Fuck Yeah Microbiology

I like viruses, bacteria, parasites, fungi, and weird other shit that invades your membranes.

[fyeahmicrobiology]

CDC Threat Report: 'We Will Soon Be in a Post-Antibiotic Era' - Wired Science

[cheesenotes]

Wired Science has a post and slideshow delving into the wonderful, wooly world of microbes and their essential role in so many of our favorite foods. Dr’s Rachel Dutton and Ben Wolfe — who by now have made many an appearance on this blog — contributed to the post. Pictured above are a few favorites, including Geotrichum Candidum at the top:  

These Funky Microbes Make Your Favorite Foods More Delicious

If you ask me, the best things to eat and drink almost always have a little something funky going on. Cucumbers are OK, but pickles are what I reach for when I want to make a kickass sandwich. Cabbage is boring, but kimchi rocks. When it comes to cheeses, a blue always trumps a jack. Edamame? Edama-meh. Give me miso soup and sake.

What makes these foods better is the hard work of bacteria and fungi.

These bugs transform the sugars and proteins in raw ingredients like fruits and grains into something else entirely, creating new flavors and more complexity. They’re the reason an aged cheese tastes more interesting than milk and a well-made craft beer tastes better than a mouthful of barley. They put the umami in miso and make pickles more piquant.

Humans have been intentionally inoculating food with microbes for millenia, says food writer Harold McGee, whose classic book On Food and Cooking is a trove of information on microbe-enhanced cuisine (and everything else you need to know about the science of cooking). It probably started by accident.

Many of the macronutrients in the foods we eat — the proteins, carbohydrates, and fats — are too big to trigger our taste and odor receptors. As the microbes go about the business of breaking these molecules down into smaller pieces they can make use of themselves, they create amino acids, fatty acids, and sugars that we can taste and smell. They also synthesize new compounds for communication and other purposes, and some of these compounds contribute to taste or aroma as well, McGee says.

"This process of breaking down and building up makes food much more complex in its sensory characteristics and more interesting."

"We’re starting to look at that in the lab right now," said Rachel Dutton, a microbiologist at Harvard who’s consulted [David] Chang and other chefs. "I don’t think there’s good evidence one way or the other."

In this gallery several scientists — including Dutton and mycologist Benjamin Wolfe, who works in her lab — helped us explore the biology of some of the microbes that make our food and drink more delicious. Isn’t it time you got to know them a little better?

check out the full post.

[23pairsofchromosomes]

Scanning electron Micrograph of Helicopterbacter pylori - as already mentioned this bacteria is found in the stomach lining and can increase the chances of stomach cancer (brown cells in photo) along with stomach ulcers. 

Photograph by Martin Oeggerli, with support from School of Life Sciences, FHNW

(Source)

[fyeahmicrobiology]

My favorite story about H. Pylori is the one about it's discoverer.  It's as follows: 

Helicobacter pylori was first discovered in the stomachs of patients with gastritis and stomach ulcers in 1982 by Dr. Barry Marshall and Dr. Robin Warren. At the time, the conventional thinking was that no bacterium could live in the stomach, as the stomach produced similar strength acid to that of a car battery. Marshall and Warren rewrote the textbooks with reference to what causes gastritis and gastric ulcers. In recognition of their discovery, they were awarded the 2005 Nobel Prize in Physiology or Medicine.

After many unsuccessful attempts at culturing the bacteria from the stomach, they finally succeeded in culturing and visualizing colonies in 1982, when they unintentionally left their Petri dishes incubating for 5 days over the Easter weekend. In their original paper, Warren and Marshall contended that most stomach ulcers and gastritis were caused by infection by this bacterium and not by stress or spicy food, as had been assumed before.

Although there was some skepticism initially, within several years numerous research groups verified the association of H. pylori with gastritis and ulcers. To demonstrate H. pylori caused gastritis and was not merely a bystander, Marshall drank a beaker of H. pylori culture. He became ill with nausea and vomiting several days later. An endoscopy ten days after inoculation revealed signs of gastritis and the presence of H. pylori. These results suggested H. pylori was the causative agent of gastritis. Marshall and Warren went on to demonstrate that antibiotics are effective in the treatment of many cases of gastritis. In 1994, the NIH published an opinion stating most recurrent duodenal and gastric ulcers were caused by H. pylori, and recommended antibiotics be included in the treatment regimen.

[scientiflix]

Why Microbiology? ASM Members Share their Stories

Members of the American Society for Microbiology share their stories of how they discovered microbiology. To learn more about becoming a member visit http://www.asm.org/advance

via Microbe World.

