Hey there, it's Liza here and I'm super glad to welcome you to a new ITTT live stream. I'm extremely excited to be a host of this session again. And if you guys tune in, please let me know if you hear and see me clearly, okay? So I'm going to wait for a couple of minutes for a moment for some people to join in. And we will get into the topic really, really soon. So let me just quickly introduce the point we are going to discuss today. So basically a new school year is coming and it is probably the best time to discuss what things have to have to be prepared in advance. So I hope that today's session will be helpful. To some extent, I know that these live streams are watched by great professionals and I am 100% sure that you guys know how to do everything and you are prepared. So, but anyway, so let me know if you guys hear and see me clearly. So we have this chat box, we have this comment section, just type in a couple of words like if you see and hear me, okay? Because I want to know that my equipment works and we won't have any issues with the technology, okay? And yeah, so also I would love to know where you guys are from because it is always interesting to learn about people from various destinations and to understand that this community is global. So I am based in Russia, in central Russia, pretty far from Moscow or cities which are big enough. So we don't have many English speakers in here. So yeah, that's pretty much. And yeah, where are you from? So let me know. Okay. Nice to see you for us. Thanks for coming. Thanks for joining the session so for us is from Egypt. I'm really glad that people from different parts of the world have time to come to my sessions. Thanks a lot.  Let me know where you guys are from. And also, yeah, what's the weather like today there in your destinations? In my place it's actually really nice in terms of the temperature. However, because of these different weather conditions, I mean, these weather conditions are not regular for this part of the world probably so they are pretty extreme to some extent. So we have a really severe smoke in here because we have a lot of forest fires, you know, so it's harsh, but yeah, it's just this nature. All right. Yeah, if you meet and hot in Egypt, yeah, for sure. And from what parts of Egypt are you? Are you from, you know, closer to your capital city or in the south? Okay. All right, I'm glad to see Puvane again. Puvane is from Malaysia. It's such a beautiful country. I have visited Malaysia a couple of years ago, and I loved it so much. I wish I could go there another time and I'm actually really impressed with the Southeast Asia. This destination is just really nice. All right, so I believe we can actually start. There are not many people today, but it's okay. So I hope guys that those who have already joined will benefit from today's session because we're actually going to discuss a really important point. So let's get prepared for this coming school year as online teachers together. And let me change the screen view. So I hope that my presentation is clear and is seen well on your way on your side. And just just a quick mention. These live streams are provided by ITTT. We are a leading internet taffle and TESOL provider. We are presented on various social networks. Right now this live stream is broadcasted on YouTube and Facebook. Yeah, if you are interested in some other social networks, feel free to join in because we try to be as consistent as it is possible in terms of sharing high quality content with you. And we try to be as useful and helpful as it is possible. And by the way, if you guys are interested in taking a taffle course with us, you can see this QR code in the right corner of your screen. So it gives you 30% discount of any ITTT taffle courses just today. So we share this promo code on the live streams only. So if you are thinking about taking a taffle course and becoming certified, just make sure you take this opportunity. And yeah, let's dive into today's topic. Well, actually, here is the first point I've introduced in here on this slide. However, before digging deeper into these details, I want to mention that every summer is just the perfect time to get prepared professionally. So it is always better to work on your self-development and on your professional development as a teacher during the summer period because this time we don't have much classes, we have less work hours, you know. So just before going into some technology details and technical points, I want to mention that teachers have to improve constantly. And if you are not a professional teacher, if you don't have a degree, like I mean an educational degree, it is totally fine. You can get certified, you can find some other ways how to improve your teaching skills. And it is vital to do in advance before you start working with students constantly without any breaks, you know. So make sure that you take this opportunity of getting taffle certified because it's a great start for new teachers or for those people who, you know, transition between different professions. So this is probably a zero point to mention because many people start teaching without any qualifications and from my point of view it is not good because we have to provide the best quality services. If it is not like this, people, I mean our clients, our potential clients, they don't realize what to expect. So I hope that you are conscious people and you know that professional education and professional development is vital, is crucial. All right. And here on this slide, I've mentioned the first point to check before you start actual teaching, teaching multiple classes every day is your equipment. So before you start your school year, make sure that your equipment works well. It's pretty obvious, but I know that many people neglect doing this thing. And then when it comes to work, when it comes to actual teaching hours, some problems start. For example, sometimes people get disconnected because of some Wi-Fi issues or even problems with the internet provider. So it is always better to be on a safe side and to get prepared with your equipment beforehand. So if you also have some problems with your laptop or personal computer, make sure you check it out before starting your school year. And yeah, you should be fine. Some other points to mention is that webcams, mics and lighting, they are not that they are actually important. But if you have a laptop with a decent camera, it's a place to start. You don't have to buy some expensive equipment. It's not necessary from my point of view because our modern laptops are equipped with all of these systems. And it's actually fine for these regular classes. However, if you notice that something is wrong, it is always better to replace it. For example, I know that on some laptops, mics might be not that sensitive and they may actually catch all the sounds behind you in your room or from somewhere else. However, they are not that sensitive to transfer your speech and it is always better to make sure that this is not a problem in your case. And that's for professional lighting. Yeah, you can actually buy a special lamp, but it's also not obligatory because you can sit in front of the window or you can switch on just this artificial lighting and it should be alright. Just make sure you don't sit like me right now. It is just in my room it is just not convenient to move the desk. So that is why I do like this. But I believe that for high quality online lessons, it is vital to lighten your face and to make sure that the picture is clear. And let's move on to the next point to look at before starting your school year. It is a platform to teach on. So there are many various platforms. So if you don't work for a teaching company, if you're a freelancing teacher, it is always better to see some options because every year new platforms appear, new platforms for online teaching, I mean. And yeah, it is necessary to be updated from this point of view. So here I've listed just a couple of options but there are actually even more ways to deliver online classes. So usually I work with Miro and Zoom. I've never worked with that Jamboard and Google Classroom, but I know some teachers really like Google Classroom, for example, because it allows to add many people in one room and then assign homeworks and stuff like that. So it's pretty convenient, especially for schools, but I've never tried that and I can't suggest anything here. So you have to test it. I just prefer Miro and Zoom. And actually the latest version of Zoom has some new features in plug and it is actually connected with Miro. I haven't tested it yet, but I have like two weeks without any classes because all my students decided to have some rest before the school year. So I'm going to investigate everything