Changing Temperatures Potentially Change Our Gut Microbiome

Contributed by: Chelsey A. Skeete, Emily F Ursini, and Sopjia T. Noble

Introduction

The gut microbiome is an incredibly complex component of the body that is still not fully understood. The microbiome can be impacted by a vast number of factors including diet, exercise, contact with others, and time spent in and outdoors (7). The gut microbiome is
impacted by the environment, which is influenced by temperature and climate (8).The temperature influences microbial diversity in a multitude of ways from common seasonal changes to the earth’s overall shift in climate (8). This is especially important to consider when thinking about the 70 million Americans currently suffering from gastrointestinal issues including irritable bowel syndrome and celiac disease (6). The information to follow explores some beneficial and detrimental influences of temperature on the gut microbiome, which are incredibly important to keep in mind when assessing the impact that temperature shift will have on the environment, as well as how to maintain a healthy microbiome throughout these changes.

Figure 1: The human microbiome is impacted by the external environment.

The Dangerous Effects of Temperature and Environment Change on the Microbiome

Growing up in microbe-rich environments, individuals can uptake microbes from the environment that colonize in the gut as commensal bacteria. Urbanization often leads to loss of biodiversity and local habitats that would be reservoirs for commensal bacteria to survive and reproduce (8). Individuals who grow up in environments with slightly lower microbial diversity are exposed to less potential commensal bacteria. Less exposure to commensals especially during child development may raise individuals’ risks for inflammatory diseases. Additionally, reduced exposure to pathogenic bacteria may result in defective or compromised immunoregulation.

Figure 2: Type II Diabetes Diagram

In a study with mice samples, the populations raised in cold environments for several days had intestinal structural changes that enabled them to have increased glucose uptake (4). The increased presence of glucose led to higher production and functioning of insulin to be recruited to the small intestine to break down glucose. Overuse of insulin led to insulin sensitivity in the mice, which raises the risks of the mice getting Type II Diabetes. These mice could also be a model for cold temperature impact on humans and how their small intestines could similarly alter to have increased glucose uptake leading to insulin sensitivity. Of course other factors must be considered in this relationship of temperature and insulin sensitivity, as diet and genetic predisposition to Diabetes would impact the results seen in humans as well. In warm, heat stressed environments, the diversity in the gut microbiome has decreased in cow subjects (11).

The Beneficial Effects of Temperature Change on the Microbiome

Cold exposure may lengthen microvilli in the small intestine where commensal bacteria may attach and grow (3). Additionally, cold exposure may improve glucose absorption in the small intestines of humans enabling more carbon resources for commensal bacteria to survive and reproduce in the gut (3). During rapid temperature changes, some species in the gut microbiota may produce heat to help animal hosts maintain their internal temperatures in cold environments (9).

Supporting Data

Figure 3: Diversity of bacterial phylums across samples isolated from mice raised in room
temperature or cold temperature (4).

One research group researched how temperature affects microbial diversity in feces and cecum samples of mice (4). Some mice were raised in room temperature or cold environments for up to 31 days and their fece samples were collected to sequence the DNA in each sample. In room temperature environments there tends to be a higher abundance of ​Verrucomicrobia ​across the feces and cecum samples. However, there is a slightly higher abundance of ​Deferribacteres ​in samples isolated from mice raised in colder environments. Such evidence demonstrates that the populations of bacteria in mammals’ microbiomes may slightly change due to extreme temperature changes in the environment. This change may be due to the fact that certain bacteria based on its structure and functions can only adapt to specific temperature ranges. These mice used in this experiment may possibly be a model for the human gut microbiome and how it may be subject to change in its diversity due to extreme temperature changes.

Tips to Maintain the Diversity and Viability of the Gut Microbiome

Figure 4: Prebiotic Rich Foods
  1. Maintain a healthy and diverse diet
    • Increase fiber consumption, as it helps to create and maintain the gut microbiome (6)
    • Try to eat what is in season as much as possible! Foods out of season often have lower levels of nutrients, as well as increased levels of harmful pesticides (7)
  2. Spend more time outdoors
    • The microbe rich environment of the outdoors increases microbial diversity in
      your gut (7)
  3. Consider utilizing prebiotic powder to support your gut (7)
    • Prebiotic powders feed species in the microbiome that struggle to survive due to the western diet and lifestyle (7)
  4. Reduce stressors whenever possible (7)
    • Stressors slow digestion, which reduces microbiome diversity by only allowing the survival of certain bacterial species
  5. Avoid sleep deprivation
    • Sleep deprivation can throw off bacterial balance, even two nights of being sleep deprived can decrease certain bacterial strains by one half (7)

Conclusion

There are quite a few studies that show how cold environments may both positively and negatively impact the gut microbiome of mice, salamanders and other animals. In these temperatures, the phyla composition of bacteria change over time due to certain selective pressures bacteria may have to survive and reproduce in such an environment. On the other extreme, heat stressors may reduce gut microbiota diversity in animals. However, there are very little research studies that demonstrate how climate change may alter the gut microbiota of humans. While these animals used in these experiments may be models for the effects of climate change on the human gut microbiome, humans have more advanced homeostatic mechanisms to rapidly adapt to environmental changes. There is still more research that needs to be conducted to show if indeed temperature change is harmful to the gut microbiota diversity in humans.

References

  1. Keesing, F. (2010). Impacts of biodiversity on the emergence and transmission of
    infectious diseases. ​Nature, ​​468,​ 648-652. doi:10.3897/bdj.4.e7720.figure2f
    https://wedocs.unep.org/bitstream/handle/20.500.11822/18895/nature09575.pdf
  2. Candela, M. (2012). Intestinal microbiota is a plastic factor responding to environmental changes. ​Science Direct,20​(8). doi:10.3897/bdj.4.e7720.figure2f
    https://www.sciencedirect.com/science/article/pii/S0966842X12000935
  3. Canny, S. G., & Rawls, J. (2015). Baby, It’s Cold Outside: Host-Microbiota
    Relationships Drive Temperature Adaptations. ​Cell Host & Microbe,​ ​18​(6), 635-636.
    doi:10.1016/j.chom.2015.11.009 https://www.sciencedirect.com/science/article/pii/S1931312815004631
  4. Chevalier, C., Stojanović, O., Colin, D., Suarez-Zamorano, N., Tarallo, V.,
    Veyrat-Durebex, C., . . . Trajkovski, M. (2015). Gut Microbiota Orchestrates
    Energy Homeostasis during Cold. ​Cell, ​​163​ (6), 1360-1374. doi:10.1016/j.cell.2015.11.004 https://www.sciencedirect.com/science/article/pii/S0092867415014841
  5. Fontaine, S. S., Novarro, A. J., & Kohl, K. D. (2018). Environmental temperature alters the digestive performance and gut microbiota of a terrestrial amphibian. ​The
    Journal of Experimental Biology,​ ​221​(20). doi:10.1242/jeb.187559 http://jeb.biologists.org/content/jexbio/221/20/jeb187559.full.pdf
  6. Davis, L. S. (2018). Gut Feeling. ​Grist.​ https://grist.org/article/climate-change-my-microbiome-and-me/
  7. Hyperbiotics. (n.d.). How Your Gut Bacteria Change With the Seasons. Retrieved from https://www.hyperbiotics.com/blogs/recent-articles/how-your-gut-bacteria-change-with-the-seasons
  8. Tasnim, Nishat, Abulizi, Jason, Hart, Gibson, & L., D. (2017, September 21). Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on
    Where We Live? Retrieved from https://www.frontiersin.org/articles/10.3389/fmicb.2017.01935/full
  9. Rosenberg, E., & Zilber-Rosenberg, I. (2016). Do microbiotas warm their hosts? ​Gut
    Microbes,​ ​7​(4), 283-285. doi:10.1080/19490976.2016.1182294
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988433/
  10. Image #1: Tuning the Microbiome Improves Melanoma Immunotherapy Response.
    (2018, October 31). Retrieved from
    https://www.genengnews.com/topics/omics/tuning-the-microbiome-improves-melanoma-immunotherapy-response/
  11. Chen, S., Wang, J., Peng, D., Li, G., Chen, J., & Gu, X. (2018). Exposure to heat-stress
    environment affects the physiology, circulation levels of cytokines, and microbiome in dairy cows. ​Scientific Reports,​ ​8​(1). doi:10.1038/s41598-018-32886-1
  12. Image #2: Nutrition: The Secret To Preventing And Reversing Type 2 Diabetes. (2018, November 20). Retrieved from https://www.marshafenwicknutrition.com/nutrition-the-secret-to-preventing-and-reversing-type-2-diabetes/
  1. Image #3: Healthy Foods High in Prebiotics. (2019, January 05). Retrieved from
    https://www.oawhealth.com/2013/09/18/healthy-foods-high-in-prebiotics/

Are Our Handbags ‘Carrying’ Around More Germs Than a Toilet?

Contributed by: Katherine Hayes, Catherine Roughneen, and Darya Kostyuchek

As early as the seventeenth century, both men and women have been utilizing soft fabric or animal hides as a means of fashioning handheld bags to carry their belongings. One early example originating in Scotland is the sporran, a satchel type accessory, that was worn under pocketless kilts. Nowadays, the modern handbag has become just as essential as any other article of clothing. Americans use handbags daily to carry their everyday needs from commuting to work to travelling through a busy airport. Consequently, purses are often kept in environments laden with bacteria, such as kitchen tables, restroom floors, and fast food counters.

It is said that the common handbag hosts more germs than a toilet seat. This is due to the vast diversity of microbiological communities and types of bacteria found both on the inside and bottom of everyday handbags. Admittedly, one probably cleans the inside of their toilet more often than the inside of their handbag.  According to a recent study done in 2015 created in order to further investigate the importance of microorganisms living in and on purses shows that pocketbooks and handbags are easily contaminated with infectious agents. Microbiologists have confirmed that about one third of handbags have fecal bacteria on them. Other strains of bacteria found included Staphylococcus, Enterococcus, Escherichia coli, Pseudomonas, and Micrococcus.

These microorganisms themselves can lead to intestine problems, chest disease, or staph infections. Therefore, people carrying around handbags can unknowingly serve as vehicles for the transmission of diseases. Purses in this way are — fomites or vectors of disease for thousands of bacterial colonies festering inside our bags. In the study, 145 handbags, 80 from women and 65 from men, were swabbed and cultured looking for the presence of certain bacteria. Bacteria were then identified by gram staining and other biochemical tests. The scientists found that 138 purses (95.2%) had bacterial contamination, with about half having single bacterial growth and the other half having mixed bacterial growth (Biranjia-Hurdoyal, Susheela D, et al.). Most bacteria found from the study was relatively harmless with the exception of Staphylococcus, Bacillus, and Micrococcus, which are considered opportunistic pathogens, infecting both healthy and immunocompromised individuals. The study also found that women were more likely to have bacterial growth in the handbags than men. This may be attributed to women being more likely to carry a purse in the first place and more likely to place said purse on kitchen tables, public restroom floors or counters. Purse carriers also never completely empty or clean their belongings and tend to keep items inside including food and hand lotions that can initiate vast microbial growth.

Why are Purses such great Fomites?

Handbags are in constant contact with our hands and a variety of surfaces, increasing the risk of germs being transferred to the bag. Once germs are on our handbags, we can easily transfer harmful germs to other people and surfaces.

One study in the United Kingdom found that the handle was the bacterial hotspot, but others report that the inside of the bag was worse, containing items like makeup or hand creams that had the toilet-flush levels of bacteria (Gerba). The inside of handbags create a perfect haven for germs because they can live in a dark, humid, and damp environment with old food crumbs floating around providing nutrients to the bacteria. Overall, scientists seem to agree that the material of the handbag is also an important factor in determining bacterial growth. Handbags with rough, braided, and grooved surfaces harbor more bacteria than handbags with smooth surfaces. This is because the bacteria can harvest themselves inside these small hard to reach places.

Your money, keys, credit cards, and mobile phones inside your handbag are no better. A study done to find the possible transmission of infectious bacteria via mobile phones, swabbed 192 phones and found that 91.7% of them showed bacterial contamination (Bhoonderowa). Furthermore, it was discovered that women’s phones, kept in purses had more colony forming bacteria compared to men’s phones that were kept in pockets. Phones themselves can be considered fomites as we take them with us to the kitchen, the restroom, hospitals, and other places that are chock-full of microorganisms. Similarly, more than 50% of coins and banknotes were found to be contaminated with bacteria. Most items in handbags are passed between many people, placed on surfaces covered with bacteria, and touched by dirty hands. This creates a vicious cycle between bacteria from our handbags contaminating our belongings, and the same belongings making the bacterial growth in our handbags worse.

How Can we Prevent the Breeding Grounds?

Experts recommend:

  • Instead of putting your handbag on the floor in restaurants, toilet stalls or train floors, you hang it on a hook or door handle.
  • Always close the toilet seat before flushing as germs can still contaminate when they are airborne.
  • Regularly clean out and wash both the insides and outsides of bags with antibacterial wipes or gel as often as possible.
  • Regularly wiping down phones with disinfecting wipes before placing them back inside bags.
  • Try not to keep food inside bags, especially decaying fruit.

These few tips can severely decrease the bacterial count on the bottom and inside of your bags. In fact, the “toilet plume,” or small particles of toxins and waste that mix together with the toilet water, is known to be able to hurl aerosolized feces into the air as high as 15 feet every time they’re flushed without closing the lid. Similarly, one communicable and vomit induced microorganism found in a lot of toilet bowls, C. difficile, can shoot up to 10 inches. As well as keeping food and fruit out of the inside of bags is extremely helpful (Lawton). This is due to the fact that as mentioned above, the insides of purses can be perfect breeding grounds for mold or other microbes that thrive off of dark and warm spaces – not to mention that food naturally have enzymes that catalyze the degradation process (Gerba).

References

Healthy Gut, Healthy Mind

Contributed by: Rafat T. Quazi, Elizabeth E. Spyrou, and Michaela J. Sorrell

Introduction

​The human gut harbors nearly 100 trillion microbes of more than 1,000 different species involved breaking down food, supporting our immune system, and as revealed by current research, have important implications on our mental health. Recent studies have yielded significant evidence of an interaction between our intestinal microbiota and the central nervous system, a connection that has been recognized as the gut-brain axis (GBA). This connection is important when we consider the high comorbidity between gastrointestinal disorders and stress-related psychiatric disorders, such as anxiety and depression. Probiotics, fecal transplants, and altered diets have been recognized as means to manipulate our microbiome and hold potential for the prevention and treatment of prevalent psychiatric diseases in today’s society.

Background

Figure 2: A simplified schematic of the microbiome–gut–brain axis. (Image courtesy of Kiran Sandhu.)

The enteric nervous system, consisting of approximately 100 million neurons embedded in the walls of our gut and acting as a ‘second brain’, is a key player in the GBA. Although it is not entirely known how gut communicates with and influences our brain, one way that it might is through the production of neurotransmitters such as Serotonin which is well-known for it’s role in mood changes. Gut bacteria can also influence the metabolism of these compounds and how much reaches the brain. Another way that gut bacteria can influence the brain is through activation of the vagus nerve. Finally, the gut microbiome may impact the brain through it’s tie to the immune system. Gut microbiota regulate levels of immune molecules like cytokines; elevated levels of inflammatory cytokines have been associated with depression. Gut-brain communication is bidirectional, meaning that patients with gastrointestinal issues have higher rates of depression and anxiety, and patients with mental health issues experience more GI problems than healthy individuals. Early life disruption of the bidirectional GBA has been associated with increased risk of depression in adulthood.

Pros/Cons of dealing with Mental Disorders through a Bacterial Lens

Pros:

  • Early nutrition can play a huge role in developing infant gut bacteria. Breastfeeding was shown to correlate with the number of bacterial organisms present in the gut, as well as other antibodies that provided protection against intestinal inflammation.
  • Prebiotics contain fibers that can help stimulate present gut bacteria. Recent studies have shown that prebiotics, along with probiotics, offer similar antidepressant effects to lower stress induced changes to our microbiota, which creates stability within bacterial populations.
  • In a recent study, patients without depressive symptoms, who were given probiotics, saw reduced cortisol levels and better psychological effects similar to patients who used an anti-anxiety medication.
  • Patients may find that using prescribed mood-altering drugs in addition to the consumption of probiotics, can help lower/fix created neurological imbalances.

Cons:

  • Mothers who have infants through Cesarean section often deal with less gut bacteria in the baby’s gut than infants delivered vaginally.
  • Infants that consumed formula their first month had a decrease in total bacteria. Breast milk has been shown to include lactose and a multitude of other molecules (such as sugars), that build the base for a strong and healthy gut environment.
  • The mechanism and long-term effects of probiotic use on humans with mood disorders have yet to be seen, or even studied. Subjects on probiotic therapy have even reported sickness, nausea, and increased bacterial challenge. This suggests that probiotics may not be a long-term cure for all patients.

Case Studies

There have been increasing amounts of case studies that serve to inspect the “bidirectional
communication” between the gut and brain, called the gut-brain axis. Scientists have theorized that a decrease in good gut bacteria leads to inflammatory responses in the immune system. This then leads to inflammatory and mental disorders, such as depression.

In the case study “Gut-Brain Axis and Mood Disorder” researchers tested the theory that intestinal microorganisms did played role in affecting the human gut-brain axis (neuro-endocrine immune pathways) and how that could cause certain mood disorders. The study also looked at the effect of pre/probiotics as well as antibiotics on mood disorders.

Previous studies show that ~60% of anxiety/depressed patients suffered from irritable bowel syndrome (IBS) which is involved with changes in intestinal microorganisms, namely a reduction of microbiota species. In fact, a study led by Park AJ, Blennerhassett, and Verdu stated that animal procedures showed gut bacterial disturbances to cause nervous system pain and brain chemistry changes and behavior. Stress can lead to gut bacteria change and therefore mood change with the HPA axis. ​Corticotrophin-releasing factor (​CRF) ​receptors in the body are used to measure intestinal permeability induced by stress. In acute stress, permeability is increased, and early life stress causes a cortisone level increase which forces bacteria to move towards your liver and spleen, furthering the idea that those with mood disorders suffer from a reduction in gut bacteria. Studies on rats showed that the lack of intestinal microbiota increased anxiety-ridden behavior when the rats were faced with challenges or unknown stimuli.

Probiotic Effects on Stress-related Disorders

While various means of regulating the gut microbiota have been considered, an interest in probiotic treatments has particularly increased in recent years. Probiotics are live microorganisms consumed with the expectation of health benefits, as they have the potential to improve and restore our gut bacteria. It is known that gut bacteria can produce metabolites for various human organ systems. The bacterias ​Lactobacillus and ​Bifidobacterium,​ for example, are able to synthesize gamma-aminobutyric acid (GABA) from monosodium glutamate, which is an important inhibitory neurotransmitter having calming effects in the central nervous system. ​A significant amount of the research has been done on germ free mice, which are entirely devoid of microorganisms, offering a more controlled setting for observation of the role of the microbiome in diseases and their treatment. In one study, it was found that a bacterium ​Bifidobacterium infantis,​ commonly found in probiotics, was able to reverse an elevated HPA-axis response and depression, leading to a general relaxation in neural processes. Other rats who were regularly administered probiotics including Lactobacillus helveticus or ​Bifidobacterium longum showed decreased psychological stress levels and cortisol levels, a hormone associated with our stress response. Studies on humans have also been able to show connections between specific gut bacteria and depression. For example, the ​Bacteriodes family has been specifically shown to be associated with depression, with low levels of this bacterium in fecal matter associated with high activity in brain areas related to depression. This makes sense, as this family has been shown to produce large quantities of GABA, which as stated before is among the most significant inhibitory neurotransmitters on the CNS. Based on studies like these, probiotics have the potential to decrease symptoms of anxiety and depression, and therefore may be an important treatment option in coming years. Without the side effects and stigma that surround antidepressants in today’s society, this could be a promising option for people suffering from these psychiatric disorders.

References

Zombie Pathogens: How Melting Permafrost Is Bringing Dormant Microbes Back to Life

Contributed by: Madison J. O’Connor, Jonathon R. Vickery, and Ernest M. Violet

Long-dormant bacteria and viruses, trapped in ice and permafrost for centuries, are
regaining life as Earth’s climate continues to warm.

What Is Permafrost?

Permafrost coverage in the Northern Hemisphere.

Permafrost is soil that has been frozen for at least 2 years. These soils cover about 25% of all
land in the Northern Hemisphere, and they store more than half of Earth’s soil carbon. Permafrost habitats can be 1-3 million years old in the Arctic and bear a variety of microorganisms, many of which remain active at subzero temperatures. This kind of habitat is ideal for keeping microbes and spores dormant, or metabolically inactive, due to its neutral pH, low temperature, and lack of both of light and oxygen.

Permafrost and Climate Change

Climate change is warming the Arctic twice as quickly as any other place on Earth. As global temperatures increase, microbial metabolism of organic carbon increases, which results in the increased production of carbon dioxide and methane. This process leads to a dangerous feedback loop. As more carbon dioxide and methane are released, greater warming occurs, which then releases more carbon dioxide and methane. This cycle results in the activation of dormant microbes present in the permafrost.

The permafrost positive feedback loop.

