Microcosm Day! Ask A Question and Win a Signed Copy

Microcosm%20cover%20150.jpgI’m in a celebratory mood. Microcosm is published today. In my mind, I can see the books moving out of warehouses onto trucks, off to book stores and front door steps. This morning I read a great review from Mykola Bilokonsky at Newsvine. (“What are you waiting for?” he asks.) And tonight I’ll be having a little get-together, with the weather cooperating in splendid fashion. To spread the cheer, let me invite you to participate in a contest to win a copy of Microcosm that I will personally sign.

To enter, you just need to ask a Microcosm-related question in the comment thread. My book is specifically about E. coli, and generally about life. By illuminating how this microbe works, I end up exploring everything from synthetic biology to the possibility of extraterrestrial life to the evolutionary history recorded in E. coli’s genome–a history that we share. For more information, you can check out the Newsvine review, or my previous Microcosm-related posts here, or my Microcosm page on my web site. Or you can just ask a question about E. coli that’s been on your mind for years. I know you have at least one…

You can post a question between now and Thursday, 5 pm EST. I will then choose five questions to answer in a post on Friday, and I’ll get in touch with the five winners for their addresses.

In the meantime, question away, and spread the word to anyone else who might be interesting in entering.

Update: Let’s keep it to one question per entry, so that the question space isn’t all gobbled up!

Update: The contest is closed. Come back Friday for winning questions and their answers.

244 thoughts on “Microcosm Day! Ask A Question and Win a Signed Copy

  1. As the first commenter can I get away with a silly question? Something like, “So, why’s E. Coli such a big deal?”

    Actually, I don’t know much about E. Coli. Why is it the bacteria we always use for experiments? What is it about that little guy that’s so amenable to being experimented upon? I think mice, drosophila and E Coli are the most experimented-upon creatures, at least that I know of.

    As a final, and definitely silly, question, “How does E. Coli illuminating how E. Coli works lead you to explore ‘everything from synthetic biology to the possibility of extraterrestrial life to the evolutionary history recorded in E. coli’s genome–a history that we share’?”

  2. OK, here’s my question: Is most of life slime? For years I’ve consoled myself with the factoid that “most of life is slime,” i.e., by weight, the bulk of living matter, past, present and future, was, is, and always will be, microbial. Is that true? If so, how do we know? (P.S., my neighbor, NPR science editor David Malakoff, says you are a great writer.) Sincerely, Dan Kowalski

  3. Hi Carl,

    How does E. coli maintain its “species identity” (for lack of a better phrase) given that it’s not a sexually-reproducing lifeform?

  4. Here’s my question:

    I’ve been hearing a lot about probiotics in health circles lately, I wonder if there is any work being done on modifying e. coli to further assist with various intestinal problems. In other words, could e. coli be made into a type of super-probiotic?

    If you happen to choose my question, my current copy of Microcosm will be given as a prize to one of my middle school science students this fall. 🙂

  5. If you happen to choose my question, my current copy of Microcosm will be given as a prize to one of my middle school science students this fall. 🙂

    Hey, now, Edman… doesn’t that constitute biasing the jury pool?!? 😉

  6. Is there a limit to the number of questions we can ask? Assuming we can ask only one question, just pick #1. If not, here’s my list:

    1. Because E. coli lives in our intestines, I would think that our health would be in its genes’ benefit. Have there been any genes or processes identified that benefit it by benefiting us? or is the environment in our intestines too competitive to allow us to get into a mutualistic relationship with our E. coli?

    2. Sort of going along with #1, are individual’s E. coli strains distinguishable from each other? could we, in theory, identify an individual (human or otherwise) by looking at the bacteria in their feces?

    3. What is your favorite thing that has been done to E. coli (making it glow, smell like bananas, etc)?

    4. Do different E. coli cells ever cooperate with each other (clones)? how about different strains?

  7. Hey, now, Edman… doesn’t that constitute biasing the jury pool?!? 😉

    Haha, actually, that was totally unintentional. I really just didn’t want people thinking I was hoarding copies of Microcosm…which might be considered pretty weird.

  8. Congrats Carl! I have already ordered the book but I would love to have a signed copy:). I know absolutely nothing about E. coli so my questions are a little basic (sorry).
    Why is E. coli so successful? Who actually benefits in our relationship with E. coli? What makes some strains harmful? And finally, are you ever coming to give a talk in Tennessee :)?

  9. There doesn’t seem to be much info that’s readily available about the genus Escherichia. Wikipedia does say:

    While E. coli is responsible for the vast majority of Escherichia-related pathogenesis, other members of the genus have also been implicated in human disease.

    Why E. coli? Is there something in particular about its evolution that accounts for its “success”? Is it that it happened to get a “foothold” and just went on from there for no particularly explicable reason, or is there something that can be pinpointed as a “success factor”?

  10. I believe it was one of your articles leading up to this book that compared E. Coli to the internet. How both E. Coli and the internet function in similar fashion, breaking information, or food, into packets that can be processed identically and then efficiently working through them all.

    So my question is, Would we be taking the analogy too far if we flipped it around and asked if the internet is showing signs of life? Can E. Coli be used as an example to show how the internet is not only mimicking life, but dealing with the same problems as a living entity?

    Are there good philosophies that can seperate the functions of E. Coli and the internet, and call one life and the other artificial?

    Ok, so I’ve asked a few questions. Maybe I’m breaking the rules, but that’s been weighing on me ever since I read the article about how the Internet is like E. Coli.

  11. I have a question about how far back we can trace E. coli in animals. Did the dinosaur-era proto-mammals have E. coli in their guts? Or does bacterial evolution occur so quickly that we don’t have the tools to look back that far?

    Does E. coli leave any kind of trace that we might find in fossilized dung, or even for ice-age remains like in a frozen mammoth or something preserved in asphalt at La Brea?

    I guess my question is best phrased as “when did E. coli first conquer our bowels?” Presumably there’s been an entire ecosystem in there since multicellular life started having a butt. When did E. coli become king of the roost, and in what way are scientists able to find this out?

  12. “How are intelligent design proponents taking the news that E. coli flagellum can be explained naturally? Have they countered with anything?”

    I think their response is something like this:

    “What? Nuh-unhhh… OH LOOK! COWS!!! Wait, what were we talking about?”

  13. Question: Is there really a clean division between E. coli and other species of bacteria? Is there really a clean division between bacteria and viruses of bacteria? Or, in general terms: what can we learn from E. coli about the boundaries we draw between organisms?

  14. In studying the mechanisms of e-coli, are there any insights that can apply to the organization of more complex entities? For example, does the responses of e-coli to environmental pressures offer ideas as to how to better organize organizations or societies to respond to danger, stress, etc.?

  15. In animals and plants transposons and other mobile elements have contributed a number of times to the evolution of advantageous traits and the birth of new genes. As E. coli has its own set of mobile elements, I was wondering if we know of any documented cases when the transposition of these sequences resulted in increased (bacterial) fitness?

  16. Hmmm … questions you want.

    As I understand it many, most?, types of E. coli are fairly benign. Some are normal and beneficial to humans and live in our guts. But some other species or subspecies, are deadly.

    Why is it that the generally beneficial ones proliferate in the human gut but the toxic ones generally don’t? What tips the balance on the playing field?

    Presumable the bad ones are all around us in small numbers. Why is it that only when you get large numbers of them all at once, like when you eat that under cooked burger with tainted beef, does that toxic sort take over.
    If the toxic sort is so strong that it can push aside the friendly version and and we are exposed to it in smaller concentrations so frequently why doesn’t win out more frequently?