and check out how it works. And the last platform I would love to mention is ProgressMe. I have tested that platform. The only disadvantage of this platform is that it is not free, so you have to pay for it. But the fee is really small, so you pay for each student who you add into the platform. It's around $2 or something for students, which is pretty affordable for a month. So if you work with students consistently, if you have regular students, this platform might be an option because it is really, really interactive. I should say it is much more interactive than Miro. And this platform has a lot of pre-saved and pre-made materials for English teachers. If you, for example, consider creating your course, it is also possible, or such options as marathons or short-term courses, they might be done on this platform. And I have this promo code if you want. And this platform offers seven days for free, like just to spend some time looking at the service and checking if it works for you. So, yeah, ProgressMe is really convenient, but you have to test it. If you need a link to this platform, I am going to send this presentation to the Facebook group after this session. So, let me know. Or I can actually send it via the chat box as well. And let's move on to the next point. So, I believe it is also vital to organize one lesson which is devoted to the use of technology only. So, what do I mean exactly? When you start working with a new student, especially with children, but sometimes usually with adults as well, because we all are different and not many people are actually digital with kids, you know. So, you have to prepare one lesson. It might be a short lesson, like a 10-minute lesson or a half-an-hour lesson, where you explain how your platform works or how your lessons are organized. For example, you meet on Zoom and then you explain to your students how Zoom is organized, how to open a chat box, how to share their screen, how to send files via Zoom and stuff like that. If you use some other platforms, for example, if you combine Zoom and Miro, you also have to show how to push the buttons on Miro as well. Like last year when I started teaching online in January, so in the beginning of 2020, when the whole pandemic was just about to start, I was new to online teaching and I neglected this step. And the first couple of lessons with all students were such a disaster. Then I realized that that was my mistake because I just didn't explain how to work with the services, how to work with the platforms.  And it is also a great opportunity to bond with your students a little bit and to have this clear way of teaching, you know, when you use English but you explain some other subjects. So I believe it's a great opportunity for both students and teachers. Don't underestimate this stage and make sure you explain at least some basics because sometimes when I work with younger students, they don't know where to find an apostrophe, for example. And I have to explain what key is to push. So it is funny. However, you want to save up some time on these issues. So just get prepared. Another way to organize this stage would be to film a video, to film a short video related to the use of technology. So you can also show everything in your demo video, not necessarily a demo class. And yeah, you just vocalize everything and you explain where to push, where to sign in and so on. So you can film a video, record a video and then send to your students. It's an option. But yeah, again, it's up to you. But I believe that it's a great way to provide some high quality services at the very beginning. The next point is your space and resources. So it's pretty clear that it is always better to work from an, not an empty room but from a quiet space. So make sure you don't have kids running around you if you work from home and if you have children or, I don't know, some noises, like from time to time, I get disturbed by my neighbors above. So they have small kids, they have two small kids, and they eventually start running all around the apartment and they don't have carpets. So I have those severe noises and I'm never sure if my students can hear them or not. So I usually ask, like, is it okay? Doesn't it disturb you or something like that? And they just confirm that it's okay because, yeah, probably my mic is really good because it doesn't catch those sounds. So yeah, as you can see, quiet spaces are better than places where you are not alone and where you can be disturbed. What else? Yeah, you also should prepare some visual aids. It is especially important for teachers working with younger students. But on some teaching platforms, it's obligatory to prepare some visual aids which teacher can use during the lesson to grab some attention on the first place. But at the same time, I know that for some teenagers or even adult students, it's important to keep focused and maybe visual aids, some visual clues might be useful as well. You can decorate your background, for example, and to start with explaining the weather, discussing the weather or the time and so on. And you don't have to use interactive materials on your Miro board, for example, or another teaching platform. You can just get some eye contact using your background or some other visual clues. So just make sure that they are close to you, that they are not somewhere in a different room. It is always better to keep them in one place, like close to your desk or maybe in a drawer at your desk. So something like that. And the last point here is files. So we have a lot of digital files to share with our students during the lessons. To begin with, we have to, yeah, if you use Zoom or Skype only, you usually share your screen and show some, I don't know, coursebooks, some PDF files or presentations. Some teachers just don't prepare in advance, but you want to make sure that everything opened before your lesson and you don't have to search on your desktop for this particular file. The same thing about audio files. Yeah, frankly speaking, I am not perfect as well. Sometimes I just forget to open audio files and then it takes like a couple of moments to find that file. And we have this, you know, moment when both of us are quiet and it's not pleasant at all. I believe that students can get daunting, yeah, can get bored and frustrated, especially younger children who can't focus for longer than like five minutes or so. So make sure everything is opened and your files are in order. Okay. And when you've prepared all of those steps, which I have mentioned previously, it is the time to think about your course design. So, basically, if you're a professional teacher, if you're qualified and certified, you know how to design a course and, yeah, you just follow those steps. However, just a couple of things to mention. Before you start designing a particular course, for example, in such cases when you work with individual students one on one. You have to consider some learning objectives. Well, basically the same point applied to groups. However, learning objectives may vary. So you have to think about different people and you have to consider if they have like similar needs or different needs and so on. So learning objectives before whatever planning you do. And you have to bear them in mind during the whole course, because when you step somewhere else, when you neglect those specific learning objectives, both you and your students may lose this focus and then lessons get really frustrating for the both sides. So make sure you think about the learning objectives before creating any materials, any curriculum, and so on. Then when you're done with the goals, with the objectives, you have to consider what materials might be suitable for this or that student or for this or that group. So course materials, they are depending on the objectives for sure. And so how to pick the right course book is actually pretty easy. You have to just read different course books, descriptions, and you would probably also check out the teacher's books to understand if the book is right in terms of the age, the needs, and the main objective. For example, I usually work with teenagers and adults, so I versatile between course books for younger adults and for adults, and they all have the same content, but it is designed slightly differently, slightly different from the age perspective. So, for example, such course books as perspectives from National Geographic or what else, Keynote, they have the same style, however, they target different age groups. And although the materials are really interesting and engaging for both teenagers and adults, it is still not very nice to take those two books for adults because of the content itself. It is just for some younger audience. So make sure you consider all of these points when you choose your perfect course book. And when you are done with the first two steps, you move on to the actual lesson planning. So probably you don't have to write multiple lesson plans for the whole year. It is probably easier to create a separate lesson plan for each coming lesson, but it's up to you. I know that some teachers just feel safer when they have everything in order and everything prepared in advance, even lesson plans, so it's actually up to you.  