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The quantification of relative and absolute taxa-specific abundances in complex microbial communities is crucial for understanding and modeling natural and engineered ecosystems. Many errors inherent to this quantification are, though well-known, still insufficiently addressed and can potentially lead to a completely different interpretation of experimental results. This review provides a critical assessment of next generation sequencing (NGS) of amplicons and quantitative real-time PCR for the quantification of relative and absolute taxa-specific genome abundances. Starting from DNA extraction, the following error sources were considered: DNA extraction efficiency, PCR-associated bias, variance of strain-specific 16S rRNA operon copy number per genome, and analysis of quantitative real-time PCR and NGS data. Tools and methods for estimating and minimizing these errors are presented and demonstrated on published data. In conclusion, amplicon sequencing and qPCR of 16S rRNA genes are valuable tools to determine relative and absolute taxa-specific genome abundances, but results can deviate by several orders of magnitudes from the true values if the reviewed error sources are ignored. Many of these errors can be minimized in a cost-efficient manner and large errors can be easily identified by plausibility checks as shown in this review. Finally, the accurate conversion of genome abundances to cell numbers and microbial biomasses was pointed out as an important future research topic for the integration of PCR-based abundances into mathematical models.

The gut microbiome is not only an indicator of different pathologies, but it also influences metabolism and overall health of the host. Recently, microorganisms inherent to the gut microbiome, such as Listeria monocytogenes, Enterococcus faecalis and Clostridium cochlearium, were demonstrated to be electroactive, i.e. to perform extracellular electron transfer (EET). To further explore the presence of electroactive microorganisms in the gut microbiome electrochemical enrichment starting from mouse feces was performed. Open circuit, abiotic and autoclaved inoculum controls were run in parallel. A maximum current density of 122±23 µA cm−2 at low coulombic efficiency ( 1%) was achieved. The presence of biofilms at the anode and microbial electrochemical activity with a formal potential of EET of 0.23±0.01 V vs. Ag/AgCl sat. KCl was demonstrated using fluorescence microscopy and cyclic voltammetry. The 16S rRNA gene sequencing and PCR-free Nanopore sequencing showed the enrichment and dominance of Shigella flexneri.