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This past weekend, I went to visit a friend and meet his twin toddler boys for the first time. Though both boys eagerly ran around the playground we visited, one was just slightly less active. “He has asthma,” his dad explained to me, “but his brother doesn’t.” Why would two boys with the same environment and genetics have different disease manifestations?
The microbial world (much larger than even originally imagined, as demonstrated in the new Tree of Life) contains an extremely wide array of biochemical reactions that various organisms use to acquire energy, release waste products, and detoxify the surrounding environment. These broad abilities allow microbes to grow in some of the harshest conditions known on Earth – from sulphuric springs to frozen tundra, there are few places that are truly sterile in this world.
Thursday, 28 April 2016 15:47

Assessing gram stain error rates

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The gram stain, also known as the Gram stain for Hans Christian Gram, is one of the first techniques budding microbiology students learn in their introductory lab courses. It’s even a good exercise for younger students (with proper supervision, of course), due to its simplicity and the colorful, beautifully stained cells that result from the procedure. The protocol is often taught in tandem with lessons on bacterial structure, since the differential staining helps determine whether an isolate is a gram-positive or gram-negative bacterium.
Tuesday, 26 April 2016 15:44

A Microbial Ocean Feast: Who Ate What?

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Single-celled organisms called bacterioplankton spend their lives drifting in open ocean, visible to the naked eye only en masse. But don't be fooled by their slight size: These minuscule critters play a hefty role in the carbon cycle. Heterotrophic microbes, by some estimates, process half of the organic carbon in the ocean fixed by phytoplankton and other autotrophs through photosynthesis.
One of the most dangerous places for an infection to occur is in the bloodstream. Septicemia, when microbes are present in the blood, not only allows bacteria access to other internal organs through the highway of our circulatory system, but also can cause a massive inflammatory response, leading to septic shock. Conditions that increase risk of bloodstream infections, such as invasive surgery or implantation of an indwelling device, are carefully monitored and are sometimes accompanied by prophylactic antimicrobial drugs to prevent this very serious condition.
Several papers published in Genome Announcements recently describe the sequences of new Zika virus isolates. Scientists have known the genomic sequence of at least one Zika virus isolate since 2007, but continue to publish newly isolated strains. What is the importance of these additional sequences?
Tuesday, 19 April 2016 15:16

Cities have Individual Microbial Signatures

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Greg Caporaso was sifting through blog posts on, which covers the microbiology of built environments, when a study idea sparked for him and colleagues Jeff Siegel, Scott Kelley and Rob Knight.
Breast milk provides an inexpensive, nutrient-filled source of food for babies. Because of this, the American Academy of Pediatrics and the WHO recommend new mothers to exclusively breast feed their babies for the first six months of life, and continue up to two years (supplemented with other foods). Breast milk provides maternal antibodies, which protect the immature immune system. It has a balance of carbohydrate, protein, and fats that are hard to reproduce in formula. It provides digestive enzymes and hormones necessary in early life. And new research published in Applied and Environmental Microbiology suggests specific components of breast milk…
Like us, bacteria have their own microbial attackers, in the form of bacteria-specific viruses called bacteriophage, or phage. These phage come in a variety of flavors but can be broadly categorized into virulent, which immediately begin to replicate and lyse (burst) the infected cell quickly, and temperate, which incorporate the phage DNA into the bacterial genome. This non-replicative state, called lysogeny, allows the phage to be passed to daughter cells when the bacterium divides, but does not generate multiple progeny phage until activated. When activated, the lysogenic phage enter the lytic cycle, killing E. coli host cells as the phage…
Pneumonia remains a serious worldwide problem, especially among the young, elderly, and immunocompromised. Over 900,000 children die each year due to the disease, and respiratory syncytial virus (RSV) is the most common viral cause (Streptococcus pneumoniae and Haemophilus influenzae type b being the most common bacterial causes). Antibiotics and antivirals can help treat sick patients, but prevention remains the ideal route of protection. Scientists are hard at work generating vaccine candidates, and a promising lead in an RSV vaccine has recently been published in Clinical and Vaccine Immunology.
Is the way to treat heart disease through a person's stomach? According to a new study, the answer is yes. Researchers have found that a compound found in red wine, resveratrol, reduces the risk of heart disease by changing the gut microbiome.
Thursday, 31 March 2016 14:55

