GDB 103 Final Flashcards


1) Student should be familiar with the following topics and concepts, be able to provide a definition or  context, and where applicable at least one example: 

Holobiont/holo genotype/holophenotype, 



  • Holobiont: symbiont conferred function, This term refers to the host organism along with all of its associated symbiotic microbes, including bacteria, fungi, viruses, and other microorganisms. The holobiont is considered a collective of species that are intimately associated and function as a single ecological unit.

  • Hologenotype: This is the sum of the genetic information of the host and its microbiota. It encompasses all the genomes within the holobiont, highlighting the idea that the host’s genome and the genomes of its symbiotic microbes are interconnected and can affect the host’s phenotype.

  • Holophenotype: , extended host phenotype This refers to the combined phenotypic traits of the holobiont, resulting from the expression of the hologenotype. It includes all the functional traits and characteristics that arise from the interaction between the host and its microbial partners.



  • symbiont-conferred functions - parasite control the host behavior 

defense offense nutrition growth reproduction dispersal

  • extended phenotype - the influence of genes can continue beyond the host body, and also takes into account the environment. 

  • emergent host phenotype - new traits that arise between the interaction of a host organism and microbiota 

symbiont-conferred/hacked dispersal, symbiont side of symbiosis, 

vertical vs horizontal  transmission of microbiota,  Darwinian vs Lamarckian evolution, hologenomic evolution, 

  • Vertical Transmission related to Lamarckian Evolution, organism acquire all kinds traits and phenotypes, and pass on to next generation

  • Horizontal transmission - microbiota received from other sources

  • Darwinian Evolution- selected traits for fitness advance, 

  • Hologenomic evolution - the selection of beneficial microbiota 

beneficial sexually  transmitted microbes, parasitic control of host behavior, 

  • Toxoplasma gondii - 

    • A single celled protozoa that has a complicated life cycle with many hosts.

    • The primary host is felines, because this is where the parasite can replicate/complete its life cycle.

    • Can infect humans via meat contaminated with fecal oocysts or from contaminated water. even via blood transfusions .



  • manipulation hypothesis - Follows the manipulation hypothesis because infected rodents show a decreased aversion to cat urine, even seem attracted to it. 

  • rabies virus - significant behavioral change -> heightened aggression

  • Agrobacterium tumefaciens - bacteria that induces rapid cell growth (Auxins cytokins) and also takes advantage of host to make Opines (carbon source bacteria cannot make itself)

  •  fermentation hypothesis - > bacteria in the scent glands of mammals generate odorous metabolites used by their hosts for communication

  •  microbiota-gut-brain axis (involving vagus nerve,  circulatory system, immune system),

Shows the connection of the gut microbiome to the brain

  1. Vagus  - connects  gut and brain via signal

    1. Vagotomy - no connection of the microbiota to the brain 

  2. circulatory system - moves chemicals from gut to brian 

  3. Immune - recognizes invaders of the body, controls certain chemicals for interaction 

  • - the hype/exaggeration surrounding microbiomes, hoopla - > questionable claim -> deception 

  • the Human Genome  Project, - the human genome can be sequences in a very quick way 

  •  the Human Microbiome Project - understood the limits of the Human Genome project, recognized which microbial exist and their impacts on human health

  •  National Microbiome Initiative - follows the One Health Principle , 

  • press releases, the pitfalls of big data  (false-positives) - finds a correlation but no reason to assume there’s a correlation between source 1 and source 2 false discovery rate, correlation versus causation - not always implied/connect- pretty easily to fool someone, reductionist approach in microbiome  research (e.g. synthetic communities or SynComs), translating animal studies to humans, common causal/lurking/hidden variable, 



  • germ theory - disease is caused by microorganisms, 

  • , beriberi - nutritional disorder caused by deficiency of thiamine (vitamin B1)

  • , fecal microbiota transplantation - low tech, transfers stool from a healthy donor to the GI tract of a patient to restore balance of bacteria in the gut 

