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.
Understanding the Microbiome and Metagenome: Key Differences and Applications
The terms “microbiome” and “metagenome” are often used interchangeably, but they represent distinct aspects of microbial research. Understanding the nuances between these concepts is crucial for designing studies and interpreting results, especially in fields such as health, agriculture, and environmental science.
The microbiome refers to the entire community of microorganisms inhabiting a specific environment, such as the human gut, soil, or ocean. It encompasses bacteria, archaea, fungi, viruses, and other microorganisms, highlighting their diversity and interactions. Microbiome studies often focus on 16S rRNA or ITS sequencing to classify and identify these microbial communities, providing insights into their composition and ecological roles.
In contrast, the metagenome delves deeper, examining the collective genetic material of all microorganisms in a sample. Metagenome sequencing uses high-throughput technologies, such as Illumina and PacBio, to analyze not just taxonomic diversity but also functional potential. This approach uncovers the metabolic pathways, resistance genes, and biochemical capabilities of microbial communities, making it a powerful tool for applications like bioremediation, nutrient cycling, and disease research.
By combining microbiome and metagenome approaches, researchers can achieve a holistic understanding of microbial ecosystems. For example, a microbiome study might reveal shifts in bacterial populations in a diseased gut, while metagenomic analysis identifies the genes involved in disease progression or resistance. At MR DNA, we offer advanced sequencing and bioinformatics solutions to explore both microbiome composition and metagenomic functionality, empowering discoveries across diverse scientific fields. Learn more at www.mrdnalab.com.