    Do we, in conjunction and cooperation with the friendly E. coli, have some sort of limited immunity?

  17. Q: What makes some bacteria, such as E-coli, beneficial in one setting (e.g., the gut) and harmful in another ?

  18. What is the energy economy of E. coli? How much energy does it burn to produce what result? When does the E. coli economy collapse (ie: too many for a given host)? Can an E. coli “colony” grow too large for its environment?

    Lots of questions to express the one idea.

    Oh, and thanks for a nice science blog.

  19. How do you distinguish between benign strains of E. Coli and pathogenic ones? I am guessing that different methods are used in research and clinical settings.

    Is it possible that life began on Earth when a space faring alien briefly stopped over and took a shit? And thus E. Coli was the first terrestrial life form? 🙂

  20. Carl:

    Congratulations on your book! Have fun at your “little get-together”. =)

    Question: What, if anything, can E. Coli teach us about swarm technology; specifically, can E. Coli provide any insights into nano-tech motility and the way nano-bots work together?

  21. My question (ooh, ooh, pick me pick me!!):

    How much of the nutrients extracted from the food we eat go to our E. coli-like gut flora, and how different are their nutrient demands from our own?

  22. Are there bioterror risks in using a species originally from intestines as such a central tool of biology? I mean, we can’t take toothpaste on an airplane, but you don’t need any kind of security clearance to genetically engineer E. coli.

  23. Oftentimes, genes will pass from a bacterium to another bacterium – or even a human. Q: What types of diseases are associated with gene transfer from E. Coli to our own cells? And is it an evolutionary battle to maintain a population of E. Coli, while at the same time protect ourselves from that (seemingly) safe population of E. Coli?

  24. How can E. coli help us conquer the universe?

    Congrats on you publications!
    Greetings from the Neotropics!

  25. How special is e-coli. Is it special enough, or are its morphs special enough, to live in planets throughout the Universe?

  26. Would we care so much about E. coli if we couldn’t infect it with bacteriophage lambda or the T-even phage?

  27. I’ll recuse myself from the contest… but congrats on the release. I’ve changed the Link on EcoliWIki from “Coming soon” to “Now available”.

    And alas, no, most of these questions are not answered at EcoliWiki.

  28. What role do phage-encoded toxins (such as Shiga) play in the evolution of the phages that infect bacteria like E. coli?

  29. A copy is already winging it’s way to me, but here goes…

    Does E Coli affected by any parasites?



  30. I dig your NYT articles and would love a copy of your book, and it is my birthday…So, heres my question: how similar is the microbial flora of the digestive system within similar phylogenetic groups and across different ones?

  31. Would a review of Microcosm: E. coli and the New Science of Life on a leading on-line review site (named something other than ‘amazon’) by a leading writer there be of interest to the E. coli bug..??

    There, I asked a question, even if annoyingly self-serving…


  32. If E. Coli can easily absorb genes from other organisms, what allows it to keep its identity? Or to say it differently, what keeps the newly mixed DNA from producing a Chimera? Under what conditions is the expression of a foreign gene allowed?

    By the way Carl, when you are in the Bay Area, why not stop into The Bone Room in Berkeley and say hello and get a free tour.

    Ron Cauble

  33. Mr.Zimmer

    I have one simple question. When will the first synethtic cell – like a an amoeba – be created by man? I thought it would take thirty years. More like in half that time or less. And that inevitablily leads to the question of what is life and what constitutes as life. Life can be based on instinct and learned response alone. But intelligent life entails awareness and the ability to learn. By that definition all living things, including viruses and bacteria have the ability to adapt not just to survive but to thrive. Read the for example for the first time in thirty years there is now type of wheat rust can potentially destroy all wheat strains and therefore cause worldwide famine.

    Thus to me the question of life is central to our quest to all our other questions. And the development of synethetic life is or will be a huge milestone and cause huge waves of change. Think how this understanding could lead to a whole new string of computers. They would be the closest thing to a synethetic human being. Thanks for opportunity. Look forward to your response or anybody esle’s. Like this kind of discussion.


  34. hi carl
    how do you think e coli is likely to evolve in the future? given the fact that the mitochondria in our cells has its origins in a bacteria, is e coli too going to lose its personality (!) and become an integral part of us?

  35. Question: Can you get sick from e coli you already have ?

    ie… you have e.coli in your digestive tract anyway, say you have poor hand washing skills after using the bathroom, can you infect yourself with a bacteria you already have ?

  36. Will learning more about E.coli / current knowledge let us use it to crack biosynthesis, code and synthesise at will letting
    E.coli be the molecular factory we are looking for ideally? And will it lead to more answers regarding the minimal-organism theory/practice?

  37. Will learning more about E.coli / current knowledge let us use it to crack biosynthesis, code and synthesise at will letting us use E.coli as a molecule factory ideally, in and out of living systems? And will it lead to more answers regarding the minimal-organism theory/practice?

  38. How can E. coli, and your book, be used in the ongoing quest to explain evolution to those who are open to learning, and how can they be used to take on the claims of creationists/IDists?

    I’ve got a copy of the book speeding toward me, but would love to have a signed copy. Mostly, though, I am really interested in an answer to the question!

  39. I suspect that my infant daughter already has E. coli and other intestinal flora in her system. My question is, how did it get there?

    Probably not through the umbilical cord, unless it’s also a blood-borne pathogen endemic to pregnant women. Probably not from the birth canal, since she was a C-section baby. And probably not from the general environment since, as paranoid first-time parents, we scrub and disinfect everything that comes into contact with anything that comes into contact with her. I don’t see E. coli listed as an ingredient in baby formula and it wouldn’t make sense for it to be lurking in breast milk, so where did Baby Alexi–and by extension the rest of us–obtain that very first dose of bacteria?

  40. How does E. coli relate to other gut flora in terms of competition? Do they have finely tuned mutually beneficial relationships, or is it a competitive environment?

  41. Creationists often point to the bacterial cell and say something to the effect of “the cell is so complicated it is highly improbable that it could have spontaneously formed – therefore God-did-it. Are there any particular features of E.coli that reveal simpler origins?

  42. Hya,

    My question (I hope it has not been asked before) is this:

    There are some people that argue that life is, fundamentally, about information. Thus, eating, reproduction, etc. should all have meaning in terms of information.

    Is there a model for chemical information exchange between organisms and their environment? How does it work? Can we look at it through microbial life?

  43. What would be the short-term and long-term effects of the total eradication of E. coli? In what ways would humans be effected, and how could you envision us adapting?

  44. How does E.Coli interact with other mammals? I know that we humans naturally have it, but, are there dangerous strains that cause food poisoning in other mammals, or is it mainly just us humans?

  45. Recently, Craig Venter has been speaking on his work in genetics, and how the recent explosion in DNA sequencing technology has allowed the creation of entirely synthetic genomes. How optimistic are you about the future of using engineered bacteria to accomplish some of the optimistic scenarios (say, to create fuels from CO2 feedstock)? Would E. Coli or, or an “engineered descendant” of it, be used in a process like this, or would it be an entirely different type of bacteria?

  46. My question, and this comes from my work to some degree, is (multi pronged), are we born with e. coli, or do we get are first amount of it after birth?

    If we get it after birth, where do we get it? Is it an indicator of what we eat or who we are related to, or both?

    If it shows who we are related to, can we use it like DNA to look for relationships?

    If it comes from what we eat, can we use it to study food consumption, and do we get more from new sources as we continue to grow and consume?

  47. How is our knowledge of E.coli and other bacteria changing our understanding of population genetics and how will we modify the 20th century synthesis of natural selection and genetics?

