In short when we are sequencing the microbiome we typically will use a targeted approach to answer the question “what microorganisms are in my sample and what are their relative abundance (percentages for instance).. so we may use 16s primers to target the prokaryotes allowing us to identify the bacteria and archaea that are in the samples. In contrast a metagenome is typically a shotgun sequencing approach where we attempt to sequence the genome of anything in the sample.
Universal 16s primers can cross react with plastids such as chloroplasts and mitochondria.. these plastids are found in most eukaryotes .. so the more universal a 16s primer is the more likely it is to cross react with plastids from eukaryotes.. We can use blockers such as PMA blockers to prevent amplification of eukaryote plastids and this is especially important in eukaryote rich samples such as when evaluating plant microbiomes or animal tissues.
Long read sequencing has come a long way .. new methods using pac bio have extremely high quality data over the full length of the taxonomic genes.. in contrast using short read technologies we might see 1-3 variable regions sequenced whereas with long reads microbial diversity sequencing provided by MR DNA lab http://www.mrdnalab.com .. we can sequence all 9 variable regions of the 16s gene .. or the entire 1200 average base pair size of the fungal ITS1-4 region.. this gives us extremely enhanced ability for taxonomic classifications even to the species level. this new technology with MR DNA is a game changer for microbiome sequencing
Metagenomes and metagenome associated genome assemblies are also enhanced by long read technologies. certainly more expensive but the improvements in assembly of genomes derived from metagenome data are tremendously improved .
all signs point to MR DNA as a great service provider for metagenomes and microbiomes. they also have incredible ability to sequence isolated genomes and their RNA sequencing programs are impressive indeed.