Weimer Micro Lab

Contributed by Narine Arabyan 

Viable but nonculturable (VBNC) state was first discovered in 1982 in the lab of Rita Colwell at University of Maryland. VBNC state in bacteria is induced by many different environmental stresses (nutrient starvation, temperature shifts, oxidative and osmotic stress and etc.). Before the discovery of VBNC state, bacterial cells were considered dead when it was unable to grow on culture media. However, we know now that cells can stop growing on media but remains viable and potentially able to regrow. VBNC state in bacteria is characterized as living cells that are unable to grow on routine media on which they normally grow, have low levels of metabolic activity and become culturable when resuscitated.

VBNC cells have many differences from the viable culturable cells. The differences are found in their cellular morphology, cell wall, metabolism, gene expression, physical and chemical resistance, adhesion properties and virulence potential. VBNC cells undergo cell size reduction in cell size and cells become round. The fatty acids and peptidoglycan change in the cell wall. There is an increase in the unsaturated fatty acids and carbon chains become less than 16 carbons. There is an increase in the peptidoglycan cross-linking which is thought to strengthen the cell wall. VBNC cells have greater physical and chemical resistance which could be due to cell wall strengthening. VBNC are able to tolerate heat, low pH, ethanol, antibiotics and heavy metals. VBNC cells are capable of retaining attachment ability and are still virulent due to faster resuscitation into culturable cells upon introduction to proper host.

Cells enter VBNC state under stressful conditions. This is an adaptive strategy for long-term survival and is advantages for bacteria. Bacteria in VBNC state stay alive for long time until conditions become favorable. The ability to enter the VBNC state poses a risk to public health. This is a serious problem for pathogen detection. The inability to culture causes problems for proper diagnosis of diseases and subsequent treatments. This is a huge problem for quality control in the food industry and water distribution systems. Risks become apparent even more when pathogenic bacteria in the VBNC state regain virulence after resuscitation. Although this state in bacteria has been discovered more than 30 years ago, we still don’t know a lot about VBNC state in bacteria.

Contributed by Azarene Foutouhi

The human gut microbiome is understood to perform useful and necessary functions that help to maintain a healthy body in a multitude of ways such as aiding in the breakdown of otherwise indigestible nutrients and providing a physical barrier against disease-causing bacteria. However, the acquisition of this dynamic community is less well understood. While it was previously thought that the womb was a sterile environment and a baby first encountered bacteria on the path through the birth canal, DNA sequencing has allowed us to detect bacteria in cord blood, amniotic fluid, and the meconium (the infant’s first bowel movement). It is yet undetermined whether the initial microbiota is delivered via the mothers blood or an ascending migration from the vagina through the cervix, but studies have shown that a mother’s milk has a great effect on her child’s microbiome, no matter where the child may have acquired it.

It has been shown that roughly one-third of human breast milk is comprised of complex sugars, which though indigestible by the baby, instead serve to enrich the ‘good bacteria’ while blocking binding sites of potentially disease causing pathogens. These components of breast milk serve as prebiotics that promote the colonization of the baby by the so-called good bacteria such as the genus bifidobacteria, which dominate the gut of breast fed infants. It is clear that breast milk has evolved to not only nourish the newborn, but also to shape its gut micobiota into a functional and protective system.

Nevertheless, the gut microbiome is dynamic and varies greatly even between healthy individuals. Understanding the development and maintenance of this complex system, especially in the individual’s early years will provide great insight into the relationship between one’s colonization by different populations and disease.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866150/

https://www.sciencedaily.com/releases/2013/01/130104083103.htm

Contributed by Alli Weis

Firstly, what is the Zika virus and how is it spread? This is part 1 of a 3 part series…

The Virus:

Zika virus is a member of the virus family Flaviviridae, genus Flavivirus. The virus was first isolated in 1947 from the Zika Forest in Uganda. It’s an enveloped single-stranded RNA virus with a positive sense genome that can be directly translated into viral proteins: three structural and seven non-structural.

The Spread:

The Zika virus is spread by the Aedes aegypti and the Aedes albopctus mosquito. These are the same mosquitos that spread the malaria parasite (Plasmodium falciparum) and the same ones that spread dengue and West Nile viruses. When the mosquitos bite into a person, the virus migrates from the mosquitos’s salivary gland into the blood stream of the person. The other route of transmission is through sexual context from a man into his partners.