Microbes Discovered in Permafrost

  • In 2005, NASA conducted a study in which bacteria that had been trapped in a frozen pond in Alaska since the Pleistocene period (~32,000 years) were successfully revived. The microbes were identified as Carnobacterium plesitocenium, a psychrotolerant, facultative anaerobe. The microbes began to move once the ice melted, and quickly became infectious once revived.
  • In 2007, scientists revived a bacterium that had been dormant for 8 million years underneath a glacier in Antarctica.
  • In 2014, scientists revived two “giant viruses,” i.e. viruses that have much larger genomes compared to other viruses as well as unique genes, Pithovirus sibericum and Mollivirus sibericum, that had been trapped in Siberian permafrost for 30,000 years. Both viruses quickly became infectious once revived. Although these specific viruses only infect amoebas, single-celled organisms, viruses that can infect humans could be similarly revived.
  • In August 2016, in a remote area of the Siberian tundra, an anthrax (Bacillus anthracis) outbreak resulted in the death of a 12-year-old boy and the hospitalization of over 70 people. Health officials concluded that an abnormal wave of heat thawed the frozen carcasses of reindeer that became infected with anthrax over 75 years ago. Once thawed, the carcasses released anthrax into nearby groundwater and soil, which was then passed on to the food supply. Scientists fear that there will be more anthrax outbreaks as permafrost continues to thaw.
  • Scientists have discovered RNA fragments of the 1918 Spanish flu virus in corpses buried in large graves in the Alaskan tundra.
  • In Siberian permafrost, fragments of smallpox DNA have been found in corpses covered in sores.

Impact on Human Health

The possibility that pathogenic microbes can be revived and infect humans is well-established. What is uncertain is whether these microbes are bacteria that can be fought with antibiotics, bacteria that are resistant to antibiotics, or viruses. Since these microbes have been trapped in permafrost for long periods of time, our immune systems would not recognize them or be able to defend against them. Therefore, these once-dormant microbes could pose a serious threat to human health.

References

  1. Burkert, Alexander, et al. “Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.” Applied and Environmental Microbiology, American Society for Microbiology, 1 Apr. 2019, aem.asm.org/content/85/7/e02646-18.
  2. Cheng, Guodong, and Tonghua Wu. “Responses of Permafrost to Climate Change and
    Their Environmental Significance, Qinghai-Tibet Plateau.” Journal of Geophysical
    Research: Earth Surface, John Wiley & Sons, Ltd, 8 June 2007,
    agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2006JF000631.
  3. Doucleff, Michaeleen. “Are There Zombie Viruses in The Thawing Permafrost?” NPR,
    NPR, 24 Jan. 2018, www.npr.org/sections/goatsandsoda/2018/01/24/575974220/are-
    there-zombie-viruses-in-the-thawing-permafrost
    .
  4. Fox-Skelly, Jasmin. “There Are Diseases Hidden in Ice, and They Are Waking Up.”
    BBC, 4 May 2017, www.bbc.com/earth/story/20170504-there-are-diseases-hidden-
    in-ice-and-they-are-waking-up
    .
  5. Goudarzi, Sara. “As Earth Warms, the Diseases That May Lie within Permafrost Become a Bigger Worry.” Scientific American, Nov. 2016, www.scientificamerican.com/article/as-earth-warms-the-diseases-that-may-lie-within-permafrost-become-a-bigger-worry/.
  6. Jansson, Janet K., and Neslihan Taş. “The Microbial Ecology of Permafrost.” Nature
    News, Nature Publishing Group, 12 May 2014, www.nature.com/articles/nrmicro3262.
  7. Koven, Charles D., et al. “Permafrost Carbon-Climate Feedbacks Accelerate Global
    Warming.” PNAS, National Academy of Sciences, 6 Sept. 2011,
    www.pnas.org/content/108/36/14769.full.
  8. Pikuta, Elena V., et al. “Carnobacterium Pleistocenium Sp. Nov., a Novel
    Psychrotolerant, Facultative Anaerobe Isolated from Permafrost of the Fox Tunnel in
    Alaska.” International Journal of Systematic and Evolutionary Microbiology,
    Microbiology Society, 1 Jan. 2005, ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.63384-0.
  9. Resnick, Brian. “Melting Permafrost in the Arctic Is Unlocking Diseases and Warping the Landscape.” Vox, 6 Feb. 2018, www.vox.com/2017/9/6/16062174/permafrost-melting.
  10. Schuur, E. A. G., et al. “Climate Change and the Permafrost Carbon Feedback.” Nature News, Nature Publishing Group, 9 Apr. 2015, www.nature.com/articles/nature14338.
  11. Taubenberger, Jeffery K et al. “Discovery and characterization of the 1918 pandemic
    influenza virus in historical context.” Antiviral therapy vol. 12,4 Pt B (2007): 581-91. https://www.ncbi.nlm.nih.gov/pubmed/17944266.
  12. Zoltai, S. C. “Tree Ring Record of Soil Movements on Permafrost.” Arctic and Alpine
    Research, vol. 7, no. 4, 1975, pp. 331–340. JSTOR, www.jstor.org/stable/1550177.

Microbial Fingerprints: Your Own Unique Population!

Contributed by: Alison A. Lemme, Kathryn H. Shaffert, and Angel E. Roman

What is a Microbial Fingerprint?

Millions of microbes are present in this one fingerprint!

Every individual has their own microbial fingerprint. This means that each individual’s microbiome has a specific makeup of species and strains. This fingerprint is largely determined by a person’s environment. Similarly, a person’s environment is also affected by their microbial fingerprint. This means that there is an exchange occurring between people and their environment as each sheds microbes onto the other. Due to this shedding and exchange, it has been shown that the proportions of bacterial species are in constant flux; however, the overall makeup of microbial strains remained the same (1).

How is Microbial Fingerprint data used?

