(Or Microbes and Matisse)
Or It Takes Guts to Alter a Brain PART I
The longest and most extensive cranial nerve in our body, the vagus nerve connects the brain to the lungs, heart, and gastrointestinal (GI) tract. Within the lungs, the bronchial branch stimulates the bronchi, while the cardiac branch impacts heart rate. The vagal fibers that reach the GI drive peristalsis, the wavelike, muscular contractions required for food to pass through the digestive system. And amazingly, this neural connection also provides a link in gut microbiome-brain interactions.
en.wikipedia.org Henry Gray (1918) Anatomy of the Human Body
First, a little history…
The record of gut-brain interactions has an ancient history. Rufus of Ephesus who lived in the 2nd century, noted that the snipping of the vagus nerve (a vagotomy) stopped peristaltic movements within the stomach. Galen of Pergamum, the great physician and philosopher, identified the vagus nerve in his De Anatomicis Administrationibus (On Anatomical Procedures). Relatively recently, a vagotomy was considered an important therapy to combat peptic ulcer disease. But what about the gut microbiota?
In 2011, Drs. Javier Bravo and Paul Forsythe reported that Lactobacillus rhamnosus* impacted brain chemistry and behavior via the vagus nerve. Researchers fed mice either a standard chow diet (SCD) or an SCD+ Lactobacillus rhamnosus diet. L. rhamnosus is a probiotic with anti-inflammatory properties. Later, the mice underwent a variety of behavioral tests. Mice fed the probiotic enriched diet exhibited reduced depressive-like and anxiety-like behaviors. Moreover, the SCD+ L. rhamnosus mice also displayed unique differences in GABA receptor levels. GABA, gamma-aminobutyric acid, is a major neurotransmitter. Deficits in GABA signaling are linked with depression. The mice that ingested L. rhamnosus displayed an increased expression of GABA receptors in the hippocampus and a decreased expression of GABA receptors in the amygdala and prefrontal cortex**. This suggests that a microbe within the gut modulates the brain—an organ far, far, away. How?! The exact mechanism is unknown, but when researchers snipped the mouse vagus nerve the L. rhamnosusdiet no longer altered behavior or GABA expression. Gut microbes produce many modulatory molecules, including neurotransmitters, these molecules may stimulate the vagus nerve, impacting brain and behavior. Remember: the vagus nerve is only one of many pathways involved in gut-brain communication.*** Could gut bacteria be a useful tool to treat depression? What do you think?
Interesting work Dr. Bravo and Dr. Forsythe!
*The lactic acid bacteria are typically found in our guts and yogurt!
**Hippocampus: brain region associated with learning, memory, and much more // Prefrontal cortex: the ‘smart’ brain region associated with cognitive thinking and much more // Amygdala: brain region associated with fear
***I’ll post about vagus-independent gut-brain communication later!
Sources + Additional Information:
Vagus Nerve: http://www.britannica.com/science/vagus-nerve
Johnson, Leonard R., Ed. Physiology of the Gastrointestinal Tract, Two Volume Set. Elsevier Limited: Oxford, 2012.
The Bravo et al. study: http://www.pnas.org/content/108/38/16050.full
For a Great Review on Gut-Brain Interactions, click: http://icds.uoregon.edu/wp-content/uploads/2011/07/CryanDinan2012_MindAlteringOrganisms.pdf
(Or Time for a Halloween Post: How Microbes Shape Behavior)
A couple weeks ago I volunteered with the UBC Let’s Talk Science Team for a Zombie-Themed Science Day at Science World. I did not know about the Let’s Talk Science (LTS) Organization until I came to Canada. LTS STEM* volunteers create and share exciting science-focused learning programs. For more information about LTS check the link below. And if you are a student or teacher in a STEM program I encourage you to volunteer with LTS!
