Metagenomics terminology can be complex and confusing. To help decipher some of the basic terminology, we compiled a list of key terms and phrases you should know. Find some interesting Metagenomics FAQs below:
Microbes are tiny living things that are found all around us and are too small to be seen by the naked eye. They live in water, soil, and in the air. The human body is home to millions of these microbes, also called microorganisms.
A microbiome is the community of microorganisms—such as bacteria, archaea, fungi, as well as viruses—that inhabit an ecosystem or organism. The microbiome is the genetic material of all the microbes – bacteria, fungi, protozoa and viruses – that live on and inside the human body. The number of genes in all the microbes in one person’s microbiome is 200 times the number of genes in the human genome.
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.
Ribosomal RNA (rRNA) is a molecule in cells that forms a part of the protein-synthesizing organelle known as a ribosome and that helps translate the information in messenger RNA (mRNA) into protein. The three major types of RNA that are present in cells include rRNA, mRNA, and transfer RNA (tRNA).
Metagenome simply refers to a collection of all genomes/genetic materials from a particular environmental sample consisting of a bunch of living organisms. Metagenomics aims to study the metagenome.
16S rRNA genes
The 16S ribosomal RNA is the part of Small Subunit (the 30S subunit) of rRNA which is present in prokaryotic cells. DNA segment coding for 16S rRNA is called 16S rRNA gene. It contains multiple conserved regions and is widely used in sequencing in order to study phylogenetic relationships between different phyla, comparison among species between the same genus, identifying a certain bacterial sample in a culture etc.
Microflora is basically a community of microorganisms like bacteria and other life-forms (fungi, algae) that live in a particular habitat or inside the body of an organism. Like human gut microflora that refers to a microflora inside the human intestines.
Alpha & Beta Diversity
Alpha diversity is metagenomics refers to the number of different species that can be detected within a microbial ecosystem. Therefore Alpha diversity deals with only one particular ecosystem. Whereas, Beta diversity refers to the difference/diversity in microbial communities between different microbial ecosystems i.e. how different is the microbial composition of one environment than another.
Hyper Variable Region (HVR)
Bacterial 16S ribosomal RNA (rRNA) genes contain nine “hypervariable regions” (V1 – V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations.
Next Generation Sequencing
Next generation sequencing (NGS), massively parallel or deep sequencing are related terms that describe a DNA sequencing technology which has revolutionised genomic research. Using NGS an entire human genome can be sequenced within a single day.
In DNA sequencing, a read is an inferred sequence of base pairs (or base pair probabilities) corresponding to all or part of a single DNA fragment. A typical sequencing experiment involves fragmentation of the genome into millions of molecules, which are size-selected and ligated to adapters.
Analysis of sequence reads from microbial samples.
Bioinformatics analysis is performed in steps, where each next step deals with an output from a previous analysis step. For example, you must align the reads to a reference before analyzing levels of expression
In 16S metagenomics approaches, OTUs are cluster of similar sequence variants of the 16S rRNA marker gene sequence. Each of these cluster is intended to represent a taxonomic unit of a bacteria species or genus depending on the sequence similarity threshold. Typically, OTU cluster are defined by a 97% identity threshold of the 16S gene sequences to distinguish bacteria at the genus level.
DADA2 is a pipeline for analysis of exact sequence variants of 16S ribosomal sequences