  •  Haybittle/Peto rule - protocol to halt a clinical trial early if initial results show a significant benefit foa  treatment being tested. Purpose is to ensure ethical conduct in clinical trials to allow patients to benefit from promoting new treatments without delay. TLDR- if something works, gotta give it to the patients

  • microbiota-based therapeutics such as VOWST, FDA,

    • FDA - When used to cure, treat, mitigate or prevent a disease, fecal microbiota for transplantation meets the legal definition of a drug and biological product 

  • Nitropenia ,disease that arise for inadequate availability of NO/NOx  (based on disease mongering 

  • ethics of microbiome science, 

  • 16S vs  metagenomics sequencing - 




16s 

Metagenomic sequencing

  • Cheaper 

  • Tracks single gene (issue that’s the only thing you know, can’t ID microbial functions

  • Sequence all the data, less bias, 

  • Can identify microbes 

Cons

  • Pricey 

  • Can’t sequence rare microbes

  • Risk of contamination from host/site 














  • informed consent - Need it for a study, gives study organizers the right to use your data for research/ opportunity for rights to be declared for research projects. 

  • , American Gut/UBiome  - microbiome project which collects Metadada, Ubiome- you submit the data, Institutional Review Board (IRB) - campus board that reviews is studies are ethical 

  • healthy vs unhealthy microbiomes,

    • Healthy- one without pathogens? one that is more diverse? one that is missing a ‘good microbe’?

  •  interactions between animal immune system - serves a protection from infections, prevents certain pathogens from invading, reinfection 

  •  (innate vs adaptive ; dendritic cells - bridge between an innate cell and adaptive cells, services as a transport, picks up antigens and transports them to help immune system)  and 

  • Innate - “first responders, takes care of incoming pathogens”

  • Adaptive - make antibodies

  • microbiome: 

  • tolerance - Self antigens Food antigens (commensal microbes?

  • immunity - pathogenic microbes 

  • homeostatic immunity - response without inflammation, immune regulation 

  • ; dysbiosis - imbalance within the microbiome, caused antimicrobial usage

  • , infections

  •  ; opportunistic pathogens  - part of normal microbiota, don’t cause disease in normal locations but causes disease to spread to other locations, needs another niche to toke over

  •  frank pathogens - always pathogenic, create its own niche to make damage there;  

  • toxic shock syndrome - microbes/toxins can spread throughout the body, create an inflammatory response (cytokine storm)

  • ; microbiome-based or -targeting treatments;

    • probiotics/prebiotics - supplements, vitamins

  • FMT ( fecal microbiota transfer) - transferring microbiota from one donor to another

  •  Transfaunation - transferring cow rumen fluid into healthy animals ; 

  • SecondGenome - Glenn Nedwin’s Company
    microbiome companies: what diseases or parts of the bodies do they target, what kind of products or services  do they offer; differences between doing (microbiome) science in academia vs industry; AnimalBiome - looks at the microbiome of cats and dogs, sequences their fecal matter, causes of and solutions to different kinds of dysbiosis; 

    • Causes: evolution of humans driving dysbiosis, transition to agricultural to the environmental societies 

  • probiotics vs FMT; 

  • impact of diet on gut microbiome - need to look at protein, fiber, and carbohydrate factors  

  • best  practices in designing microbiome studies (crossover vs parallel vs single-arm); 

    • Crossover - A type of clinical trial in which all participants receive the same two or more treatments, but the order in which they receive them depends on the group to which they are randomly assigned.

    • Parallel - a type of clinical study in which two or more groups of participants receive different interventions.



  • biologicals (categories, active ingredients, business model);

  1. Biopesticides, Biocontrol Bioprotection - regulated by EPA 

  2. Biostimulants 

  3. Bio Fertilizers, bionutrients

2,3 regulated by EPA 

 Marrone Bio Innovations - discovers, develops and markets effective and environmentally responsible biologically based products for pest management in agriculture and water.

