(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


ANTONIE VAN LEEUWENHOEK: The Father of Microbiology Part 1

Jan_Verkolje_-_Antonie_van_Leeuwenhoek Portrait by Jan Verkolje

(The Draper, and trader, and microscope maker)

ˈɑntɔni vɑn ˈleːwənhuːk

Antonie van Leeuwenhoek (24 Oct 1632-26 Aug 1723) lived in Delft, Netherlands and worked in drapery and haberdashery. (Alternative subtitles included: Or how a haberdasher developed microscopy). His parents Margaretha (Bel van den Berch) and Philips Antonysz van Leeuwenhoek were middle class merchants. Following the death of his father, young Antonie was sent to live with relatives in Benthuizen and later apprenticed as a draper in Amsterdam. His shrewd business mind enabled him to start his own haberdashery shop back in Delft and he was soon appointed the prestigious position of Chamberlain for the Delft Sheriff’s Assembly.*

While running his drapery and haberdashery shop, van Leeuwenhoek developed an interest in the creation of magnifying lens. Then, he started producing simple microscopes. He became enthralled by the images of the microscopic world. His friend Renier de Graaf, a Delft physician, urged Antonie to submit his findings to the Royal Society in London. And throughout his lifetime, nearly 200 letters were exchanged from the country village of Delft to the great English capital. Unlike the learned members of the Royal Society, Van Leeuwenhoek received no formal training in either the sciences or Latin. Moreover, he only spoke and wrote Dutch and his letters had to be translated before the meetings. Although initially enthusiastic about his pursuits, Antonie’s discovery of single-celled organisms was regarded with disbelief and ridicule by the Royal Society.

Dear Mr. Anthony van Leeuwenhoek,

Your letter of October 10th has been received here with amusement. Your account of myriad “little animals” seen swimming in rainwater, with the aid of your so-called “microscope,” caused the members of the society considerable merriment when read at our most recent meeting. Your novel descriptions of the sundry anatomies and occupations of these invisible creatures led one member to imagine that your “rainwater” might have contained an ample portion of distilled spirits–imbibed by the investigator. Another member raised a glass of clear water and exclaimed, “Behold, the Africk of Leeuwenhoek.” For myself, I withhold judgment as to the sobriety of your observations and the veracity of your instrument. However, a vote having been taken among the members–accompanied I regret to inform you, by considerable giggling—it has been decided not to publish your communication in the Proceedings of this esteemed society. However, all here wish your “little animals” health, prodigality and good husbandry by their ingenious discoverer.

You could have cut the sarcasm with a snicker. But Antonie insisted on the veracity of his findings and the Royal Society eventually sent an envoy to Delft. Van Leeuwenhoek’s credibility and genius was restored. Years later van Leeuwenhoek would write, “my work, which I’ve done for a long time, was not pursued in order to gain the praise I now enjoy, but chiefly from a craving after knowledge, which I notice resides in me more than in most other men.” A good reminder for all researchers: work hard, stay true, and embrace the wondrous!

Heavily Abbreviated List of Antonie van Leeuwenhoek’s Accomplishments:

First to record microscopic observations of

  • Capillaries
  • Muscle fibers
  • Bacteria
  • Sperm
  • Compound eyes (insects!)
  • Single-celled organisms

*This same business acumen would be later put to use in his lensmaking endeavors. When invited by Tsar Peter the Great he refrained from showing the court his most advanced microscopes, thus preventing others from learning his techniques and creating rival lenses. FYI: his method involved soda lime glass. Robert Hooke, the great English microbiologist bemoaned that the entire field of microscopy, and by extension the financial profits, rested on the shoulders of one Dutch man.

For more information on van Leeuwenhoek see:, and


The Skope

Welcome to the Skope! The blog dedicated to the human microbiota, the collection of microorganisms that reside with and on the human body. Described as the “forgotten organ”, the human microbiota launches at birth. Soon trillions of microbes colonize the human host enabling our survival. These microbes digest dietary starches, aid immune system development, and synthesize essential vitamins. Even our mood and behavior may be linked to microbial communities. Most Skope entries cover the gut microbiota, the microbes that inhabit the intestinal tract, click Gutsy Topics. But I will also include articles on the oral microbiota, skin microbiota, ocean microbiota, soil microbiota, and many more microbial habitats. Articles in An American (US!) in Vancouver describe my graduate/international experiences, while Biologs features brief histories of microbiology and also reviews/summaries of interesting microbial articles and books. Happy exploring!



(AKA: What is this? Why is it important?)

When I typed “Gut Microbiota” in Google Scholar and limited publication dates from 1900-1950, I discovered 16 articles. 1951-1980: 291 hits. 1981-1990: 497 hits. 1991-2000: 2,130. 2001-2010: 26,100. Publications from 2015 alone: 5,030 and counting! I thought about producing a graph, but it seemed pretty pointless. On second thought, why not?

[A Pretty Pointless Graph: The Rise of Microbiome Research]

Pretty Pointless

During the 19th and 20th century, most microbiologists studies focused on pathogenic bacteria. This led researchers O’Hara and Shanahan to label the gut microbiota, as the ultimate “forgotten organ.” In the abstract of their 2006 EMBO publication, O’Hara and Shanahan noted the gut microbiota “is a positive health asset” that “has a collective metabolic activity equal to a virtual organ within an organ.” Germ-free animals exhibited marked physical changes (decreased muscle thickness and smaller Peyer’s patches*) and increased susceptibility to infections. However, these microbes might also contribute to diseased states, such as Crohn’s or IBD, if an individual displayed an immune intolerance towards certain microbes. O’Hara and Shanahan speculated that further study of the gut microbiota might reveal undiscovered methods vital to understanding host-pathogen interactions. Indeed, 2006 appeared to be a major milestone in microbiology research; the age of microbiome research had emerged. Within the next decade microbiologists examined the impact of the gut microbiota on obesity, metabolism, depression, autism, immunology, and behavior. More to come in the following blogs!

*Peyer’s Patches: these are lymph node “islands” located in the mammalian large intestine

Sources + Additional Information