I’ve been blogging elsewhere about microbiome research, and collecting a ridiculous number of links and articles about it. I’ve been lucky enough to have long conversations with some of our faculty who are publishing in this area. This week one of the faculty asked me to proofread a chapter they are writing about the microbiome, which was a great treat for me. Beautifully written, engaging and educational, I’m really looking forward to seeing it in print.
Midway through the process of writing about the microbiome, the faculty member was asked to include the virome. Oh. Well, let’s mix things up a bit, shall we? By the time I saw the draft, the mycobiome had also been added in. A brief ‘glossary’ for those not currently working in this space. Also note that because of the lack of a true glossary for some of these terms, I am intuiting definitions from a scan of the writings using the term. In other words, doing the best I can, but part of this is sort of made up*, even though the terms exist and are being used. While we don’t have enough for an alphabet book, there were enough that I felt compelled to alphabetize.
Biome = community of living things in a particular space or habitat
Exobiome = a community of living things external to the Earth’s air space
Exposome = measuring and assessing health impacts of environmental exposures external to the individual (beginning in utero)
Genome = genes of an organism
Metabolome = “small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules” [Wikipedia]
Microbiome = genomes of a community of microbial or bacterial living things etc.
Mycobiome = genomes of the community of fungi …
Parisitome = genomes of the community of parisites …
Pathobiome = genomes of the pathological components of a microbiome; behaviors and changes in a microbiome that lead it toward a pathological state
Proteome = proteins produced by a genome
Retrovirome = genomes of the community of retroviruses …
Transcriptome = a subset of the genome comprised of the transcripts or various types of RNA fragments from a given cell
Virome = genomes of the community of viruses …
Xenome = genomes of microbiomes involved in xenografts or xenotransplants
And then there are the specific microbiomes for body regions, such as the vaginal biome, oral microbiome, aural microbiome, nasal microbiome, and the skin microbiome. I’m not aware of specialized terms for microbiomes of external locations (hospital, home, school, jungle, waterways, etc.) and other species (canine, feline, various bird species, various rodent species, etc). Most of the other Omes also are studied across species and locations. And there are more.
Here’s a tutorial for an introduction to just the genomics part.
The Human Genome, DNA, Chromosomes & Gene Structure – Excellent genomics tutorial & figs by Dr. Carol Guzé – http://t.co/puUDdgJi7T
— Awesomics (@Awesomics) July 27, 2013
And while this isn’t a tutorial, these are videos from the recent conference on Human Microbiome Science: Vision for the Future. That should give you an overview of that portion.
— Andrew Su (@andrewsu) July 25, 2013
So let’s take a look via Twitter at some of the other “Ome”s and omics. As you might guess, these are BUSY topics, with formal Twitter chats discussing fine points of methods, sharing articles, conference presentations, news, and general buzz.
— BF Francis Ouellette (@bffo) July 26, 2013
— Jason Anthony Tetro (@JATetro) July 30, 2013
— Genomics Trap (@GenomicsTrap) August 1, 2013
— Genome Biology (@GenomeBiology) July 29, 2013
— McGill Alumni (@McGillAlumni) August 1, 2013
— BioTechniques (@MyBioTechniques) June 17, 2013
— Bioline (@thepcrcompany) August 1, 2013
— Mcknick (@mcknick85) July 31, 2013
— Robert West PhD (@westr) July 22, 2013
— Jonathan Eisen (@phylogenomics) July 27, 2013
— Marco Manca (@markomanka) July 31, 2013
— Genome Biology (@GenomeBiology) July 26, 2013
— Galen Bodenhausen (@GVBodenhausen) July 9, 2013
— ironorehopper (@ironorehopper) July 2, 2013
— Dominick Lemas (@dominicklemas) June 9, 2013
— Robert West PhD (@westr) July 30, 2013
— Gaurav Arora (@GA77tweets) July 22, 2013
— Eric Topol (@EricTopol) July 31, 2013
— Robert West PhD (@westr) July 30, 2013
— Sherri Rose (@sherrirose) July 25, 2013
— Michael Schatz (@mike_schatz) July 31, 2013
— Genome Biology (@GenomeBiology) July 31, 2013
— Genome Biology (@GenomeBiology) August 1, 2013
— Adam Phillippy (@aphillippy) July 31, 2013
— Eric Topol (@EricTopol) July 30, 2013
— Nick Loman (@pathogenomenick) May 23, 2013
— Matt Landau (@Matt_Landau) May 1, 2013
An accessible database for mouse and human whole transcriptome qPCR primers. http://t.co/UOwz2Z0gIY
— Nicholas Mark Murphy (@NicholasMMurphy) March 31, 2013
— humanexposomeproject (@exposome) July 3, 2013
— Ken Kubo (@kmkubo) July 19, 2013
— Microbiome (@MicrobiomeJ) July 15, 2013
— Seth Bordenstein (@Symbionticism) July 25, 2013
— Robert Brucker (@liveinsymbiosis) July 23, 2013
— Seth Bordenstein (@Symbionticism) July 28, 2013
— Seth Bordenstein (@Symbionticism) July 31, 2013
"The CRAPome: a contaminant repository for affinity purification–mass spectrometry data" http://t.co/Mw00xsvmKe
— Brett Baker (@archaeal) July 31, 2013
Personally, I find this hysterically funny.
FYI I'm claiming the name: "gentillome" – the collection of biological entities working together in harmony to attain health. #microbiome
— Jason Anthony Tetro (@JATetro) July 26, 2013
* A proper glossary for these types of terms was just brought to my attention by Ian Bosdet.
— Ian Bosdet (@ianbosdet) August 2, 2013