  48. A nurse friend of mine once told me that out gut flora has a circadian rhythm of 24 hours.

    Is this true? If it is, is it then dependant on the rhythm of human activity and metabolism? Or do bacteria that live their entire lives in the darkness of our intestines have an internal clockwork independent of us?

  49. Now that we know so much about E.coli, is it possible to prevent diseases of gastrointestinal tract? Maybe somehow by changing the DNA of E.Coli using the transduction of specifically created DNA information?

  50. Do E. Coli populations in the gut remain there on their own or is their spread to other areas of the body limited by the immune system?

  51. I have no real knowledge about E.coli (so my question may be quite silly?) but I am very interested in your book. All I know about E.coli is the horror stories I have heard about E. coli 0157:H7. What is it that makes E. coli 0157:H7 harmful to consume for humans, while other strains of E. coli are ok/helpful?

  52. Isn’t there a virus (or viruses) in our intestines that attacks the E. coli bacteria? When a person gets sick from E. coli, is it because favorable conditions have allowed it to reproduce faster than the virus?

    Sorry, that’s more than one question and not even really related to your book (congratulations, by the way!) but one question always leads me to another. Good luck with your book!

  53. E. coli is used quite a bit in biotechnology, specifically for use with recombinant DNA technology. Why is E. coli used so frequently in this field? Is the nature of the E. coli organism condusive to recombinant DNA or is it simply that E. coli has a long history in laboratories so scientists are very familiar with how to work with it?

  54. The synthetic capability of E. coli to produce peptides introduced following transduction/transformation is well established, but with obvious short-comings. One such short-coming is the inability to enact comprehensive post-transcriptional modification, or provide an adequate environment for adequate post-translational mechanisms. One example is the formation of inclusion bodies following insulin synthesis because of the absence of chaperones.

    Do you see a way to overcome this without moving to yeast or other eukaryotes? Would introduction of Hsp90 family proteins address this issue? or is the demand associated with proper chaperoning in excess of what e. coli can support (with or without major genetic engineering)?

  55. Probably the best well known , famous bacteria on earth. Is it the most common & is it found outside the guts of animals on a routine basis?

  56. I am mentally drained from finals, so I don’t feel up to the challenge of finding a question worthy of receiving a free book. But I just wanted to comment that I saw a link to this on PZ’s blog (Although I was thrown off for a second & thought that PZ was plugging Margulis’s 30 year old pop-sci book Microcosmos), and I’m definitely going to go buy this book. I’m a microbio student who loves to read popular science, so this is right up my alley. 🙂

  57. How can our understanding of the microcosm be applied to our understanding of the macrocosm. Particularly I am thinking about adaptations and mutations. Can we use this knowledge to improve living situations around the world and make Earth a safer place?

  58. Is E.Coli the only species that fills this particular niche in our gut flora? ie could we do without it, if we were never exposed to the bacteria, or if it was wiped from our gut by a bacteriophage etc?

  59. Why do we seem to suddenly have such a problem with e. coli? Is it because of big business or just nature?

  60. How has E. coli persisted as a species? Especially how did it persist pre-animal digestive tract? With the constant onslaught of E. coli phage that E. coli has persisted through….its remarkable there are any E. coli (or any bacteria) around to write your book about.

  61. I’ve heard different stories about e. coli in the human gut, and I’m curious about e. coli’s normal, non-virulent behaviour. Is it, under ideal circumstances a helpful addition to the host organism in some direct way, or is it merely a somewhat schizophrenic room mate that could just throw all your shit out and set fire to the place?

    (pun totally intentional)

    Seriously; what’s stopping us from all out biological warfare against this potentially treasonous organism?

  62. Congrats on the new book! I’m not a scientist. I’m not even very smart, for that matter.

    We have a symbiotic relationship with E. coli. Does E. coli have symbiotic relationships with any other bacteria? Have we seen any symbiotic relationships among any bacteria and, if so, do any of those relationships likely show the beginnings of the evolution of a new multicellular life form? Maybe I should’ve first asked if that’s the probable method for the early evolution of multicellular life.

  63. I know nothing about E.Coli, so just to enter into the spirt of the thing, my question has to be the pathetic:

    Is the E. Coli bug a microcosm of Ben Stein’s brain and, if not, what is the difference between those two things?

  64. Are there E. Coli strains which are benign or even beneficial in other species which are harmful to humans, or vice-versa?

  65. So, if E. coli traditionally colonizes inside of an infant’s GI tract within about 2 days of birth as part of the normal flora of the gut that aids the host by producing vitamin K2, and/or by preventing the establishment of pathogenic bacteria within the intestine, then how would virulent and toxic strains, like O157:H7, O121 and O104:H21 come into existence? If E. coli is naturally a part of the environment of the gut that is adapted to aid the host, what factor came into play that cause the genetic material of E. coli to code for harmful strains in order to boast its own survival rate? Also, are these harmful strains only found in the human gut, or is this something that is seen in the various other species which have a gut that E. coli inhabits? Thank you and looking forward to reading your book.

  66. At the risk of answering (in part) some of the questions above:
    Are there any clues in the E. coli genome as to the possible origins of its phage-virus parasites (e.g. lambda)?

  67. I haven’t read all of the questions, so maybe this is a repeat, but here it is.

    It is my understanding that pathogenic strains of E. coli are dangerous because they produce toxic metabolites. Is this true? If so, what kinds of products do they make and how do they harm us? Is there any benefit to the bacteria for producing these metabolites (ie, they evolved somewhere outside the human body where it was useful), or are they just sort of accidental? If damage is not due to toxic metabolites, what is the source of their pathogenicity?

  68. Q. How does the e. coli in our bodies get there?

    It’s not there during fetal development, so is it passed somehow from the mother or is it ingested?

  69. When I first moved out into the country and had a well drilled I had my water tested. One of the things tested for was “coliform” bacteria. Is that the same as E. coli? What are the specific concerns about this “coliform” bacteria? What are the usual sources of it?

    Thanks very much.

  70. I have not read all of the previous questions, so forgive me if this has been asked already…
    Why E. coli? From a historical perspective, why do we study E. coli? There are countless easily culturable microbes out there, so how did the scientific community select this particular species as “the model” for microbiology?

  71. Historically we have been using E. coli for many applications in research, one being secretion of recombinant proteins, but recently modified E. coli have been created to produced oil and other hydrocarbons. While this procedure is not cost effective at the moment, do you see this new field as one that will become more important in the future, perhaps overshadowing current uses for E. coli? If E. coli can create chains of hydrocarbons, is it possible that we can use them to create other organic molecules? What do you see as the future of E. coli in research?

  72. To my e-coli, I must be an omnipotent creator god. As such it’s important to me that my e-coli act morally and worship me.

    My question is: “How can I tell if my e-coli are being good?”

  73. Question:

    Do you think a microbial zoo could be a popular tourist attraction?

    Imagine enlarged photos, diagrams and gigantic models of viruses and bacteria.

  74. E. coli is a bacteria commonly found in the intestines of some animals. What distinguishes the common and harmless strains from those that can cause illness and death?

  75. Simple model organisms are sometimes used to study more complex biological processes. (Yeast were/are studied to better understand eukaryotic cell division and its implications in cancer, for example.)

    Besides using E. coli as “factories” to express large amounts of protein for biochemical analysis, how are (or how could) the cellular mechanisms of E. coli be studied to gain insight into more complex biological systems?

  76. What does the future hold for E.coli? Specifically, where is this famous bug going in the lab and our lives as we nudge closer and closer to artificially creating little beasts of our own with similar utility.