Our team discussed brain anatomy with young Science World visitors–we even got to decorate awesome brain-shaped cookies. Plus, we received complimentary zombie make-up for the day! Working at Science World reminded me about Amazonian zombie ants. When Cephalotes atratus ants get infected with the Cordyceps fungus, the insects begin displaying fatal, zombie behavior. Cordyceps spores infiltrate the ant brain and force the ant to climb nearby plants and stay put. The ant eventually dies and “a vigorous, silky, greyish-white mycelium* emerg[es] from the body joints and orifices” (Sampson and Evans, 1982). The Cordyceps are now in the perfect position to release ‘zombie’ spores, which drift down and infect more unsuspecting ants.
Did you know that microbiome communities can also shape behaviors? Researchers at the Karolinska Institutet in Sweden found that germ-free mice, which lack a gut microbiota (or any microbiota for that matter!) exhibited increased activity and less anxiety-like behavior compared with mice exposed to microbes. Moreover, researchers discovered that the germ-free mice showed elevated levels of important neurotransmitters, including serotonin and dopamine. Another research group at McMaster University in Canada found that antibiotic-treated mice displayed increased exploratory behavior. Very odd, considering that mice are neophobic (afraid of new things). The antibiotics had altered the gut microbiota composition. When mice were taken off antibiotics, the gut composition and strange behavior returned to normal. Researchers noted that the mice treated with antibiotics also displayed a decrease in brain-derived neurotropic factor, or BDNF. BDNF is a protein that promotes neuron growth and is important for memory and learning. Researchers think that shifts in microbial composition impacted BDNF levels, which changed mouse behavior. Complicated, right?
Lastly (for this post), a recent Bioessays review article discussed whether our gut microbiota manipulates dietary cravings in order for us to eat (unhealthy?!) foods that promote microbial fitness. But feeding gut microbes high-fat and high-sugar treats doesn’t help our waistline! Describing the study, one journalist asked “Are we food zombies controlled by our gut bacteria?” I’m not sure, but maybe that is why I’m craving some Halloween goodies…
Stay tuned for more gut-brain research!
*Science Technology Engineering and Mathematics
**a mass of filamentous-like structures (the vegetative fungal growth)
Sources + Additional Information
Zombie Ants, Anyone? http://www.sciencedirect.com/science/article/pii/S0007153682800375
Germ-free mice: http://www.pnas.org/content/108/7/3047.long
Antibiotics and Microbes: http://www.ncbi.nlm.nih.gov/pubmed/21683077
(Thanks EY for the cookies!)
(Or every field needs a good dose of healthy skepticism!)
In 2013, experts of the emerging human microbiome field gathered at the National Institutes of Health (NIH) campus in Bethesda, Maryland. The NIH-sponsored conference entitled “Human Microbiome Science: Vision for the Future” highlighted both the successes and challenges of the microbiome field. Speakers noted that “A challenge in microbiome research is to move beyond identification of microbiota community structures that correlate with disease states to establishing a causal link between structural changes and the functions of microbiota in disease.” The “hype” of correlation studies, especially ‘hot topic research’ will always remain. Scientists need to be cautious when interpreting their results and presenting results to the public. In a 2014 Nature Comment, William Hanage lists five questions that microbiome researchers should ask when planning an experiment. I think these five questions also serve as a solid framework for readers (that’s us!) when examining microbiome research. I’ve listed the the questions below. For a more detailed read, check out the link to Hanage’s article.
- Can experiments detect differences that matter?
- Does the study show causation or just correlation?
- What is the mechanism?
- How much do experiments reflect reality?
- Could anything else explain the results?
Lastly, I have to share with you this awesome article. Did you know that the microbiome totally caused the financial crisis in 2008!! What??! #Microbiomehype #SEC_NIHworkingtogetheratlast #BewaretheBacoTell
Thanks to NM for sharing, and great job EB representing at the NIH!
Human Microbiome Science: Vision for the Future Report: http://www.microbiomejournal.com/content/2/1/16
Financial Crisis and the Microbiome: http://www.theallium.com/biology/report-human-microbiome-totally-responsible-for-financial-crisis-of-2008/
(October is Here–Bloody, Ruddy, Muddy, and More!)
Aesthetics and microbes: check out the following snaps* to see microbial communities in nature!
