MiSciWriters is proud to partner with the UM Center for Microbial Systems to provide live coverage of the 2016 Michigan Meeting “Unseen Partners: Manipulating Microbial Communities that Support Life on Earth.”
We will be live-blogging the event here, and live-tweeting from @MiSciWriters today 9:00am-3:30pm, 7:00-8:30pm.
We hope you’ll join in the conversation by commenting below or tweeting with the hashtag #MiMicrobe. Enjoy!
“Ethical and Scientific Considerations of Fecal Transplants”
Pilar Ossorio, J.D., Ph.D., University of Wisconsin Law School and Vincent Young, M.D., Ph.D., University of Michigan
Moderator: Emilia Askari, Journalist, University of Michigan
Editor: Irene Park
Blogger: Ada Hagan
Young and Ossorio spent some time at the end of the session answering questions from the audience.
Q: What is the stability of an FMT?
Young: The exact donor microbiome doesn’t seem to stay there long term. There are longer studies being conducted, but really a physician only needs to get the recurrent C. difficile patients through the infection, then it doesn’t matter. The issue arises if particular microbes associated with other illnesses hang out long-term putting you at risk for those.
Q: Many of these patients are desperate, what is our role as semi-cautious experts in harm reduction?
Ossorio: Obligation of physician is patient health, of course.
Q: Do we have an ethical obligation in translational research to eliminate the use of antibiotics wherever possible to help prevent antibiotic resistance?
O: Be careful with “obligation.” It would be a good thing to advance science that controls pathogenic bacteria without antibiotics.
Y: Where antibiotics have proven efficacy, I don’t hesitate. When a patient comes before me, a physician has to focus on the patient and can’t necessarily apply Spock’s concept that the needs of the many outweigh the needs of the few.
Q: Have there been reported FMT “rejections”?
Y: “I don’t like that they call it a transplant” since many of the requirements for organ transplants don’t apply for FMT, and we don’t understand the immunological effects behind it.
Q: How do we balance the “risk-reward”?
O: There isn’t a standard method for this. It’s difficult to first decide who is responsible for balancing risk and reward, in many cases of human health, the FDA becomes responsible..
Q: Where do FMT’s stand in the medical field?
Y: It’s a mixed bag. At U of M, physicians will do it, but only for recurrent C. difficile (at least 2 episodes).
O: It can be done for recurrent C. difficile with a locally screened donor, but otherwise an IND is required.
Q: What should the conversation be if there’s a doctor unwilling to perform an FMT?
Y: No physician is required to perform a treatment that they consider unethical. Many patients have to travel, either because the doctor can’t or won’t do it.
O: There seem to be many more patients that want FMTs than there are doctors who will perform it.
Q: What do donor screenings entail? Is sequencing done to help learn more about the system?
Y: Clinical application is FDA approved tests for pathogens or relevant antibodies. Sequencing is only done by researchers.
Q: Fecal transplants are a sledgehammer solution for C. difficile treatment. Can we narrow it down?
Y: Some are working to narrow it down, but it shows our ignorance. FMTs probably work because they give hundreds of microbes, one or more of which are helpful. Which ones, we don’t know.
Q: What is driving these patients to FMTs? Because it’s “all natural”?
Y: I have no idea.
O: There are a variety of motives, but in one study patients receiving FMTs repeatedly, and spontaneously, discussed it’s the “naturalness.”
Q: How do we move forward? What is the “best way”?
O: I’m not sure I have a good answer, there’s probably more than one “best way” to move forward with this. We have to acknowledge and respect that buy-in by DIYers and physicians alters our clinical trials and accordingly focus on developing good clinical trials.
Y: We need to do good research in teams and promote it properly. Don’t oversell or be afraid to call BS on someone who is so we can move forward as fast as we can.
The FDA is a huge component of the “regulator” category. Fecal microbiota is regulated by the FDA since it is used to “cure, treat, mitigate or prevent a disease” and thus meets the legal definition of “a drug and biological product.” What this means is that everyone who wants to use FMT has to fill out an Investigational New Drug application, which enforces the patients to wait at least 30 calendar days before any clinical trials can be initiated. Because of the current evidence, however, the FDA has said that they will use “enforcement discretion” in enforcing these requirements for recurrent C. difficile if the donor gives an informed consent, the product doesn’t come from a stool bank, and the product has been screened.
Critics state that such strict regulation pushes FMTs into the DIY world and that they should not be so strict. Ossorio said
because of the strict FDA regulations, we don’t have the evidence to show that FMT is effective in the first place for the FDA to be less strict.
Cautious “experts” believe that “we don’t know enough yet” about FMTs. Those in this group find the use of donor feces unscreened for human pathogens is unnecessarily risky. Ossorio notes that FMT’s don’t only include microbes, but also gut mucus and other “ingredients” that can affect patients either positively or negatively.
Because the gut microbiome appears to have global health effects (e.g. depression, obesity, type 2 diabetes, etc), cautious experts might also advocate for screening donors for those conditions.
As stated by Young and others, “The best evidence for the effectiveness for FMTs is in the treatment of patients with recurrent C. difficile.” Ossorio, as a cautious expert, argues that even in that case, the evidence that the microbiota is the “active ingredient” in the cure is not very strong. She doesn’t agree that FMT is truly the standard of care in these situations. There are many roadblocks to FMTs for patients, including availability of donor screening or a insurance provider willing to cover the treatment. She argues that the current literature makes grandiose claims based on small, uncontrolled, and biased studies.
What if enema or colonoscopy alone is sufficient to help resolve recurrent C. difficile infections? Something Ossorio clearly feels is lacking in the scientific research about FMT efficacy, as she emphasized it is important to “develop good evidence we need to run well-designed clinical trials.” Of 159 studies found for “fecal transplant” on Clinicaltrials.gov, Ossorio stated that very few involved C. difficile, suggesting that the matter appears to be closed.
It seems like the general public has already accepted that using FMTs is the new best way to treat C. difficile infections. In fact, recent clinical trials have been virtually sabotaged by patients who lied to drop out of the control group in order to receive FMT.
Many consider FMT as an “interim solution.” Ossorio said “we should be working to develop better data on safety and effectiveness. And we should develop better characterized and standardized products based on the ‘active ingredients’ of feces.”
Ossorio states that there are three major contesting groups in the FMT conversation: patient advocates, regulators, and more cautious experts (i.e. physicians). What are their roles?
Patient advocates tend to have the feeling that “regulators, scientists, insurers and ethicists are preventing [them] from accessing an effective, cheap, safe, and natural intervention that can treat many gut-related medical conditions.” Many claim that there has never been an adverse event associated with FMTs. But that’s not the case! And so began the rise of the do-it-yourself FMT. As an aside for the record, your pets can carry human pathogens and probably shouldn’t be used as your FMT stool donor.
However, some patient advocates do recognize that DIY FMT isn’t entirely safe. A patient advocate who has worked with the Food and Drug Administration on FMTs reported infections in DIYer’s, who suffered from serious stomach infections from improper administrations of feces.
So how do you administer an FMT? Well, fortunately, we weren’t given a live demonstration.
The feces from a donor, usually someone in the same household as the patient, can be delivered from the “top” i.e. in a pill or from the “bottom” i.e. a colonoscopy. But there are a number of questions to be addressed: What if there isn’t a healthy donor available? Can we use feces from an anonymous donor? There are a number of illnesses transmitted by poop (e.g. hepatitis A and cholera), how do we ensure that we don’t accidentally create new problems? Are fresh feces better than frozen feces? Can we improve on feces? Some companies have published studies attempting to refine feces. Some use a mixture of bacteria, ranging from 8 to 33 different species. Which bacteria are the best? Ossorio will attempt to focus on these, and similar ethical questions.
In summary, we know that the indigenous microbiota of the gut is part of a complex, balanced ecosystem, disturbances in this balance play a key role in the pathogenesis of C. difficile infection, and the use of microbiota transplantation provides a unique treatment for C. difficile.
Askari, a U of M lecturer in Environmental and Public Health journalism and former reporter for the Detroit Free Press where she covered microbes and their various interactions with humans, kicked off the session. She commended the organizers and the university for putting together such a successful and accessible event. She pointed out that many consumers of microbiology, (i.e. journalists, politicians, and the general public), are not very well versed in microbiology, and she appreciates the opportunity for them to participate in important microbial conversations.
Young’s goal was to introduce the audience to the point of view of a physician on our “inner ecosystem”. He opened with mentioning that the National Microbiome Initiative was announced last week, noting that the initiative included researching more than just the human microbiome. There are different definitions of the microbiome, usually limited to the community of microbes, but Young argued that it should also include the given environment that the microbes inhabit.
Many have heard of microbiomes but often through the lens of the media. Young wanted to give us the view from behind the white physician’s coat. He was taught that “the only good microbe is a dead microbe.”
Young’s lab focuses on Clostridium difficile, a bacterium that can form spores, a dormant form of the bacteria that are easily spread and extremely resistant to disinfectants like hand sanitizer. Exposure to C. difficile spores, usually in hospitals, can lead to infection in antibiotic-treated patients since their microbiota have been impacted by the antibiotics. Most patients can then be treated with new antibiotics to get rid of the C. difficile, but in many patients the C. difficile keeps coming back. How do we help these patients? One way is to give them back a normal microbiome.
Fecal transplant is not a new idea. The idea of human microbiome protecting us from disease was discussed as early as 1916 by a German physician Alfred Nissle, and fecal transplants to treat a variety of gastrointestinal illnesses were documented by Chinese physicians as early as the fourth century. The modern age of FMT began in 1958 when it was used as a treatment of pseudomembranous colitis by Eisemen et al. The first study on FMTs, however, wasn’t published until three years ago.
If you’ve heard anything about microbiomes at all, then what you have heard has probably been about the one that resides in your gut. And with fairly good reason. The intestinal microbiome, a collection of bacteria, parasites and viruses, has been linked to a number of human health issues like depression, obesity, autoimmune diseases, cancer and even neurological ones like autism. One of the most pressing issues regarding the gut microbiome is its importance in protecting us from bacterial infections such as Clostridium difficile infections. A “healthy” microbiome protects us, and microbiome that’s been partially wiped out by antibiotics leaves us susceptible to infections and diseases.
In recent years, researchers have found that Fecal Microbiota Transplantation (FMT) has been useful in treating patients plagued by recurrent C. difficile infections. FMTs involve taking stool from a healthy donor and giving it to the patient. The idea is that this somehow restores balance to the patient’s microbiome, loosening C. difficile’s foothold in their bowels.
While FMT is quite effective in curing various gastrointestinal disorders, the nebulous link between the intestinal microbiota and other aspects of human health make it a tricky subject for both medicine and law. The final session of the Michigan Meeting day 2 will attempt to shed light on the issues at stake with FMTs. In this session we will hear from Vince Young, M.D., Assistant Professor in Microbiology and Immunology at the University of Michigan, and Pilar Ossorio, Ph.D., J.D., Professor of Law and Bioethics at the University of Wisconsin Law School.
“Microbiome at the Tap: From Ann Arbor to Addis Ababa”
Nancy Love, Ph. D., University of Michigan
Editor: Ada Hagan
Blogger: Jimmy Brancho
Love goes on to show how her findings differ between “one A-A city and another A-A city,” Ann Arbor and Addis Ababa. The point-of-use filters studied in Addis Ababa were different than those in Ann Arbor, but they shared the common element of activated carbon. Activated carbon is a common and cheap material, similar to charcoal, that is used in many water filtration devices.
Again, Love’s group saw that the kinds of bacteria in the water before and after filtration are different. The results are very new, but they point to the importance of understanding not only how point-of-use filters affect the dissolved chemicals in tap water, but how they might set the stage for unexpected kinds of microbes to thrive.
Love seems excited to get the ball rolling on this research. Her findings on microbial changes induced by point-of-use filters might seem like answers to microbiology questions. But, as an engineer, she sees them going on to inform how point-of-use filters are employed, or even what they might be made of.
Pat Schloss saw a connection between this research and the water crisis happening in Flint, asking what types of questions she would like to see answered as a microbial engineer. Love noted that, from a microbial standpoint, the problems between the three areas (Ann Arbor, Addis Ababa and Flint) are similar, and that
EPA* recommendations on changing the filters every two weeks [is important, but communities] might not be well-informed [regarding that recommendation]. Her group has plans to investigate that problem but has not yet begun to collect samples.
[Updated for clarification, 11:19pm 5/17/16 A.Hagan]
[*Updated 12:40am 5/18/16 A. Hagan. Dr. Love later notified us via email that she may have misspoken, these recommendations may be from a source other than the EPA, but “based on [her] knowledge about balancing microbial counts in the effluent (faucet flow-through) and conforming to manufacturer limits for use (100 gallons, which may take a typical family about 2 months)”, this is the best recommendation we have so far. This also highlights the need for studies conducted directly in Flint.]
“In the United States, we have a love affair with our point-of-use filters, it seems,” Love says. Her group tested the effectiveness of the kind of filter you might have attached to your faucet, but in the presence of chlorinated phenols. Chlorinated phenols, such as triclosan, are common environmental contaminants in otherwise normal Ann Arbor tap water. Chlorinated phenols have the unfortunate side effect of acting on bacterial machinery in such a way that enhances antibiotic resistance. Love’s group found that the water coming out of point-of-use filters lacked chlorinated phenols, but contained a lot of bacteria. The reason? Some bacteria can thrive inside the filters. The filter traps the chlorinated phenols, but when the water shuts off, certain kinds of bacteria use the phenols in the filter to live off of. This, in turn, affects the wastewater supply by selecting for bacteria resistant to chlorinated phenols that may also be resistant to antibiotic drugs.
That could be bad news. Researchers are still working to figure out what the effects of point-of-use filters are on the environment, but Love’s work definitely suggests that they might contradict the overall goals of water purity.
At today’s Michigan Meeting, Love will present on her work engineering the “urban water cycle” – the interaction of water from storms, drinking water from freshwater sources, and wastewater.
Stormwater, or water from rainfall, is an important water source in dry places where fresh water is relatively scarce, such as the southwest United States or, more relevant to Love’s research, Addis Ababa, Ethiopia. When it hits the ground, stormwater can pick up all kinds of contaminants, from metals like lead and mercury to disease-causing microorganisms. Systems that collect stormwater for eventual use by humans need to eliminate these contaminants, or collect the water in such a way that prevents introduction in the first place.
Moving on from stormwater, Love notes, “Wastewater is the first step in an effective drinking water treatment.” She cites the Roosevelt quote that Dick gave at the end of his talk, saying, “But this [adding wastewater back to the water supply] is how it works on this planet.”
Mastering the interaction between stormwater, wastewater, and fresh water is the mission of civil engineers who design water supply systems for our use. Love studies ways to make those systems better.
This morning, getting ready for the trip into lab, I washed hair conditioner, soap, and toothpaste down the drain and out into the wastewater stream. I was thinking about the smell of coffee wafting out from my kitchen and an impending presentation – certainly not about how the personal care products I just used would affect the biology of water supplies I’m connected to.
Nancy Love, a University of Michigan professor of civil and environmental engineering, thinks about that a great deal. Her research focuses on understanding how wastewater affects the environment with the goal of developing biological technologies for wastewater treatment. Another portion of her effort is dedicated to finding reliable ways to measure, and/or predict by modelling, how much of a given chemical might be in a wastewater stream. By expanding the toolbox, so to speak, Love’s research expedites developing biotechnology – in which microbes could do the work traditionally done by chemicals – for water treatment.
“Unintended Manipulation of Microbial Communities in Lake Erie”
Gregory Dick, Ph.D., University of Michigan
Editor: Ada Hagan
Blogger: Jimmy Brancho
Dick suggests that other bacteria in the bloom have defenses against hydrogen peroxide that protect Microcystis from attack. But, when hydrogen peroxide levels get too high, the nearby microbes can’t protect Microcystis, and it’s every microorganism for itself – the bloom environment turns to favor the non-toxic organisms that have their own defenses.
Dick concludes his talk by pointing out that algal blooms are a serious environmental problem that seem to be getting worse. Understanding how they work is critical, but changes in farming and industrial practices will be necessary to keep harmful algal blooms under control. There are joint initiatives by the United States and Canada to control the amount of phosphorous that gets into Lake Erie, but that’s just a start. He quotes Theodore Roosevelt: “Civilized people should be able to dispose of sewage in a better way than putting it in the drinking water.”
Returning to reactive oxygen species, Dick notes that nobody knows for sure why some Microcystis strains produce microcystin. Its biological function isn’t known. That’s part of the reason that his group studies the effect of reactive oxygen species on the algal blooms. His central example is hydrogen peroxide, which you might have in your house as a disinfectant. Concentrated hydrogen peroxide kills the kinds of microbes responsible for toxic algal blooms. But, the considerably lower amounts of hydrogen peroxide found during Lake Erie blooms actually create an environment where toxic Microcystis thrives, relative to other species of microbe.
Dick’s group measured the overall toxicity of the 2014 Lake Erie bloom over time. The amount of microcystin hit its peak in early August and went down again. But, the total amount of bacteria in the water didn’t exactly track with the microcystin spike, which points to some other complication. Observing a spike in nitrates and hydrogen peroxide close to the peak of bloom toxicity, Dick zeroed in on those for this project.
