(A hopefully useful, but definitely not über technical, microbial-related set of definitions)

While blog-planning, I decided to include a blog post containing microbiology-related definitions. Some define common techniques used in lab research, others are Microbiology-related, and still others define the microbes/microbial components themselves. If you are a scientist (kudos!) you probably can skip these! And let me know if there are definitions I should include.

Cell culture: The process of growing and maintaining cell lines in a laboratory setting. Common techniques utilized in cell culture include passaging (transferring cells from one container to another to prolong cell life or expand cell numbers) and calculating plating density (determining the cell number per volume of the culture media).

Commensal VS Pathogenic VS Symbiotic*: Commensal organisms benefit their host (whale and barnacles, pathogenic organisms cause disease in the host (Salmonella and you), and symbiotic organisms are benefited by/benefit the host (clownfish and sea anemone). The healthy gut microbiota consists of primarily symbiotic and commensal organisms.

Genomics (Meta, Proteo): The study of the genome-the complete set of DNA within a cell. Metagenomics is the study of a collection of genomes from a set community (e.g. the microbial community within your gut). Proteomics refers to the study of all the proteins produced by an organism. So metaproteomics is—bingo!—the study of all the proteins produced by a set community.

Gram-negative bacteria: These bacteria have a thin layer of peptidoglycan-a meshlike polymer—between their inner and outer cell membrane. Gram negative and gram positive bacteria are differentiated by Gram staining (gram negative bacteria appear pink after identification staining). Example: E. coli

Gram-positive bacteria: These bacteria have a thick layer of peptidoglycan surrounding the plasma membrane. Gram stain: purple. Example: S. aureus

2000px-Gram-Cell-wall Source:

Holobiont: The symbiotic organism: an organism + their micro-species. For example: a human+ any bacteria, fungus, parasite that share the human’s body space. The hologenome theory of evolution suggests that evolution is driven by natural selection of the holobiont, not just the organism.

Human microbiome project: Launched in 2008, the HMP characterized microbial communities found within the nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract. Additional HMP goals included the development of new techniques to study and analyze the microbiome and projects to examine the role of the microbiome in human health and disease. The Human Genome Project, the famous ‘older sister’ of the HMP was completed in April 2003.

Hygiene hypothesis: (also called the Lost Friends Theory or the Biome Depletion Theory) The hypothesis that lack of microbial exposure in young children might lead to an increased susceptibility to allergic/autoimmune/behavioral diseases. The recent emphasis on germ-free lifestyles prevent children from being exposed to microbes, preventing the full development of their immune system.

Metabolites: Small molecules that are intermediate components of the metabolic pathway.

Microbiome vs. Microbiota: Although these words are often used interchangeably, microbiome refers to the collection of microbial genes, while microbiota refers to the microbial organisms themselves.

Gut microbiota: The trillions of microbes that reside throughout the host digestive tract.

Flow cytometry: A laser-based technique utilized to determine cell size, granularity, and molecular characteristics. Suspended cells pass through the cytometer’s laser, a sensor detects differences in the light scattered/emitted from the cells and the data is recorded for analysis.

PCR: Polymerase chain reaction: Developed by Kary Mullis**, PCR is a common laboratory technique used to amplify a segment of DNA. PCR steps include: denaturing (the double-stranded DNA sample separates), annealing (a DNA primer attaches that corresponds to the beginning or end of the DNA sample binds to the single-stranded DNA), and extension/elongation (DNA nucleotides—the DNA building blocks—are added onto the primer to create a complementary strand). This process is typically repeated 35 times.

Screen Shot 2015-08-13 at 8.05.35 AM

Sequencing: This refers to any technique used to determine an unknown sequence of nucleic acids (DNA or RNA). Common techniques include:16SrRNA (see below), chain termination, shotgun sequencing, and 454 pyrosequencing.

Scanning electron microscope (SEM): This type of microscope utilizes electrons to probe the surface of a metallic-coated object, producing a 3D image.

Transmission electron microscope (TEM): Unlike SEM, the transmission electron microscope emits electrons that pass through an object, producing a detailed cross-section of the sample.

Western Blot: A common lab technique: This method utilizes electric charge or molecular weight to identify proteins in an unknown sample. Other blots include the Southern blot to identify DNA sequences and the northern blot to detect RNA.

Xenobiotics: This refers to any substance that is not naturally produced by the host/microbiome. For example: pharmaceutical drugs.

16S rRNA sequencing: This technique is used to determine evolutionary relatedness between bacterial sequences. 16S rRNA is a highly conserved component of bacteria.

*this type of symbiosis is technically mutualistic symbiosis, as symbiotic refers to any species interaction, pleasant or unpleasant.

**Check out an upcoming Biolog on Kary

By KCBauer

Hello! My name is KCBauer and I am a PhD candidate at the University of British Columbia. I am a researcher, writer, musician, and explorer. Originally from Washington DC, I graduated with a BA in Music and BS in Biology in 2014. This blog focuses on the gut microbiota, the trillions of microorganisms that reside along the digestive tract. My grad research at UBC examines the role of the gut microbiota on human health, brain development, and anthropology. When I am not in the lab, I enjoy ambling through Vancity, listening to music, reading science journals, and hiking. If you have questions, ideas for blog topics, suggestions for place to visit in BC, or corrections send me an email at

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