  77. Given its importance in biology and the conservative approach of my school district, what’s the best activity or simulation you could think that I could use to teach 7th graders about the nature of E. Coli?

  78. E. Coli borrows genes from other organisms in its environment.

    Do any known strains of (natural) E. Coli have explicitly human genetic sequences, and if so, how do we determine where that code originated in the first place?

    If E. Coli are so prolific, and act as DNA duplicators, I wonder if they may have been a sort of filter, collecting DNA from other creatures and then through some mechanism (possibly by a virus that can infect both E. Coli and human cells) manage to copy DNA into our cells.

    I ask, because I doubt that viruses are the only lifeforms that have been directly tampering with our DNA since our ancestors became multicellular.

    I wonder if we are alive today, only because our ancestors were ‘given’ genetic information by our many parasites, like how we improve and redecorate our homes to better suit our needs. It might explain our tolerance for certain bacteria.

    Is this possible, or am I going way out on a limb, here? Is there a virus/mechanism that copies bits of genes from bacteria into mammalian cells?

  79. Since the Republican Party has done so much, through deregulation, to bring more and more people into daily contact with E.coli, does this mean the GOP elephant should be replaced with a microbe?

  80. I cannot think of a good question – but reading these comments I now want to know more. I’ll have to check out your book!

  81. One of my favorite science fiction stories is “Microcosmic God” by Theodore Sturgeon. Assuming that genetic engineering allows us to become “Microcosmic Gods”, how do you think this will change the future societies of the human race, morally, spiritually and politically?

  82. In his essay, Planet of Bacteria, Stephen Gould writes:

    “Writer Dorion Sagan and biologist Lynn Margulis write in their book, Garden of Microbial Delights, that ‘human skin harbors some 100,000 microbes per square centimeter’ (‘microbes’ includes nonbacterial unicells, but the overwhelming majority of ‘microbes’ are bacteria.

    I was particularly impressed with their statement about our colonial status: ‘Fully 10 percent of our own dry body weight consists of bacteria, some of which, although they are not a congenital part of our bodies, we can’t live without.'”

    I’ve always been fascinated by such estimates. Do they take into account ERVs? Do they include all micro-organisms, or just bacteria? What is meant by “dry weight”? Is this estimate still considered accurate?

  83. I would like to know if there is any evidence to suggest that viruses evolved from single-cell creatures rather than the other way around.

  84. The book sounds really interesting.

    My question is: do we have any idea how many human beings E coli used to kill (oh, say, 200 to 500 years ago), as opposed to today?

  85. I have a long question but I assure you that it’s basically just one.

    Okay, so as I understand it the species concept in a nutshell is “a reproductively isolated group”. But, and this question goes for stuff like bdelloid rotifers as well, how do you distinguish and define species among asexually reproducing critters?

    Morphology? Gene families (in rotifers, I suppose it’d be plasmids for E. coli)? Morphology? Gene expression? What’s the line at which you can say “Yes, this level of distinction is definitely a species-level distinction, and that level of distinction is merely ‘strains’ within E. Coli.”
    I mean, aren’t they all arguably just in a sort of transitory quasi-speciation state, just like sexually reproducing creatures, but without the benefit of reproductive isolation to tell em apart?

    In asexual reproduction, what differentiates species from one another, as opposed to strains?

  86. I hope nobody has asked this question, but I’m too impatient to read through all the comments (that’s generation Y for you). Apologies if it has.

    Would it be possible to replicate microbes synthetically and how difficult would it be for us to build new ones? What is the potential of microbes in biotechnology?

  87. Will there be a genetic engineering revolution in the same sense there was a computer revolution? That is, will we see rapid, exponential development driven by individuals working from their garages?

  88. My question is this: How do you suggest we combat E. Coli and the effects of it, while at the same time not encouraging its evolution into something even more dangerous or into something we don’t yet have the means to face?

  89. In every episode of “How clean is your house?” the hostesses find colonies of e-coli, which obvious is a trademark of dirtiness!So, my question is:How dirty does one have to be in order to have a house with e-coli lurking in every corner?

  90. I was just wondering about an evolutionary link between free living E. coli and the E. coli found in our bodies. How did it get there? Was it just sort of caught up in the development of multicellular organisms and we had to find a way to get along? Or did it jump in later with a random mutation that allowed it to form a symbiotic relationship?

  91. Maybe the answer to this question is in the book. In which case I doubly deserve a free copy.

    Here’s my question:

    If there’s lots of e coli in our guts already, not making us sick, then how does e coli-infected meat or water make us sick?

    I understand that not all bacteria make us sick, and that harmless e coli in meat or water is more an indicator of general contamination, which includes other strains of bacteria that actually do make us sick. Fine. But where do the other dangerous strains of bacteria come from then, if not from fecal contamination? If dangerous bacteria are not in our gut, and the e coli in our gut are not dangerous, then why do we worry about fecal contamination at all?

    Seems that meat & water contamination tests are misdirected, and that neighborhood coprophilia parties might actually be recommended now and then, particularly after a course of antibiotics.

  92. A simple one: How can I best use your book to combat the forces of anti-evolutionary “education” in Louisiana?

  93. Okay, this is a more basic question than a lot of them, but here goes: Since families share strains of E. coli, when two people with different strains begin to cohabit, do the strains of E. coli merge into a smaller number (than the addition of person a and person b’s strains together) of new strains?

  94. Hi Carl,

    Longtime reader, first time writer:

    Given that E. coli is widely experimented upon, are there thoughts about using it to ease the burden of malnutrition in the developing world? According to wikipedia, E. coli in the gut produces vitamin K. Would it be possible to manufacture strains that also manufacture vitamin A, or E, or vitamin C? If so, innoculating people with these strains could potentially eliminate disease caused by vitamin deficiencies.

  95. Hello,
    I’m kinda taking the direction of asking about your science writing experience, the kind of folk you had in mind when you were writing and who you hoping will enjoy the book. And hoping you’ll elaborate a little bit about the whole experience, really.

    So my question is, what sort of person can enjoy this book and really get the most out of it – did you write for good old nature lovers who don’t know a lot of detailed science but are curious, or is it more for people who already read a lot of science writing and are pretty up on the play?

  96. What insight do you think the differing patterns of cell-adhesion lectins between different pathogenic strains of E. coli and non-pathogenic strains can give us regarding the co-evolution of E. coli, its host(s), and other microbes competing in its environment?

  97. My question:

    How did E. coli (or it’s ancestors) and other gram-negative bacteria evolve the periplasmic membrane? Was the generation of the second membrane an internal adaptation or did one (gram-positive) bacterium invade another, in a similar fashion to that which has been hypothesized for acquisition of mitochondria by eukaryotes? Note – mitochondria have a double membrane as well!

    This is the stuff that keeps me up at night.

  98. Do you think that our focus on E. coli has biased our view of the prokaryotic world, and, if so, in what direction? If, long ago, we had chosen a different model organism– Geobacter, say– do you think microbiology would look different today?

    And a few (even more) vague, general questions, just for fun:

    Is microbial senescence a real phenomenon?

    Ecologically speaking, why do we see three domains of life, rather than two, four, or more? (Is it a matter of evolutionary contingency, with a wide variety of other arrangements having been possible?) If another domain existed, but went extinct long ago, how would we learn about it?

  99. I know that plasmids can come with benefits, but given that they do take advantage of bacteria for their own replication, is there any way in which plasmids behave, at least in part, like parasites?

