Lecture 3: maurice Flashcards
humans are made up of what
-eukaryotes
-bacteria
-archaeabacteria
-viruses
-parasites
what is commensalism
one organism benefits and the other is unaffected
what is mutualism
both organisms benefit
what is parasitm
one organism benefits at the expense of the other
true or false: interactions between microbes and humans can fall anywhere on the symbiosis spectrum between beneficial and neutral
false it is beteween beneficial and harmful
genome: who’s there. what is the tool?
amplicon sequencing/16 s rDNA sequencing
genome: what can happen. what is the tool?
metagenomics/shotgun sequencing
transcriptome: what is happening/what are they doing: what is the tool?
metatranscriptomics
proteome: what makes it happen/how does it happen?: what is the tool
metaproteomics
metabolome: what has and is still happening?: what is the tool
metabolomics
how many phyla exist
more than 5o
the human microbiota is dominated by how many phyla
3-5
true or false: microbial communities are site specific
true
70% of total microbiome is in the….
colon…..
which bacteria dominate the stomach
-lactobacillus
-veillonella
-helicobacter
True or false: microbiota composition is highly variable between individuals, the functional gene profiles are similar
true
Oral and fecal communities analyzed by
16S rna seq
Bacteroidota formely known as
Bacteroidetes
how many species in Bacteroidota
70000
Most common genera are….
Bacteroides, Prevotella, Porphyromonas,
and Xilanibacter
what is the shape of the Bacteroidota
-gram -, anaerobic and rod shaped bacteria
which bacteria is known to degrade a variety of complex glycans (polysaccharide utilization loci, starch utilization system)
Bacteroidota
what is the most gram - bacteria of the gut microbiota
Bacteroides
true or false: bacteroides are non-flagellated and non-fimbriated bacteria
true
give the % of Bacteroides vulgatus
31%
give the % Bacteroides thetaiotaomicron
12%
give the % Bacteroides fragilis
5%
Bacillota is formely known as the…
Firmicutes
is Bacillota gram + or -
mostly gram +
is Bacillota spore forming
yeah
are Bacillota anaerobe
nah they are obligate anaerobes
which species does Bacillota contain
Clostridium
Ruminococcus
Lactococcus
Lactobacillus
Eubacterium
Roseburia (butyrate-producing)
Faecalibacterium (butyrateproducing)
Veillonella (Gram-negative).
Pseudomonadota (form. Proteobacteria) in clude what…
Escherichia and Desulfovibrio (sulfate-reducing bacteria)
Actinomycetota (form. Actinobacteria): includes …..
Collinsella species and Bifidobacterium species (probiotics)
Verrucomicrobiota (form. Verrucomicrobia): includes….
the species Akkermansia muciniphila, specialized in mucus degradation
Main Functions of the Human Microbiome
ü Colonization resistance.
ü Production of vitamins.
ü Metabolism of xenobiotics.
ü Generation of metabolites.
ü Digestion of dietary fibers and generation of shortchain fatty acids.
ü Development of the immune system.
Bacterial metabolite production
ü Dietary phosphatidylcholine is hydrolyzed in the intestine by lipases to generate choline.
ü In the colon, the microbial choline utilization (cut) gene cluster is responsible for the formation of trimethylamine (TMA).
ü TMA is absorbed and oxydized in the liver into TMA N-oxide (TMAO), which is linked to higher risk of cardiovascular disease.
ü The cut gene cluster was identified in 20 members of the human gut microbiota, including members of the Bacillota, Pseudomonadota and Actinomycetota phyla.
Primary bile acids (e.g. cholic acid) are synthesized in the….
liver from cholesterol and excreted in bile
some of the primary bile acids the large intestine, where several species of….
Bacillota (e.g. Clostridial species from cluster XI, Clostridium scindens and Clostridium hylemonae) generate secondary bile acid using the bai genes
These secondary bile acids (e.g. deoxycholic acid) inhibit the growth of….
C. difficile, but were shown to mediate tumor development in a mouse model of
liver cancer
The gut microbiota degrades indigestible dietary….
carbohydrates from plants (pectin, cellulose, xilan, and starch)
Bacterial metabolism of plant carbohydrates generates…
short-chain fatty acids (acetate, propionate and butyrate) that account for over 10% of our daily calories
name microbiota scfas
-acetate
-propionate
-butyrate
Short chain fatty acids (SCFAs) are the fermentation end products of…
dietary carbohydrates
what is the concentration of scfa’s
can reach up to 100 mM in the distal colon
Although all SCFAs influence colonic health, …. appears to have important specific functions.
butyrate
what is the role of butyrate
-acts as an energy source for enterocytes
-Butyrate inhibits histone deacetylases (HDAC), leading to increased histone acetylation and epigenetic modification of gene expression.
-Butyrate induces TGF-b secretion by epithelial cells
-stimulates dendritic cells and macrophages to produce IL-10 and retinoic acids
Butyrate-producing bacteria are widely distributed in the …. class
Clostridia
butyrate inhibits what?
histone deacetylases (HDAC), leading to increased histone acetylation and epigenetic modification of gene expression.
Butyrate and niacin bind ….
GPR109a on epithelial cells to trigger production of the cytokine IL-18.
Low-fiber diet promotes
expansion of….
colonic mucus-degrading bacteria (Akkermansia muciniphila)
Low-fiber diet increases the susceptibility of mice to
colitis caused by the enteric pathogen citrobacter rodentium
Bacteriocins produced by the microbiota
Consist of lantibiotics, thiopeptides, microcins,
true or false: bacteriocins are toxic for a specific set of bacterial species, excluding the producer
true
Mutacin 1140 is one of the 4 lantibiotics produced by…..
