequences.

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