[drsohm]

Public health success story: rotavirus vaccines protects more than just babies (LA Times)

The rotavirus vaccine is a relatively new vaccine to the market (2006) that is given to babies in their first year.  Rotavirus causes watery diarrhea, vomiting, fever and used to be contracted by nearly all children by age 5.  Incidence of rotavirus in children under 5 has dropped 80% since the vaccine was introduced.  While the vaccine is only being given to infants, significant reduction in rotavirus have been seen in people of all age groups.  Herd immunity in action!

[nprglobalhealth]

Antibody Cocktail Cures Ebola In Monkeys, Even After Symptoms Appear

Ebola, your days as one of the world’s scariest diseases may be numbered.

A team of U.S. government researchers has shown that deadly Ebola hemorrhagic fever can be vanquished in monkeys by an experimental drug given up to five days after infection — even when symptoms have already developed.

An antibody cocktail aimed at Ebola’s outer surface rescued three of seven macaques infected with lethal doses of the hemorrhagic virus in the U.S. Army’s high-security labs at Fort Detrick, Md.

Looked at the other way, Ebola killed nearly 60 percent of the monkeys despite the experimental treatment. So there’s still a long way to go before the infection can be reliably treated — in monkeys or humans.

Still, this experiment, whose results were publishedWednesday in the journal Science Translational Medicine, marks the first time researchers have shown that Ebola can be successfully treated after the infection is well underway.

Continue reading.

Image of the Ebola virus from Cynthia Goldsmith/CDC.

[currentsinbiology]

Bacteria in Mouth Implicated in Colorectal Cancer (Science Daily)

Gut microbes have recently been linked to colorectal cancer, but it has not been clear whether and how they might cause tumors to form in the first place. Two studies published by Cell Press on August 14th in the journal Cell Host & Microbe reveal how gut microbes known as fusobacteria, which are found in the mouth, stimulate bad immune responses and turn on cancer growth genes to generate colorectal tumors. The findings could lead to more effective strategies for the early diagnosis, prevention, and treatment of colorectal cancer.

“Fusobacteria may provide not only a new way to group or describe colon cancers but also, more importantly, a new perspective on how to target pathways to halt tumor growth and spread,” says senior study author Wendy Garrett of the Harvard School of Public Health and the Dana-Farber Cancer Institute.

Dental plaque. Coloured scanning electron micrograph (SEM) of plaque, which consists of a film of bacteria (green) embedded in a matrix of glycoprotein (brown). The bacteria shown are mainly spindle-shaped Fusobacteria. If left untreated, bacteria in the plaque produce acids which erode dental enamel, leading to decay and infection.

[superbloodbanker]

A strain of bacteria that causes skin and soft tissue infections in humans originally came from cattle, according to a study to be published in mBio®, the online open-access journal of the American Society for Microbiology. The researchers who conducted the genetic analysis of strains of Staphylococcus aureus known as CC97 say these strains developed resistance to methicillin after they crossed over into humans around forty years ago. Today, methicillin-resistant S. aureus (MRSA) strain CC97 is an emerging human pathogen in Europe, North and South America, Africa, and Asia. The findings highlight the potential for cows to serve as a reservoir for bacteria with the capacity for pandemic spread in humans. The researchers sequenced the genomes of 43 different CC97 isolates from humans, cattle, and other animals, and plotted their genetic relationships in a phylogenetic tree. Corresponding author Ross Fitzgerald of the Roslin Institute and the University of Edinburgh in Scotland says strains of CC97 found in cows appear to be the ancestors of CC97 strains from humans.

Primary source: mBio

[ofscienceandgeeks-deactivated20]

"But these viruses, described today in Science1, are more than mere record-breakers — they also hint at unknown parts of the tree of life. Just 7% of their genes match those in existing databases."

“The researchers are now trying to determine the viruses’ origins by characterizing the unknown genes and the proteins they encode. They have long suspected that giant viruses evolved from cells; if they are right, the ancestors of Pandoraviruses must have been very different from the bacteria, archaea and eukaryotes we have today. “We think that at some point, the dynasty on Earth was much bigger than those three domains,” says Abergel. Some cells gave rise to modern life, and others survived by parasitizing them and evolving into viruses."

Guys. GUYS! READ THIS ARTICLE BECAUSE IT’S IMPORTANT AS BALLS! THERE IS A POSSIBILITY THAT THERE MIGHT BE A NEED TO RECONSIDER THE DOMAINS OF LIFE, AND THAT’S PRETTY DOPE SHIT YO!