, Invasive Species Corporation - another company by Pam Maroone 

healthy vs unhealthy vs  conditionally unhealthy microbiomes;

 autism spectrum disorder -

  •  Shares course behavior impairments 

  • A subset of these individuals have gastrointestinal (GI) abnormalities including altered gut permeability mouse models for ASD also has GI abnormalities

  • Treatment of these mice with Bacteroides fragilis corrects gut permeability alters the microbiome to a new state and corrects ASD related anxiety and motor skill behaviors



This suggests a gut-microbiome-brain connections may lead to pharmacological therapies for ASD and other GI and behaviors maladies

  • Autism leads to less diverse microbiome 

  • Pathobiome- taking the microbiome of a diseased individual

  • ; effect size, microbiome-based diagnostic  indicators, Clostridium difficile infections, 

  • resistance  - insensitivity to perturbation 

  • resilience rate of recovery after perturbation 

  • perturbation – stability - function of residence and resilience 



  • press disturbance - change in condition (meat to veggie diet) 

  •  pulse disturbance - short time, antibiotic 

  •  cardiovascular disease - leading cause of death and morbidity worldwide, 



  • autologous fecal matter transplantation - you can store your fecal matter/ to get more info for your data 

  • humanized/personalized gut microbiomes in mice -/ see the effect of your microbiota in mice giving an autism donor gut microbiome into mic, causes behavioral alterations in mice

    • Giving normal mice chemicals, normal, germ free mice, inhibited functions future directions in human microbiomics. 

2) Students should know about the composition, assembly, acquisition, function, succession and/or impact  of microbiota associated with the following hosts, host tissues, or other sources, insofar these were  presented in class: 

Plant leaf nodules - located on the plant (symbiotic organ for the plant) 

 flowers, Rhizopus microsporus,

 wild baboons - shapes gut microbiota by behavior (grooming0 rather than same environment/ diet 

kittiwakes, carpenter ants, felines/rodents, dogs  - Inflammatory Bowel Disease  -> gut dysbiosis,  hyenas, Arabidopsis/soil, human gut

human placenta - resembles the oral microbiome 

 fecal microbiota transplantation sample, AO+  Restorative Mist (a Mother Dirt product), 

the New York Subway system 

- samples collected from trains or just any object people can touch (kiosk, benches, turnstiles 1) swab, 2) mark 3) upload *include time/location, found mostly bacteria, but other unknown stuff 

, the Yanomami Amerindians - isolated tribe, different microbiome, conclusion was more diverse/different microbiome than that of US peoples 

, coprolite  samples, sick animals; Gut Restore; 

Zequanox; human patients, 

IBD-diagnosed dogs - inflammatory bowel disease leads to gut dysbiosis 

CLas-infected citrus trees- bacterial infection for trees, microbial groups that are infected and are not infected are significantly different

 

mice, 

Burmese python - 

, sheep - produce methane,, linked to differential gene expression in sheep rumen microbiome 

, animals in the wild - microbiome sampled for 180 animal species, metagenome was isolated and sequenced, assempl 1209 bacterial genomes 75% of assembled genomes belong to previously undescribed bacterial species , 

carrion eaters, birds and bats - bats have a similar gut microbiome to those of birds, suggests a convergence for them to fly 

With lots of data, if matches, can infer a relationship beaten bacteria phylum and species 



3) Students are expected to recognize the names of the following individuals, and explain their contribution  to the study of microbiomes/microbiota, in connection to material presented in class: 

R.A. Fisher, Statistician and biologist who combined Mendelian genetics and Natural Selection

Robert Koch 

  • Founder of modern bacteriology 

  • ID’s causes of TB, cholera, 

  • Kochs postulates 4 general principles linked 

, Christiaan Eijkman - worked with Koch, set oto prove beriberi was microbial (geom theory), wrong since it was anto-beriberi (vitamin base, 

Set out to prove that the cause of beriberi was microbial, but was wrong. But discovered anti-beriberi factor (vitamin B1)

David Whitlock; 

Glenn Nedwin - CEO and president of 2nd Microbiome

Holly Ganz - founder of animal microbiome company, sequence microbiome of dogs and cats ;

 Pam Marrone - plant microbiome lady founder of Invasive Species Corporation and Marrone Bio Innovations