Exploring Microbial Diversity: The Ubiquity of Microbes
School
University of Ottawa**We aren't endorsed by this school
Course
BIO 3124
Subject
Biology
Date
Dec 12, 2024
Pages
17
Uploaded by fearlessfoxyroxy
9/4/241Art by David Goodsell (Ebola)Welcome to General Microbiology12Microbes are ancientAnd they changed our planet3
9/4/242Microbes are ancientHow old is our planet? 2:46minDerek Muller - Veritasium4Brock – Biology of Microorganisms, Chapter 1, Pearson.Feb 25th(start producing O2)July 15thSept 17th (Sexual reproduction ~1.3 bya)Dec 13thDec 31st 11:30pmIndustrial revolution: 23:59:58Land based fungi ~1 bya (that’s way before land plants!)March 21sthttps://www.youtube.com/watch?v=I_ssiZCoRAsEarth’s life calendar5Microbes are numerous and ubiquitous6
9/4/243Microbes are numerousWorld population: Over 8 billion or 8 x 109as of Nov. 2022 (wikipedia)Microbial population: 5,000,000,000,000,000,000,000,000,000,000 or 5 x 1030 more then there are stars in the universe (~6-8 order of magnitude).If a microbe is 1µm in length, stacked next to each other in a row, microorganisms would cover the distance between the earth and the sun about 200 trillion times (1012). In 1ml of sea water, you can find up to 10-50 million viruses, and they kill about 20% of the living material in the oceans, every day! There are more viruses than people on earth in 1L of sea water. (ref Dr Patrick Keeling unverified and Dr Mya Breitbart)Ref: Prokaryotes: the unseen majority, PNAS, 1998, 95:6578-65837Microbes are diverse8Some bacteria are BIG!Some have complex structures!MyxobacteriaFisher, P.R. (2005). M icrobial Developm ent. In Encyclopedia of M olecular Cell Biology and M olecular M edicine. Vol. 8, pp. 289-342.100mmComplex organizationComplex inner structuresType 4 secretion systemAlejandro Peña Ignacio Arechaga, M olecular M otors in Bacterial Secretion, J M ol M icrobiol Biotechnol 2013;23:357–3699
9/4/244Their immense diversity allows them to be everywhere in huge numbers•Use different sources of energy•Use other organisms in symbiotic relationships•“Developed” inventive chemistry and biochemistryin order to obtain or produce the metabolites they need•“Developed” geneticsthat allow adaptationMicroorganisms have evolvedand adapted to every type of environment found on Earth 10Microbes can live in extreme environmentsNASAOther planet extreme?Marina Cvetkovska11Hyperthermophiles can live in near boiling temperatures12
9/4/245Blood falls: Psychrophiles pumping out Fe3+ in Antarctica13Some acidophiles can live where the pH is close to 014Alkaliphile can survive a pH range from 8.5-1215
9/4/246FungiZombified ant: Cordyceps fungal infection http://berkeleysciencereview.com/read/fall-2012/manipulative-microbes/16Choanoflagellates: beginnings of multicellularity?https://www.hhmi.org/research/choanoflagellates-and-origin-animals17Heart worm in dogshttps://w w w .countryhillspets.com /heartw orm -prevention/https://erinm illsvet.ca/2015/06/18/the-truth-about-heartw orm /Parasites18
9/4/247You are your very own microbial planetsAnd that is a good thing!Image source: Eighteen.B blogpost19Just how many microbes? Heaps!Where and how many?_______________________________________Skin: 5-50 x 103/sq. inchGroin, axilla: 5 x 106/sq. inchTeeth: 5-50 x 106/sq. inchColon: 300 x 106/g_______________________________________Total bacteria (70Kg normal person): 40-70 trillion, 70 x 1012Total human cells: ~30-40 trillion, 30-40 x 1012That’s 2-6lbs of bacteria per 200lbs adult, not counting fungi and viruses.Not sure where I got this data, presumably Brock – Biology of Microorganisms, Pearson. or Wessner – Microbiology, Wiley.20The living arrangements are in constant fluxWhen the equilibrium fails between symbiotic communities, we call it dysbiosis.When one species takes over the community, it can sometimes result in pathogenesis.Gut Homeostasis, Microbial Dysbiosis, and Opioids, Wang and Roy, Toxicologic Pathology, 2017, Vol. 45 (1) 150-156.21
9/4/248We think of microbes a lot in relation to our health. We have good reasons to!Norton, Microbiology, 6thed.FIGURE 1.8 ■Infectious disease pandemics throughout human history.22Animal symbiosis: Bacteria fermenting cellulose in ruminants are the animal's major source of lipids (and farts!)23Plant symbiosis: Native Mexican corn, mucus and nitrogen fixing bacteria https://atpeacewithpink.blogspot.com/2018/08/sierra-mixe-corn.html24