  100. So many questions I had have already been asked, really looking forward to the answers post. 🙂

    Question: Are there other common Escherichia? And if so, why is E. coli so important compared to the other species? (If not, what is it about E. coli that makes it the only common species in its genus)

  101. Long ago, in bacteriology class, the teacher (an ex-nun at an ex-Catholic college) was telling us about the type “F” pili that are used to pass DNA so coli can have sex. One of the students asked “Why do they call them type F?” The teacher started to answer, but stopped, and then she turned bright red. The class start laughing, and then she did as well, and then someone asked, “What other kinds of pili are there?” She pulled herself together, said “Thank you” and class continued.

    I would like to know both the answer to the original question, and also when in evolutionary history these tiny beings started having sex.

  102. I am currently working with a professor on developing a mathematical model to determine the targets genes of the global regulator CsrA. To develop this model, we have relied heavily on what are the known targets in E. coli. My question is how effective do you think it is predict target genes of CsrA in other organisms based on the regulon of E. coli?

  103. First of all, I loved your book Evolution. I keep it prominently on the shelf, and reading it has led me to become an adjunct researcher for a pediatric medical institute. So, already, thank you so much!

    Now for the question.. let’s go simple here: What would happen if E. coli didn’t exist, and what effect would that have had on human evolution?

  104. Hi Carl,
    Many of your previous posts have explored the dynamics between the micro and the macro realms. To me this is the most fascinating aspect of research in this area: in the overall scheme of things how much pressure do the micro creatures exert on the macro ones? i.e.to what extent do they go in shaping the larger level behaviors that we see? Thanks!

  105. This isn’t a science question, per se, but I must ask it. When are you going to get an E. coli tattoo so you can post your science tattoo in your collection?

  106. This isn’t a science question, per se, but I must ask it. When are you going to get an E. coli tattoo so you can post your science tattoo in your collection?

  107. Okay, I’ll admit it! I’m microbiotically challenged. Isn’t E-coli what them Swiss Mountaineers call to each other across the Alps?

  108. You mentioned that you explored synthetic biology while writing the book: Do you believe that synthetic biology has the potential to revolutionize our society in much the same way as computing has since the 1970s?

  109. Well, my question is more about Microcosm itself than E. coli or the science. The review you linked mentions that you do a great job at making the science in your book easy to understand. How do you manage to go over a topic as inherently scientific as a microbe, and explain its relevancy to so many facets of science, without getting bogged down in the technical?

  110. This is actually somewhat inspired by the post I’ve linked below, but: Obviously, E. coli produces substances for the benefit of its host, but is there any evidence that it’s had direct or indirect effects on the human genome itself (e.g., gene transfer, epigenetic effects, etc.)?

  111. Could the prions be the first (or at least previous) replicators, from which DNA-bearing bacteria wrested the control of life on this planet? And: do we see prions in bacteria? Thanks!

  112. Have you ever studied the E. coli from your own body? If so, how and where did you obtain the sample from, what did you learn from it, and how did your hands smell afterwards?

    twas, a joke.

  113. So it turns out that most of the genome of organisms is “junk” or redundancy (or at least non-coding). What percentage of the E. coli genome is non-coding, or do we know to any certainty? (I would assume the number to be much lower than estimates for, say, the human genome.) And what kinds of avenues are people exploring in an effort to tie this into the paradigm of human evolution (so, WHY do we have huge numbers of transposons and non-coding DNA that still gets transcribed anyway)?

  114. As I understand it E. Coli is commonly used in labs to test genetic code expression (frequently what proteins are built as a result of that bit of genetic code) using samples from other organisms, like animals or plants. What’s the most interesting thing you’ve learned from this type of E. Coli research?

    (Looking forward to reading your book, regardless of the contest results.)

  115. I would love to get a signed copy of your book (I happen to work with E. coli and other pathogens, and your book sounds great).

    So, my question:

    How applicable is it to use this organism for the study of human disease pathology and evolution? A great number of bacterial species are very different from a gram-negative enteric like E. coli, and those differences are probably evolutionarily greater than the separation between humans and plants.

    I understand that this was one of the first organisms to be artificially genetically altered, and that because of some of the evolutionary adaptations it possesses, it makes for an easy subject for genetic manipulation and study. But how well do the results and effects of such study transfer to tremendously different bacterial species — like Clostridium difficile or Streptococcus pneumoniae — especially in regards to toxins, secretion systems and adherence?

  116. my knowledge of e. coli is pretty scanty, seeing as I’m actually a computer scientist. but…ummm…

    what does e. coli contribute to the science behind the relation of multi-celled organisms and the cultures of bacteria that cohabit with them?

  117. There is a prolific woo psuedo-science therapy called ‘colonic flushing’.

    What would happen to someone if all their e. coli got somehow cleaned out?

  118. As you mentioned the new field of synthetic biology :
    do you think we will soon be able to create a new E.coli-type cell from scratch, or more simply to “boot” a DNA-deprived cell on an artificial chromosome, as Craig Venter claims ?

  119. I’m finishing up my pre-req’s to eventually become a PA (until I change my mind again), so I don’t have much under my belt other than a&p and basic micro. However, here goes!

    I am curious as to why certain strains of e.coli evolved to affect the people the way they do. That is, if e.coli is already found in food, what’s the evolutionary advantage of making someone sick? I suppose my question is much broader than I initially thought, but why don’t bacterial organisms evolve to all benefit one another? Why the need for harmful bacteria at all?

  120. Tough to come up with a good question! We think of E. coli as a gut species but clearly it can survive “in the wild”, since otherwise we would not be able to test water supplies for it or other coliforms. So – my question – are the populations outside a gut able to sustain themselves or do they depend on continuous replenishment? To rephrase – if all the guts (and feces!) were to suddenly disappear, would E. coli survive or go extinct?

  121. A fairly weak question, but the only one I can think of at the moment: How long can E. coli survive outside the gut? In other words, how long is it viable once it hits a spinach leaf or some other place in the great outdoors where it normally does not live?

  122. Congratulations on your new book!

    My question isn’t about E. coli, but it did come up during my intro biology lecture. I was telling my students about Streptococcus and necrotizing fasciitis, and that the species of Streptococcus that causes “flesh-eating” is carried by a small percent of the population without affecting the carriers. The question was “so if one of the carriers coughed on themselves, could they give themselves flesh-eating disease?” I couldn’t see why not, but I can’t find the answer anywhere…

  123. Is it possible to trace the evolutionary divergence of species by testing the rate of mutation in the e-coli within the digestive system? In other words, can we use e-coli as an evolutionary clock to give us another data point in terms of how long ago species diverged from each other? Further, are there certain genes within the e-coli that we’ve identified which mutate at a known fixed rate, and fit the profile as a possible evolutionary clock?

  124. I’ve already ordered the book. My question is when are you going to write a book about a subject I can illustrate again?

  125. One of the things that really excites me about biology is emergent properties. How simple components can interact to create something marvelous. I was wondering whether there are examples of emergent properties happening among a colony of single celled organisms, E. coli of otherwise?

    Does multicellular life have a monopoly on cells collaborating to accomplish a task or is there more to those ubiquitous bacteria than I thought?

  126. Hello,

    Your book is called “Microcosm”…this label made me think a little.

    We know quite a good bit of information about the behavior of animals around our order of magnitude, such as chimps (Jane Goodall, of course), birds, ants, dolphins, etc. The list goes on. I’d assume that bacteria, being the “primitive”, microscopic creatures that they are, show no significantly interesting behavior. Is this true? Or are there actually any bacteria (E. Coli, perhaps?) that exhibit strange and wonderful behavior as we animals do?