Antarctica’s Blood Falls, located at the tip of Taylor Glacier spurts a rusty curtain of briny water rich in iron-oxide. Autotrophic microbes (these fellows obtain energy from inorganic substances) live in this frigid, anaerobic environment. The microbes metabolize the ferrous and sulfate ions present in the water.
One of the quintessential Yellowstone National Park landmarks, Morning Glory pool awes millions of visitors each year. The hot spring contains beautiful, blue, gold, and purple tones thanks to the thermophilic* microbes that live in the 69.8 °C/157.6 °F waters. Unfortunately, the trash, coins, and other mementos tossed by tourists have blocked some of the thermal vents. This blockage lowers the temperature of the pool allowing brown/yellow bacteria that survive in cooler temperatures to thrive, diminishing MG’s original brilliant colors.
Female Anglerfish (Lophius piscatorius) have a ‘fishing rod’ apparatus on the top of their head. At the end of the rod is a short bulb-like structure, filled with bioluminescent bacteria (typically Vibrio or Photobacteria). The glowing bacteria lure prey: deep-sea dining made possible by microbes! Male anglerfish are much smaller and lack the rod/bait structure. In order to survive, the male anglerfish becomes a parasitic partner. The male latches onto a female anglerfish-permanently-his internal organs and eyeballs eventually atrophy as the male fuses to his mate!
*snaps a Skope term meaning, an informative, short blog+photo note
**organisms that thrive in very hot temperatures (45-800C)
BREATHE: Asthma and the Microbiota
(Antibiotics, Asthma, and an Idea)
Approximately 250,000 people die prematurely each year from asthma. Over the past century, asthma prevalence has continued to rise in developed countries. And prevalence is predicted to continue rising. According to the American Academy of Allergy, Asthma, and Immunology, the number of people living with asthma will likely reach 100 million by 2025. Recent studies have linked antibiotic use with allergic airway disease.* For Brett Finlay (University of British Columbia) the lightbulb moment occurred when his wife, a pediatrician, mentioned that children exposed to antibiotics as infants were more likely to develop asthma. Antibiotic treatment can result in massive changes in the gut microbiota community. Could our gut microbes impact asthma?
The Finlay Lab decided to conduct experiments examining the potential role of the gut microbiota on asthma susceptibility. The research, spearheaded by Shannon Russell, a UBC grad student, utilized an asthma mouse model. Russell found that mice treated with vancomycin, a commercial antibiotic, exhibited a decrease in gut microbes and increase in asthma severity. Changes in microbial composition were most pronounced in perinatal exposure (meaning the mama mice received antibiotics and the antibiotic exposure continued after birth). In contrast, the impact of vancomycin on the gut microbiota of adult mice was less severe. Furthermore, infant mice (but not adult mice!) exposed to vancomycin were significantly more susceptible to asthma.
According to the Finlay Lab, gut microbes have the greatest influence on immune development during a “critical window” from birth to three weeks of age in mice. Antibiotic treatment during this time frame impacts the development of the immune system and may contribute to the development of allergic diseases, including asthma.
The next step involves the development of better antibiotic and/or microbial therapies to treat bacterial infections without promoting asthma development. The gut-lung axis was (and is) a relatively new and unexplored field. I am excited to learn what my fellow lab mates discover next!
