We are some of the foremost leaders of the microbiology field, three of us are national academy members. Dan Portnoy is working on Listeria and collaborating with Aduro Biotech to help reach a cure for cancer. Michael Thomashow works to understand the mechanisms to help plants handle freezes and drought, in order to reach the potential of crops. Steven Lory works to understand how soil based bacteria cause diseases. John Mekalanos is the former chair of microbiology at Harvard and works on the mechanisms and vaccine development for cholera.

Here is the link to each of our labs and proof: https://mcb.berkeley.edu/labs/portnoy/Portnoy_Lab/Welcome.html








Comments: 537 • Responses: 57  • Date: 

efg3q9hrf08e285 karma

Does the microbiology community have any plans to analyze Donald Trump's "hands"?

Microbiology_ama281 karma

HAHA, They are all refraining from answering that one.

gusmoreno15206 karma

How cooperative are you with other scientists working on the same subject? Do you help each other and share ideas if you share the same goal?

Microbiology_ama242 karma

Sorry for deleting my comment it was an accident. but what i said was that i really do my best to help my ex students and collaborators, and I said less helpful to competitors, as the first response quotes. this does not mean not helpful it means less helpful than the extreme amount that I grant to my students.

Microbiology_ama25 karma


thelimetownjack55 karma

I am less helpful to my competitors.

That's a shame for science.

Microbiology_ama325 karma

There is a degree of helpfulness and of course I am going to be more enthusiastic to collaborate with those who I have worked with in the past. This is unfortunately a competitive field and sometimes information is privileged.

melaniebeale167 karma

How do you simply but adequately describe the dangers of antibiotic resistance to the lay public? Every time I try to describe it, people don't listen, don't fully understand, or both.

Microbiology_ama145 karma

Dan Portnoy: among the problems is that bacteria that are normally of no threat, but are resistant to antibiotics, can then pose a very large threat especially to those who are immunocompromised once the antibiotics are administered.

lvanDrago43 karma

Stupid question, but is it possible that some peoples immune system is strong enough to kill off Gonorrhea on it's own? Couldn't we start searching for people who have stronger antibodies to create new vaccines? As an example of James Harrison.

Microbiology_ama51 karma

Dan Portnoy: That is difficult, and is actually part of of the problem in finding a cure for HIV. generally for our purposes though the answer is no

knightking558677 karma

Is there any chance that malaria & dengue wil be having vaccines in near future? Also why is it so important to memorize the life cycle of parasites rather than just disease?

Microbiology_ama172 karma

John M.:

There is a high possibility that both diseases will have a vaccine in the next 10 years. And it is important to memorize because that is what we memorized back in the day and you should to :)

sushiiallday66 karma

What is the coolest thing you have seen or learned in regards to microbio?

Microbiology_ama192 karma

Mike Thomashow: That there are some naturally occurring bacteria that exchange genetic information with plants, and actually change the plants genetics in a way that benefits the bacteria.

Steve Lory: the power of bacteria to cause the death of humans, and the power of humans to combat that.

jesusonabicycle13 karma

This has peaked my interest, what do you think is an interesting example of this happening?

Microbiology_ama40 karma

Mike Thomashow: Crown Gall Disease.

Keep-reefer-illegal60 karma

How have inventions like the life straw and other water filters helped the fight against Cholera.

Also, what are some major hurdles in the development of a Cholera vaccine?

Microbiology_ama72 karma

John Mekalanos: 1.anything that provides pure water is an effective intervention in controlling cholera, especially in epidemic situations 2.The major hurdles: there are vaccines already in existence, however they are very difficult to manufacture. This means that the largest hurdle is developing a cheap and easy to vaccine that does not require a cold chain (does not have to stay cold until the admission)

tribe_segundo48 karma

What have been the most impressive recent discoveries in terms understanding how soil microbes affect human beings? Or how they affect crop development?

Microbiology_ama35 karma

Steve Lory: Soil micro bioms - better understanding of the community of bacteria that is involved in harming or benefiting crops and human health

herptydurr12 karma

Can you say anything regarding what that understanding is?

Microbiology_ama17 karma

There is a correlation between those communities and the health, but we do not have evidence of causation yet.

UnsubstantiatedClaim44 karma

How do microorganisms get lead in them in the first place?

Microbiology_ama59 karma

John M: It is just in the environment around them and enters through diffusion. Most microorganisms actually pump out lead to stay healthy.

Christopher_Ocean43 karma

Do you believe in aliens? if so, do you think aliens could be more advanced than humans?

Microbiology_ama85 karma

John M: I actually am very open to that possibility and am under the belief that life will be found on another planet in my lifetime, the details of which I of course dont know.

Microbiology_ama66 karma

Steve Lory: no to the first part, but yes to the second

Christopher_Ocean30 karma

Why do you disbelieve in aliens?

Microbiology_ama165 karma

I am a scientist, I would like to see evidence.

secretwarmonger38 karma

What percentage of your PhD candidates end up doing lab work they truly enjoy? How many of them actually make 50k+ for annual salary?

Microbiology_ama52 karma

Dan Portnoy/John Mekalanos: I believe the majority of my students enjoy their work while in the lab, after that point, in their first real position perhapse half truly enjoy what they do., and the vast majority make an excess of 50k

holymilk0938 karma

About 4 years ago in my microbiology class i asked why not manipulate virus's to kill cancer cells? Is that idea still in the air?

Microbiology_ama66 karma

John Mekalanos/Dan Portnoy: They are. It is very much in the works and that was a very good idea. One interesting example is that the herpes virus could have some applications for certain brain cancers. There are currently no examples that are FDA approved however to the best of our knowledge.

Microbiology_ama36 karma

Due to all the questions we have returned to answer more

pussgurka36 karma

What are some common misconceptions about microbes?

Microbiology_ama65 karma

Dan Portnoy: the misconception is that they are simple, however they are extremely complex.

genyul35 karma

Do you think the Spartans will beat the Wolverines next year?

Microbiology_ama63 karma

We have asked a MD/PHD, who practices medicine, their opinion on this question, and she said that you really need to have a love for medicine, if you have a preference for research perhaps you should consider moving to another field.

genyul53 karma

I dont know if im too dumb to grasp the answer (or if you are just blatantly ignoring my question as a joke, but its ask me anything so that would be kinda rude), or if it doesnt make sense

Microbiology_ama70 karma

OH, our bad we meant to send this response to another question. haha.

Conneron31 karma

Weird question, but what is your favourite microorganism and why?

Microbiology_ama63 karma

Sorry for not including this person in the bio but Raphael Martinez, was a microbiologist at UCLA for many years and he wanted to answer this one. His answer was Yersinia, because he spent many years researching it.

John M: Cholera, because I fell in love with it 40 years ago and have worked with it ever since

JustKerta24 karma

Will this cure for cancer ever become ineffective? For the example, the Flu virus had evolved and the vaccinations at the time became ineffective.

Microbiology_ama78 karma

Cancer is not an evolving system, so it cannot develop across the population to become resistant, however within the particular person the cancer can mutate to be more resistant. edit: The type of cure we are referring to is that of immunotherapy.

pighalf22 karma

Thank you very much for doing this AMA! What advice to you have for a senior post doc that would like to stay in academia (in the process of applying for assistant professorships now) but is worried about getting funding in the future? I should mention my postdoctoral advisor consistently had anywhere between 3-4 R01s in the past, however is down to only one and hasn't been able to obtain anymore in the last 3 years despite publishing in immunity, nature immunology, cell host microbe and plos pathogens.

Microbiology_ama30 karma

Dan Portnoy/John Mekalanos: I think if you truly love science you should just go for it, make sure to hold on to much of your post doc research to get you ahead, and do your best to join a program that matches your interests and goals. There will always be money for creative and interesting science with possible applications, however the future of funding is unclear to us as well.

Edit: Please feel free to ask more questions, we love to help people in your situation.

pighalf6 karma

Thanks Dan and John for your honest responses, particularly concerning the future of funding. I have interests in cyclic dinucleotide signaling independent of sting or ddx41 as well as examining additional P. aeuruginosa derived pamps in the context of innate immunity. Do you think this is considered "too basic science", particularly since my postdoctoral advisor thinks I should focus more on disease models?

Microbiology_ama25 karma

We don't want to interfere the advice of your advisor as there are many different approaches. Dan enjoys advising and would be happy to help on a more private level, please private message for a more specific response as we don't want to step on any toes.

billythegruffgoat20 karma

How worried are you guys about antibiotic resistance, a potential 'superbug' of sorts?

Microbiology_ama35 karma

Everybody: We all believe this is a very relevant and imminent problem.

regulusblackismycat15 karma

Thanks for doing this! I was wondering if you could recommend any books that are must haves for people interested in microbiology? I have my old textbook from university but I'd like to learn more for fun.