9/4/249Humans and microorganisms' relationshipsTaking into consideration the genetic potential of organisms only in our gut provides 100X the genetic potential of all our cellsMicrobial genes2 to 20 millions genesHuman genome~23,000 genes(That’s 99.9% greater than the genetic capacity of humans!)Grice, E. A. & Segre, J. A. The human microbiome: our second genome. Annu. Rev. Genomics Hum. Genet. 13, 151–170 (2012).25Environmental MicrobiologyPlant microbiologyMicrobial ecologyBiogeochemistryWater and marine microbiologyAeromicrobiologyAstrobiology26What we know about microbesKnown species: ~6 x 106Predicted: 1 trillion (1012) speciesOf which about 104have been culturedThe entire Earth Microbiome Project (EMP) sequence bank covers less then 107species, 29% of which have only been detected twiceWhich means 99.999% of microbial species still need to be identified! And we haven’t even discussed viruses yet!Scaling law s predict global m icrobial diversity. Kenneth J. Loceya and Jay T. Lennon, PN AS M ay 24, 2016. 113 (21) 5970-5975; published ahead of print M ay 2, 2016. https://doi.org/10.1073/pnas.152129111327
9/4/2410Course Logistics28Request for a note-takerNote-Taker’s Responsibilities •Maintain the confidentiality of the student for whom you are taking notes. •Make sure that notes are legible and comprehensive. •Attend each class. •Provide a copy of your notes promptly following classes. •Using a shared drive may facilitate notes-sharing. •If for some reason you are unable to attend class or continue as a note-taker, contact the student so that other arrangements can be made.If you can be a note-taker, please email me (elaine.beaulieu@uottawa.ca) and I’ll forward your email to the person needing the notes.29SubjectWeekIntroductionCase studyAbx resistanceCase study SporulationBacteria 2Regulation 1Midterm 1 (10%)Case study Spatial OrganizationGrowth 1Microbiome1Revision?Midterm 2 (20%)Reading week (quorum sensing case study)MetabolismRevision?2 Sept9 Sept16 Sept23 Sept30 Sept7 Oct14 Oct21 Oct28 Oct4 Nov11 Nov18 Nov25 Nov2 DecMonday Tuesday Wednesday Thursday Friday Bacteria 1ArchaeaCase Studies due dateSmartworkVirusGrowth 2 Case Studies due dateGenesCase Studies due dateRegulation 2Host-pathogen 1Microbiome2Case study whooping coughCase study We are not aloneSmartworkOr Micro What?Host-pathogen 2Microbial worldBacterial cellsArchaea and EukaryaVirusesMetabolismQuorum sensingMicrobial geneticsMicrobiomeHost-pathogen interactionsFinal exam (cumulative)Module 1Module 2Module 3Final exam prepBacterial GrowthSpatial organizationGene transferMolecular regulationSmartworkCourse schedule:30
9/4/2411TextbookMicrobiology – An Evolving Science, 5ed, by Slonczewski, Foster and Zinser,from WWNorton publishings. DO NOT BUY IT FROM THE UNI STORE!!!!!Buy paper or online version directly from Norton:•Click on the following link https://digital.wwnorton.com/microbio5. •Once the page opens, you will have the click on the “purchase options” button.•The eBook with Smartwork option is $104CAD.•The Smartwork only version (no hardcopy or ebook) is $39CAD.Rice University Openstax free textbook.Local library : managed by Matthieu Delcourt and myself, in our office, BSC10831Help resourcesHow to register to a Student Set:https://wwnorton.com/common/mplay/6.11/?p=/digital/registration/video/&f=adding-yourself-to-a-set&ft=mp4&cdn=1How to register for Smartworkhttps://youtu.be/WPXcHtWBcSESee a whole list of tutorials here:https://wwnorton.knowledgeowl.com/help/student-help-notes-23c713932Course evaluations•Midterm 1: 10% of final mark •Midterm 2: 20% of final mark•Final Exam: 50% of final mark•Case studies: 10%•Smartwork: 10%The averageof all the midterms and final put together must be 50% or over to pass the class, regardless of the grades obtained from formative assessments.Summative 80%(in person exams)Formative 20%(homework)33
9/4/2412Does the cumulative mark of all my exams average over 50%?NoYesYou have not met basic course expectations and need to redo the course.You have met basic course expectations!Your Smartwork mark will be added to your total course mark.Your case study mark will be added to your total course mark.Course evaluations34Case studies (10% total course mark)•These home assignments replace a few lectures•Assignments will be posted in Brightspace•All assignment questions must be answered to be marked.•Not all questions will be marked, and you will not know which questions will be marked.•The cumulative number of points you obtain over the semester will dictate your overall mark for this part of the course.•For example, if there is a total number of 130 points to accumulate over the semester and you have accumulated 115 points:•115*100/130 = 88.5%•No late submission will be accepted. An important professional skill is to be able to manage your time, so submitting homework on time is me measuring this intangible learning goal of “time management”.35Smartwork (10% total course mark)•Choose between Smartwork or Micro What?