Streptococcus
mutans, active against other Streptococci
This mutacin undergoes post-translational modifications. Eleven genes are required for its biosynthesis
mutacin 1140
Disease can result from loss of ..
beneficial functions or new maladapted functions.
what can cause ibs, psoriasis and acne
microbial imbalance: dysbiosis
The vagus nerve, which connects the
CNS to the ENS, has both … and
… neurons
afferent and efferent
Production of bacterial metabolites that access the bloodstream and cross the BBB can directly regulate
neurological functions (e.g. SCFAs and
neurotransmitters).
Immune cells and cytokines, which cross the BBB, can regulate
neurological functions, including thev hypothalamic-pituitary-adrenal axis (HPA)
which neurotransmitters does bacillus produce?
Dopamine, norepinephrine
which neurotransmitters does Bifidobacterium produce?
GABA (gamma-aminobutyric acid)
which neurotransmitters does Enterococcus produce?
serotonin
which neurotransmitters does Escherichia produce?
Norepinephrine, serotonin
which neurotransmitters does Lactobacillus produce?
Acetylcholine, GABA
which neurotransmitters does Streptococcus produce?
Serotonin
ASD is a neurodevelopmental disease diagnosed by
behavior impairments, deficits in language and social interactions
true or false: people with asd have gastrointestibnal probles
yeah
altered GI mobility and increased gut permeabilityy
Gut microbial dysbiosis is often observed in individuals with….
ASD
Large epidemiological studies linked maternal infection to increased
autism risk in the kid
WHAT is maternal immune activation
-mouse model: Pregnant females are treated with poly(I:C) to mimic viral infection.
-resulted in TLR3 activation and inflammation.
-offspring showed some symptoms of ASD (increased gut permeability and behavior impairments
MIA offspring had lower levels of …..
bacteroides fragilis
True or false: Feeding B. fragilis to the mice induced ASD symptoms
false it reversed the symptoms
MIA offspring also displayed an altered profile of serum
MIA offspring also displayed an altered
profile of serum metabolites with
increased levels of the metabolite 4-
ethylphenylsulfate (4EPS).
true or false: injection of 4EPS into normal mice caused the same behavioral problems
true
4eps is most likely a … metabolite since gf mice don’t produce it
bacterial
ü 4EPS is related to p-cresol, a tyrosine …
metabolite found in urine of children
with ASD.
Maternal high-fat diet (MHFD)
induces…..
behavioral alretarions inb kids
MHFD causes alterations in….
in gut microbiota, reduction of oxytocin production, and deficient
synaptic plasticity
ü Presence of Lactobacillus reuteri
was reduced by …fold in the
MHFD offspring gut microbiota
> 9
L. reuteri treatment restores
oxytocin levels,… and ….
synaptic plasticity and social behaviors
name types of IBD in their respective spots
ü Crohn’s disease (mainly ileum).
ü Ulcerative colitis (colon).
ü Multifactorial diseases, with known
genetic component (NOD2)
what are the changes in microbiota composition in ibd
increase Bacteroides, adherent-invasive E. coli (AIEC), Helicobacter hepaticus,
Overall a decrease in gut microbial diversity and an …… in the
numbers of pathobionts are observed
increase
true or false: IL-10-/- SPF mice are susceptible to IBD ad why
true
Susceptible germ-free IL-10-/- mice do not develop IBD
true or false: Susceptible IL-10-/- mice that lack TLRs or MYD88 do not develop IBD
true
what is important for the devlopment of tbd
Recognition of commensal bacteria by the innate immune system
what is: Faecalibacterium prausnitzii
-butyrate-producing Gram-positive
bacterium part of the Bacillota phylum
whichis: One of the most abundant bacterium in the human gut microbiota representing up to 5% of the total bacterial population
Faecalibacterium prausnitzii
Oral administration of live F. prausnitzii or culture supernatants …. the severity of trinitrobenzenesulfonic acid (TNBS)-induced colitis in mice
reduced
what could be used as a probiotic to prevent IB?
Together with Bacteroides fragilis and other butyrate-producing bacteria, F.
prausnitzii
Probiotic colonization is ….c
site-specific
Probiotics colonization is …
person-specific`
Probiotic colonization is predictable by…..
host features (pathways associated with anti-bacterial defense, antigen presentation, etc
which is the second mpst common cancer
colorectal
Specific species of the gut microbiota have been linked to CRC:
- Streptococcus gallolyticus
- Enterotoxigenic Bacteroides fragilis.
- Colibactin-producing Escherichia coli.
- Fusobacterium nucleatum (Fn).
Fn is…. detected in stool. However, it is ….. in colorectal cancer tissues
rarely and abundant
what does fn do
ü Fn adheres to and invades intestinal cells through its FadA surface adhesin.
ü FadA binds to the EC5 domain of E-cadherin and activates β-catenin signaling.
what does fada do.
ü Fn adheres to and invades intestinal cells through its FadA surface adhesin.
ü FadA binds to the EC5 domain of E-cadherin and activates β-catenin signaling
what does fap2 adhesin do
ü Fn adheres to and invades intestinal cells through its FadA surface adhesin.
ü FadA binds to the EC5 domain of E-cadherin and activates β-catenin signaling
true or falce: ü Gal-GalNAc is highly expressed in adenomas and adenocarcinomas, but not in normal tissues.
true: This explains the abundance of F.
nucleatum in malignant tissues
ü Fn was abundant in CRC tissues in
patients with…..
recurrence post chemotherapy
true or false: fn decreased crc resistance tio chemi
false: it promoted
Fn …. the autophagy
pathway in a TLR4-dependent
manner and, in turn, ….
chemotherapy-induced apoptosis
Fn activated the autophagy
pathway in a TLR4-dependent
manner and, in turn, inhibited
chemotherapy-induced apoptosis