Where does the hydrogen peroxide come from? When the sun shines on a body of water, certain chemicals can react with water itself, or with oxygen in the water, to produce hydrogen peroxide. Organisms living in water also produce hydrogen peroxide over the course of their lives. Due to the potentially damaging effects of hydrogen peroxide, many organisms are equipped with “defenses” against hydrogen peroxide. Usually these are in the form of proteins that break the molecule down, such as catalase. Dick’s group looked for the signatures of hydrogen peroxide defenses in the Lake Erie bloom and found an increase in their concentration that, curiously, came after the August hydrogen peroxide spike. Moreover, Microcystis doesn’t have any built-in defenses against hydrogen peroxide.
So what’s going on?
Today, Dick will talk in more detail about measurements made by his group to learn how hydrogen peroxide, and other harsh oxygen-containing chemicals called reactive oxygen species, affect toxic algal blooms like the ones in Lake Erie. The key player in Lake Erie blooms, and other toxic algal blooms around the world, is Microcystis aeruginosa. Microcystis are cyanobacteria that produce a compound highly toxic to human and livestock livers, microcystin.
Dick clarifies that Microcystis blooms are initiated by the presence of phosphates in the environment. The growth of these bacteria is kick-started by phosphorous – bloom growth won’t start without it – but can then be intensified by the presence of other nutrients like nitrates. Phosphorous gets into the water from “the effluent of human civilization” – meaning fertilizer runoff, manure from livestock farming, and sewage dumping.
You may have heard of “red tide,” or seen spectacular satellite images of colorful swirls in open water. These enormous aquatic disturbances, called algal blooms, are caused by tiny aquatic algae or bacteria.
Greg Dick, Associate Professor of Earth and Environmental Sciences at the College of LS&A, University of Michigan brings his expertise in marine microbiology to bear in an attempt to understand the inner workings of an algal bloom. His recent work has taken him to Lake Erie, where in 2014 the largest algal bloom the lake had ever seen threatened the water supply of over 500,000 people.
An algal bloom starts when an excess of nutrients, like phosphates and nitrates, get into a freshwater source. Industrial waste and runoff from fertilized fields are huge contributors of such chemicals. When algae find themselves in fresh water with large amounts of these chemicals, their growth goes wild, resulting in a spectacular bloom. The problem is that algal blooms use up all of the water’s nutrients and oxygen for themselves, restricting the growth of other microbes. Some blooms exude toxic substances into the water as well, a problem for the animals living in it, and the humans who want to drink it.
Dick’s research focuses on how other environmental factors, such as dissolved hydrogen peroxide, can affect the course of algal blooms. Recently, his group showed that there was a spike in hydrogen peroxide concentration in Lake Erie just before the harmful algal bloom hit its peak. Normally, hydrogen peroxide is harmful to microorganisms, but Dick and others are learning that certain toxic algae and bacteria and use their toxins to survive the hydrogen peroxide stress, which just makes the bloom worse.
“Debating Life’s Family Tree”
Norman Pace, Ph.D., University of Colorado and W. Ford Doolittle, Ph.D., Dalhousie University
Conveners: Thomas Schmidt, Ph.D., and Matthew Chapman, Ph.D, University of Michigan
Editor: Ada Hagan
Blogger: Alisha John
Question 3: How do contrasting interpretations of trees influence sequence-based explorations of complex microbial communities?
According to his first slide, “At this stage, not much.” He states that if you want to use environmental sequences to establish evolutionary relationships, that’s fine as long as you appreciate the limitations.
Doolittle leans on a presentation from Adam Martiny on a very similar question. In this presentation, Martiny asked “Is phylogeny predictive of traits?”, suggesting that Pace would answer “Yes!” and Doolittle would answer “No!”.
Doolittle continues using Martiny’s slides to discuss the answer to question 3 and seems to agree with the idea that both the Norman Paces and Ford Doolittles of the world are correct. Sometimes phylogeny predicts traits, other times it does not. This is due to a variety of reasons, including the number of genes controlling a particular trait. More variable traits tend to be controlled by a smaller number of genes than those traits that are more conserved (and often more complex).
By quickly addressing question 3, Doolittle was able to move into addressing a topic of his choice: Holobiosis – Hope or Hype? With this, he discussed his opinions on the hologenome theory of evolution, which proposes that instead of acting on an individual organism, evolution acts on the “holobiont” – an individual plus all of its microbial buddies.