The Symptoms:

About 1 in 5 people that are exposed to the Zika virus become ill. Common symptoms are fever, rash, conjunctivitis (pink eye), and joint pain (CDC). These symptoms are usually mild and last from a few days to a week. In severe cases, hospitalization is required; however, this is generally rare (CDC). The devastating impact of Zika virus is when a pregnant woman becomes infected with the virus. Zika virus is linked to a serious brain birth defect called microcephaly, meaning small brain. Babies associated with viral infection during pregnancy have displayed a range of phenotypes, mostly related to brain development, many of which are still being investigated as an effect of infection. Zika virus has been recovered from the brain of babies born with microcephaly; however, it has not yet been proven that the virus caused this phenotype.

Danger for the United States:

While most of the impact on humans so far has been contained to Brazil, at this time the CDC reports that 30 states have been infected with the Zika Virus. That is, there have been evidence that mosquitos have been carrying and humans have been infected by the virus in over half of the nation states. This poses significant threat to the public health of the country.

“Everything we look at with this virus seems to be a bit scarier than we initially thought,” said Dr. Anne Schuchat, principal deputy director at the Centers for Disease Control and Prevention. “Most of what we’ve learned is not reassuring,”

The map linked below shows the US States currently affected by the Zika Virus.

https://www.graphiq.com/wlp/20hcjIF479H

Source of information: Centers for Disease Control and Prevention

The US Action:

Recently the Obama Administration asked Congress for $1.9 billion for Zika virus aid. This funding would include science research grants, health work funds, and others. While Congress is discussing the plan, the Obama Administration is considering appropriating left over Ebola funds into aiding with the Zika virus.

Stay tuned for part 2 and 3 of the Zika Virus Blog series…

All of us at The Weimer Micro Lab would like to congratulate Alli Weis for two awards she recently won at the 2016 UC Davis Interdisciplinary Graduate and Professional Student Symposium.  Alli won the Dean’s Prize for Best Oral Presentation in Medicine, Genomic Comparisons and Zoonotic Potential of Campylobacter isolates around Davis, California,  awarded by Dean Julie Ann Freischlag .  Alli also won the People’s Choice for Best Oral Presentation, Genomic Comparisons and Zoonotic Potential of Campylobacter isolates around Davis, California,  awarded by Vice Chancellor for Student Affairs Adela de la Torre.

CONGRATULATIONS on a job well done, Alli!  We are all very proud of you and your accomplishment.

Contributed by Nguyet Kong

Recent research has been done to understand why wine can reduce the risk of heart disease and it’s all about the gut microbiome. Red wine has a compound called resveratrol that reduce the risk of heart disease because it appears to have impact of the development of atherosclerosis. Atherosclerosis is when the plague arteries get harden and narrow, so basically the arteries slowly get block putting the blood flow at risk due to the limiting flow of oxygen-rich blood moving to the organs. The plaques are made from fat, calcium and other items found in the bloodstream. This is a high cause of heart attacks, strokes and other vascular diseases.

Resveratrol is a natural plant compound that can be found in red wine. It is believed to have antioxidant properties that can protect against some diseases. Researchers at the Research Center for Nutrition and Food Safety in Chongqing, China wanted to learn how resveratrol might protect against atherosclerosis by doing a mouse study to see how resveratrol will alter the bacterial community in the gut that it can provide protection. The finding show it reduce the level of trimethylamine-N-oxide (TMAO) and inhibit gut bacteria production of TMA, which is a factor for atherosclerosis. The results indicate that the gut microbiota will be an interesting target for pharmacological and dietary developments to decrease the risk of heart disease. For the future, the researchers believe a natural polyphenol could be used to treat heart disease, so now the role of resveratrol need be more defined and the study need to be replicated in humans.

http://circ.ahajournals.org/content/111/2/e10.full

http://www.mayoclinic.org/diseases-conditions/heart-disease/in-depth/red-wine/art-20048281

http://www.webmd.com/heart-disease/news/20100621/how-red-wine-helps-the-heart

http://www.nutritioninsight.com/news/Uncovered-Why-Drinking-Red-Wine-May-Reduce-Risk-of-Heart-Disease.html?tracking=Nutrition%20and%20Health%20News-Related%20Articles

http://www.nhlbi.nih.gov/health/health-topics/topics/atherosclerosis

http://www.webmd.com/heart-disease/what-is-atherosclerosis

Contributed by Bart Weimer:

A fuel that keeps people and science moving is coffee. Humans have had a fascination with coffee for over 9000 years! We have long recognized that coffee flavor is extremely different among regions f the world, but also by brewing method. The exact same coffee variety can have different flavors depending on the soil, cultivation elevation, region of the world, roasting method, extraction temperature, and contact with metal during the brewing process. The popularity of coffee has boomed in recent years. Until recently, the microbiome of coffee was not widely characterized. Most knew that it was a fermentation process that altered the flavor, but a recent study by Ludlow et al. (2016) demonstrated that the flavor can be manipulated and tracked based on the fungal microbiome. This is a great step forward in the coffee world since the industry largely depends on the native biota to ferment the beans right after harvest. This could enable use of starter cultures to alter the microbiome so that it can direct the community diversity. Ludlow et al. demonstrated that the microbiome of coffee (oh and by the way, cocao) is directed by Saccharomyces cerevisiae – the common bread yeast!! They also demonstrated the the genomic variation was distinct between regions of the world and aligned with human migration around the world as we trekked out of Africa. Since coffee is native to Ethiopia they postulated that humans distributed coffee and variations in the microbiome around the world and that the microbiome adapted to the new locals. As a coffee snob, this work is fascinating because it starts to describe a microevolution for a commodity that humans have persisted with for thousands of years.

Ludlow, Catherine L., Gareth A. Cromie, Cecilia Garmendia-Torres, Amy Sirr, Michelle Hays, Colburn Field, Eric W. Jeffery, Justin C. Fay, Aimée M. Dudley. 2016. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation. Current Biology (http://dx.doi.org/10.1016/j.cub.2016.02.012)

Contributed by Carol Huang

The rarely seen bloodstream infection bacteria, Elizabethkingiam, has sickened 54 in Wisconsin since November, 2015. Seventeen of those patients are dead, although direct causes of their deaths remain unclear. It was recently confirmed to have claimed a life in Michigan. This brings the total death toll of the illness to 18 since the outbreak first occurred in November 2015

Elizabethkingia anopheles is named after the microbiologist who first identified and isolated it in the 1950s. Although found in the guts of mosquitoes, it is not a dangerous bacteria for anyone with a healthy immune system. It is commonly existed in the environment, including in water and soil, it rarely causes infections, and the risk is very low in young or healthy people but can cause life-threatening infections in young babies, the elderly, and those with pre-existing health conditions like compromised immune system, cancer, liver disease or kidney disease.

Symptoms of the blood infection include shortness of breath, fever, chills and cellulitis. It is proven to be extremely tricky to treat as it is resistant to a lot of antibiotics.

Most previous outbreaks have occurred in a specific place, such as a hospital. Since the outbreak began in November, 54 people in 12 southeastern Wisconsin counties have been sickened. It is not associated with any particular location or facility. More perplexing is that health officials confirmed that a Michigan resident died after contracting a bloodstream infection that matches the one detected in Wisconsin. These patients are in different places around southeastern Wisconsin and Michigan. Many aren’t even mobile because they are homebound or in a nursing home. They’re on different water systems, some have their own private wells. There’s no commonality for some particular environmental exposure that people had. The source remains mystery.

Health official cautions that people ought to practice good infection control and good hygiene practices.

http://www.upi.com/Health_News/2016/03/19/CDC-Obscure-blood-infection-spreads-to-second-state/7131458414735/

http://www.startribune.com/scientists-search-to-unravel-mystery-behind-blood-infection-outbreak-in-wisconsin/372610031/

Contributed by Nguyet Kong

I’m a fan of pistachio and I can use them with my baked goods and dinner entrees, but now I have to be careful with the brand and type of pistachio I’ll be purchasing in the near future. Centers of Disease Control and Prevention (CDC) have recommend people to stop eating Wonderful Pistachios because it have been linked to a Salmonella Montevideo outbreak. There have been 11 cases across multiple states were two people have been hospitalized for the consumption. The Wonderful Pistachios include products that are even sold at Traders Joe, which I frequently visit to purchase my food products to make my meals. One location is down the street from the UC Davis campus, where many undergraduate students shop for their food. Pistachio is a healthy snack that have many health benefits such as heart health, weight management, protection of diabetes and hypertension and improve digestion. It has lots of vitamins, minerals and good fats and protein. Hopefully, Wonderful Pistachios can find its cause for the contaminated pistachios and fix the issues.

