 Okay, thank you very much for inviting me and thank you very much for the nice words I really look forward to come here and talk about the new revolution in the DNA sequence sequencing technologies and so on I've actually changed the title a little bit to more about how can we use the secret lives also in what engineering in different aspects You may probably Remember around ten years ago the human genome was sequenced and A lot of stuff has come out of that. We have learned a lot about our disease the genes we have talked about evolution and that's all things and That was really fantastic at that time. You may also remember about the the other genome the microbes because Over maybe five years ago. It was the first reports about our Micro microbe genome was was presented and we learned a lot about interaction between bacteria and and and norcell remember We have ten times more bacteria than cells in our body so to speak, so they are certainly important for whatever we're doing and And this was really a huge undertaking. It took Ten years to make the first genome It took two hundred people ten years for a cost of three billion dollars Think about that was a lot of money And how come That we now talk about revolution. That's because I can go to my lab today. I can Put in a sample. I have a human genome completely sequenced in just a few days To a cost of a few thousand dollars So that's quite amazing. I would say That's due to the sequencing revolution As you see here, that's the price for for a human genome Around hundred million in 2001 that was they learned something during the first ten years and then The the the price for sequencing has decreased according to more slow as you know It's a the computer power is doubled every second year and that means the price is dropped to the half That onto two thousand seven eight Illumina such special company they came up with some new technologies and you just see it really dropped the prices So that means now you can go and sequence anything very fast to almost no money And we believe that in just a few years you can make your own genome in a day or so and it costs maybe one one thousand dollars So that makes completely new possibilities for for anything People have now started to sequence anything you know I've had about plants animals and so on and of course we go to the engineer systems We can now do a lot on Low system to learn about the microbes We can start asking questions. We couldn't ask before what sort of microbes are present What are they doing? What sort of what controls the person in the activity and that's all things so For instance in wastewater treatment drinking water treatment and so on people are now starting or have been working on this the last few years but if you if you were a little bit into more locker by all the let's say Three or four years ago. You are hopeless out there today. I mean it has really changed a lot and we have new methods Can different things today? So what I'm going to do is to talk a little bit about How to identify those bacteria give some examples and how we can use that I would talk about How can we investigate what they do in those bacteria and I'll give you some take-home messages in the medium So we can now identify all bacteria in any sample reliably fast and cheap and I'm often asked why care Why do you care about a long list of names and it's actually quite easy to to answer this First of all, we need a link to any bacterium to its function What does it do? think If you get an infection Would you be satisfied, but just know it's a bacterium. I would love to know it's a Salmonella or Echola or whatever because if you got treated you should know what it is the same goes for any other system And our thing is when you find a certain bacterium It's nice to know where it's the same in China in Lisbon in Denmark because if you have notice about the function You can apply that anyway. So yes, we need name and link it to function So how do you do that? well, all bacteria they have a chromosome or DNA or genome as we have and typically one bacterium has For 5,000 genes and those genes determine whatever the bacteria can do as genes do in humans and just as a small question a Bacterium has 5,000 genes to know how many human how many do we have many genes Did I hear something around 20,000 so in terms of genes we are only five times more complex than a bacterium just so you know One of those genes that's a this called 16 s RNA and a strange name I'll not explain you why it has a name, but this one is the one we are using for the ID and that's because it's existing all sort of bacteria and It it's slightly different the composition of this gene. It's slightly different different bacteria due to mutations or And evolution so this gene is what we use for the identification so what we do we simply sequence those genes and The way we do it is by using what we call next generation sequencing And the workflow is here that you take a sample and you extract the DNA from the sample you get then the mixed DNA from all bacteria in the system and You amplify that means you make a lot of copies of this particular gene and that called the PCR products and Then you can sequence this and you get what we call an Amplicon library that's simply all the when when you'd sequence you get all the bases in the DNA and then you go into a Database using bioinformatics and get a long list of names So you get a list of names, but also the quantity so it's quantitative as well And that might be up to maybe 50,000 bacteria in just one sample So a list and quantitation very fast very cheap. I can do it from day to day it costs One to two hundred for one same So having this tool in hand you can go and sequence wherever to get the identity of any bacterium and We are