Several methods are used to analyse 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.
- 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 which are assembled by computers. Using WGS, taxa can be defined at the species level. WGS is more expensive than 16S rRNA amplicon sequencing.
- Macrogen
- Microbiome Insights
- LC Sciences
- Swift Biosciences
- Omega Bioservices
- Novogene
- BGI
- Genewiz
- Mr DNA
- CD Genomics
- Illumina
- Laragen
- The Sequencing Center
- Eurofins
- MG-RAST
- 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) which 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.
- VSL#3 Probiotic distributed by Sigma-Tau Healthscience USA and VSL Pharmaceuticals
- Prescript Assist
- Visbiome
- Kombucha
- Ajuvis Labs
- Adare Pharmaceuticals
A drug, not a food, that is mined from host–microbe–dietary interactions in the gut.
These companies are using gut health and microbiome science to diagnosis, treat, or cure disease.
The use of bacteriophages or phages therapeutically as antimicrobial treatments against bacteria.
- Concentric (company)
- Indigo Agriculture
- AgBiome
- Pando Nutrition
- Seventure Partners
- Flagship Pioneering
- OrbiMed Advisors
- Alexandria
- Illumina Accelerator
- Johnson & Johnson Innovation
- Monsanto Growth Ventures
- Kaleido BioSciences
- Pivot Bio
- Second Genome
- Ample
- Animal Microbiome Analytics
- Anokion
- Artizan Biosciences
- Axial Biotherapeutics
- Biomx
- Caelus Health
- Cambrooke Therapeutics
- Inception IBD
- Indigo Agriculture
- Inocucor
- Mucovax
- PanTheryx
- Realbio Technology
- Rhythm Metabolics
- TargEDys
Timeline
People
Chris Kresser
David Perlmutter
Elizabeth Bik
Science Editor
Jessica Richman
Co-founder and CEO
Mark Pimentel
Executive Director
Mary Shenouda
Rhonda Patrick
Rob Knight
Professor, UCSD
Roshini Raj
Susan Lynch
Further reading
'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 microbes eat our medication
Caitlin McDermott-Murphy
Web
June 13, 2019
Gut microbiota are related to Parkinson's disease and clinical phenotype.
Scheperjans F , et al.
How Your Gut Microbiota Can Make You Fat (or thin)
Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial.
Paramsothy S , et al.
Natural compound coupled with specific gut microbes may prevent severe flu: Mouse study reveals how gut microbes fight influenza
Penn researchers single out bacterial enzyme behind gut microbiome imbalance linked to Crohn's disease
Personalized Nutrition by Prediction of Glycemic Responses
Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention
Israeli D, da Silva IT, Ward TL, Hjorth MF, Tolhurst G, Zhao L, Knights D, Chen T, Zmora N, Ana D, Long W, Kovatcheva-Datchary P, Juan José A, Ko G, Langin D, Mayer EA, Lim MY, Saris WHM, Blaak EE, Gonzalez A, Zeevi D, Lee K, Almeida-Pititto B, Gomes EP, Akrami R
Probiotic Bacteria Could Protect Newborns From Deadly Infection
Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota
Edgar, R. C., Tiedje, J. M., Matziouridou, C., DeSantis, T. Z., Bercik, P., Gill, K. D., M. Jucker, Jeffery, I. B., Cattaneo, A., Garrity, G. M., Berer, K., Taylor, V. H., Hooper, L. V., Bienenstock, J., V. Cheatham, Nguyen, T. D., Ishibashi, K., Love, S., Ishiwata, K., K. D. Mc Coy, Leal, M. C., Mahdi, A. A., Morelli, L., Klipper-Aurbach, Y., T. Harach
Research Links Gut Health to Neurodegeneration
Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study.
Staley C , et al.
The Big List of Microbiome Companies and Investors
Web
Documentaries, videos and podcasts
Companies
Avaxia Biologics
USA
Healthcare
Bezoar Laboratories
Probiotic
BioResource International
USA
Agriculture
DayTwo
Israel
Nutrition