The data collected from microbial fingerprints is used to learn which microbes are present in the surrounding environment and how they live and function in these specific environmental conditions. These fingerprint methods are very important in the bioremediation field (3), by indicating whether or not bioremediation will be effective for a specific surface depending on the makeup of the microbial population. Bioremediation is the introduction of microbes to break down environmental pollutants! In addition, these fingerprints can account for changes in the microbial community over a period of time or period of bioremediation. They are basically environmental markers that indicate if the bioremediation was successful or not!

Three Microbial Fingerprinting Methods

PLFA: Phospholipid Fatty Acid Analysis

PLFA analysis measures the total biomass of a microbial community and creates a profile or ‘fingerprint’ of its composition, including several microbial species (except for archaea). PLFA analysis is most commonly used to determine how varying conditions impact total biomass (2).

DGGE: Denaturing Gradient Gel Electrophoresis

DGGE amplifies DNA and analyzes its molecular weight to demonstrate how the genetic composition of a microbial fingerprint is altered in varying conditions. These results are extrapolated to identify the family or genus of the organisms present at the highest abundance. Subsequent sequence analysis of the dominant bands provides more information regarding the identity of the abundant species. Because DGGE can only identify the family or genus level of only the most abundant species present, it is typically utilized as a first step in microbial fingerprint identification (2).

T-RFLP: Terminal Restriction Fragment Length Polymorphism

T-RFLP is a qualitative method of microbial fingerprinting that uses restriction enzymes to break apart DNA at sites that are species-specific. Therefore, the lengths of the fragments that are produced are indicative of the specific organisms present (2). T-RFLP is able to detect microorganisms that are present at lower concentrations in a sample than DGGE techniques (4).

Applications of Microbial Fingerprinting

Due to the uniqueness of each individual’s microbial fingerprint, research is being conducted on its possible application as an emerging tool for forensics. Because the average person sheds approximately 15 million bacteria per hour, their microbial fingerprint may be present at a crime scene after their departure for testing by forensic officials. By sequencing the species present at the crime scene, forensic officials are able to create a microbial profile of a suspect.

The proportions of microbial species present also provide a potential opportunity for further specification of the identification of the criminal’s lifestyle, because certain species will thrive more in specific lifestyles (1). While this is still an area of active research, it represents an exciting innovation that can be used to complement traditional methods of identification, such as DNA sequencing, in order to enhance the reliability of identification of perpetrators. 

Advantages of Microbial Fingerprints

Microbial fingerprinting methods do not require the growth of a microbe in a laboratory setting. This saves time and resources! These methods can be used to identify and track specific phenotypes of organisms that have never before been cultured or identified (3).

In a global environment where new unknown contaminants are constantly emerging and being produced, microbial fingerprints can be a useful tool. Since very little background information is needed to identify microbial species of interest, these methods can help to track these newly emerging contaminants!

Limitations of Microbial Fingerprints

PLFA analysis is unable to identify specific microorganisms. On the other hand, genetic fingerprinting methods like DGGE or T-RFLP can in fact identify specific microorganisms, but can not always determine the exact number of that microorganism that exists in the given environment (3). Lastly, microbial fingerprints are very detailed, and as a result are very subjective in their interpretation from person to person. The more microbial communities that are analyzed using these methods, the more accurately scientists will be able to identify the microorganisms. So it’s up to us to keep these methods relevant!

Our microbial fingerprints don’t just identify us, they even reveal information about the microbes living in, on, and around us!

References:

  1. Gilbert, Jack; Hampton-Marcell, Jarrad; Lopez, Jose. “The human microbiome: an emerging tool in forensics.” Microbial Technology, US National Library of Medicine, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328825/, April 22, 2019.
  2. ITRC. “Microbial Fingerprinting Methods.” Environmental Molecular Diagnostics, ITRC, https://www.itrcweb.org/emd-2/Content/5%20Microbial%20Fingerprinting.htm, April 22, 2019
  3. ITRC. “Microbial Fingerprinting Methods: EMD Team Fact Sheet.” Environmental Molecular Diagnostics, ITRC, https://www.itrcweb.org/documents/team_emd/Microbial_Fingerprinting_Fact_Sheet.pdf, April 22, 2019.
  4. Sinha, Moumita. “Microbial Fingerprinting – A current vogue in Microbial Forensics.” Research Gate, Research gate, https://www.researchgate.net/publication/315665338_Microbial_Fingerprinting_-_A_current_vogue_in_Microbial_Forensics, April 22, 2019.

Venom: Friend or Foe?

Contributed by: Kayleigh S. Clermont, Jeremiah Seo, and Yanlin Zi

Almost everyone loves dogs, cats, and bunnies, but other animals or insects such as wasps, scorpions, and snakes are usually not the “beloved” superstar in the animal world. They are neither cute nor friendly, and moreover, their venom even threatens our health. However, scientists recently have discovered that the venom of these “malicious” creatures could be beneficial to us.

Wasps

Buzzzzzz…Buzzzzzzz…

When people hear this sound in their house, most people’s first reaction is “Uh-oh.” Then, perhaps, they would start freaking out and trying desperately to get this annoying intruder out of their house as soon as possible. Admittedly, unlike honey bees, who are both friendly and beneficial workers, wasps are considered mostly as dangerous and frightening. However, scientists have recently found out the wasp’s venom can be extremely beneficial in the field of medicine.

If stung, wasp venom could cause swelling of the skin, hives, and itching as well as many other symptoms. In severe cases, the potent venom could also cause dizziness, breathing difficulties, vomiting, or even loss of consciousness. However, even though wasp venom poses such a threat to human health, it could also help doctors fight some complicated infections.