You implement this specific strategy, which is called dogme, when you don't plan anything and you just go with the flow. For some people, it is normal, but not on a regular basis. So it is always better to prepare. And this point might be even more crucial for the, even more crucial in all of the mentioned before. So what do I mean? So when we start teaching, sometimes we explain everything and then students still have this huge eyes and they don't understand.  And they usually say yes. This is our failure in terms of giving the right instructions. So when you instruct students, you want to make sure they get you clearly. However, asking them, like, do you understand is not useful at all. So what you have to do on this stage even before this happens is think about ICQ and CCQ. So ICQ instruction checking questions and CCQ concept checking questions. So instruction checking questions are important for that part of your lesson when you give actual instructions and when your students are just about to start some activity. So at this stage, you ask them a couple of questions to check out if they got your instructions correctly. And as for the concept checking questions, they might be applied when you explain some specific concepts like some vocabulary or grammar, for example, or something linguistic. So probably it's a great idea to think about some specific ICQs and CCQs before you start teaching. Just when you create your lesson plan, it's a great idea to write down a couple of questions like that close to the task or, I don't know, maybe in the lesson plan itself, so on some stage. The next point is evaluation. So when you work as a freelance teacher, you are not the same teacher as that one working in a real classroom at school. So you probably don't have this need to grade your students, to give them specific scores or marks.  So probably it's a great idea to think of your special grading system. It may be really helpful when you work with younger children because they still need this, you know, marks or stars at least. They don't have to be, you know, A's or B's or C's. Grades might be just some stars or stickers you give to celebrate students' achievements together and to praise your student. Because this is the only way to cheer your students up sometime when you work online because they don't have the same experiences in the real classroom when you can give them a gift or something like that. So maybe it's a great idea to create some specific system and to keep it somewhere on your, you know, platform, on your teaching platform. For example, I do this with my younger students. I create this chart. And if I work with groups, I write down the names and then I keep the score of the stars they get. So basically the same as teachers do in real classrooms to see the progress, to see their achievements and to celebrate together. And the last idea which is crucial as well is the feedback. So I know that especially some, yeah, just let me collect my thoughts quickly. So many teachers believe that feedback is only about correcting errors. That's not true. Feedback should be reasonable and ecological in the way it is given. So when you think about giving some feedback to your students, think about some different strategies, some psychological strategies to make it in a nice and friendly manner in a nice and friendly way. Because if you only correct their mistakes, if you only, you know, mark everything red, it is not pleasant and they might feel bad about themselves because they would see it that they've done everything wrong only and that's all. So think about the way to give them some nice feedback first and then probably draw their attention to mistakes. Actually, last time, so a couple of weeks ago, I asked my student to give me her feedback on my work. And that was the point she mentioned. She said that she liked that I never said that you are wrong here and you did it incorrect here. She mentioned that she appreciated that my feedback was always cheerful and motivating. So because I didn't focus on the mistakes only, I actually never focused on mistakes. I focused more on something that has been done really well. And only after that I pointed some gaps, some issues that might be corrected. But after that, after that positive feedback, students usually corrected themselves and they explained everything like what mistakes they did and how to solve all of those problems. So this is also a teaching strategy. Feedback may be not just your feedback, but also a tool to make your students think and to make your student self-correct. And I believe this is the last slide for today. So classroom management, when we work online, it is not easy to manage classrooms sometimes, especially if you work with bigger groups. So basically before starting any teaching, for example, if you work with parents, it is nice to suggest them that they have to be in a quiet room as well, that they have to sit down, not lie down. They have to have a laptop instead of a cell phone. You know, everything happens in this world and I actually had such cases. A couple of days ago I agreed to teach one girl and her mom asked, is it okay to study from a cell phone? And I was like, no, it's not okay because it's absolutely inconvenient for the student. The screen is small and if I share any materials, she just doesn't see it. So classroom management begins before the actual teaching. So make sure you discuss all these points before the lessons with your clients. However, when you work in an online way, so when you teach, you have to also consider some problems that may happen. They usually depend on some concept checking questions or instructions you give. However, at the same time, there is this specific pace you have to control. Some students may work faster than the other students. So you want to make sure that they are busy all the time and they don't have this breaks, these periods when they can look somewhere else, when they get disturbed with their cell phones or something like that. So consider some problems before your course, discuss everything with your clients, explain some rules which you have in terms of managing your classroom, and then you should be good. So we do have classroom management during online classes, but it's not the same as in the real classroom, right? So you have to consider some strategies, but they are always subjective. Sometimes there are some issues we may anticipate. However, it is always something else happening, so you have to be really flexible. But at the same time, you know, at ITTT we have this new course related to online teaching, and we have this part related to classroom management online. So if you feel like it is something you would improve in your teaching, yeah, you can check out that course. So basically that is it for today, and let's now have a quick Q&A session. Here you can see this QR code, but I'm also going to send a link to the chat box. So if you feel like it's time to get TAPL certified, feel free to use the link from the chat box, or feel free to scan this QR code. Now I'm going to check out the questions from the chat box, and if you have any questions or any concerns related to today's topic, which is getting prepared for a coming school year as an online teacher, let me know. So let's do a quick Q&A session. And by the way, guys, thanks a lot for joining in. I am really, really grateful for having you all here. I see there are 12 people, so some people come and go, but it's okay. I hope that the things that I discussed today were useful for you. Yeah, so let me check out the questions. That's a great question, Puvana, thanks a lot. I am not confident in suggesting some specific area because it is really subjective. You know, it depends on many factors, and probably one which is above all of them these days is the pandemic situation. So you have to check out different countries, different governmental sites, like where you check out the visa requirements and so on, if the countries are opened or not, because I know that countries like, let me see, like China for sure, what else, Thailand. So some countries in the Southeast Asia are still closed. They don't open borders for tourists, for expats, so it is subjective to this situation. But at the same time, if you look for some quick experience, if you look for some easy ways how to get your first teaching experience, I would definitely suggest you going online. Start teaching online as soon as it is possible, because it is the easiest way today, and the demand is huge. You can work for an online teaching company. They don't have strict requirements. Some companies do. Some companies want to hire native speakers only, but those companies that understand that ESL teaching is not just about proficiency in teaching, in proficiency in English, they actually hire non-native speakers really well. So, or otherwise, you can work as a freelancer. My general suggestion is to create social media, to choose a perfect social media in your country or, I don't know, in some nearest countries, and start promoting your services. So, just show everyone that you are confident, that you know how to teach, that you are creative, and I believe that you will be really fine and you won't wait for students too long. And let's move on. So, basically, I have already mentioned all of the tools and all of the equipment you need for teaching online at the beginning of today's presentation. If you were absent at that time, I would suggest you watching the recording of this live stream, because I have already mentioned everything. So, I do mind explaining everything again, because it took me like an hour. Yeah, I am going to share this presentation. It actually has some links and, you know, it contains the names necessary for this use. Let me just quickly copy the link, and I'm going to share it. So, yeah, check out the presentation from the chat box, see if you can open it. I think it should work. So, this is the same presentation I've used during the session. Yeah, just let me know if you see it. Okay. Do you guys have any further questions related to today's topic, or to Tefl in general? Let me know. By the way, if you are interested in online teaching, make sure you check out my previous live streams, because I talked a lot about online teaching. I overview different teaching platforms, teaching companies. I also did some overview of the best coursebooks of materials. I also showed how to create materials with your online tools. So, make sure you check out the previous live streams. Let me send you a link. So, I'm going to send a link to the YouTube channel, because I think YouTube has the most convenient way to store live streams compared to Facebook. But we do have the same folder on Facebook, so just feel free to check out. Okay, let's see. Just one second. I haven't prepared my files before this live stream, but I didn't expect any questions related to the previous... Well, actually, I usually refer to my previous live streams, so I had to prepare in advance, but I'm sorry. I'm not perfect too, so where it is. By the way, our YouTube channel contains a lot of useful presentations and videos related to all possible topics in online teaching and what else. So, there are a lot of things which might be useful. I have found this folder, but I'm not sure how to copy the link. So, let me see. Okay, I think like this. No, I'm not sure how to do that. Okay, I'm going to send the link to one of the videos, one of the first videos. Yeah, so I think if you follow this link from the chat box, you will see the whole folder full of previous live streams. And yeah, it is here. So, you can check it out. And by the way, did you manage to open the link to the Canva presentation? Can you see everything? Let me know. Yeah, I think that today's topic was really interesting to discuss and I hope that you found something useful for yourself in today's live stream. I hope to see you guys next week. I am not completely sure about the topic for the next week, but if you have any suggestions, feel free to comment right down below. Yeah, I think that is all for today. And yeah, let's wrap up and I hope to see you next week. Oh, and by the way, I have a Facebook group for English teachers. If you want to join this community, this small community, feel free to follow this link from the chat box as well. So, the community isn't that big yet. And for some reason people are not active there. They probably expect me to, you know, share content, which is my plan for future. But if you have any questions related to teaching to the use of materials or something like that, you can actually write your question on the group. And I hope that somebody out of the community will reach you out. Yeah, so it's a great way to network as well. Yeah, just feel free to join in the group. And thanks for coming today. As I mentioned, see you next week. And yeah, that's all. Bye bye guys.


Thanks Michelle and I should be able to rise to your challenge. I'm from New Zealand originally and we're allegedly among the world's fastest native English speakers, so I guess we'll be putting that to the test. Anyway, so what I'm going to talk about is how we can move from these association patterns, many of which are intriguing, but only suggestive to ideas more about causation and mechanism. And as we've seen over and over again today, there's a tremendous amount of diversity in the microbiome between different subjects. So in this 2005 paper from Dave Rowman's lab, you see a lot of bands that are unique to the groups of samples from individual subjects, A, B, and C. We confirmed this with Jeff Gordon's group and in a study of Lena de Bees twins where we see these very large filing level differences between different individuals. And META had seen the same thing in other populations. Even the species they define as core vary in abundance by orders of magnitude between different people. So anything that makes up 10% of the microbiome in one person is as rare as one cell in 10,000 in other people. And of course the HMP has extended this to other body sites. So Keata showed you some of this data before, colored by bacterial genus, where essentially even in one body site, any genus that you find a lot of in some people is very rare in others. So this leads us to some of the key questions in the field. We need to be able to figure out what aspects of this diversity actually matter. This other diversity, are we seeing these differences because they do matter or because they don't matter? How can you tell cause from effect? So which of the differences you see between individuals are causes of as opposed to consequences of the phenotypes that they differ in? And then finally, a lot of people want to know how they can leverage large existing investments in data sets such as the HMP data set that have cost millions of dollars and could really complement their studies. So let's go through these one by one. So let's start with this first question. How can I tell what aspects of diversity matter? So as we've been hearing throughout the conference, there's a lot of reasons why you should care about your microbes. And I've just picked out a few of my favorite stories here. Apparently they determine whether Tylenol is toxic to your liver. Pete Tenbaugh is going to talk more about drug interactions and then Luca Essel, one of my students who's also been working with Pete, has a poster on that as well if you want to hear more about drug effects. And Drosophila, at least, they determine mate preferences. This hasn't yet been established in humans, but maybe it's just a matter of time. There's all this exciting gut brain access stuff going on. And it turns out that your anecdotal experiences of camping are true. Different people really are tenfold differentially attractive to mosquitoes. And what they're zooming in on is basically VOCs produced by your skin microbes. But to get to these stories, what you have to start with is a whole lot of sequence data and phylogenetic trees. So what I'm showing you here is just the first nine out of 130,000 sequences from a study we did recently with No Affairs Group. Here's the piece of the phylogenetic tree file. And here's the visualization of the tree. And you can just tell immediately that you've really got your work cut out for you, right? It doesn't help you that much if I tell you the study design. We were looking at biogeography, but not on the grand scale of Darwin and Wallace and the other 19th century explorers who mapped macro organisms across the Earth. But being microbiologists, we did it on a smaller scale. So we looked at computer keyboards. And initially, the idea was, you know, does the space bar have more kinds of microbes simply because it's larger than the other keys? Are the keys a desert where a few microbes survive compared to the lush valleys of your fingerprints? And so on. So anyway, another view of the same data makes the main things going on immediately clear. So now each point represents an entire microbial community, either from a key or from a fingertip. And if I color them by person, you see the first, the second, and the third person, all their keys and all their fingertips clustered together. Whereas if I color the points by what's a key in blue versus a fingertip in red, you see no separation. So you can tell immediately that each of us has a unique skin community. We transfer from our fingertips to our keyboards as we type. It's part of the same study we showed we could match the palm of the hand up to the computer mouse someone uses with up to 95% accuracy. So this came out in PNAS a couple of years ago, but more importantly, it was on CSI Miami. So you really know it's true. So how do we do this? Well, so Greg Caporesso and a number of others who were in my lab at the moment, Greg's here at the meeting in the second row, developed this pipeline called CHIME, which stands for Quantitative Insights into Microbial Ecology, which like the tools Curtis showed you make it much, much easier to integrate analysis from hundreds of samples together. And what I'm going to show you in this talk is essentially all 16S data, although the same tools work for metagenomic data and other multiomic data as well. And basically it provides a complete pipeline from sample. So once you have sequence of samples, basically it takes the data right off the instrument, performs a whole bunch of statistical analyses, and then winds up with pictures and statistics that you can tell these stories about. So this lets us start getting at the effect size of different phenomena. So for example, when we reanalyze Dave's 2005 data, what we're looking at here is six sites along the distal gut from three different subjects plus a matched tool sample. When I color those by subject, you see all the samples from the same subject clustered together nicely.  But the distance between the stool and the other samples from the same subject is less than the distance between subjects. So we can tell this technical variability is less important than the biological variability that we're hoping to uncover. And this will be a recurring theme throughout the talk. So Liz Costello, who was in my lab at the time, now working with Dave. And as you've seen a couple of times already, put together this first overall map. And the reason I'm showing this again, because you've seen it several times today, is just to point out that we can use this kind of display to figure out which variables are important and which aren't important in the same data set. So what you can see immediately here is a lot of clustering by body sites, so the mouth and the gut are very distinct from the skin, for example. When we take the samples and color them by person, sorry, color them by sex or by person or by day, you see much less separation by those variables. Although antibiotics have a large enough effect to be visible even on the scale of different human body sites. And so we can use this kind of thing to start putting an explicit scale using the distances between microbial community samples. So here a bigger bar means greater distance. So two samples from the same body habitat are less different than two from the same habitat. Within a habitat, two from the same person are less different than two from different people. And then within a person in the habitat, two samples a day apart, are less different than two, three months apart. Then the mouth was the most stable habitat we looked at, the skin the least stable and the gut in between. But this is kind of frustrating with a handful of time points, right? Because what you'd really like to do, as you'd really like to go to some of the same, what you'd really like to do is you'd like to figure out dynamics. As again, we've had several times already during the meeting. And so this is a viewer we use for this. So the guts down there, the mouths over there and so forth. If I rotate this around to give you an explicit access for time, you can kind of see the three months separation. You can't see the one day intervals. And it looks like there might be some changes, but it's kind of hard to figure out what they are. So what you'd really like to do is go back to some of the same people, as Dave mentioned earlier, sample them every single day for like a year and a half. And so with a switch from 454 to Illumina, we could afford to do that. And it looks like that. And the correlation between the 454 and the Illumina data is really nice, right? So the difference between platforms is a lot less than the difference between body sites. And so when you have data this dense, Greg and Antonio figured out how to process it and animate it. So what we're doing now is we're using the Castello et al. data frame, all these little points. And then we're looking at an animation, each frame is one day over six months of two people's skin, mouth, and gut communities. And so you can just immediately see how variable the skin is, how static the mouth is, and how the guts intermediate. So this is all kind of fun, but you might wonder, can you do the same thing for something that's actually clinically relevant? And so with Alex Kuritz and Mike Sadeski, we just recently did the same sort of thing for Clostridium difficile infection. And so what we're looking at here is a bunch of samples from C. diff patients, a bunch of samples from healthy subjects. And what we're about to look at is the results of fecal microbiota transplant. And so what you can see is almost immediately the subjects receiving FMT wind up much more towards a healthy distribution. And then they bounce around within that healthy distribution, but they maintain that healthy state for the four weeks that they were followed in this animation. And so this prospect for being able to track in a very detailed way changes in the microbiota associated with health and disease now exists with access to higher throughput sequencing and more samples. And you can imagine building an index that would be useful for clinicians to track this kind of property and to ask how stably do you stay in the healthy state after FMT? So this might lead you to wonder where our microbes come from in the first place. And if you have dogs or kids as I do, you probably have some dark suspicions about that, all of which it turns out are completely true by the way. So we can match up people to their pets pretty accurately according to the microbes they share as well. And with Maria Gloria Dominguez, who's going to be speaking as a keynote tomorrow, so I won't say too much about this, we were able to show that baby's vest microbes depend very heavily on delivery mode. So basically if you deliver the regular way all of your microbes resemble the vaginal microbiota. If you're delivered by C section, all of your microbes look like skin. And so fascinatingly, despite the very high degree of differentiation in adult body sites that you've heard about several times during this meeting, so here's some others mouth, then the mother's vaginal samples in red over here and skin samples in dark blue, the baby no body habitats at least initially are not differentiated. And so you can see that all of the body habitats from all the vaginal babies cluster with the vaginal samples, then all the body habitats from all the C section babies cluster with the skin samples from all the mothers.  And as I think Ruth mentioned, we can also start to understand how the microbiome develops in infants. So we see what looks on this scale like a very very steady progression from the meconium towards the mother over the first two and a half years of life. That's coupled with a steady increase in diversity. Although all you can really see on this plot is change and resemblance to the mother's stool, it's hard to tell what's going on and I'll return to this later. We can also do the same sort of thing across cultures which I'm basically going to skip since Dave went through it. I do want to make the point that we converge on very different end points between between Americans versus Amerindian and Malawian populations. And in this context it's important to remember that the HMP, despite the fact that it's a very valuable project, it only covers the start of human diversity, right? It's only looking at Western adults who are healthy. There's all the rest of the space of possible microbial configurations that it does not yet cover. And so what we're starting to do at the moment is to cover the rest of the diversity by crowdfunding with projects like American Gut. And so what's exciting about this is it gives members of the general public the ability to participate directly in microbiome research. And so it's generated an enormous amount of excitement by this point. This is Daniel McDonald in my lab handing out kits at the PGP meeting earlier this year. So we've raised about half a million dollars, had about 6,000 people sign up. We've had 1,200 kits returned, including about 400 samples from participants in the personal genome project who either have or will have their complete genome sequenced. But you can imagine how spectacular this will be with tens or hundreds of thousands of samples with a really detailed sense of what kinds of microbes are out there linked to all kinds of different conditions. So this leads us to this critical question, how can I tell which of this diversity matters in a sense that's going to allow us to tell cause from effect? And so there's a sense that we should be establishing causality with COCK's postulates. Basically the idea that you find the microbe in sick individuals, you isolate it, then you reintroduce it into healthy individuals and make them sick and then you get it back out of the healthy individuals. But even COCK didn't believe his own postulates right, because even as far back as when he was doing this original work he noticed that a lot of subjects were asymptomatic carriers of what we think of as pathogens. This was reinforced by the HMP work on pathogen carriage where a lot of alleged pathogens in fact are prevalent in the healthy population. So obviously your IRB is not going to let you try to do COCK's postulates in humans but we can use mice. And one thing that's been especially effective has been the use of notobiotic isolators. So these are the ones in Jeff Gordon's lab at WashU which I'll describe some research from. We also collaborate with a number of other notobiotic facilities around the country. So basically you're growing the mice in a bubble with no microbes of their own. You can then introduce a defined microbial community from a person or specific strains. So do these differences matter? Well in mass models they matter a lot. So these are the OB-OB leptomutant mice that have a defect in an appetite hormone so they're much heavier than a regular mouse. They also have a profound shift in the ratio of two of the major groups in the gut, the femicutes to the bacteridetes. Now just from this data alone you can't tell whether that shift in the community is a cause or an effect of the obesity. But an additional work in Jeff's lab what they did is they took fecal pellets from the leptomutant and transplanted it to a genetically normal mouse with no microbes of its own and found that that genetically normal mouse gained weight substantially faster than an equivalent mouse that was inoculated with fecal pellets from the normal mouse showing that you could transmit the adiposity phenotype by transmitting the microbes. And more recently with Andrew Gewitz's group we looked at a different mouse model the TLR5 knockouts that are unable to that are unable to make tolite receptor 5 which normally recognizes bacterial flagellin. And so again you see an obesity phenotype, you see larger fat pads in males and females, high triglycerides, high cholesterol, high blood pressure and again you see this profound alteration in the microbiome between the between the knockouts and the wild types. And again you can transmit it to a genetically normal mouse by transmitting the microbiota. What's fascinating here though is that instead of an energy balance phenotype which is what it appears to be in the OBOB mutants and the TLR5 knockouts if you do obon calorimetry on the fecal pallets what you find is the same amount of energy left behind. And fascinatingly what's going on instead is that it seems to be a behavioral phenotype. So the TLR5 knockouts eat more than a regular mouse does. Additionally gem-free mice that receive the TLR5 knockout community also eat more than a regular mouse. So Andrew found that you could cure them with antibiotics or you could cure them by putting in their cage the amount of food a normal mouse would eat. And so just as a reminder we've got about 10 times as many microbial cells as we have our own cells associated with our bodies. Andrew had this cartoon commission to reinforce the point that perhaps they are voting you when it comes time to make choices in the cafeteria line. You might be wondering if these results extend to humans. So some work that Ruth and Pete did when they were in Jeff's lab suggests that perhaps they do. So subjects on a fat restricted or carbohydrate restricted diet for a year started to resemble lean subjects more microbially. And fascinatingly Dan Knights who's now working with Robin Xavier showed when he was in my lab that you could actually classify people as lean or obese with 90% accuracy using their microbiome. So this might not seem like a very impressive test given how accurately you can do it with a mirror and a set of bottom scales right. But it does establish the plausibility that microbes are involved in the mechanism. And what's interesting in this context is that if you take all the genes ever identified by GWAS and build a predictive model for obesity the area under the curve is only about 58%.  So can we actually do something with us and change the microbiome in a way that lets us cure disease. Well where we're taking the work on the the microbiome associated with disease is to develop in countries. So this is this is a photo that Tanya Yatsunenko one of Jeff Gordon's grad students took at one of the field sites that we work with in Malawi. And so this is malnutrition clinic. You'll notice that although food is scarce in this population they are able to have access to cell phones for example. And the remarkable fact about this is there are now over 5 billion active cell phones on earth which is pretty impressive when you consider this only about 7 billion people. Of the billion poorest people in the world 20% of them have their own cell phone. I was reading a couple of weeks ago that the current penetrance of cell phones in Kenya is 95% of households have one. Right so this is a technology that just penetrated everywhere. A large part of the reason for that is Moore's law the decline in the cost of computation. So the digital signaling processing that supports that technology is so cheap that it's effectively free. And this is true not just in Malawi but everywhere basically so I took this photo in Bangladesh a little over a year ago. So even in relatively bad parts of Dhaka you can buy a sizeable hunk of a cow and then right next to that you can have your cell phone minutes recharged. So one thing that's getting a lot cheaper, faster than computation though is the cost of DNA sequencing. So I think you're all probably sick of this diagram showing the decrease in the cost of computation versus the decrease in the cost of sequencing. And this is on a log scale so in the time that computation has got about 100 fold cheaper DNA sequencing has got about a million fold cheaper. So what we're doing at the moment is studies in humanized mice. So the idea is to take fecal samples from individuals transplant them into mice. So from our Gates funded study on malnutrition our NIDDK funded study again with Jeff Gordon on obesity transplant those microbes into germ free mice and then look at how those mice gain or lose weight depending on who's microbes they got. And so this works really nicely. So this is data from Jeff's lab. Each interval is about two weeks. Five different mice. This access is principle one of the principle component one of the community. So starting off on mouse chow you switch them over to the Malawi diet which is 90 percent corn 10 percent leaves. You see this rapid decline consistent across mice along PC1 that you can just model with a single exponential decay curve. You switch them to ready to use therapeutic food so the peanut butter supplement a base supplement that's used in the clinic. They start to recover. You switch them back to the Malawi diet and very reproducibly they go back to the same state. And so the first data from this we published in science earlier this year so Michelle Smith and Jeff's lab was the first author on that. And basically what you can see so we're looking at we're looking at members of a twin pair who are either healthy the red line or have quashia core severe amount severe nutritional deficiency which is this blue line the mice that receive the quash community do really badly they lose more than 30 percent of their body mass they recover with our UTF this is coupled with a very distinct change in the microbiota and also in the functional response although I won't get into that so basically what we can start to do is we can take we can take microbial communities from individuals put them into mice and then how those mice respond to treatment depends on whose microbial community they got. Now taking us a step further what we can do now is we can use these things called personalized culture collections where instead of transplanting the primary fecal specimen what you can do instead and this was really pioneered by Andy Goodman who's here at the meeting and Jay Faith when they were in Jeff's lab is this idea that instead of taking the primary fecal specimen what you can do instead is that you can dilute you can dilute the cells down into a 384 well plate coax them through a few cell divisions and then you can sequence their genomes but unlike single cell sequencing you don't destroy the whole organism when you sequence it you only take part of the culture so you have the rest left over so you could potentially mix them together and test ecological hypotheses about which species are important and to put this in perspective for example wolves greatly affect the Yellowstone ecological system but we didn't find this out by going out to Yellowstone taking a cubic mile of stuff grinding it up and looking for the wolf DNA right the reason we know that is that people shot all the wolves the ecosystem changed profoundly then they were reintroduced and the ecosystem came back and so the ability to instead of trying to get rid of a species by antibiotics to leave it out of the community in the first place see if there's a functional difference and then reintroduce it and see if the function changes is really exciting prospective longitudinal studies can also be critical for testing causality so basically the idea is that you want to enroll subjects prior to disease and figure out if you can predict who's going to get the disease and who isn't from the microbes of their earlier time points and so there's some examples like risk, Teddy, BMMI and so forth that are doing this now as Robbie Klein pointed out to me earlier for this instead of cox postulates you want to use Hills criteria so looking for the strength and consistency of association whether the association is plausible based on what you know about mechanism and so forth rather than necessarily being able to prove transmission so just in the last couple of minutes I'm going to say a little bit about leveraging existing investments and large data sets and there's a lot of technical factors that could affect readouts of the microbiome including things like storage conditions DNA extraction conditions PCR primers what sequencing platform you used analysis software and all the rest and we know for sure that all of these factors are going to affect the results so the question is will they affect it so much that you can't see the biological pattern you're looking for and so one thing that's really exciting in this respect is standards like those produced by the genomic standards consortium and by the earth microbiome project that allow us to do a lot more data integration by having a standardized data set where often we don't need to worry about these things another key aspect to this is being able to take chime into the cloud and so NIH is currently running a running a cloud pilot through NAID with Amazon that allows us to make these techniques accessible to a lot of people who don't necessarily want to set up their own cluster and for example the reason why we were in Bangladesh was it's very hard to set up computational infrastructure in darkest so whereas in contrast you can basically give Amazon your credit card number and I'm guessing they already have your credit card number right and use that to put together an instant cluster run your jobs on it and then let it dissipate without having to set up your own set up your own supercomputer so anyway so the vision here is to see your samples in the universe of other samples and there's a data integration workflow that I'll skip in the interest of time when we use that they're basically what we can see is that the HMP cluster patterns so these are across different body sites match very nicely with the community clustering pattern so this was work with Curtis's group and with Ruth Lee's group so on the scale of the differences between body sites all of the technical variability between these different studies didn't actually matter all that much and so this kind of makes sense right on that scale the different body sites that we're seeing here are very distinct from one another and then that outweighs things like the differences between the v1 versus the v3 primers and the HMP so the primers have an effect but they're smaller than that effect however as soon as you start going into stool specifically so this is still in mucosa you start to see things you don't like so here we have the stool clustering into these two completely separate categories and what's going on there is actually that we're seeing the separation between the v1, 3 and the v3, 5 primers and the HMP that greatly outweighs the variation that we're trying to see in these individuals like whether they have IBD or colon cancer so when you're starting to get more specific questions you suddenly care a lot about this technical variation that will otherwise obscure what's going on and so Cata's talked to you about integrating multi-omics data is just as important when you're integrating data of the same data type to have some consistency in how you do that integration now this is just another view now of some more refined data where we're just looking at the Illumina platform and so when we look across body site you can see a lot of separation there and what you can see is these different experiments including in this case the HMP experiments which were on 454 separate not by project but by body site like you would hope but again when you go into stool and in this case what we're doing is we're restricting it just to Illumina data what we see here and you can see we have a ton of metadata about these individuals what you can see here is that you see pretty clear clustering by study rather than clustering by clinical variables which is what you'd like and this is very disappointing because we know there are some interesting clinical variables in here so for example when we went to Bangladesh we tracked ourselves over time so what we're looking at here is a cross body site effect which is very large and then if we look at country on this scale you can see that there's basically nothing that really separates the time we were in Bangladesh from anything else when you look at cross body sites but if you zoom on the stool specifically and we scroll down here so we're all looking at stool and we look at what happened with travel what you can see now is that that trip to Bangladesh caused some substantial shifts in the microbiota of some of our individuals who then wandered off into different regions of configuration space after that and did not return despite lack of treatment with antibiotics so being able to integrate this kind of data across many studies because for this kind of experiment it's often difficult to get enough volunteers within one study to do it many times is really important and again to cut a long story short taking this same data I showed you before with that very clear per study clustering and doing some additional analyses with it what we're able to do is we're able to bring it all back into the same distribution and we're able to now go looking for variables that are potentially clinically interesting that vary in that cloud including the American gut data which we're currently cleaning up at the moment one problem that this points out though and you see some examples of this is that there's a lot of cases where we have no data and there's a lot of cases where the data are not consistently annotated so you have for example NA versus no data as separate categories rather than integrated into the same category and that's something we're cleaning up at the moment so anyway so I'm going to talk a little about gaps needs and challenges and I assume about it out of time but the major gaps that we're facing are that we don't know what effect sizes to expect the techniques for dynamic analysis are just emerging we don't know yet whether prospective human studies or mechanistic animal studies will in general yield more information and most of the sample information is not yet in the standard format and databases including SRA so what we need we need standardized scales for effect size and better ways of doing power calculations to power microbiome studies going forward we need better ways to relate the animal to animal data to humans we need prospective longitudinal studies a huge library of microbial strains of known provenance that we can use for those kinds of microbial wolf hunting experiments and better annotations at all scales as Curtis mentioned and so the challenges are how can we balance subject privacy issues against the utility of having rich clinical metadata publicly available how can we integrate the data across omics levels in these longitudinal studies and how much data do we need of each type and how can we integrate the knowledge of gene and taxon functions produced by multiple