microbiota and IBD

what is the commensal microbiota

microorganisms that inhabit all barrier surfaces of the organism

what can affect microbiota diversity in the body from birth to grave

• genetics

• environment

• diet

• illness

• antibiotics

what does initial bacteria depend on

delivery mode

1. vaginal delivery- lactobacillus, vertical inheritance from mother

2. c-section- staphylococcus, higher susceptibility to certain pathogens, higher risk of atopic disease

what happens to the microbiota in early childhood

• new strains outcompete old ones

• rapid increase in diversity

• early microbiota = high instability

• shifts in response to diet, illness

what happens to the microbiota in adulthood

• high distinct, differentiated microbiota

• microbial community may continue to change, but at a slower rate than in childhood

• changes in the last trimester of pregnancy

what happens to the microbiota in the elderly

substantially different gut communities than in younger adults

how have humans co-evolved

with microbial partners

humans are a composite of which species

• bacteria

• fungi

• viruses

• bacteriophages

how much do microorganisms that inhabit all barrier surfaces of the organism outnumber human cells

by about 10 fold

how many more genes do the total microbial DNA contain compared to our ‘own’ human genome

contains 100 times more

what does the microbiome play a central role in

the maintenance and control of host homeostasis

what is the development of the immune system dependent on

dependent on the interactions with the commensal microbiota

what are the 2 major phyla

• firmicutes

• bacteroidetes

what are some examples of proteobacteria

• E.coli

• H. pylori

what is an example of actinobacteria

bifidobacterium

what factors affect the normal flora

1. local environment

2. diet

3. age

4. health conditions

5. antibiotics

what does the commensal bacteria aid in

• aids in digestion of food

• the type and amount produced is influences by the diet and intestinal flora

what are vitamins B12 and K and gas produced by

bacteria

what does the commensal bacteria protect the host from

colonisation with pathogenic microbes through occupation of an ecological niche

what type of relationship do commensal bacteria have

• mutualistic

• normal flora derive from their host a steady supply of nutrients, a stable environment and protection

• the host obtains nutritional and digestive benefits, stimulation of the immune system and protection from colonisation and infection by pathogenic microbes

what do commensal bacteria help with

• the development of mucosal immunity

• normal flora can induce immunological responses

what are the different types of colonisation

1. transient colonisation

2. permanent colonisation

what is colonisation

the presence, growth, and multiplication of the organism without observable clinical symptoms or immune reaction

what is infection

• infection refers to the invasion of bacteria into tissue with replication of the organism

• infection is characterised by isolation of the organism accompanied by clinical signs of illness such as fever, elevated white blood count, purulence, and clinical expression of disease e.g. pneumonia

what can MRSA be

a colonisation or infection

what is the percentage of bacteria that are anaerobic

99%

define obligate aerobe

bacteria that must have oxygen

define obligate anaerobe

bacteria that need to be in oxygen-free environments such as the human gut or they will die

define facultative anaerobe

these bacteria can live in either an oxygen or oxygen free environment

what can bacteria of the normal flora act as

opportunistic pathogens at times of lowered immunity

what does a steep oxygen gradient influence

which bacteria are capable of surviving close to the epithelial surface

what must anaerobic gut bacteria contend with

must contend with reactive oxygen species produced by aerobic host metabolism

what does rapid dilution and consumption of oxygen secreted from the host tissue generate

generates a gradient of oxygen which decreases in concentration from tissue to lumen

what do paneth cells secrete

anti-microbial peptides

what do goblet cells secrete

mucus

how many layers of mucus are there

2

is the inner mucus layer thick or thin

thin

is the outer mucus layer thick or thin

thick

what is the mucus mainly comprised of

• water

• glycoproteins

• lipids

• other proteins and nucleic acids

what is indispensable for the maintenance of an intact barrier function for the GI mucus

phospholipids

what are the main phospholipid classes found in the mucus

• phosphatidylcholine (PC)

• lysophosphatidylcholine (LPC)

what phospholipid represents more than 90% of the phospholipids in the mucus

PC

how is PC arranged and why

• arranged in lamellar structures as surfactant-like particles which provide a hydrophobic surface on top of the hydrated mucus Gell

• prevent invasion of bacteria from the intestinal lumen- PROTECTIVE

what is PC

• anti-inflammatory

• blocks pro-inflammatory cell signalling responses to TNF-alpha

what does the barrier function also contain

IgA antibodies

how much of the IgA antibody is produced per day to protect the gut mucosal membranes