To begin the research on the medicinal values of wasp venom, Leite et. al did a study in which they studied that the venom of ​Polybia paulista​, a kind of social wasp (wasps that lived in colonies) from South America that is normally found in the tropical areas of Brazil, Argentina, and Paraguay. Researchers found that this specific wasp venom contains a peptide, a small chain of amino acids, that they called Polybia-MP1. They discovered that this peptide could potentially be used as a chemotherapeutic substance. The peptide was observed to have the ability to eliminate cancer cells. However, the exact mechanism of this elimination process is still not fully understood. Just like other animals’ venom, wasp venom contains a multitude of compounds that have the ability to kill various kinds of bacteria. However, in most cases, the venom is so toxic that it cannot be used in humans.

In 2018, scientists from MIT elaborated on the previous studies of ​Polybia paulista​ venom with the intention of using it to formulate a drug that could be used on humans. From this study, MIT researchers successfully developed a method to modify the antimicrobial peptides extracted from ​P. paulista​ venom so that they would not be toxic to humans but still retain their bacteria-killing properties. To achieve this, scientists extracted a very small amount of the antimicrobial peptide from the wasp venom. De la Fuente-Nunez, one of the scientists from this MIT project, explains, “it’s a small enough peptide that you can try to mutate as many amino acid residues as possible to try to figure out how each building block is contributing to antimicrobial activity and toxicity.”

The modified wasp venom-derived peptide has the ability to kill the bacteria by disrupting the bacterial cell membrane, just like attacking a citadel during a war. ​The venom-derived drug has already been proven be able ​to successfully fight against Pseudomonas aeruginosa, a bacteria that commonly causes respiratory and urinary tract infections.

Pit Vipers

Sssssssss… Ssssssssssss…

Most people jump at the sound of a snake nearby out of fear of getting bitten and having toxic venom injected into their tissues and bloodstream. Though many snakes are nothing to be afraid of, pit vipers pose a massive threat because of their powerful bite and potent venom. Pit vipers are a family of snakes that are found in various habitats in Europe, Asia, and the Americas. A bite from a pit viper can have many consequences including but not limited to pain, swelling, bruising, numbness, respiratory distress, and shock.

Despite all of these consequences, scientists have found a way to manipulate the venom of the Brazilian pit viper and turn it into a helpful drug for humans. It all started when John Vane tested small amounts of Brazilian pit viper venom on dog lungs in Vane recognized that compounds from the venom inhibited the enzyme that causes high blood pressure. Soon after, in 1974, Squibb, a US drug company, tested the ability of one of the compounds in the venom to lower blood pressure. In 1981, Squibb had an FDA-approved drug which they called Captopril.

By lowering high blood pressure with Captopril, the risk of heart attack, stroke, and kidney issues are all consequently reduced. Captopril does this by easing the blood vessels, thereby allowing blood to flow through more easily. Additionally, some bacterial and viral infections can cause high blood pressure, in which cases, Captopril could be used to treat that symptom. Although Captopril has its benefits, it also has potentially harmful side effects. Some of the consequences of using this drug may include dizziness, fainting, tachycardia (fast heartbeat), muscle weakness, or liver problems.

Conclusion

As seen in the example of the wasp and the Brazilian pit viper, venom of all sorts of animals can potentially be manipulated and used in small doses for medicinal purposes. By targeting species whose venom is not well researched, amazing drugs could possibly be created to target bacterial infections, viral infections, fungal infections, and even maybe cancer. More research needs to be done on species who seem scary because they could actually prove to be helpful to humankind as the wasp and the Brazilian pit viper have.

References

So What Really ​Are​ Vaccines?

Contributed by: Nicole Bell, Tara Beckwith, and Kelly Cavan

Vaccines have been a hot topic for scientists, researchers, healthcare professionals, and
parents alike. While many people have learned that vaccines do not cause autism or changes in intelligence, personality, or behavior, there is still a lot of skepticism surrounding them. ​What really are vaccines, what is being put in my or my child’s body, and why do we need them?

Vaccines protect people against severe or life-threatening diseases that spread easily and have very serious side-effects or a high mortality (death) rate. Vaccines are made by taking the disease-causing bacteria or virus and turning it into a form that is not harmful to the body, also known as an antigen. The antigen does not injure the body, but there is enough
material the body can fight off, and remember how it fought it. This makes the immune response from the body the next time the virus or bacteria comes much more efficient!

Production of Vaccines

Vaccines are made in a five step process: generating​, ​releasing and isolating​, ​purifying​,
strengthening​, and ​distributing​ the antigen: Generating​ the antigen is the first step, which
is made using one of the processes you will read about in the table below, and then growing the antigen in different cells, including a chicken egg, human cell, or bacteria. Next, the antigen is ​isolated from the cell where it is grown and is ​released​ from it. The antigen is then ​purified​, by ​filters​ or by being inactivated​, so it can be used on people. After this, the antigen is ​strengthened​ by adding ​adjuvant (which enhances the body’s immune response), stabilizers ​(to increase the ability of the vaccine to be stored), and/or ​preservatives​ (especially if the vaccine is multi-dose). Finally, the antigen is packaged, put in a vessel, and ​sent out​ for use (“How Vaccines are Made”).

The ​type​ of vaccine used is different depending on the virus and bacteria:

History of Vaccines

Contrary to popular belief, the story of vaccines does not begin with Edward Jenner’s invention of the smallpox vaccine in 1796. Rather, it begins with a long history of infectious disease in humans, and specifically, with early uses of smallpox material to provide immunity against that disease (“All Timelines Overview”).