•Quizzes in Smartwork platform ($$ - 21 days free trial). •Almost weekly, 10-20 questions per quiz.•You have 2 tries for each questions.•The cumulative number of points you obtain over the semester will dictate your overall mark for this part of the course.•For example, if there is a total number of 130 points to accumulate over the semester and you have accumulated 115 points:•115*100/130 = 88.5%•Again, no late submission will be accepted. An important professional skill is to be able to manage your time, so submitting homework on time is me measuring this intangible learning goal of “time management”.36
9/4/241337uOttawa email!!!!If buying onlineIf not sure whether you will stick with micro or don’t have the cash right now.38Reenter your uOttawa email address 39
9/4/241440Click on your address to enter the “student set” codeClick on “Add yourself to a student set”41Student set code is 83273142
9/4/2415Professional work-like assignment opportunity – designing course material•Spots for 5 students or teams of 2 – you must tell me why this is something you would like to do (either record a video or write it in an email). 3rdyear student will be preferred.•This work would count toward replacing 5% of your final exam in a pass or fail fashion. This means your final will be calculated on 45%, and you’ll either have 5% or 0% added to your final mark separately for the work. •Build a “Micro what?” short case study type of learning exercise for students to do next year. I have several ideas and resources to share to help you start your project.•Detailed instructions will follow to those wishing to participate. I have made an example of what I think you should aim for as a format and depth.•We will need to meet frequently throughout the semester to track progress and develop the “products” in an iterative way as a group, so you must be available. You will be helped and supported along the way, but it will take a chunk of your time.•The passing criteria is delivering a fully usable short case study for microbiology students, well referenced, well designed, interesting and with learning goals and assessment strategy that will add to the student’s learning experience. 43Absences During midterms: •You do not need to submit a medical note or even let me know why you haven’t been able to do the midterm. The weight of the midterm will automatically be added to the final exam.During final exams:•Contact theFaculty asap.Prolonged absence affecting coursework: •Come talk to me or email me if you are absent for a week or more and you worry it will affect your course performance, we’ll see what we can do.44Course expectationsTeamwork/Individual workYou will not be assigned specific teamwork. However, case studies can be done in small groups, but each member must submit their own copy, stating who they have worked with, and your answers on your copies must be in your own words, ie, you can’t simply copy off each other. Also, the material in the case studies is on the exam, so do them carefully.For Smartwork, help each other out constructively if you wish, but straight copying off each other serves no one in the longer term…Professional skillsI expect you to be accountable for your learning, I expect you to be self-efficient, set goals and coordinate tasks, to work with integrity, to problem-solve or immediately seek help when needed, reflect on your learning and yourself. Sometimes what we expect of students is not explicit, some call it the Hidden Curriculum. If you are interested in knowing more here is a good start.45
9/4/2416Course expectationsWhat you can expect of meMy priority is always my students. I will be available should you need my help. I will reflect on my own teaching and always listen to your side of things. I will be prepared for exams and prepare you for them. I will try my best to idenmfy and explain the main concepts you should take from this course. I will do my best to give you as much flexibility for your learning as you need, but within a structured course (the balance is hard to get). I do not know everything and somemmes make mistakes, just like you. Live and learn ࠾?.46“Trying to remember something is a wickedly effective way of actually remembering that thing”Benjamin Keep4748
9/4/2417Don’t forget to email me if you can take notes for someone else.If you can be a note-taker, please email me (elaine.beaulieu@uottawa.ca) and I’ll forward your email to the person needing the notes.49