THE IDEA THAT THERE EXISTS ORGANISMS THAT SHARE 7% OF OUR GENOME IMPLIES IT IS COMPLETELY DIFFERENT LIFE (well, distantly related to us) BUT STILL ITS ALMOST COMPLETELY NEW AND ITS EXCITING AND THIS IS WHY I SCIENCE!

But seriously, if you’re interested in evolutionary biology, this paper is worth a read.

[currentsinbiology]

Copper Nanoparticles Could Protect Food from Bacteria (Science Daily)

Microbes lurk almost everywhere; most of the time, they are harmless to humans. But sometimes they aren’t. Every year, thousands of people sicken from E. coli infections and hundreds die in the US alone. Now Michigan Technological University scientist Jaroslaw Drelich has found a new way to get them before they get us.

His innovation relies on copper, an element valued for centuries for its antibiotic properties. Drelich, a professor of materials science and engineering, has discovered how to embed nanoparticles of the red metal into vermiculite, an inexpensive, inert compound sometimes used in potting soil. In preliminary tests on local lake water, it killed 100 percent of E. coli bacteria in the sample. Drelich also found that it was effective in killing Staphylococcus aureus, the common staph bacteria.

Scanning electron micrograph of Staphylococcus aureus

[heythereuniverse]

MRSA | NIAID

[fyeahmicrobiology]

MRSA covered in what appears to be Neutrophil Extracellular Traps and other Leukocytes...

[wildcat2030]

Amoeba farms bacteria for food and weapons

There are new details about how the world’s smallest farmer picks up edible bacteria and then harvests them like crops.

The organism, a social amoeba called Dictyostelium discoideum, carries not one but two strains of bacteria. One strain is the “seed corn” for a crop of edible bacteria, and the other strain is a weapon that produces defensive chemicals.

The edible bacteria, the scientists found, evolved from the toxic one. The two strains differ by many mutations but a single key mutation, which hit an important controller in the genome of the nonfood strain, alters expression of 10 percent of its genome. This alteration increases the expression of some genes and decreases the expression of others.

A mutation that affects this much of a genome could be lethal, but in this case it had the surprising effect of making the bacterium edible by changing its chemical profile.

Scientists at Washington University in St. Louis and Harvard University describe their findings in the Proceedings of the National Academy of Sciences. (via Futurity.org – Amoeba farms bacteria for food and weapons)

[fyeahmicrobiology]

I guess a lot of that has to do with whether or not being edible helps their life cycle, doesn't it?

[fyeahmicrobiology]

Macrophage (red) engulfing tuberculosis bacteria (yellow), taken with ZEISS FE-SEM. Courtesy of Dr. Volker Brinkmann, Max Planck Institute for Infection Biology, Berlin/ Germany.

What you can see here is the body trying to cure itself.  The yellow cigar shaped objects are tuberculosis bacteria.  Around it is macrophage.  A macrophage is a phagocyte, and these are the cells that protect us by attempting to ingest and harmful foreign objects.  The name comes from the Greek phagein – to devour and the word cyte which denotes a cell in biology.

From Kuriositas.

[fyeahmicrobiology]

In this electron microscope image of green-leaf lettuce, rod-shaped E. coli bacteria nestle inside a minute pore in the leaf called a stoma. Conventional produce sterilization techniques cannot reach pathogens such as E. coli in stomas, said Dr. Rosana Moreira, Texas A&M AgriLife Research food safety engineer. (Texas A&M AgriLife Research photo) See more images like this at Kuriositas.

Most of the time these e. Coli bacteria are harmless, in fact e. Coli are among the most common bacteria easily culturered out of the bowel.  However, certain conditions that change the molecular genetic pattern of expression in e. Coli in the bowel can cause food poisoning and pathogenesis.

This change is usually brought on by the consumption of certain genetic material in the form of plasmids.  The e. Coli themselves are always absorbing genetic material through a process known as transformation, one of four well known ways that bacteria consume DNA.  This material helps promote genetic diversity in a species of animal that divides instead of using sexual reproduction.  

ETEC (enterotoxigenic e. Coli) and EPEC (enteropathogenic e. Coli) are the most common form of this foodborne illness.  Pathogenic E. coli are not distinguishable from other strains or from each other by appearance on agar plates or by the results of the usual biochemical tests.