Reference:

Wonderful Co. recalls pistachios because of link to Salmonella outbreak; Trader Joe’s brand included

http://www.americanpistachios.org/nutrition-and-health

Contributed by Azarene Foutouhi

Very little is known at this time of the mechanisms and interactions between the fetal and maternal systems and their resultant effects on the health a pregnancy. While some research has indicated complex relationships between the role of fetal placental stem cells and the hormones they produce from maternally derived compounds in the maintenance of a pregnancy, there is yet little information regarding the pathways and parties responsible when things go wrong. Recently, interest in describing the microbiome of the placenta in a healthy pregnancy has led to questions on the potential involvement of bacteria in placental health, namely spontaneous abortion and preterm birth.

More specifically, research has linked certain strains of bacteria responsible for periodontal disease, an infectious disease of various severity affecting the majority of individuals, to premature and term stillbirths. One such bacteria associated with periodontal disease, Fusobacterium nucleatum, is a gram negative anaerobic bacteria with superior adhesion capabilities that is found in the amniotic fluid of 30% of women in preterm labor. These levels greatly outnumber any other bacteria present.

While it has previously been supposed that any bacteria found in the placenta or amniotic fluid is a result of infection from an ascending route through the cervix, this particular species of Fusobacterium differs from those isolated from the lower genital tract, suggesting its presence in amniotic fluid is due to hematogenic transfer from the mother to the fetus through the placenta. By describing a normal placental microbiome and detailing the interactions between host and microbe, we will be better able to explore the potential effect of bacteria on the maintenance of pregnancy and in the development of the fetus, as well as any indications of their effects on the long term health of the child.

Yiping W. Han. 2004 April. Fusobacterium nucleatum Induces Premature and Term Stillbirths in Pregnant Mice: Implication of Oral Bacteria in Preterm Birth. Infection and Immunity. 72(4): 2272-2279

Yiping W. Han. 2000 June. Interactions between Periodontal Bacteria and Human Oral Epithelial Cells: Fusobacterium nucleatum Adheres to and Invades Epithelial Cells. Infection and Immunity. 68(6):3140-3146.

Contributed by Robin Jones

I have a great job! I get to work in a research lab at a top University. I get to rub shoulders with people who are making the world a safer place and with young people who are starting their journey toward their future. It can be exciting, challenging, exhilarating, and stressful to say the least. Everyone who knows me knows that I am the token ‘non-science’ person in the lab, but I find that being an administrative assistant is what I was cut out to be. I admire those who are doing the science and I like working in the shadows to do what others might consider mundane. Setting schedules, bringing coffee (I actually LIKE to do this), booking travel, and keeping calendars glitch free and meetings straight. All of this is what I happen to be good at so others don’t have to think about it and can go about their day doing what they are good at. I find at this stage in life I look forward to waking and working, it’s not only fulfilling but there is something new every day!

Another thing I enjoy is snacking! I have discovered while working in the lab that everyone has some sort of snack at his or her desk. I hear the crunch of chips, the rattle of plastic as a tasty snack is torn open (usually mine), and the thud of paper cups and energy drink cans as they are dropped into the recycle bin. Occasionally I hear the crunch of an apple, catch the smell of a banana or heart healthy homemade muffins. But with all the time spent sitting at our desks, I notice the one thing we all seem to do is snack!

In an attempt to find something beautiful in the snacking realm (and since none of us will likely give it up) I thought perhaps my contribution to this blog might be to add a couple of ‘healthy’ snack recipes. I hope to take my own advice and start gravitating toward them and away from those dangerous yet tasty prepackaged death bombs.

Below are a couple of links I found for Healthy Snacks to have at your desk. Enjoy!

http://www.foodnetwork.com/recipes/trisha-yearwood/power-balls.html

http://www.myrecipes.com/recipe/chewy-caramel-apple-cookies

http://communitytable.parade.com/366238/kellyhunt/make-your-own-delicious-homemade-kind-bars/