mod review 2

what is the human microbiome

collection of all microorganisms associated with the human body (bacteria, eukaryotes, archaea and viruses)

staphylococcus aureus

commonly found on the skin and its nasal passages

associated with skin infections but can cause more serious infections it enters the bloodstream

escherichia coli

a normal inhabitant of the human gut

some strains aid digestion and other cause UTI, food poising and other infections

helicobacter pylori

found in the stomach lining associated with peptic ulcers and some forms of stomach cancer

lactobacillus species

commonly found in the gut, mouth, vagina

plays a role in maintain a healthy microbiome and preventing infections by outcompeting pathogens

clostridium difficile

presented in some individuals without causing issues but can lead to severe colitis especially after antibiotic use disrupts normal gut flora

bacteroides fragilis

part of the normal gut microbiome

critical for breaking down complex molecules

propionibacterium

found on the skin in sebaceous glands and commonly associated with acne

what is the human microbiome project 1

figuring out and characterization of who lives on and inside of us (taxonomy) and what those microbes are actually doing across different body part (metagenomics)

what is the human microbiome project 2

normal baseline studies to how microbial changes correspond to health breakdowns and specific diseases

what is the superorganism concept

a concept that describes that microbial cells and the human host engage in signaling and share metabolic pathways to form one whole functional organism

diseases associated with dysbioses in the microbiome

IBS, MS, diabetes, allergies, asthma and cancer

what factors influence the human microbiome

geography, age and microbe-host diversification (climate, diet exposures)

how does migration impact the microbiome

a study showed that immigrants moving from a non western country to the US had an increased antibiotic resistance genes

skin microbiome

it is a physical barrier against invasion of pathogens

mostly dry but some humid areas

commensalism relationships between bacteria and skin

factors contributing to variation in the skin microbiome

environment, immune system, sex/age, lifestyle and underlying health conditions

oral microbiome

1000 bacterial species identified

three major habitats

commensalism and parasitism

dysbiosis of oral community associated with disease

cavities, oral pathogens that cause inflammation, gingivitis, etc

what is fluorescence in situ hydbridication (FISH)

a technique that allows scientists to take a high resolution color coded photograph of a microbial community while keeping its physical structure intact

how does FISH work in oral biofilms

the fluoresenctly labeled probe sequences (oligonucleotides) bind to specific 16S rRNA sequences

taxa are detected by probes with different colors and then those probes reveal the structure of a dental plaque biofilm

vaginal microbiome

dominated by Lactobacilli and associated with environmental factors of low oxygen, low pH and glycogen

the communities change with age (pre-puberty, premeno and postmeno)

what factors are associated with vaginal microbiome

hormonal and anatomical changes which include prepuberty, premenopausal and post menapausal

what is hormone replacement therapy

partially restores vaginal habitat to premenopausal conditions and colonization of Lactobacilli

normal functions of iNKT (invariant natural killer T) cells

detecting and responding to lipid antigens of pathogens and killing tumor cells

disregulation of iNKT cells

autoimmunity, allergies and asthma

IgE

respond to allergens and parasite infections

binds to allergens such as dust, pollen, dust mites, ultimately triggering inflammatory chemicals to be released

IgA

mainly protects mucosal surfaces and binding to pathogens

they are present in breast milk which provides with early immune system

IgE and IgA

both immunoglobin antibodies have been linked to gut microbiome diversity in infants

factors that affect infants developing gut microbiota and microflora

babys diet (breast versus formula)

delivery pattern (vagina versus c section

antibiotics

breast milk

is a probiotic that delivers several microbiota to the infant

contains prebiotic human oligosaccharides

contains IgA antibodies

what are lipopolysaccharides

a key component of the outer membrane of gram negative bacteria

structure of lipopolyssacharide

lipid A (hydrophobic)

the core oligio (hydriphilic)

the o antigen (variable)

commensal bacteria

interact with immune cells and help establish normal development of innate and adaptive immune systems

pathogenic bacteria

disrupt normal flora in gut and stimulate inflammatory responses

what is butyrate

a food allergy in infants

short chain fatty acid that is produced by several key gut bacteria

suppressed overactive immune response to foods

eubiosis

healthy lung microbiome

dysbiosis

long inflammatory disease

scope of the primary research article

the gut microbiome is responsible for contributing to many processes of human health and disease

there are responses to environment and lifestyle

westernized diet on gut microbiome (primary article)