working quite a bit in wastewater treatment, but also in many other systems and We have always been interested in knowing what sort of bacteria are actually present in wastewater plants Is it so that Do we have a lot of them or few and is it so that it's very different from one plant to another one? And we did a survey in many different Danish plants and here you can see that's a summary of the bacterial species we found and Surprisingly we found that in all those in this case 30 plants. We had more or less the same Abundant bacteria that means we had specter that were In high abundance. So in well see we just have to look at maybe 100 bacteria Just 100 maybe 150 species make up the vast majority of biomass in all Danish wastewater treatment That was surprising of course in each plant you have several thousands But they are just present in tiny amount and not really important And that means we have here system. Let's say the the the the wastewater treatment plants and That's you can already now start learning the words Michael by all I mean a micro-barone. That's the microp in a defined system. We could have it in humans You can also have wastewater treatment plants. So this is a human or the wastewater treatment plants Michael by all that can be started in a great deal because when we only have maybe 100 species and It's possible to to to study those in great detail. Remember those bacteria cannot be isolated. So we've got to do it using those methods so We want to know identity, but also link function to to those and one way we have applied quite a bit is using single cell techniques and That's for instance to make a marker markers that can label specific bacteria So you can visualize them in in the microscope. Those nice red ones are specific species And then you can combine this with other methods that can inform you about visuality how they grow What they eat and and other things so in this way you can actually get a lot of information about what they do Among those one or whatever and we have said wow in a microbarone It's very similar. We made similar experiments in China in Australia in US and in other parts of world we get more less the same maybe not 150, but maybe 200 So we can make what we call a field guide to the microbes of activites I guess you have all heard about field guides of birds in Australia and so on so why not a field guide of bacteria in accurate loss So that's a resource for anyone who wants to learn more about bacteria in accurate slots and It gives you information about the taxonomy. What's the names of those it gives you? information about the function the distribution and also the morphology. How do they look like? so you can also Go and search for specific species Exactly what what is known about those species you can go and look for protocols to make the DNA extraction to make the sequencing so you apply same method as we do to make it unified so this is actually I Think very useful. It's a has been running now for Half a year in reality and it would be extended with a lot of collaborators worldwide in the future So we get very extensive study of this Having this in hand we can start looking at other things now know something about the bacteria some of the function of at least at a certain level so we are interested in such thing as stability of the plants and Since we now can sequence fast and cheap we can make time-series that's all things so Here you see a list of bacteria in in One plant is a list of bacteria and it's maybe 1,000 species It's just the top 15 and you see the green shows the abundance over years from 2009 to 2011 and We're really dealing with big data here. Remember, maybe Still a thousand measurements in each point. So how to get an idea? Well, this is constant I'm not how it changes then use statistics and trust analysis and try to to Convert the one time point for one point in such a Plus and then those that cluster together. They are very similar So that's a way to make a fingerprint of the entire community and see where they vary or are similar or not so we have Investigate a lot of treating plans over many years more than 500 samples and I'll show you one example here of Some of those plants So here see how each Plant has a specific micro population and you see that they cluster together over time So it's not so that one plant change population a lot and it becomes like another one It's really pretty stable over the years. That was quite surprising for us So we have now a common core of bacteria where most in all those plants. We do also have very high stability So that means again, it's nice to to study those and and Run them. So so so what can that be used for? Yeah, the slide here showing that Well, although you think they are very similar if you here are three You can also if you go and look at the specific years, you can actually see that some plants Make some changes. Some plants are The same over over the years. So that's a difference So how can you use this to also to to to to handle operational problems that could be done by By those times years, I will give you an example Here there was a treating plant. They one of the biggest in Denmark a huge plant and they experienced once in a while very bad Performance and the slots did not perform well those That's the bacteria and they grow in those small flocks and they fall apart And that was very annoying for for everyone in this plant But I didn't really know why I had a suspicion that there was an oil refinery that had some load to the system By just by chance, we had a lot of samples from this particular plant in the freezer So we took them up and then we sequenced and you can see again with this plot you can see it moves from Before it went back bad to a new situation when it was bad and then recently it