Despite our microbiomes getting antsy for lunch (as joked by Tom Schmidt), we have time for a few questions.
Q: We’ve gone from using whole 16S RNA sequence, to using a small, hyper variable region of 16S. Can you comment on this shift?
Pace: The issue is one of resolution. You have to have enough nucleotides to determine relationships.
Q: Matt Chapman asks both speakers to acknowledge that there may be caveats in everything discussed today, including concatenated gene trees, the eocyte theory, and Lokiarchaea.
Pace: Responds first by asking “What’s the question?” Continues to say “I have no doubts about the ribosomal RNA tree.” He does, however, concede that concatenated gene trees have a role to play in determining more recent evolutionary relationships. Pace remains firm in his belief that ribosomal RNA is the correct molecule for determining more distant relationships.
Doolittle: “I have doubts about everything, of course.”
The session ends with a vigorous applause from the attendees before filing out to feed their microbiomes.
Question 2: What are Prokaryotes? Did Eukaryotes arise from Prokaryotes?
The name “prokaryote” itself suggests that prokaryotes are the precursor to eukaryotes. Pace states that with the three domain Tree of Life “prokaryote” lost taxonomic legitimacy as both Archaea and Bacteria fit into the prokaryote category, though Archaea and Eukaryotes are more closely related. And he “doesn’t care what you say.” He affirms that the term prokaryote means “non-eukaryote” and nothing more. In just a few slides, it has become very apparent that Pace isn’t pro-prokaryotes.
So, where did the eukaryotic cell come from? The answer is complicated. Ribosomal RNA trees don’t provide the whole answer and we have to turn to concatenated gene trees, where many genes are strung together to determine evolutionary relationships. Pace warns that concatenated gene trees are “lethal”; their problems are many: alignment issues arise, lateral gene transfers add another layer of complication, and the fact that the rate of change in sequence is not constant between genes creates a statistical nightmare.
Pace has a strong stance: Concatenated gene trees are a bad idea. But they have some utility, especially for shorter evolutionary time scales. He warns that if you use concatenated gene trees to establish deep evolutionary relationships, “You’re going to screw yourself”.
Pace spent a significant amount of his time arguing against the eocyte hypothesis.
He ended his talk with the conclusions that 1) Woese was correct, and 2) the term “prokaryote” fails both phylogenetically and taxonomically.
Doolittle starts his address to question 2 by stating something along the lines of, “Well we disagree on this one”.
Doolittle continues on to the longstanding question of whether there are two or three domains in the Tree of Life. Here, Ernst Mayr and Carl Woese enter our discussion, the “King Kong vs Godzilla” in phylogenetics. Doolittle shares an entertaining letter he received from Mayr, a
supporter of the two domain view (Prokaryotes and Eukaryotes).
Doolittle described Woese, who supports the three domain view, as “¾ of a cladist.” Doolittle argues that a pure cladist would argue for a two domain Tree of Life, consisting of 1) Bacteria and 2) Archaea and Eukarya.
Doolittle combines his talking points into a single slide: The traditional view, where eukaryotes derived from within prokaryotes. Doolittle suggests that a simple organizational shift moved this into the two domain (prokaryotes and eukaryotes). From here, the three domain “Tree of Life” emerged. Since that time, a more nuanced “post-Lokiarchaeota” tree emerged that suggests eukaryotes arise from within archaea.
Doolittle ended his discussion with a variation of Pace’s final slide.
Pace is quick to point out that Lokiarchaeota is only a proposed branch of Archaea. Doolittle fires back by pulling up a supplemental slide with reasons for the audience to “drink the Lokiarchaeota Kool-Aid”. In my own interpretation, Doolittle’s favorite beverage is Kool-Aid, but I can’t postulate on which flavor in particular.
Q: Pat Schloss brings up an ongoing Twitter discussion between Brett Baker & Laura Hug, stating that she faced a lot of criticism for not choosing a side in the two vs three domain debate.
A:Pace responded with an apology for the letter he sent her regarding the publication but defended his stance on the matter.
Q: What’s the homology between Archaea and Eukarya 16s RNA?
The stage is set with a second podium at the front of the auditorium and two whiteboards providing a buffer between podiums.
Thomas Schmidt begins with a historical perspective. In the early 1990s, Carl Woese and colleagues rocked the biological world with their proposal on the evolutionary relationships between domains of life – Bacteria, Archaea, and Eukarya.