To determine whether the isolated strain is one of the pathogenic strains or a constituent of the normal flora, additional identification techniques must be employed.  Generally this testing involves a PCR (polymerase chain reaction) which replicates the pathogenic plasmid of DNA millions of times until it can be read by sequencing and identified as a strain containing the harmful set of DNA instructions.

Doctors can readily do this test for only one strain of pathogenic EPEC in the clinical laboratory, EHC 0157, which has been readily identified in millions of cases.

  Source 

[staceythinx]

Some of the fascinating images from the Kuriositas gallery Under the Electron Microscope. Check it out for more photos and a great explanation of the techniques used to get them. Click on the images above for descriptions of what’s pictured.

[scinewsnetwork-blog]

Bacteria That Cause Gum Disease Linked To Alzheimer's

Toothy Fun Maryland Department of Health and Mental Hygiene

Could Alzheimer's disease originate in your mouth?

It sounds like a strange idea, but scientists have recently found one small clue that dental bacteria may play a role in some cases of Alzheimer's.

A team of researchers from the U.K. and the U.S. found gum-disease bacteria in the brains of four people with Alzheimer's disease. The bacteria didn't appear in the brains of 10 people who didn't have Alzheimer's disease and had donated their brains to science. Six more people in the study who had Alzheimer's disease didn't have the bacteria.

The study wasn't set up to show whether the bacterium—Porphyromonas gingivalis, a major cause of severe gum and tooth diseases—causes Alzheimer's. Instead, researchers were just aiming to see if the buggers could appear in the brain. And there they were.

Bacteria in the mouth could hop into the bloodstream and travel to the brain after someone loses a tooth, Bloomberg explains. Chewing, brushing and flossing are also able to transfer oral bacteria into the bloodstream, but the study's lead scientist, StJohn Crean of the University of Central Lancashire, told Bloomberg that people should keep brushing and flossing. Keeping your mouth clean reduces the number of bacteria in there and the likelihood that they'll travel elsewhere. (Anyway, Porphyromonas gingivalis seems to be rare in the mouths of those without periodontal disease.)

Crean's team isn't the only one that's looking for a connection between gum disease and Alzheimer's. Decades of research have shown that those with Alzheimer's have chronic inflammation in the brain. Some scientists think that perhaps inflammation elsewhere in the body, such as in the gums, could affect the central nervous system.

The Porphyromonas gingivalis study was published in the Journal of Alzheimer's Disease in May.

[fyeahmicrobiology]

I'm pretty sure most scientists knew that bacteria could travel from the gums to the brain.  It's also been shown in the past that bacteria found in facial lesions in a certain triangle of the face can be found in the brain. 

Seen here and explained here.

[fyeahmicrobiology]

Codenamed: Zeus' Revenge.  

This week in Science, Authors Philippe et al. describe the discovery of the World's Largest Virus.  Ten years ago, a virus infecting Acanthamoeba known as the Mimivirus caused scientists to reassess the upper limits of the viral world.  The mimivirus expanded both the largest known particle size (>0.7 micrometers) and genome complexity (>1000 genes), which are the dimensions of a typical intracellular bacteria.  These Megaviridae were sampled from aquatic environments and associated sediments from around the world.  In this new paper, however, they report on the isolation of two new giant viruses, which change everything we know about life.  These viruses, with micrometer sized ovoid particles and DNA genomes of at least 2.5 and 1.9 megabases, are without any morphological or genomic resemblance to any previously defined virus family.  

These two viruses are part of the newly proposed "Pandoravirus" genus, a term which reflects the surprise and newness held in this discovery.  

Sediment dwelling amoebae have had a bad track record for possessing newly discovered massive viruses.  These giant viruses are visible by light microscopy and are generally phagocytosed by target cells.  From there, they fuse with the phagosomal membrane and release their contents into the cytoplasm where they take over the machinery of the nucleus.  They have a solidified classification as viridae since they lack ATP generation, binary fission, or protein translation machinery.  

Perhaps most interesting is the complete uniqueness of the genetic material inside the viral particle.  The authors describe how the DNA held within is so different that it probably comes from a new domain of life.  Scientists have long held the belief that there were once many more domains of life than the three known: Archaea, Prokaryota and Eukaryota.  In sequencing the DNA held within the Pandoravirus, it's clear that this virus originates from a host which held few if any similarities with the extant domains of life.

This has incredible implications for future Virologists and techniques of gene therapy/proteomics.  The genome of this little critter is completely unrecognizable.  

Here's the article itself from Science and here's a news comment from Nature.