    Truly curious,

  127. NPR recently reported on an MIT team of bioengineers who created a strain of minty-smelling e. coli. I can’t believe that the interviewer didn’t ask the obvious: Could they introduce that strain into the human gut and produce relatively pleasant-smelling excrement?

    So I’m asking you.

  128. Some E. coli strains are symbiotic with humans, and some are pathogenic. Why the huge difference in virulence of various E. coli strains?

  129. How are morality and the capacity for religious belief selected for in an evolutionary sense, and could these selection pressures produce one without the other?

  130. How big is E. coli? I mean is it one of those that’s 1/100th the size of a human body cell, so they outnumber our cells? Or do bugs with tails have to be bigger?

    and a comment: I’d pay real money for a non-DRM electronic copy of your book. I’d even promise not to share it, except by pointing to your for-sale site. I’ll even write a review on my blog, for what it’s worth. I’ve got a pocket computer that i bring everywhere, and it’s smaller than any book made of paper, and it can cope with HTML, PDF, text, Palm docs, and dozens of other formats.

  131. Dr. Zimmer, I’m an undergraduate in Microbiology who wants to know how you would define of life.

    Would viruses fall into your definition?


  132. Are E. coli more sensitive to mutations because they have relatively non-repetitive DNA and are generally haploid, or do they rely on them for rapid evolution?

  133. Question:
    What has your research, and your educated-guess-fantasies about life, told you so far about how artificial life (nonorganical lab units) would interact with the human and other natural species?

  134. Why do so many non-scientists get upset about directed genetic engineering? To be more specific, what is it about directly synthesizing genes (for E. coli, or any other bug) that is more upsetting than making random mutations by treatment with mutagens (as has been done for decades) or even just picking out random beneficial mutations (as has been done for millenia). Why do people get queasy about directly mutating and constructing artificial genes?

    (I know this is phrased as multiple questions, but it’s really one question that I had a hard time articulating).

  135. I haven’t read all of the above questions, I hope mine is not a repeat (if it is, please disregard mine in favour of whoever asked first).

    Would a completely synthetic genome (all bases of DNA assembled in a non-living system e.g. test-tube) inserted into a single E. coli cell that had previously had its genome removed, qualify as a synthetic organism in your opinion, or would other cellular components (membranes, proteins, etc.) also have to be synthetically produced and included?

    Thank you.

  136. Basic bonehead question:

    If humans have 46 chromosomes and chimpanzees have 48 chromosomes, and if chimps and humans shared a common ancestor, then that ancestor likely had 46 or 48 chromosomes. Considering the developmental problems that occur when there is a chromosomal mismatch (Downs, for example) how did the population with the different number of chromosomes arise?

    That mutations and mistakes happen I understand. That they might occasionally be advantageous I understand. How that first creature with the extra or missing pair successfully mated I don’t understand.

  137. What is the earliest example of a symbiotic relationship between a bacterium (or other prokaryote) and a eukaryote? I know the endosymbiosis theory for origin of mitochondria and chloroplasts, but am more curious about when eukaryotes began using prokaryotes as helpers.

  138. How close are we to completely modeling a living e.coli cell computationally? What are the key discoveries that still need to be made to achieve this feat of modeling a complete living system?

  139. The question I’ve been waiting to ask is about an earlier book: “evolution the triumph of an idea”. My copy (a paperback version bought in a perfectly normal manner from Amazon, rather than anything obviously pirated or dodgy) is missing nearly all the illustrations, diagrams, photographs or whatever it was meant to have. The text makes specific reference to various figures but they simply aren’t there – not on neighbouring pages, nor even quarantined into special inserts anywhere else in the book.

    Although I have a fair idea of what each one was meant to convey (because I already have the relevant education), it’s rather annoying not to have the illustrations. I certainly couldn’t recommend the book to anyone else as educational material in its current published form. So that’s something over which you (Carl Zimmer) need to monitor the printers etc for future editions of that and other books of yours – including your latest one.

  140. Oops – in case it wasn’t obvious, the question is: what happened to the illustrations and is my copy some sort of one-off mutant in lacking them?

  141. If we ever absorbed e.coli into our own cells/DNA etc so they became a part of us (as opposed to living in us), are there any processes/selection pressures which could then reverse the ‘splicing’? What would/could they be?

    Something that would make the e.coli material think ‘actually, it’s not so great in this human cell after all, i’m outta here’?

  142. Some microbiologists have proposed that certain bacterial colonies should be regarded as multicellular organisms rather than a group of unicellular organisms.

    Do you feel that this approach has any merit when it comes to E. coli?

    If so, do E.coli colonies exhibit any sort of division of labour, coordinated behavioural responses, etc?

  143. I’m looking forward to your book because I’m fascinated by biology, evolution, and science in general. I work at a large produce company in Salinas CA that grows lettuce, broccoli, spinach and many other leafy green vegetables. My company was not directly implicated in the spinach e. coli scare a little while back, but it hurt our business nonetheless. My question is this:

    Is there any scientific research going on that would enable produce growers to somehow genetically alter e.coli to render it harmless?


  144. I am curious about E. coli. It’s my understanding that it is a normal part of intestinal flora. Yet, it causes serious illness and death when ingested. Why this dichotomy? I look forward to finding out by reading your book.

  145. Is there any evidence of quorum sensing in E. coli? And, if so, do scientists know if the bugs can talk to each other both inside and outside of the gut habitat?

  146. Found my way here via Pharyngula, and it just so happens I do have an e. coli-related question. My great grandfather was Theodore Eserich, and I’ve always enjoyed telling people that he’s the ‘E’ in E. coli. (People never seem sure quite how to react to that…) So here’s my question: What’s the ‘coli’ part of the name refer to? There was a time when I thought maybe Dr. Coli was a cohort of Theo’s, but I’m guessing that ain’t it. So, book or no book, I would love to know.

  147. I can answer your question, flaq (#173): The “coli” stands for “colon”, because that’s where it can be found.
    It’s why when you’re testing for sewage leaks, you test for “coliforms”. It’s poop bacteria.

  148. If the dog licks his butt and then licks my face, (a) why doesn’t the dog get sick and (b) why don’t I (usually)?

  149. Heya. I saw this book in Barnes & Noble two (!) days ago and *almost* bought it (I’m sorry!). Your publisher is lying to you!

    My question: How does E. coli move through its environment? I know it uses flagella, however how do they work in tandem to create such diverse and relatively quick movements?

  150. Hi Carl,
    I have been curious about microorganism “intelligence” since I read this.

    How can a primitive unicellular organism like E. Coli behave like it had some kind of intelligence, anticipating changes in their environment?

  151. So, we all want free stuff, I suppose.

    To what extent has E. Coli lost functional capability as compared to ancestor microbes over time since it is primarily a parasite.

  152. How can E. coli be harmless in the intestine and yet toxic if ingested? Is it possible for a bacterium to mutate in the intestinal tract to become pathological?

  153. Boy do I like free books!

    If an alloy is stronger, more flexible, and more resistant to corrosion than their component metals, then a bioalloy is a living system that is stronger, more flexible, and more resistant to corrosion than it’s component life forms.
    What bioalloys are E. coli a part of?
    How does E. coli contribute to each property of these bioalloys?
    Steel is an iron alloy with .2-2.04% carbon, what is the optimum amount of E.coli to make the best bioalloy?

  154. Which of its genes or non-coding sequences have been used as molecular clocks to determine the age of E. coli, and does that estimate jibe with the appearance of the earliest animals with which it currently symbioses or parasitizes?

    I would hypothesize that it would; what is that estimated age?