2-3g per day

when does secreted IgA production occur

in response to mucosal antigens in the GALT (gut-associated lymphoid tissue) and can shape the microbial composition and distribution int he gut

what are secretory antibodies associated with

• enteric pathogens i.e. infection and their virulence factors- toxins

• commensal microbes

what do secretory antibodies prevent

microorganisms and food substances from binding to absorptive enterocytes

what does IgA attach to

invading bacteria and trap them in the mucus to prevent their invasion into mucosal tissues

what is the term for microbiota being altered

dysbiosis

what is a really common firmicute

faecalibacterium prasnifzii

what is dysbiosis

• decrease in gut microbial diversity owing to a shift in the balance between commensal and potentially pathogenic microorganisms

• loss of anti-inflammatory bacteria rather than gain of virulent bacteria may cause IBD

what is reduced in IBD in regards to microbiota

• proportion of phylum firmicutes

• proportion of phylum bacteroidetes

what is increased in IBD in regards to microbiota

proportion of phylum proteobacteria

how does inflammation in IBD promote dysbiosis

immune system- altered immune and microbial interactions

what does use of antibiotics in early childhood increase the risk of

Crohn’s disease

what could antibiotics potentiate

the expansion of pathobionts such as clostridium difficle (FMT)

what does the microbiota do

1. suppresses pathogens

2. promotes immune tolerance

3. initiates epithelial repair

4. ensures development of balanced immune subsets

what immune cells are involved in IBD

• T cells

• neutrophils and macrophages

• dendritic cells

what do Th1 cells do

fight intracellular infections by helping macrophages

what do Th2 cells do

main function to fight infection by parasites

what are Th17 cells induced by

fungi or extracellular bacteria infection

what do Treg cells communicate with

immune cells to regulate their functions

what happens to barrier function in IBD

barrier function is compromised

what can gut microbes stimulate

immune cells (macrophages to secrete cytokines)

what does inflammation result in

the production of ROS

what happens to the oxygen environment in inflammation

it is reduced

what are the consequences of inflammation to the gut microbiota

1. intestinal inflammation induces the production of ROS by inflammatory cells

2. intestinal inflammation can also induce the production of small molecule products DMSO TMAO that serve as terminal electron acceptors for facultative anaerobes

3. outgrowth of facultative anaerobic bacteria such as including an increased relative abundance of enterobacteriacae and a marked decrease in obligate anaerbic clostridia and bacteroidia

4. thus, metabolic alterations associated with inflammation and/or pathobiont colonisation might act as microbial stressors and promote the outgrowth of dysbiotic species

what is the mycobiome

the fungi in the gut

what are dysbiotic microbiota associated with

the outgrowth of fungi which can then modify Th1 activation through chitin and B-glucan antigen presenting cell or the bacterial microbiota via gene transfer

what is virome

the virus present in the gut

what is the concept of feral microbial transplantation (FMT)

replace imbalanced microbiota of IBD patient with the microbiota of a healthy patient

what is the goal of FMT

the stool suspension obtained from a healthy patient added into the GI tract of an IBD patient restoring essential components of the microbiota that could revert inflammation

in which patients does FMT work in

C.difficle patients

what is the concept of probiotics

restore balance to the microbial community

examples of probiotics

• lactic acid bacteria- lactobacillus species, bifidobacterium

• non-lactic acid bacteria- bacillus

• non-pathogenic yeast- saccharomyces

what are probiotics

live microbial food and beverage supplements that beneficially influence intestinal microbial balance

what do probiotics inhibit

• inhibits growth of pathogenic bacteria

• blocks epithelial attachment or invasion by pathogens

what do probiotics enhance

• hosts immune respinse and intestinal barrier function

• improves epithelial and mucosal barrier function

• alters hosts response

what anti-microbial effects are there on beta-defensins

strengthens tight junctions between epithelial cells therefore increasing barrier function

what is the concept of prebiotics

promote the growth of existing beneficial microbes that confer benefit to the host

what are prebiotics

non-digestible oligosaccharides that stimulate the growth and/or metabolic activity of selected GI microbes according to health benefits

examples of prebiotics

• inulin

• lactulose

• fructooligosaccharides

• galactooligosaccharides

what is an example of PC as a drug target

LT-02

what is LT-02

a modified release drug that reconstitutes the low mucus PC reservoir and restoring the structure and density of the mucus, improving the barrier function and preventing inflammation in UC

how does helminthic therapy work

• helminths are large metazoan organisms

• can cause significant tissue injury to the host, parasites can persist in the host for many years

• the immune response to intestinal helminth infection drives a potent physiologic response with dual aims of parasite expulsion and mucus healing

what does diet influence

microbial fermentation and total bacteria in the intestine