has been Has changed again and actually went good and That's fit very well with the oil industry So and the load and we could also go and see for specific bacteria that made it very likely that this industry actually caused the Bad performance so one example that by sequencing the entire community in times years You can go and help for troubleshooting and come up with ideas about it can be handled So those sequencing technology those Cheap time series and so on can really be used for Plant now I say which one didn't plant but it could be any system in the water in this case we can say What about plant is it probably instability? We can say something about whether When we can expect stable information. We can go for indicator species early warning systems We can go for bio augmentation. That means adding bacteria with specific functions into the system. We can follow whether survive or not We can look for specific patterns and how they behave and bacteria that degrade Microlubus so a lot of things also Using the experiment for similar plans because using this statistic You can see which plant is similar to yours and that means you can learn from this particular one And you should really think or we should think Google we should think all this information We get of this should go into some sort of public resource So anyone can can use it and apply it in China in Australia when they have similar problems Of course, it's not that easy. There are still some problems with the data generation handling and expectation That's something we are working hard on and and it will definitely be sold in the in the near future All this Was based on wastewater treatment plant, but it could be any system. It could be soil bioremodation It could be resource recovery as we live a starter will talk about In a few minutes So those methods can be used anywhere and for instance in in the water distribution system It's obvious to use that sort of time series and is right now We often look using the specific method that just goes for certain deans or certain bacteria. We can just take all of it bacteria viruses and innocent And that could be any place in the distribution system So What we need to do is to define those let's say similar ecosystems what we also called a microbiome They are so similar that you have more this is in bacteria in those and then ensure this expertise is available That knows something about the system something about the sequencing methods and then of course find join resources and funding And then we should also consider really to establish those biobanks with loads of samples in the freezer You can take up And then simply to do it we can do it in all the engineered system in the water system and we should do it We can do it in a few years That was a little bit about the identity a little bit of the function but we can do a lot more in relation to what do the bacteria do and Then we are coming into a bit more heavy DNA Stuff, but let's try What do they do? That's also what we could call systems community systems market quality and I will give you some examples DNA is a blueprint for whatever any bacterium can do or any organism So going into the the organism you will end and see the DNA as I briefly mentioned before We have the genes and they code for all the proteins and the proteins will learn It's the machinery of the bacterium and make sure the bacteria do whatever it should do So if we know the genome We can go and look at the genes and we can predict what can this bacterium do And sometimes there's some unknown genes. We don't know about but all we can predict pretty Precisely what a certain bacteria can do. Let me give you an example Nitro spire that's a bacterium that carry out nitrification and Nitrification is very important to convert ammonia to nitrate in all water systems drinking water systems in soil in wastewater treatment plants and so on and this is the key organism this nitro spire and many of you know it So it was sequenced by Horga-Diams group in Vienna a few years ago and by digging into the denomes Of course, it was possible to see that they can denitrify Also, the 95 as I've written there, but Several surprises were there for instance. They were sensitive to high oxygen levels It was possible to see some some genes coding for instance that are very sensitive to oxygen. That means Today people think about if the nitrification doesn't work turn on the oxygen more oxygen But that's exactly what you should not do. You should make maybe reduce it because they don't like how high oxygen And another thing that could we could see is that They can actually consume organics usually you've considered nitrifiers as some bacteria that can fix CO2 and grow in that way It's not true. They can also grow on organics. That can explain many observations where things did not fit to what we what we thought And another surprise was actually that they are not nitrifiers. They can grow on hydrogen so actually we published this paper in science just three weeks ago showing that this nitrifier Can grow on hydrogen and that means the perception we have today that Present of those bacteria is the same as nitrification takes place. It's not true anymore It can do a lot of other things So that was an example of how we can go into the genome and get a lot of a lot of Useful information about the bacteria That can also be used specific to treat problems in this case I will give you an example with foaming and bulking. I think many of you have been at a treatment plant and if you ask the operators they do not like this all this foaming. It's really annoying and It's quite common and if you dig down a little bit you see it's often due to filamentous bacteria and by Making the molecular tools figure out what they are we can see it's