Sources + Additional Information:
* For a nice review, check out Noverr and Huffnagle’s “The ‘microflora hypothesis’ of allergic diseases” published in Clinical and Experimental Allergy: http://www.ncbi.nlm.nih.gov/pubmed/16393316
The Skope on Microbial Communities, particularly the Human Microbiota
(Or…Causation, Correlation, and Critters)
Michaeleen Doucleff recently posted about the gut microbiome in the NPR blog chronicling global health and development, “Goats and Soda: Stories of Life in a Changing World.” (If you haven’t visited “Goats and Soda” yet, check out the link below—G&S is one my favorites!) In How Modern Life Depletes Our Gut Microbes, Doucleff relates a New York University School of Medicine study characterizing the gut microbiome of the Yanomami tribe, a hunter-gatherer society that has lived for over 11,000 years in the Amazonian Mountains. Doucleff’s story begins in 2009, when Maria Gloria Dominguez-Bello, NYU colleagues, and a Venezuelan medical team first journeyed to the Venezuelan-Brazilian border to contact the Yanomami. Dominguez-Bello collected fecal samples from the tribe and used DNA sequencing to determine the Yanomami gut microbial profile. The Dominguez-Bello lab discovered that the Yanomami has roughly 50 percent more microbial diversity than the American gut. Or as Doucleff states, “Americans’ digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.” As societies “Westernize”, communities lose microbial species. This loss of microbial diversity is typically accompanied by an increased incidence of autoimmune disorders and chronic diseases (think allergies and GI tract disorders). But are these facts related? Researchers don’t have a conclusive answer.
Indeed, microbiologists are still untangling the different factors that drive microbial diversity. Certainly dietary habits and antibiotic usage play an important role. Other researchers emphasize the hygiene hypothesis theory, noting that improved sanitation limit microbial diversity. Of course, Dominguez-Bello noted that these findings shouldn’t give license to romanticize the Yanomami lifestyle. The modern medical and hygiene advancements that may negatively impact microbial diversity have also enabled Western societies to enjoy a relatively healthy living and high life expectancy.
Dominguez-Bello’s study of modernization/urbanization and the gut microbiota is shared by her husband, Martin Blaser MD, the author of Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. A theme of the lively comments G&S section was the delineation between causation and correlation in microbiome research. Do our microbes drive specific autoimmune disorders (causation)? Or do the modern plagues arise from lifestyle/carcinogens/endocrine imbalance—resulting in subsequent microbial changes (correlation)?
Both the researcher and reader must distinguish between causation and correlation. And both Doucleff and Dominguez-Bello do an admirable job to avoid blurring of the two. When reading a journal/article, here are a few questions I ask to differentiate between cause and correlation:
- Is there a mechanism/possible mechanism to suggest causation?
- What are the limitations of the research?
- Do other studies support the conclusions of the authors?
- What further studies are necessary to demonstrate causation?
The best way to answer these questions is to be well-read in the field and/or have amazing research friends. As for now, I am excited to learn about the next developments in Dominguez-Bello’s project!
Sources + Additional Information
PASS THE MICROBIOME PLEASE: The Gut Microbiome and Energy Harvest
(A Tale of Two Mice)
Weight Loss and Gut Microbes: the (well-deserved!) reigning poster child of human microbiome research.
The story of how gut microbes impact host weight began at Washington University in Jeffrey Gordon’s Lab. In 2005, PNAS* published Ruth Ley’s “Obesity alters gut microbial ecology.” Ley, a post-doc in Gordon’s Lab, noted that certain gut microbes produce a variety of enzymes that enable the human host to extract calories from polysaccharides (think starch-rich foods, like potatoes). Without these microbes, humans are not able to digest many complex starches. Ergo, people predisposed to obesity may have über calorie-extracting microbes! Ley and members of Gordon’s Lab analyzed more than 5,000 gut bacterial genome sequences from the intestines of genetically obese mice (ob/ob mice) and their lean, wild-type siblings. The ob/ob mice eat excessively and develop obesity, high blood pressure, and increased insulin. Compared with their lean counterparts, ob/ob mice had a distinct microbiota, exhibiting a 50% decrease in Bacteroidetes abundance and a comparative increase in Firmicutes abundance.
