Summary Catalysed reporter deposition–fluorescence in situ hybridization ( CARD‐FISH ) is a powerful approach to quantify bacterial taxa. I n this study, we compare the performance of the widely used B acteroidetes CF 319 a probe with the new CF 968 probe. In silico analyses and tests with isolates demonstrate that CF 319 a hybridizes with non‐ B acteroidetes sequences from the R hodobacteraceae and A lteromonadaceae families....

Summary Sequencing of 16S rDNA polymerase chain reaction ( PCR ) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR . Here we show that 16S rDNA fragments derived from Illumina‐sequenced environmental metagenomes ( mi tag s) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryo...