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The study of all the DNA sequenced from a community (eg of bacteria in gut)

Metagenomics

HLA

Human Leukocyte antigen

Obligate aerobes and facultative anaerobes usually have which two enzymes for detoxifying ROSs

SOD and Catalase

Aerotolerant anaerobes have:

SOD and peroxidase

some obligate anaerobes have

SOD

The cardinal temps:

Min, Max and optimum

What bacteria go into when the temperature is too low for them

Protective dormancy

Effect on bacteria of too high temperatures

Thermal lysis

Mean generation time fastest at:

optimum temp

Lowest temp required to kill all cells in a standard suspension of bacteria in a liquid culture within a period of 10 mins

thermal death point

Length of time required to kill all cells in a standard suspension of bacteria in a liquid culture at a given temp

thermal death time

Length of time required to obtain a ten-fold reduction (1 log diff) in the numebr of bacteria in a standard suspension of bacteria in a liquid culture

decimal reduction time (d value)

can benefit from associations with humans but do not provide benefits for, nor harm, the host

commensals

nutrition, niche exclusion, & GI tract & Immune system functions boosted

benefits from mutualistic bacteria

parasitism vs pathogenesis

parasite cannot grow outside host

if given antibiotics, a commensal clostridium can rise up and cause:

ulcerative colitis

fungi & green algae/cyanobacteria. GA/C provide carbon for fungi, fungi provides water, minerals and substrate for GA/C to grow.

Lichen

Another eg of mutualism, like lichen, but with a mammalian organ.

Bovine Rumen

E. coli using O2 in intestine andallowing only strict anaerobes to grow is an eg of what? (E. coli derives no obvious benefit from coexistance with anaerobes)

commensalism

what % mass are bacteria and how many kg of them in our GI tract are there?

2.5, 2

Which 3 types of bacteria are usually found in our oral cavities?

Strep, Fuso, Actinomyces

Which 3 types of bacteria are usually in our upper resp. tract?

Strep, Staph, Neisseria meningitidis

Which 6 types of bacteria are usually in our GI Tract?

Lactobacillus, Bacteriodes, Bifidobacterium, Clostridium, Escherichia, Enterococcus

Type of bac usually an early coloniser of oral cavity?

Strep

Function of early colonisers

Secrete polysaccharides to make biofilm

Surface proteins on strep (ECs) help them:

stick to the biofilm

why is it an example of commensalism that the ECs make a biofilm?

LCs can't bind directly to teeth

Type of bac usually a late coloniser of oral cavity?

Fusobacterium

Fusobac bind to what?

surface proteins on ECs

Early in colonisation of OC, ph is

3-4

late in colonisation of OC, environment is

anoxic

ECs are

facultative anaerobes

LCs are

obligate anaerobes

specific type of EC plaque bac

strep. mutans

s. mutans has 3 mechanisms of acid tolerance. What are the two things it exports?

Protons and lactic acid

the third thing strep. mutans has to increase its acid tolerance is:

Low membrane permeability to protons

Duodenum, Jejunum and Ileum make up the:

small intestine

Colon aka

Large intestine

does the colon (LI) have a presence or absence of oxygen?

absence

site of continued digestion of monosacchs, AAs, fatty acids, water, with a pH of roughly 4-5

Small intestine

Helicobacter pylori attempts to maintain an intracellular pH of around 7 by making the enzyme ______ which converts urea to CO2 and _____ which reacts with protons to form ammonium ions.

urease, NH3

transporter of urea into H. pylori cells called

urel

by which mechanism does NH4+ then exit the cell?

not known

GI microflora help make which 5 vitamins?

thiamine, riboflavin, B12, pyridoxine and k

GI microflora also increase this type of reaction to be carried out:

glycosidase reactions

human gut contains how many bacterial species?

500-1000

classic approach to identifying bacteria in/on our body:

culturing

modern approach

DNA sequencing of 16S rRNA

Sequencing 16S rRNA allows which level identification of bacteria?

genus

Gram positive bacterial phylum, eg clostridia, that inhabits the bowel

Firmicutes

Gram negative bacterial phylum eg Bacillus fragilis that digest plant polysaccharides in the bowel

Bacteroidetes

Gram negative bac phylum eg E. coli that synthesise vitamins in the bowel

Proteobacteria

Bac phylum in bowel eg bifidobacteria, that digest milk oligosaccharides and synthesise vitamins

Actinobacteria

The only archabacteria present in the bowel that consumes hydrogen gas in the gut, and produces methane

methanobrevibacter smithii

What percentage of bacteria found by a full metagenomic study were a) novel and b) not able to be cultured?

22, 83

against toxic compounds

xenobiotic

bacteria are how many times more xenobiotic for us than we are ourselves?

twice

germ-free

gnotobiotic

when are humans and other mammals still sterile?

in utero

in human neonates the intestine is colonised primarily with which type of bacteria?

facultative anaerobes

during weaning, another type of bacteria takes over:

obligate anaerobes

main type and phylum of bacterium by adulthood

obligate anaerobes, bacteroides

the presence of this bacterial species increases intestinal surface area, development of blood vessels and therefore better digestion and absorption.

bacteroidetes

these symptoms were found in what?: higher susceptibility to infections, diminished cytokine levels, reduced serum immunoglobulin and CD4 T cell levels

gnotobiotic mice

a bacterial capsular polysaccharide antigen, causes expansion of splenic CD4 T cells, - what's it shortened to?

PSA

what's the benefit of aiding development of CD4 T cells for bacteroides?

longer colonisation period

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