  155. This isn’t specifically about E.coli, but it is something I’ve been wondering about lately. What exactly is it about some foods that allows them to keep without refrigeration, but not other similar foods? For example, peanut butter seems (naively) like it might make a good medium for critters to grow in, but it does fine in the pantry; however jam does not. On the other hand, pastries containing jam-like fillings are often sold unrefrigerated. I realize that things like water and sugar concentrations are at work here, but it still often seems pretty random. Are there good rules-of-thumb that can be used to decide if something is safe to leave unrefrigerated?

  156. Can you say something about our “Inner E. coli” (as opposed to the the E. coli within us)

  157. This area of science is not my strong point, so I don’t know a lot about E. coli to begin with. But I do know it’s been altered and experimented with frequently for potentially positive uses in medicine and elsewhere. So what I want to know is, what’s the most successful use of altered E. coli in scientific research thus far?

    By the way, I had hoped to meet you at the Knight Fellows’ symposium earlier this year, but I had to catch a train about the same time your talk started. Some other time, some other place, I hope. Congrats on the new book!

  158. Congratulations on the new book, Carl! That’s great. I love the cover. My question:

    Did you choose E. coli or did E.coli choose you?

  159. How do development control mechanisms in multicellular animals relate to, are derived from, and possibly reuse methods, molecules, genes, switches etc., from single celled eukaryotes and ultimately, prokaryotes, like E. Coli? In other words, how is Evo connected to Devo?

  160. Yes, Carl, My neighbor’s son died of unspecified reasons– they seem to think it’s an infection or something–and she said, “God has a reason for everything.” “Some reason”, I said, and felt bad. I read your Parasite Rex. and I said, perhaps unkindly, this God dude’s got a crazy mind.

    Anyway, my question is, what is the best thing humans can do for each other each day, when we’ve got bacteria like you depict and other horrid things that can trip us up?

  161. We know an aweful lot about E. coli and we continue to learn more each year. In your opinion, what would it mean to completely understand this organism? In other words, how would you define a complete biological characterization of E. coli, and how far away are we?

  162. Hi Carl,

    I know the bodies of animals contain googles of bacteria. My question is – why do we have friendly bacteria living within us? Wouldn’t the immune system have fought the friendly microbes off just as they fight the unfriendly ones now? Was it because bodies gained friendly bacteria before an immune system was established?

  163. Nothing about multiple questions, right? 🙂 The second isn’t E. coli specific.

    Prokaryotic cells are often described as “simple” compared to “complex” eukaryotic cells with membrane-bound compartments. Do we have a good understanding of how prokaryotic cells remain organized? Are we biased by ignorance?

    (A copy is on order so I get to read it one way or the other)

  164. My question: Given that the most virulent strains of E. coli reside in cattle without apparent harm to the animals, is there any way we can control their evolution (as per the ideas of Paul Ewald and others) to force those strains to become more mild? It seems that since their main reservoir is not suffering from the virulence that attacks us as collateral damage, that there is no way to apply selection for mildness in the strains.

  165. Lynn Margulis goes so far as to speculate that existence of macro-organisms is enabled by the collusion of microflora; a close co-operation of a microbial community with the eukaryotic host. If this were true then evidence of co-evolution should be seen in the genomes and physiology of both humans and resident microbes. To your knowledge and aside from the ever-present immunological arms race, is such evidence known? A purely hypothetical example would be adaptation of a gut epithelium receptor to respond in mutually beneficial ways to a metabolite or other molecule of microbial origin.

  166. Here’s a relatively simple question, one that I hope hasn’t been asked already. (There are just too many questions to pick through at this point.)

    E. coli and other bacteria can live happily enough within us or they can sicken us. Just what is the dividing line between mutualism/commensalism and pathogenicity? Why do some of our bacterial guests decide to up and attack us?

  167. How can E. coli live stably in the gut without causing a significant immune response or inflammation, if it must express common bacterial antigens?

  168. Actually, there is indeed one question I have…

    With the mutation rate in E. coli (I seem to recall 10^-5 or 10^-9 from my first year), there are bound to be mutations all around that are advantageous a) for E. coli itself b) for the host (let’s say, us) and c) for research. Yet we work with a rather fixed (if very very broad) spectrum of strains for any given project, with some strains taking precedence over others for certain tasks (e.g. BL21 or Rosetta gami for expressing proteins over DH5α), so why is that exactly? Sure, they have proven to be up to the task but what if a mutation or a series of mutations would produce a strain that is even better at it than what we have in our freezers and no one is looking for it…

  169. It is known that there are many different “strains” of e. coli.
    Presumably, it is possible to “direct” the changes in those strains in the lab, by altering the environmental conditions, as is normal.
    However, is there any prospect (maybe it has aleady happened, & I don’t know about it) that the sufficently-altered survivors could no longer be regarded as E. coli any more, but a new species?
    Or even more than one new species?

    Analagous to the fact that all domestic dogs are descended from wolves, but are now regarded as a separate species, for instance.

  170. My question is more about book writing I suppose, Where does the passion come from? It is hard enough for me to write about the things I love in school, so I was wondering what about the topic made this come to fruition?

  171. If I recall, E. coli don’t have introns, and there is specualtion on whether their ancestors had them and subsequently lost them, or that they never had them at all.

    Where do you stand on this debate?

    Sorry if this has been asked, or if it’s already in your books. Have onyl just found out about it all, and they’re on the reading list whatever happens.

    Thanks and good luck with the new book!

  172. I’m curious about how E. coli and other microbes react to their environment and how that compares to animal behavior. That is, aside from obvious differences like the presence of a nervous system (and setting aside sophisticated behaviors which require brains), are the behavioral strategies of microbes and animals generally comparable?

  173. I work with another common model system (D. melanogaster). Given the huge amount of diversity in the microbial world, how applicable are the results obtained from E.coli to other microbes and even more complex systems? How do we know E.coli is a good model?

  174. The first E. coli genome to be sequenced and by-far the most studied bacterial strain probably “Of All Time”, is K-12. Unfortunately, K-12 is non-pathogenic. The reason behind it’s sequencing, which didn’t exactly come without debate, was because it was such a widely adopted laboratory strain.

    So, my question is … with a majority of the work being performed in K-12, is this desire to work in a strain which doesn’t cause any disease, delaying scientific progress? In addition, would it make sense for research communities to literally sit down and discuss a particular strain, or strains, for study within the community? Perhaps with re-evaluation (removing or adding strains) every 5 to 10 years depending on the insights which have been discovered over that period of time?

  175. If e. coli is so infectious and so endemic, why do predators not suffer regularly from e. coli infection? And why when we used it regularly in college bio lab to infect vegetable matter is it not a threat to plants in the wild?

  176. When did the most common ancestor of E. coli strains live? E. coli is known to be living in the intestine of warm-blooded animals. Did E. coli join to the common ancestor of birds, reptiles and mammals? Otherwise the commensalism evolved two times separately? How can we regard E. coli as one species, even though they seems to be diverged deeper than class level of vertebrates?

  177. What is known about how, exactly, we get our gut normal flora? I suppose it must be fecal-oral transmission but somehow that seems haphazard — and I imagine fecal-oral transmission to be an occasional thing, but is it perhaps the rule rather than the exception (i.e. perhaps we’re constantly transmitting our fecal germs to others)? Well, that’s jolly to think about.

    I think question #201 is a great one. And no, I don’t know the fellow who posted it.

  178. What are your thoughts on why E. coli has evolved into so many different strains of the same species, and yet other organisms have actually become different species through their differentiations? Do you think it likely that some E. coli strains do in fact become (or will become) wholly different species?