Bigplankton @ en.wikipedia
(An ob/ob mouse and wild-type mouse)
Bacteria belonging to the Firmicutes or Bacteroidetes phylum* dominate both the mouse and human gut microbiota. Did the Firmicutes contribute to the ob/ob mouse’s efficient caloric/energy harvest and increased adiposity? Another post-doc, Peter J. Turnbaugh, further examined the ob/ob microbiome in a 2006 Nature paper entitled “An obesity-associated gut microbiome with increased capacity for energy harvest.” Using sequencing and comparative metagenomics, Turnbaugh found that the ob/ob microbiota contained higher levels of methanogenic microbes*** that increase bacterial fermentation efficiency, contributing to mouse adiposity. In addition, the ob/ob microbiome contained enriched DNA sequences of enzymes and proteins involved in microbial starch digestion. Next, the team transplanted either a wildtype or ob/ob microbiome in germ-free mice. Both groups of mice were maintained on the same diet. Two weeks after transplant, the mice that received the ob/ob microbiome had a higher abundance of Firmicutes and a greater increase of body fat percentage, compared with the mice that received the “normal” microbiome. Very cool. Perhaps future diets will include a serving of lean microbiome!
In 2013, I spent a summer interning at Turnbaugh’s Lab examining the role of antibiotics and diet on the gut microbiota. It was a wonderful experience that solidified my interest in pursuing microbiology for grad school. For more information, check out some of the amazing research at Jeff Gordon’s lab (WU), Ruth Ley’s Lab (Cornell), and Peter Turnbaugh’s lab (UCSF).
For a similarly awesome Microbiota and Obesity story: check out this image and the last link below
From: Walker, Alan W., and Julian Parkhill. “Fighting obesity with bacteria.” Science341.6150 (2013): 1069-1070. Reprinted with permission from AAAS.
*Proceedings of the National Academy of Sciences of the United States of America. Established in 2007, PNAS Online publishes all PNAS articles from 1915 to the present. This is a great source for free, peer-reviewed articles.
** Remember King Philip Came Over for Ginger Snaps (Classification System: Kingdom, Phylum, Class, Order, Genus, Species)? Bacteriodetes: gram-negative, rod-shaped bacteria // Firmicutes: typically gram-positive and are usually rod-shaped or circular.
*** these archaea methanogens produce methane and derive energy from carbon dioxide.
Sources + Additional Information:
(A hopefully useful, but definitely not über technical, microbial-related set of definitions)
While blog-planning, I decided to include a blog post containing microbiology-related definitions. Some define common techniques used in lab research, others are Microbiology-related, and still others define the microbes/microbial components themselves. If you are a scientist (kudos!) you probably can skip these! And let me know if there are definitions I should include.
Cell culture: The process of growing and maintaining cell lines in a laboratory setting. Common techniques utilized in cell culture include passaging (transferring cells from one container to another to prolong cell life or expand cell numbers) and calculating plating density (determining the cell number per volume of the culture media).
Commensal VS Pathogenic VS Symbiotic*: Commensal organisms benefit their host (whale and barnacles, pathogenic organisms cause disease in the host (Salmonella and you), and symbiotic organisms are benefited by/benefit the host (clownfish and sea anemone). The healthy gut microbiota consists of primarily symbiotic and commensal organisms.
Genomics (Meta, Proteo): The study of the genome-the complete set of DNA within a cell. Metagenomics is the study of a collection of genomes from a set community (e.g. the microbial community within your gut). Proteomics refers to the study of all the proteins produced by an organism. So metaproteomics is—bingo!—the study of all the proteins produced by a set community.
Gram-negative bacteria: These bacteria have a thin layer of peptidoglycan-a meshlike polymer—between their inner and outer cell membrane. Gram negative and gram positive bacteria are differentiated by Gram staining (gram negative bacteria appear pink after identification staining). Example: E. coli
Gram-positive bacteria: These bacteria have a thick layer of peptidoglycan surrounding the plasma membrane. Gram stain: purple. Example: S. aureus
Holobiont: The symbiotic organism: an organism + their micro-species. For example: a human+ any bacteria, fungus, parasite that share the human’s body space. The hologenome theory of evolution suggests that evolution is driven by natural selection of the holobiont, not just the organism.
Human microbiome project: Launched in 2008, the HMP characterized microbial communities found within the nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract. Additional HMP goals included the development of new techniques to study and analyze the microbiome and projects to examine the role of the microbiome in human health and disease. The Human Genome Project, the famous ‘older sister’ of the HMP was completed in April 2003.
