GDB 103 Final Flashcards

Charecteristics for a Healthy Microbiome

1. High Diversity

2. High Balance/Sanitation

3. Functional Richness

Holobiont

The host organism along with all its associated symbiotic microbes, functioning as a single ecological unit.

Hologenotype

The sum of genetic information of the host and its microbiota, highlighting the interconnectedness of their genomes.

Holophenotype

The combined phenotypic traits of the holobiont resulting from the expression of the hologenotype.

Symbiont-conferred functions

Functions such as defense, offense, nutrition, growth, reproduction, and dispersal controlled by symbionts.

Extended phenotype

The influence of genes beyond the host body, considering environmental factors.

Emergent host phenotype

New traits resulting from the interaction between a host organism and its microbiota.

Vertical transmission

Passing microbiota from parent to offspring, related to Lamarckian evolution.

Horizontal transmission

Receiving microbiota from sources other than direct lineage.

Darwinian evolution

Selection of traits for fitness advancement.

Hologenomic evolution

Selection of beneficial microbiota for the holobiont's advantage.

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

e: , 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 types

defense offense nutrition growth reproduction dispersal

symbiont

conferred/hacked dispersal, symbiont side of symbiosis,

Vertical Transmission

This 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

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 agression, transmitted via bites from an infected organism

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

Vagus system

connects gut and brain via signal

Vagotomy

no connection of the microbiota to the brain

circulatory system

moves chemicals from gut to brian

Immune system

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

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

16S vs metagenomics sequencing

There are differences in price, how DNA is sequenced and stuff

16s

• Cheaper

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

Metagenomic sequencing

Pros

• 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

Healthy Microbiome

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

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 cells

“first responders, takes care of incoming pathogens”

Adaptive cells

make antibodies

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

; 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 probiotics/prebiotics

supplements, vitamins

Transfaunation

transferring cow rumen fluid into healthy animals ;

SecondGenome

Glenn Nedwin’s Company

AnimalBiome

looks at the microbiome of cats and dogs, sequences their fecal matter, causes of and solutions to different kinds of dysbiosis;

• solutions to different kinds of dysbiosis; 

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

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

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.

Biopesticides, Biocontrol Bioprotection

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

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

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

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 → but you can then do the Fecal Transplant on yourself

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.

Plant leaf nodules

located on the plant (symbiotic organ for the plant)

wild baboons

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

kittiwakes, carpenter ants, felines/rodents, dogs

Inflammatory Bowel Disease

human placenta

resembles the oral microbiome

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

Samples from mummies, part of the ethical dilema whether it’s okay to sequence someone’s microbiome if they can’t give consent

IBD

 inflammatory bowel disease leads to gut dysbiosis, present in dogs

CLas-infected citrus trees

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

Burmese python

eats prey at long intervals. The study asked if a fasting snake would eat? 

, 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 ,

birds and bats

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

R.A. Fisher

r, Statistician and biologist who combined Mendelian genetics and Natural Selection

Robert Koch

• Founder of modern bacteriology

• Identified causes of TB, cholera,

• Kochs postulates 4 general principles linked

, Christiaan Eijkman

worked with Koch, set oto prove beriberi was microbial (geom theory), wrongm, Set out to prove that the cause of beriberi was microbial, but was wrong. But discovered antiberiberi factor (vitamin B1)

Glenn Nedwin

CEO and president of 2nd Microbiome

Holly Ganz

founder of animal microbiome company, sequence microbiome of dogs and cats ;