This session will be structured around three questions:
- What is the Tree of Life?
- What are Prokaryotes? Did Eukaryotes arise from Prokaryotes?
- How do contrasting interpretations of trees influence sequence-based explorations of complex microbial communities?
Question 1: What is the Tree of Life?
Pace: For 100 years, textbooks discussed the four kingdoms tree until the late 1960s when fungi expanded this to a five kingdom tree. Around the same time, Steiner and colleagues hypothesized a model of evolution where eukaryotes evolved from prokaryotic organisms.
Molecular phylogenetics is often used to establish evolutionary relationships. Pace breaks this into three steps: Align genetic sequences, count the number of differences, use this information to determine relatedness. But, he questions, what molecule (DNA vs. RNA) or gene do you use to establish the “Tree of Life”?
Carl Woese decided to use ribosomal RNA for many reasons, including that it is present in all cells and is one of the most conserved sequences in biology. Woese used these sequences to establish a Tree of Life which established the classical groupings of organisms (i.e. archaea, bacteria and eukaryotes). One criticism of this tree is that it is not a tree of organisms, but instead a tree of ribosomal RNA.
Pace poses the question: Are there alternatives to the Woese ribosomal RNA Tree of Life? In short, yes.
Doolitte: He begins addressing Question 1 with a warning that he and Norm disagree most on Question 2. He also states, “Many debates in biology as philosophical.”
Doolittle believes believes that the traditional vertical trees aren’t the “truth” of the Tree of life. Instead, we should look “between” the trees, at lateral gene transfer, where there may not be a tree at all.
Doolittle believes that lateral gene transfer, also known as horizontal gene transfer, is more substantial than most give it credit for. In fact, he argues lateral gene transfer, especially in microbes, may be rampant enough to disrupt the ability to determine a meaningful “Tree of Life”.
Now we’re moving into the public Q&A for Question 1:
Q: How do you view the updated “Tree of Life” (published in April)? Pace indicated that we’d discuss the updated “Tree of Life” during Question 2. However, Pace did state, “It is BS” in regards to the updated tree. Doolittle, on the other hand, stated that he has “swallowed the koolaid.”
We began a little after 10:30am on Day Two of the Michigan Meeting on microbial communities. Attendees are settled into their oversized, velvety green chairs in the Rackham Amphitheater. We are one talk into our second day of #MiMicrobe, and for the next hour and a half, we’ll be listening to Norman Pace and W. Ford Doolittle contrast their views on the “Tree of Life”.
Pace is a Distinguished Professor of Molecular, Cellular, and Developmental Biology at the University of Colorado, Boulder.
Doolittle is a Professor Emeritus at Dalhousie University in Halifax, Nova Scotia.
Both men received their Ph.D. in 1967 – Pace from the University of Illinois, Doolittle from Stanford University. Both men have also had successful research careers, focusing on the evolutionary “Tree of Life” and the placement of various microbes within this tree. Perhaps this shared interest is due, in part, to the fact that Pace and Doolittle have worked together in the past; Doolittle was a postdoctoral fellow in the Pace Laboratory at the University of Colorado before starting his own research lab at Dalhousie University. Despite working together, Pace and Doolittle have differing opinions on the “Tree of Life”.
Since the Middle Ages, tree-like diagrams have been used to represent relationships between individuals, the so-called “Family Tree”. By the 19th century, this branching metaphor expanded into evolutionary relationships. Charles Darwin used a tree metaphor in describing his theory of Natural Selection in Origin of Species and his notebooks contain a famous sketch of the Tree of Life.
Today, these diagrams are known as phylogenetic trees and are a visual representation of the relationship between species, individuals, populations, etc. In April of this year, scientists published, “A new view of the tree of life”, a “dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included.” Bacteria, Archaea, and Eukarya are classically clumped into two groups: Prokaryotes, single-celled organisms that lack a nucleus (Bacteria & Archaea) and Eukaryotes, which have a nucleus and organelles.
Pace and Doolittle have differing opinions on the validity of these groupings and the “Tree of Life” itself. Let’s see what they have to say…
“Is There ’Just Enough’ Iron in the Ocean?”
Mick Follows, PhD, Massachusetts Institute of Technology
Editor: Ada Hagan
Blogger: Ellyn Schinke
Since the addition of iron into iron-limited oceans has such an impact on the carbon dioxide in the atmosphere, it has been proposed as a strategy to mitigate global warming. However, the model simulations done by Dr. Follows’ group have shown that, long-term, this strategy will not work. This is due to the fact that not just iron is limited in this environment. There are other limiting components as well. Not only is the iron limiting, but the particles that bind iron and facilitate diffusion into the ocean are limited as well.