researchers using multiple techniques in an efficient way but I don't want to put you off doing this so combining studies is hard but as I mentioned some biological effects are really large so this is from a recent genome research paper we did with Janet and with Jeff where even across different studies so this is colored by study effects like the effects of age are still very visible even against that background and going back to Ruth's data set of that infant development you can get so much more out of that by combining it with the HMP data set and when I do that what we can see immediately and this was put together by Antonio and Joshiki in my lab you can see that the baby starts are very much in the vaginal distribution so these are all the adult samples from all the HMP subjects showing the vagina, the skin, the mouth, and the stool and so initially what you can see is a whole lot of inoculation of the baby gut with sequences from the skin and from the vagina probably with ongoing inoculation from the skin you can see an approach towards the adult gut microbiota so the scale here is from birth up to 27 months and what you can see is an approach to the adult microbiota state although it's much less stable than it looked like on the previous slide fascinatingly and this is very relevant to Marty's talk you can see treatment with antibiotics for an ear infection followed by a rapid recovery in the microbiota so there's a lot of resilience there and by the time we get up to two and a half years you can see that infant is basically in the adult stool distribution and you could never have seen this by looking at the infant data alone right you can only get this by being able to integrate that data set with the HMP so with that I'd like to thank the large number of people currently or formally in my lab many of whom I've thanked throughout this talk our many collaborators on various projects including the CDEF project and the IBD project that I talked about briefly our various sources of support including of course NIH and the HMP specifically so thank you I'd be delighted to take a question or two of this time thank you Rob for a very nice talk as usual so when you travel you have shown that there is a shift in your microbes but of course there is a shift in your diet so the first thing most people think is you are getting new microbes from the local place but how much is it just the shift of the new diet you are ingesting there that's a great question in this case we're pretty sure it was a shift in the microbes because we all got sick on the same day and had some substantial had some substantial diarrhea and so forth which was probably not which was excuse me which was about a week into the visit so in that particular case we think we have a really we think it's really likely to be a specific microbial cause and through the sequencing we know what that microbe was in terms of the dietary shifts in patient studies that have done diet over the short term like the WWR one that I dropped from this in the interest of time generally show that you can get a statistically significant effect in humans that's relatively small but you can see it however it's really diet over the longer term that causes a big shift and who goes where thanks thank you Rob my name is Maria Giovanni I'm from the National Institutes of Allergy and Infectious Diseases and it is my great pleasure to introduce Owen White who's from the University of Maryland School of Medicine and he's going to talk to us today about large data management data standards and data sharing Owen


Greetings and salutations friends. Today's is a little bit of a different video. I'm going to be reacting to my brother's college decision reaction video. He actually just got into Princeton. I've mentioned this before but he's a senior in high school now and so getting his decision back was obviously a big moment for all of us and he decided to record it. He's also starting a YouTube channel which I will have linked down below. Make sure to go check it out if you enjoy this video but yeah let's just jump into it. Just this year. So that's Stanford Early Action and then UT Austin University of Southern California Princeton Yale and Columbia. He only applied to colleges to be fair. I applied to like 14. It's currently 6 10 p.m. Stanford results came out 10 minutes ago. I know that exact same feeling. Okay so rejected from Stanford.  Take a picture. So you got into UT Austin which is super cool. He also got in the engineering honors program which is honestly a great program for the University of Texas so that's a big deal. New updates were posted. Sincerely regret that we can offer you a place in the class of this time. You know what? It's all good. Good for you Chimp. You took it like a man. It is what it is. Who needs you? You know what?  We don't need Yale. That's what's up. Oh wait it's weightless. He's taking it back. He said you know you're not that bad. That's funny. We are sorry to offer you a place. I literally hate opening letters and then saying we are sorry or we regret to inform.  Wow Justin is handling this a lot better than I did because I remember opening all my rejections and I was so livid. I was pissed I was literally good times good times and then of course he saves the best for last. Alright this is Princeton. He looks so nervous. I'm a little nervous for this one. Definitely one of my top choices so it'd be really nice if I got in but let's see can't hold this off anymore. New updates to your application. Hey that's what's up baby.  Dude he's so happy. He's so happy. I can't be too loud right now. I lied to my mom and told her that. Okay quick side note this will lie to our mom and said decisions when coming out until Friday and they're released on Thursday so we had to wait an entire 24 hours and just lied to her like no they're not coming out today no they're coming out tomorrow.  Just watch. I'm gonna lie to him and tell him that I didn't get in. I want to see what his reaction is. I got waitlisted at Yale and then I got rejected from Columbia and Princeton. That's actually? Yeah. He really put in that Oscar meme because he thinks I'm gullible. I totally believed him I totally believed him like why would I know the first thing I said was actually because I knew Justin would pull something. Yeah let's walk. Damn he really does the... And then what am I supposed to say?  I can be mad. You know um someone from our school got into Princeton. Oh man I got into that. Oh actually there is one other person who got in. Nick. I'm not even sending you to you right now. Really he really got me good. Jesus Justin god damn. I'm recording right now. Alright he also recorded surprising our mom and this one's pretty good too so. He's got a good music choice.  I think I would know when he comes out. My mom was so confused she was calling me she was calling Justin. Like I thought they come out around 7, 8 p.m. Like don't you know anything can you ask people. No I don't know he said he told you I don't know anything. Time zones. Time zones yeah that's what's up. She said you'll call me as soon as you check. So what he decided to do was go to our mom's restaurant while she was working wearing this Princeton University sweatshirt. My mom is so happy oh my gosh this is so cute. Of course the first question she has what about the other school. Yo for real though shout out to our mom because she really just got two sons into Princeton. That's insane. Honestly if it weren't for her both him and I would be nowhere near we are so always remember to be thankful for your parents. Make sure to tell them you guys love them. It means more to them than you actually guys realize. I have a confession. What? I actually knew about these. My mom was dressed the entire day but honestly so was I I literally was trying not to text Justin at all because I knew that it would put more pressure on him. But I was like Justin can you give me your password so I can log in. He's like no I'll just tell you. Yeah I don't need your stress. Me too. Justin really threw me under the bus. He says yeah yeah Nick knew. What you mean you don't know boy.  My mom loves doing that. That's awesome. Once again congratulations to Justin and everyone else in the class of 2023. I know you guys put in a lot of hours and having that finally pay off for you guys is one of the best feelings so make sure to enjoy it. Make sure to cherish it. Live in the moment. And congrats to Justin. Hopefully I see him here next year. Once again I will have his channel linked down below. Not gonna lie guys his video editing is very much on par with someone else he might or may not look up to or have helped him along the way. Make sure to go drop a comment on his video. Let him know that I sent you guys and as always don't stress. Bye.