Several methods are used to analyze microbiota and identify and quantify the members of a microbial community. Analysis can be done at the DNA, RNA, protein, and metabolite level.
There are several methods/techniques for DNA sequencing and RNA sequencing of microbiota and individual microorganisms present in the human microbiome. Next-generation sequencing (NGS) applied to DNA in human feces samples is the predominant method, and there are several strategies for NGS of the microbiome.
Sequencing of microbiomes is sometimes referred to as metagenomics or metagenomic sequencing. The term metagenomics refers to gene-level and genome-level characterization of communities and their members using genomics methods and other “omics” methods that do not require cultivation of organisms.
NGS platforms sequence millions of small DNA fragments in parallel. Bioinformatics uses sequence maps to figure out where the sequenced fragments fit. NGS can sequence entire genomes or target specific regions. Amplicon sequencing targets specific regions by PCR, which are then sequenced with NGS.
- 16s sequencing: The highly conserved region of the genome that codes for 16S ribosomal RNA in bacteria and archaea is amplified by PCR and sequenced. Specific sequence differences correspond to a taxa at an operational taxonomic unit (OTU). OTUs correspond to organisms at the phyla and genera level and can be less precise at the species level.
- 18s sequencing: Used for eukaryotes, homologous to the 16S rRNA region used for bacterial and archaea.
- Internal transcribed sequence (ITS): ITS sequences ITS1 and ITS2 are used for amplicon sequencing and identification of fungal DNA.
In whole genome shotgun sequencing (WGS), also called metagenomic shotgun sequencing, all genes in all organisms within the sample are sequenced. Random primers are used to sequence regions of the genome in overlapping reads that are assembled by computers. Using WGS, taxa can be defined at the species level. WGS is more expensive than 16S rRNA amplicon sequencing.
- Microbiome Insights
- LC Sciences
- Swift Biosciences
- Omega Bioservices
- Mr DNA
- CD Genomics
- The Sequencing Center
- HUMAnN: The HMP Unified Metabolic Analysis Network
- MEGAN (MEtaGenome ANalyzer)
- EBI Metagenomics
Metatranscriptomic analysis is concerned with transcribed genes, which provides a snapshot of active genes within a microbial community.
- meta-total RNA sequencing (MeTRS): MeTRS requires a reverse transcription reaction step to convert it into cDNA for sequencing.
- RNA-Seq with NGS: Conversion of mRNA to cDNA is followed by NGS.
- SSU rRNA-based RNA-seq: The target is small subunit rRNA.
The investigation of all proteins in one organism is termed proteomics, or metaproteomics when multiple organisms are analysed.
- MALDI-TOF mass spectrometry: Matrix assisted laser desorption ionization (MALDI) is a form of mass spectrometry that is used to generate a protein mass fingerprint (PMF) that is compared to a database. Mass spectrometry is a technique that uses ionization to categorize chemical compounds based on their mass to charge ratio. Microbial applications usually use time of flight (TOF) analyzers to measure mass.
- LC‐MS/MS (liquid chromatography combined with mass spectrometry)
- Shotgun metaproteomics
Metabolomic research is concerned with the metabolic profile including identification and classification of metabolites produced by microbes and deducing the biochemical pathways of those metabolites. The main technologies used in metabolomics are mass spectrometry and nuclear magnetic resonance spectroscopy. Metametabolomics is the analysis of metabolites in a community of microbes.
- GC-MS (Gas Chromatography Mass Spectrometry)
- Tandem Mass Spectral Library (NIST)
- Wiley Registry of Mass Spectral Data
- Human Metabolome Database
- Global Natural Product Social Molecular Networking (GNPS)
Bacteria, archaea, yeast, fungi, protists, helminths and viruses are all found in the human gut.
- Human virome
- The gut phageome is the community of phage viruses associated with the gut microbiome
- Many commensal and pathogenic gut bacteria possess invertons which help them colonize and/or contribute to persistance of antibiotic resistance
- Parasporobacterium - Irritable Bowel Syndrome, Down Syndrome
- Crohn's disease
- Ulcerative colitis
- MetaHIT (Metagenomics of the Human Intestinal Tract)
- Human Gastrointestinal Bacteria Genome Collection (HBC)
- Human Microbiome Project (HMP)
- International Human Microbiome Standards (IHMS) project
- The Microbiome Quality Control project
Probiotics are a live microbe. Some probiotics are classified as medical foods. Kombucha is a popular probiotic drink.
Prebiotics are classified as compounds in food that positively influence the composition of the gut microbiome.
Pharmabiotics are a drug, not a food, that is mined from host–microbe–dietary interactions in the gut.
Bioinformatics companies researching the microbiome
These companies are using gut health and microbiome science to diagnosis, treat, or cure disease.
Much of the products for animal and pet microbiome health are focused on diet change, antibiotics, and steroids that are able to provide temporary assistance to the pets microbiome. Whereas the innovations into animal microbiome health are focused on supplements to restore the pet's microbiome and supplements to combat digestive issues to restore an animal's microbiome balance. Other innovations are in pet and animal foods that have ingredients including oligosaccharides and glycopeptides.
Companies investigating the relationship between the microbiome and skincare
Companies investigating the relationship between the microbiome and therapeutics
The use of bacteriophages or phages therapeutically as antimicrobial treatments against bacteria.
Companies working on AgTech or livestock research related to the microbiome
- Seventure Partners
- Flagship Pioneering
- OrbiMed Advisors
- Illumina Accelerator
- Johnson & Johnson Innovation
- Monsanto Growth Ventures
- Kaleido BioSciences
- Pivot Bio
- Second Genome
- Animal Microbiome Analytics
- Artizan Biosciences
- Axial Biotherapeutics
- Caelus Health
- Cambrooke Therapeutics
- Inception IBD
- Indigo Agriculture
- Realbio Technology
- Rhythm Metabolics
'Ridiculously healthy' elderly have the same gut microbiome as healthy 30-year-olds
Computational methods for high-throughput comparative analyses of natural microbial communities.
Preheim SP , et al.
Exercise changes gut microbial composition independent of diet, team reports
Fecal Microbiota Transplantation
Gut bug enzyme turns blood into type-O