Dr. Follows called this the “iron-microbe feedback hypothesis.” Basically, his hypothesis states that when iron is naturally deposited into the ocean, the system has balance. In addition to iron, there needs to be a certain amount of microorganisms and the iron binding particles. He tested this hypothesis using his computer models. These simulations show that this hypothesis seems to be the case.
So, is there just enough iron in the ocean? The answer seems to be yes. The feedback between iron, other nutrients, and ocean’s microbiome ensures that the system stays balanced, and the ocean stays at its most productive.
How does the iron fertilizer get utilized? As the iron sinks into the water, plankton are able to use it to produce nutrients. However, not all organisms can utilize the iron in this particular form. Plankton also capture the iron from sinking sediments, incorporating it into complexes with other particles (i.e. siderophores) in the water. The process of iron binding by these other particles in the water is crucial, as it allows more iron to be bioavailable in the ocean. Without it, the concentrations of iron in the ocean water would be significantly less, and the ocean ecosystem would be quite different.
Using this information, Dr. Follows has built a model of global ocean iron, phosphorus, and carbon cycles. This is a simplified model which doesn’t take into consideration the microorganisms themselves, but instead how they affect these elements. In this model, they can simulate how much iron is present in varying parts of the ocean. Importantly, this computer simulation not only captures how much iron they have observed in various ocean regions, but also provides significantly more data than sampling the ocean ever could.
Some surface regions are rich with un-utilized macronutrients, but why is this? Part of it has to do with wind. The wind drives circulation of ocean waters, which propels nutrient-rich waters from the deeper parts of the ocean up toward the surface. At this point, the nutrient cycle can progress. However, in these newly mixed waters, a lack of iron and nitrogen might limit the growth of phytoplankton. In regions with strong wind currents, iron-rich dust can be deposited to compensate for the iron deficit.
Since the proposal of this “Iron Hypothesis”, originally proposed by Dr. John Martin, a number of groups have conducted iron enrichment experiments. In these experiments, ships would dump iron into the water, and look at the response of plankton by measuring the fixation, and subsequent sedimentation, of atmospheric carbon dioxide. These experiments included the 1999 SOIREE, and 2004 EIFEX experiment. These experiments demonstrated that enhanced iron availability leads to enhanced generation of organic material, which is important for nutrient cycling in the ocean.
“All models are wrong but some are useful,” Dr. Greg Dick said during his introduction to Dr. Follows’ talk.
“All are wrong.” Dr. Follows said, eliciting a chuckle from the audience.
Is there enough iron in the ocean? Dr. Follows, a physicist-by-training, is curious about the balance of iron in the ocean and how it influences the production of macronutrients. Using a unique, computational approach (and many pretty pictures!), he brings a new perspective to the talks from yesterday.
The ocean microbiome combines phytoplankton, bacteria, their predators (protozooplankton and phage), and mesozooplankton, zooplankton restricted by ocean salinity and temperature. These microorganisms participate in nutrient cycling (i.e. iron, nitrogen, phosphorus) which results from the sinking of iron-rich sediments in the ocean. Since it’s a microbiome conference and we have to talk about poop, the feces of these zooplankton are appropriately crucial for this process.
Dr. Mick Follows, an Associate Professor of Earth, Atmospheric, and Planetary Sciences at MIT, was originally slated to discuss the biogeography and competition of marine plankton, but decided to change his topic to one that he was more passionate about. Of course, Dr. Follow! Today, he will talk about iron and the role it plays in the productivity of our oceans. I doubt he even realized when making the change that this would have a fantastic tie-in to Dr. Tom Schmidt’s introduction from earlier in the conference. But I’ll get back to that in a moment…
Since the 1980s, it has been thought that iron might be a limiting nutrient in parts of the ocean, a theory which was tested by dumping ferrous iron into the ocean to assess phytoplankton productivity. The result was a highly productive algal bloom, which many thought could be a means of dealing with the overabundance of atmospheric carbon dioxide and global warming. But how does climate affect that? Today, Follows will discuss the effect that climate has, particularly windy climates which produce atmospheric, iron-rich dust, on the sensitivity of atmospheric iron and the storage of carbon in the ocean.