  179. I know that E. coli plays a significant role in our digestive system metabolizing the milk sugar lactose which evolutionarily opened a niche in the mammalian colon. How fast is E. coli undergoing horizontal gene transfer and can we expect more strains like 0157?

  180. Escherichia coli colonizes the newborn’s GI tract in the first day or two of birth. Most sources I’ve found suggest this is a necessary event for the proper development of the child. But how necessary is this event? If it was possible to prevent E. coli (or Lactobacillus or any other mutualistic microflora) from colonizing, how negative an impact would this have on the child’s development?

  181. We know that there are many subtypes of E. coli that can cause enterohemorrhagic colitis and HUS, however E. coli O157:H7 remains the primary identified subtype. We know that because of inadequate screening methods many of the subtypes are not readily diagnosed. My question is this: Is E. coli O157:H7, being more readily identified by screening, truly the most significant pathogen of the pathogenic subtypes, or is E. coli O157:H7 truly more virulent and thus causes more morbidity than the lesser well-known E. coli paghogenic subtypes? In other words, are we significantly underdiagnosing E. coli morbidity because of inadequate screening methods?

    Thanks for the opportunity to ask a question that has been in my mind for awhile.

  182. Hi,
    Many of the questions I have revolve around this species genetics. Has this species undergone a significant genomic reduction during it’s co-evolution with mammals?

  183. I thought I once heard in lecture that the E. coli genome is very similar to that of Salamonella. How could a slightly “tweaked” genome turn a relatively harmless organism into one that can cause drastic disease?

  184. Hi, Congrats on the publication! I’ve had your book on my ‘to read’ list for a while now, so I’m excited that it’s hitting the shelves.

    My question is what fraction of the E. coli genome has been inherited vertically since the last common ancestor of all E. coli strains, and what fraction has been inherited horizontally? How could you determine this?


  185. One from the field of synthetic biology (I’m taking Drew Endy & Natalie Kuldell’s class right now):

    Do you think it’s a good thing that so much synthbio work is done in E. coli as opposed to a wider variety of organisms? On the one hand, having a “canonical organism” makes it easier to have something like the Registry of Standard Biological Parts. (My design project for the aforementioned class is in yeast, which means for every part I pull out of the Registry, I have to worry about whether it works in yeast.) On the other hand, having a “canonical organism” means we may miss out on the awesome natural abilities of more diverse organisms. (Another group is trying to make their project solar-powered, so they’re putting everything in a cyanobacterium.) What are your thoughts?

  186. Could you recommend a book that might prove enlightening to someone who knows very little about E. coli, but would love to learn..?

  187. Can the possibility that E. coli learn to utilize plastic be eliminated? If not, then should we keep a close eye on the Giant Pacific Plastic Vortex for Andromeda Strain 2.0?

  188. Whoops, one more.
    In the lab, we have to make E. coli cells competent to take up plasmids — I haven’t done this in a while but I seem to remember some protocols involving heat shocks and Ca2+. I also recall purchasing vials of already competent cells (this when I was in the better-funded lab!). Yet we’re always hearing about how bacteria in the wild are madly swapping genes back and forth. What’s the difference here — why do we have to force E. coli to be competent in the lab, and how is lab-produced competence different from “naturally occurring” competence?

  189. Much of our investigations into the biology of e.coli seem to occur in the petri dish, at a temperature of 37 degrees centigrade, with the gas concentrations you would expect to find in the human body.
    However, When one extracts any bacteria from an environment, and plate it on a petri dish, any bacteria unable to adapt to this new environment will not grow, so you may end up getting a biased sample of bacteria.

    Do you think this has affected/biased the study of E.coli since it’s discovery ?

  190. question:

    Has there been work on the evolution of E. coli inside the guts of various organisms? It seems like a lot could be learned about how E. coli has evolved throughout the years within other evolving species, but it doesn’t seem like there’s been a lot of work in that area.

  191. I know that microbes aren’t necessarily organized into the same Linnean classifications which multicellular organisms are, but since so much is known about E. coli, I wondered two things:
    1. Has E. Coli ever been seen to evolve into something which is clearly no longer E. coli – into what would be considered another family or order? How would it be determined that such a change had taken place?
    2. Since we know so much about the genome of E. Coli, has any progress been made into understanding the “individualised” behaviors described in the NYT article:

    Presumably if the genes are the same, then regulatory DNA or epigentic factors are in play here. How much have we learned from E. Coli about the power of these two extra-genetic forces?

  192. We harbor e.coli in our gut–a sort of symbiotic relationship. What are your thoughts on how such symbiotic relationships arise with what would otherwise be a harmful parasite? Is the parasite evolving a mechanism by which is helps (or at least doesn’t hurt) the host because that is adaptive for the parasite? Or is the host somehow responding in a different way so as to promote a non-pathogenic relationship?

  193. I do have a question since very long. Why does E.coli not have such a high mutation rate as lets say…the common cold virus. The virus has such a great advantage in dodging everything we throw at it. Why wouldn’t E.coli have this? What determines how much the mutation rate of an organism is?

  194. I remember the idea of plasmids being a major part of our ability to manipulate E. coli, but I’ve always wondered how genetic material goes from the main gob, the “nuclear” DNA of E. coli, to become tiny plasmids that can be transmitted from cell to cell?

  195. One of the things I took very much to heart in grad school was that in bacteria, everything function was as efficient as possible. No gene is present nor protein created at a specific time without a damn good reason.

    This is presumably due to highly competitive microbial environments and obscenely quick generation times – thus allowing natural selection to happen exceedingly rapidly. Any mutation giving a bacterium even a tiny competitive/growth advantage, including any permissible decrease in DNA/protein synthesis, would take over a population very quickly.

    I’ve always assumed this does not hold true as strongly in multicellular Eukaryotic species, especially those that emerged more recently, simply due to less time on Earth and much longer generation periods. But I never really looked it up to address the issue.

    So the question: Is it safe to say that we, as humans, are not nearly as efficient with our cellular functions as bacteria are with theirs? If we aren’t, are there any examples of slow progress in that direction? Or do inefficiencies creep in faster than selection can prune them away? (For instance, the amount of junk DNA we have is so much – huge amount of DNA synthesis for things of unclear use. If we were E. coli, I would have assumed that if it really was un-used, it would have been either scavanged to become something useful and retained or, alternatively, deleted a long long time ago)

  196. My question: It was jut reported that the platypus, a billed, egg-laying, venomous mammal, shares genes with birds related to production of hard-shelled eggs, and it also shares genes related to venom production with some reptiles. We also know that chickens have genes for teeth which can be induced to be expressed under some conditions. What does this tell us about life on this planet? How much of the genetic toolkits of reptiles, birds, or even e.coli. are we carrying around, perhaps unexpressed? Will people someday be able to “order” children with venomous fangs?

  197. Given rampant horizontal gene exchange between E. coli and closely related bacteria species, how do we distinguish E. coli from closely related organisms like Salmonella and Shigella. Is the species concept of bacteria arbitrary?

  198. Does e. coli compete with any other organism to maintain its seemingly comfortable spot inside my tummy?

  199. Given the ubiquity of bacteria, they can clearly outcompete eukaryotes in some environments or circumstances. Why is this, since eukaryotes would seem to have a much more diverse set of tools to work from? Is it just that bacteria are smaller, have lower energy needs, and can replicate faster than even the smallest eukaryotes?

  200. Here is my Question;

    Why octopus has 8 arms ? what is the survival (or sexual?!) advantage of 8 over 6,7,9 and 10?

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