L17: the Human Microbiome Flashcards
What is the microbiome? What does it contain?
collection of microbes, their genetic information and their gene products within a colonised site.
Contains:
- bacteria
- archaea
- virus
- fungi
- protozoa
Why does Next Generation Sequencing have a huge impact on the study of the microbiome?
before bacteria needed to be cultivated, isolated, then DNA extracted and sequenced, this wouldn’t allow uncultivatable bacteria to be sequenced.
In NGS don’t need to isolate bacteria, can identify straight away
What is Single-cell microbiome sequencing?
an approach that allows for the culture-independent whole-genome sequencing of microorganisms. Cells are isolated through flow cytometry, compartmentalised in microwells, bacteria lysed and genome amplified
What is metagenomic sequencing? What are its strengths and weaknesses?
Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample. Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample.
Strengths:
- inclusion of a large number of samples
- time to result
- detection of differentially abundant taxa
- detection of uncultured bacteria
Weaknesses:
- Extraction bias (the bacterial diversity that is captured is a function of the extraction protocol
- cannot discriminate between live bacteria and transient DNA
- minority populations are insufficiently detected
What is culturomics sequencing?
‘Culturomics’ uses multiple high-throughput culture conditions with mass spectroscopy or 16S ribosomal RNA sequencing for the identification of previously unculturable bacterial species.
Multiple culture conditions mimic the natural habitats.
- new approach –> high-throughput culture
- potential to detect minority populations
- provides strains –> characterization of new species
What is metatranscriptomics?
Metatranscriptomics serves to analyze the entire transcriptome of an environment to obtain a comprehensive view of gene expression profiles and functional data.
What is metabolomics?
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms.
Weakness - hard to tell where the metabolite is coming from, i.e. could be from food
What is multi-omic analysis?
Multiomics, multi-omics, integrative omics, “panomics” or “pan-omics” is a biological analysis approach in which the data sets are multiple “omes”, such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome (i.e., a meta-genome and/or meta-transcriptome, depending upon how it is sequenced)
Metaomics methods summary
See L17 slides 31 and 32