a species called micro tricks And it turns out to be a worldwide problem a lot of foam form micro tricks all the entire globe and It has been very hard to control it We have done a lot of studies and we have also got the genome and by making what we call a Metabolic reconstruction we can go and see exactly what they do We can get information about the the facility and what we could see is that they do only eat lipids Nothing else and that's very rare for a bacterium just to eat one single substrate So to control it we can either remove the lipids. That's usually not easy Or we can add some specific chemicals that prevent the bacteria for taking up the Lipids and it works very well when this is implemented Worldwide this method it works very well, and it is based on a genome knowledge, but also a lot of let's say in situ experiments So this is just examples On two genomes in reality we would like to have let's say in the active loss systems We would like to have all hundred and fifty all the key ones because they're important But in drinking water there would be another hundred and fifty and anywhere there would be a number We would really like to have a genome. How do we get it? well You should you would take a sample from that particular place you would put on an aga plate you would grow the bacteria and then you will extract DNA sequence and you have a genome and The problem is that many bacteria do not really like to grow on an aga plate and you may Of course you want to have the really important one in the system You want to have the strong guy who is really important in the system, but you may end up getting something else And this little nice dog really doesn't tell too much about The bad guy who is the dominant one in the system so It's hard to get So if you get some it is often the wrong one and in reality It's almost impossible. We know today. There are between 1 million or 10 million different species and We have only isolated maybe 10,000 and we have only denials of 5,000. That's a long way to go but There's a solution called meta dynamics That is not just to look at the genome of one bacterium, but to look at entire community So as you can see here There might be pieces of deans from maybe a thousand bacteria and That's that cover all this so instead of looking at one bacterium We can look at all the deans for the entire community and get very good ideas about what this community does Usually we like to get the denials of the individual bacteria and not the entire system So there are some new methods coming on where it's possible to from this genome to extract So this is the one one to extract the genome So we can again get the species specific denials and that's really what we want for many purposes It's still only for let's say specialists very few groups can do it But in the near future a lot more will be able to do this. So That means in any system we can get the denials of the key players It has not been possible. It's just a year ago. It has been possible, but we can do it now We can get it a lot of them. We can get them fast just one example we have now most of the important ones from the activation loss system and a lot more on the way in this system and in our systems When we have those in hand we can use it to what we call Community systems microbiology. That means we try to integrate the knowledge about all the different bacteria by By let's say the novel methods. That's let's say the future. That is what can we do with our system? Again, we can extract DNA Get the media genomics. We can also look at Deans or sort of deans are expressed. We can see what sort of proteins Enzymes are expressed. We can see what sort of metabolites are turning around or shuttling around in the system by Sequencing of different ways. All this can also be done in let's say day scale And you can integrate the data and get another Notice about individual bacteria into action and the entire community. This works nicely in let's say Simple system in which reactors not the very complex, but they will come in just a few years and that can be used For any ecosystem manipulation when you know about the system So that's where we are heading and that has really will have huge Of huge importance for the entire system. So I think I will Yeah, I will just summarize that of course when we get those new data from the genome from the system My world we added into this database and that was should be done to any database because What I would like to say is that now you can you have to think big You should not think about one sample anymore. You think about hundreds or thousands samples and it can be done in very short time We can identify very fast and reliable function is coming. It's coming, but it will not take that long time It's important to define those similar engineer systems which what we can find digest as soil drinking water Microbiomes so we have to learn that words the microbar room and We should really join Resources to establish those things and we should establish biobinds in each system with loads of samples we can use for all of us for experience and Just do it as I mentioned before and if you think this is it sounds exciting What I hope then there's a chance to learn more about it to hear more about it later today because we have our bioclust activities that is activities between Iran and The is me that's a the international society for my copicology who are making all those fancy methods So we have a method there and we have we will give some awards So that would be a very interesting session and we have also some other workshop this afternoon on same topics to join us if you'd like to hear more I like to thank the people in my lab that made most of the results you have seen today and I think I will start Thank you