Microbiology_ama41 karma

Dan Portnoy: Microbe Hunters by Paul DeKruif, it is the book that made me excited about science, and I give it to every single student who leaves my lab.

orangeman3315 karma

Do any of you brew beer and if so what is your favorite yeast strain?

Microbiology_ama12 karma

No, sorry.

SamJakes12 karma

When you've researched bacteria, have you found any interesting bacteriophages which blew your mind?

Microbiology_ama12 karma

Dan Portnoy: Not recently, sorry for the bad response edit: a word

aresman9 karma

any chance ever that celiac disease can be cured?

Microbiology_ama46 karma

Everybody: None of us feel qualified to answer that question

MyPenisIsaWMD9 karma

With the way that academia is going these days, are you becoming more likely to suggest industry to grads/postdocs than previously? It's approaching 100s of good applicants/tenure track gig at decent schools. As a recent postdoc on the academic job hunt from one of your schools (rhymes with 'Barvard'), shit's getting real out there.

Microbiology_ama13 karma

John M: You are correct, that is the way it is going. I am more likely to suggest it but it is of course not the only option. Industry is somewhat high pressure due to need for a product.

Dan Portnoy: They are very different, If you have any interest in teaching you should definitely stick with academia. if you want strict research both will fit your purposes. Personally we all prefer academia due to the cutting edge nature of the science and the freedom of academic pursuit.

MyPenisIsaWMD7 karma

Why is there no crystal structure (or any structure for that matter) available for T4 DNA ligase? Like, what the hell? There are dozens of ligase structures available but not even a homology model for the one that is most relevant to molecular biology. Blind spot or is it somehow weird?

Secondary question: With the way that academia is going these days, are you becoming more likely to suggest industry to grads/postdocs than previously? It's approaching 500 applicants/tenure track gig at decent schools. As a recent postdoc on the academic job hunt from one of your schools (rhymes with 'Barvard'), shit's getting real out there.

(Grad students looking for a project, this would be a good one).

Microbiology_ama11 karma

We are not structural biologists and therefore do not feel qualified to answer

wooki_cooki7 karma

What do you think of veganism as a cure to cancer?

Microbiology_ama57 karma

resounding laughter

luxii46 karma

I got a microscope for my 7 and 8 year old. They are bored of the prepared slides that came with it. I remember peeling onion skins and looking at them in biology. Do you have other interesting suggestions?

Microbiology_ama16 karma

dirty pond water under the right microscope will be flush with bacteria. besides that you can have them scrape the inside of their cheek to try to see their own cells.

theexplosivecandle6 karma

What do you guys think is the future of probiotics in topical applications?

Microbiology_ama12 karma

John Mekalanos:Topical applications and probiotics are not strongly related because probiotics are generally ingested. That being said there could be a probiotic to help our skin or other topical locations. I am optimistic about probiotics because it is an unexplored field that will largely be impacted by synthetic biology.

thethermals6 karma

What advice do you have for medical students? Have you ever seen "sketchy micro" and what do you think of it?

Microbiology_ama4 karma

We have asked a MD/PHD, who practices medicine, their opinion on this question, and she said that you really need to have a love for medicine, if you have a preference for research perhaps you should consider moving to another field.

Microbiology_ama5 karma

Alright, thank you all for your questions, sorry if we weren't able to answer some and perhaps didn't give adequate responses to others. We were very impressed by many of the questions and encourage those who are interested in science to pursue that as we are always looking for bright young minds to enhance the world we live in.

puntloos4 karma

For some people, especially the elderly, it is sometimes advised to be on permanent penicillin. Ignoring the antibiotic-resistance facts for one moment, is this sound advice? I always thought that keeping a healthy gut flora is just as important (and gut flora has been linked to immunity too!).. thoughts?

Microbiology_ama3 karma

Resident MD: Certain people with take antibiotics prophylactics. Generally speaking the less antibiotics the better, even in the case of some infections.

Ghidoran3 karma

The microbiome seems like it's an emerging field, with lots of different kinds of research. How important do you tihnk the field is going to be moving forward? Are things like novel therapeutics and even microbiota manipulation going to become a primary focus of researchers or is it simply too nebulous?

Microbiology_ama5 karma

John M: we generally have quite a lot of enthusiasm for microbiom research.

felixthemaster13 karma

Microbiology is my goal. Do you have any tips? I graduate this year and need to put together a CV and list of skills.