Using citizen science to engage students

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A long-standing innate curiosity can drive students to explore their world through observation, and may lead to a career in science for some people. But more commonly, students enjoy learning about science as elementary students and that interest wanes with time. There are many factors involved in keeping students engaged with learning, but participation in citizen science projects is a movement underway to introduce science as a dynamic, evolving field with many questions left to explore.
Fecal transplants are increasingly being used for refractory Clostridium difficile and other gastrointestinal disorders. While fecal donors are screened for various infectious diseases, it is unclear whether viruses can in fact be transmitted during fecal transplants. Now a new study shows that communities of viruses can be transferred during fecal transplants, but that the viruses that are transmitted are harmless to humans. The study was published this week in mBio, an online open-access journal of the American Society for Microbiology.
Whether you’ve Google-searched “biofilm” to learn more yourself, taken courses covering the subject, or are deeply embedded in biofilm-related research, you’ve probably encountered a model similar to the one below, which represents biofilm maturation. In the current model, a biofilm begins with a planktonic cell attaching to a surface, which multiplies and develops into a three-dimensional structure that includes both cells and extracellular matrix. Eventually, the biofilm releases planktonic cells, which can seed new biofilms by attaching and reinitiating the cycle. This model has been helpful in understanding the developmental stages of biofilm formation.
Thursday, 24 March 2016 14:34

Shiga toxin: no preassembly required

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Making something requires connecting parts in a particular order. Baking: dry ingredients must be mixed before adding wet ingredients. Puzzles: much easier if the border is assembled first. Legos. Ikea products. Similarly, the order of biological interactions at the molecular level can determine whether a complex has the correct structure or activity for its function: translation is a simple example. If the small and large ribosomal subunits formed before interacting with an mRNA, there would be no message to scan for instructions on amino acid incorporation into proteins.
Tuesday, 22 March 2016 14:32

Communicating your science via social media

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ASM aims to promote and advance the microbial sciences in a myriad of ways. In addition to promoting scientific education and discoveries, we also hope to engage the public with the diverse world of microbes! Last year, we held our first Agar Art contest, to highlight the often-overlooked beauty of microbial growth. We were amazed at member participation, including both the number and quality of the art works! Every submission required a short explanation in lay language, which helped garner public interest in the beautiful microbial pictures.
What kinds of microbes do you associate with hot springs? Maybe microbial mats? Thermus aquaticus and the discovery of Taq polymerase? Archaea, previously (and erroneously) thought to be strict extremophiles? Viruses may not be the first microbial subtype that springs to mind (pun intended) but rest assured, where cells exist, so do viruses. A recent paper published in the Journal of Virology describes a newly discovered virus, originally characterized based its genome sequence.
Because of its safety, efficacy, and affordability, chloroquine remains the treatment of choice for all Plasmodium species, except in regions with chloroquine-resistant P. falciparum. Chloroquine-resistant protists are treated with combination therapy, which includes artemisinin-derived molecules in some cases. But one drug is easier to administer than two, and scientists working on chloroquine resistance have found a clever mechanism that may lead to a new, two-birds-with-one-stone malaria treatment.
Tuesday, 15 March 2016 12:12

Microbial Communication Over the Airwaves

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Jean-Paul Latgé originally wanted to know if he could test the breath of patients with Aspergillus infections for volatile compounds produced by the fungus. His group at the Pasteur Institute in Paris thought this might be a new way of diagnosing fungal culprits like Aspergillus fumigatus that often colonize the lungs of cystic fibrosis (CF) and immunocompromised patients.
This blog discusses food safety quite a bit because microbial contaminants in one part of the food chain can have a major impact on human health. Since the last post on Chipotle contamination, there’s been a major recall at Starbucks, Wonderful brand Pistachios, and another scare at a Chipotle restaurant.