Hygiene hypothesis: (also called the Lost Friends Theory or the Biome Depletion Theory) The hypothesis that lack of microbial exposure in young children might lead to an increased susceptibility to allergic/autoimmune/behavioral diseases. The recent emphasis on germ-free lifestyles further removes children from microbial exposure, precluding the full development of their immune system.
Metabolites: Small molecules that are intermediate components of the metabolic pathway.
Microbiome vs. Microbiota: Although these words are often used interchangeably, microbiome refers to the collection of microbial genes, while microbiota refers to the microbial organisms themselves.
Gut microbiota: The trillions of microbes that reside throughout the host digestive tract.
Flow cytometry: A laser-based technique utilized to determine cell size, granularity, and molecular characteristics. Suspended cells pass through the cytometer’s laser, a sensor detects differences in the light scattered/emitted from the cells and the data is recorded for analysis.
PCR: Polymerase chain reaction: Developed by Kary Mullis**, PCR is a common laboratory technique used to amplify a segment of DNA. PCR steps include: denaturing (the double-stranded DNA sample separates), annealing (a DNA primer attaches that corresponds to the beginning or end of the DNA sample binds to the single-stranded DNA), and extension/elongation (DNA nucleotides—the DNA building blocks—are added onto the primer to create a complementary strand). This process is typically repeated 35 times.
Sequencing: This refers to any technique used to determine an unknown sequence of nucleic acids (DNA or RNA). Common techniques include:16SrRNA (see below), chain termination, shotgun sequencing, and 454 pyrosequencing.
Scanning electron microscope (SEM): This type of microscope utilizes electrons to probe the surface of a metallic-coated object, producing a 3D image.
Transmission electron microscope (TEM): Unlike SEM, the transmission electron microscope emits electrons that pass through an object, producing a detailed cross-section of the sample.
Western Blot: A common lab technique: This method utilizes electric charge or molecular weight to identify proteins in an unknown sample. Other blots include the Southern blot to identify DNA sequences and the northern blot to detect RNA.
Xenobiotics: This refers to any substance that is not naturally produced by the host/microbiome. For example: pharmaceutical drugs.
16S rRNA sequencing: This technique is used to determine evolutionary relatedness between bacterial sequences. 16S rRNA is a highly conserved component of bacteria.
*this type of symbiosis is technically mutualistic symbiosis, as symbiotic refers to any species interaction, pleasant or unpleasant.
**Check out an upcoming Biolog on Kary
THE “FORGOTTEN ORGAN”
(AKA: What is this? Why is it important?)
When I typed “Gut Microbiota” in Google Scholar and limited publication dates from 1900-1950, I discovered 16 articles. 1951-1980: 291 hits. 1981-1990: 497 hits. 1991-2000: 2,130. 2001-2010: 26,100. Publications from 2015 alone: 5,030 and counting! I thought about producing a graph, but it seemed pretty pointless. On second thought, why not?
[A Pretty Pointless Graph: The Rise of Microbiome Research]
During the 19th and 20th century, most microbiologists studies focused on pathogenic bacteria. This led researchers O’Hara and Shanahan to label the gut microbiota, as the ultimate “forgotten organ.” In the abstract of their 2006 EMBO publication, O’Hara and Shanahan noted the gut microbiota “is a positive health asset” that “has a collective metabolic activity equal to a virtual organ within an organ.” Germ-free animals exhibited marked physical changes (decreased muscle thickness and smaller Peyer’s patches*) and increased susceptibility to infections. However, these microbes might also contribute to diseased states, such as Crohn’s or IBD, if an individual displayed an immune intolerance towards certain microbes. O’Hara and Shanahan speculated that further study of the gut microbiota might reveal undiscovered methods vital to understanding host-pathogen interactions. Indeed, 2006 appeared to be a major milestone in microbiology research; the age of microbiome research had emerged. Within the next decade microbiologists examined the impact of the gut microbiota on obesity, metabolism, depression, autism, immunology, and behavior. More to come in the following blogs!
*Peyer’s Patches: these are lymph node “islands” located in the mammalian large intestine
Sources + Additional Information