Early Origins:

  • Several accounts dating back to ​1000 C.E.​ detailed the early method of Chinese inoculation​: smallpox scabs would be collected, ground into pieces, and inhaled through the nostrils
  • In ​1661​, Emperor K’ang Hsi, who survived ​smallpox​ as a child, had his children inoculated with smallpox scabs
  • Lady Mary Wortley of Montagu had been disfigured by smallpox in 1715. Upon hearing that an inoculation had come to Turkey, she immediately had her six-year-old son undergo the procedure:
    • A “useful invention . . . for the ​good of mankind​” (“All Timelines Overview”)

Significant Breakthroughs:

  • 1796​: Edward Jenner successfully tested his hypothesis: inoculation of ​cowpox​ sores from milkmaids ​protects​ a person from ​smallpox​ infection. 200 years after Jenner’s discovery, the eradication of smallpox was achieved!
  • 1800​: Harvard professor Benjamin Waterhouse performed the first​ U.S. vaccinations on his children! Vaccines gained momentum in the U.S.:
    • In ​1815​, the U.S. Vaccine Agency was established with the endorsement of notable figures, such as Thomas Jefferson, as an “act to encourage vaccination”
    • In ​1855​, Massachusetts became the very first U.S. state to enact a ​law​ mandating the ​vaccination​ of children
  • There were also numerous breakthroughs occurring in Europe, particularly in ​France​. For instance, in ​1879​ Louis Pasteur created the first laboratory-developed vaccine, which was the vaccine for chicken cholera (​Pasteurella multocida​). More effective methods developed within the heart of Paris:
    • 1909​: Development of ​air-dried ​vaccines from smallpox vaccine pulp for tropical areas, where the temperature would destroy non-dried vaccine material. Nine years later, a more effective ​freeze-dried​, vacuum-packed smallpox vaccine was created
    • 1936​: Development of attenuated vaccine for ​yellow fever​ using chicken egg tissue cultures (“All Timelines Overview”)

U.S. Vaccine Licensing in the Latter Half of the 20th Century:

  • The middle of the 20th century was an active time for vaccine research and development, with rapid discoveries and innovations:
    • 1945​: The ​Influenza​ Vaccine became the ​first​ ​vaccine​ ​approved​ for military use​ in the U.S. in 1945 and in 1946 for civilian use
    • 1971​: The Measles, Mumps, Rubella Vaccine (MMR), a combined trivalent​ vaccine, became licensed by the U.S. government. This eliminated the need for several separate injections, and reduced the costs of shipping and stocking multiple containers
    • 1981​: The Chickenpox Strain and Hepatitis B Vaccine became licensed. The human-blood-derived hepatitis B vaccine became the first​ ​subunit​ ​viral​ ​vaccine ​licensed by the FDA (“All Timelines Overview”)

21st Century Innovations, Events, and Outcomes:

  • 2008​: The U.S. military shifted its vaccine stock from freeze-dried Dryvax vaccine to an Acambis vaccine stock that is grown in ​cell cultures​, rather than on the ​flanks​ of calves
  • 2009​: ​Diphtheria​ (leading cause of premature death in children) was declared ​eliminated​ in the U.S. There have been no cases of respiratory diphtheria since 2004
  • 2014​: the WHO certified the ​Southeast Asia​ region ​polio-free! ​(“All Timelines Overview”)

Contents of Vaccines

The contents of vaccines can be broken up into a few categories:

  • Ingredients that provide immunity to specific diseases
    • Antigens​ are very small amounts of weak or dead germ cells that can cause very minor diseases. They help your immune system learn how to fight off infections faster and more effectively. An example of an antigen present in a vaccine is the flu virus present in the influenza vaccine
    • Adjuvants ​help your immune system respond more strongly to a vaccine and thus increase your immunity against that disease and decrease the number of doses needed to build immunity. An example of an adjuvant is aluminum (“Vaccine Ingredients”)
  • Ingredients that keep the vaccines long lasting, safe, and free of outside bacteria
    • Preservatives ​protect vaccines from outside bacteria or fungus and are only used in vials of vaccines that contain more than 1 dose, because each time an individual dose is taken from the vial, it is possible for harmful germs to infiltrate the vial
    • Stabilizers ​help active ingredients in vaccines continue to work while the vaccine is made, stored, and moved. Stabilizers help to keep active ingredients in vaccines from changing because of something like a shift in the temperature where the vaccine is being stored. An example of a stabilizer is sugar or gelatin (Writers)
  • Ingredients necessary for production and then removed (but remain in small amounts)
    • Cell culture (growth) material, ​such as eggs, help to grow the vaccine antigens
    • Inactivating (germ-killing) ingredients,​ such as formaldehyde, weaken and kill viruses, bacteria, or toxins in the vaccine. The amount of formaldehyde present in vaccines is very small and diluted down to residual amounts, which has proven to be harmless (“Vaccine Ingredients”)
    • Antibiotics,​ such as neomycin, keep outside germs and bacteria from growing in the vaccine and thus prevent contamination during manufacturing (Writers)

Vaccines have a long-standing history as life-saving inventions. Using the body’s own
processes to create an immune response and recognition, vaccines allow people of many different states of health to protect themselves from diseases that could normally kill them. Vaccines will only improve over time and will remain a safe and effective way of keeping the body protected from many dangerous bacteria and viruses.

References

Picture Sources