Microbiology_ama8 karma

Everybody: do as much research in undergrad as possible, that will open many doors.

Accidentallystoned3 karma

As someone graduating this spring with a Bachelors degree in Biology and wanting to work in the microbio field, do you have any advice for getting my foot in the door in the field?

Microbiology_ama6 karma

John/Dan: Do your best to do some undergrad research, whether that means finding an internship or otherwise.

supermikefun3 karma

Is harvard actually that much better than a state college?

Microbiology_ama6 karma

Depends on the person and the school.

ConfusedBuffalo3 karma

Hello! I am a microbiology major currently because I like the idea of immunology and more! What are some interesting new developments/research in this field related to immunology?

Microbiology_ama6 karma

Everybody: the microbiom influence on the immune system, nervous system and metabolic system. But that is just one of many.

Gwuc3 karma

Hi guys I'm a surface chemist, have you guys done much work into antibacterial surfaces? It's the field I'm hoping to do my pHD in! If you guys have had anu exposure to the field, what do you think of using surfaces to combat AMR?

Microbiology_ama4 karma

John M: It is an extremely exciting field that has only scratched the surface of its potential. it seems to have potential for AMR but we need to see results before we can say anything else.

Chief_Rocket_Man2 karma

This is to Dan specifically I guess because it's specific to listeria. So do you work with the food industry or the FDA, or has your work helped, to combat listeria. Also if not what are you specifically researching in regards to listeria?

Microbiology_ama2 karma

No, I do not. The vast majority of my research for cancer in some way.

jefferlewpew2 karma

What do you foresee as the biggest threat microbiologically (is that a word?) to a) humans and b) the ecosystem?

Microbiology_ama5 karma

One very big one would be that of antibiotic resistant bacteria, besides that its the continuing emergence of viruses, including new strains of flu.

billdietrich12 karma

Is there, or why isn't there, a high priority on developing microbes that would produce fuels (octane, hexane, butane, toluene, etc) to replace fossil gasoline, diesel, kerosene ? I've heard of some labs working on it, but it seems to me this should be a very high priority in the fight against climate change. What are the prospects for achieving such a development ?

Microbiology_ama9 karma

Everybody: That is actually very much in the works, but that is not the field of any of us, so we don't feel comfortable responding.

hannson2 karma

Could your research be reproduced in most university microbiology labs (or a semi-advanced home lab) or does it require equipment that's very expensive or otherwise hard to gain access to?

Microbiology_ama3 karma

Yes it is reproducible, but there are some pieces of equipment that are used is expensive.

MuscleCoder2 karma

Do you publish what you tried to do and didn't work? So that others can come along after you and continue?

Microbiology_ama6 karma

John/Dan: generally not but sometimes in the context of another paper it will find it's way in. Research is driven by hypothesis, and we are often wrong in the beginning but that leads to something else.

Bocote2 karma

I understand that this isn't the focus of your field, but just out of curiosity; say if we were to make Mars habitable for humans, do you think we have to first make soil on Mars to host some microbes?

I always thought it would be interesting to sends some soil microbes and see how Mars changes.

Microbiology_ama3 karma

We think microbes enhance growth on this planet, we and others do not know what will happen on mars.

Drew12312 karma

How are you planning to use listeria to treat cancer? I'm interested in the specific science because I'm somewhat familiar with the virulence factors. As far as I understand, monocytogenes is a pretty bad bug, but I imagine that leaves a lot of systems to take advantage of.

Microbiology_ama3 karma

It's well beyond the planning stage. There are two biotech companies already in phase 2 clinical trails using attenuated Listeria-based vaccines. There have been promising results. I feel compelled to disclose that I am a consultant for one of these companies.

Blueyduey2 karma

What are the current big topics of debate among microbiologists?

Microbiology_ama3 karma


Quaid330 karma

I've heard cancer is just caused by acidic and stagnant lymphatic system which can all be corrected by proper diet. Is cancer caused by viruses and bacteria or poor elimination of toxins? And if cancer is caused by poor elimination of toxins, wouldn't a vaccine just make that worse?

Microbiology_ama6 karma

Dan Portnoy: Cancer is not just one disease and generalizing like this is not possible. The lymphatic system can connect to it but can not be linked to causation, however if there is an issue with your white blood cells then it will be very connected to the lymphatic system. Vaccines work in many ways besides dealing with toxins, and toxins are just small molecules that are not necessarily in vaccines. Vaccines work against protein toxins not the same as small molecule toxins that can cause cancer.