as more countries move towards industrialization and urban environments, western diets are preferred over traditional foods from rural environments

what is alpha diversity

metrics used to assess diversity within a single sample, community or habitat

common alpha diversity metrics

observing amplicon sequence variants by counting

richness and evenness

richness of alpha diversity metrics

number of different species in a sample

evenness of alpha diversity metrics

describes how uniformly individuals are disturbed among different taxa

what is chao 1 index

alpha diversity estimator relying on species richness, it accounts for undetected species by incorporating rare taxa

what is shannon index of alpha diversity

diversity estimator accounting for evenness and richness

what is beta diversity

describes variation in species composition between different communities

bray curtis dissimilarity of beta diversity metrics

measures compositional differences (abundance) between two samples

unifrac of beta diversity metrics

incorporates both abundance and phylogeny to measure differences

weighted of unifrac

accounts for absolute abundances

unweighted of unifrac

accounts for presence and absense

takehome with mothers in primary article

the urban groups had higher BMI’s and increased abundance of microbial taxa previously found to associate with obesity (lachnospiracaea and enterobacter)

takehome of infants in primary article

urbanization was associated with slowed development of microbiome gut diversity in infants from T1 and T2 and urban babies were more susceptible to infectious diseases and allergies

what does the gastointestinal tract include

the mouth, the throat, esophagus, the stomach, small and large intestine, the rectum and anus

gastrointestinal tract functions

ingestion/digestion of food

nutrient absorption

immune defense

production of essential molecules

waste elimination

habitats of GI tract

firmicutes and bacteroidetes

what are the primary fermenters of the colon microbiome

bacteriodes and bifiobacterium (complex carbohydrates)

what are the secondary, tertiary and quad fermenters in the colon microbiome

Clostridium (glucose and lactose)

acetongenesis (make acetate)

methanogenic archaea (methane and hydrogen sulfide)

gut brain axis

the three way communication exits between the brain, the gut and the microbiome

what is the major point of communication between the CNS, the brain and the gut microbiota

the vagus nerve

this is linked to inflammatory diseases such as IBS

SAD (social anxiety disorder)

a highly disabling anxiety disorder with intense fear

the patients have distinct microbiomes (16s rRNA) from healthy control patients

complex ways to engineering and modulate the gut microbiome

whole diets, tailored diets, pre pro and synbiotics, fecal transplants and personalized nutrition

diet in terms of microbiome

has a pivot role in shaping the composition, function and diversity of the gut microbiome

diet impacts on gut microbiome

can have considerable negative influences or beneficial influences on the composition and functionality of the gut microbiome

mediterranean diet (the gold standard in preventative medicine)

high intake of unprocessed foods, whole plant foods, olive oils, dairy products, low amounts of red meat w

what does mediterranean diet do

increase secondary bile acids, increase SCFA fermentation pathway, increase dietary degradation and increase SCFA production

high fiber diet

rich in fiber, whole grain foods, fruits veggies, grains, beans, peas

what does high fiber diet do

increased lipid profile, decrease in colon transit time, decrease in inflammatory markers and increase of SCFA production

western diet

enriched in animal protein, saturated fats, simple sugars and ultra processed foods

what does western diet do

decreases SCFA production and decrease in intestinal T cells

ketogenic diet

loe carbs with moderate protein and high fat dietary (fasting)

what does ketogenic diet do

increased chronic inflammation, increased oxidative stress, increased dysrefulation and increased risk of metabolic disorders

metabolic disorders

red meat containing choline can lead to increased TMAO, a compound promoting atherosclerosis

intestinal disorders

animal production consumption is associated with reduced SCFA production and mucosal damage

what is the low FODMAP diet

low fermentable oligio, disacch, monosacc and polyoligios

this is used in treatment for IBS

prebiotics

the addition of one or more live beneficial bacterial strains to correct gut microbiome dysfunction

probiotic benefits

inhibits pathogens by competing for nutrition and binding sites

enhance tight junctions

contribute to immune homeostasis

prebiotics

fermentable carbohydrates with wide variety of chemical structures that promote growth of health gut microbes

ex is additional fibers

dietary fiber impacts

SCFA can reach circulation and have advantages to host health

g protein couple receptors are activated and trigger secretion of gut hormones

SCFA enhance gut barrier function

synbiotics

products that contain both pre and probiotics

designed to overcome issues with growth and survival of probiotic strains

fecal microbial transplants

a transfer of healthy donor gut microbiota to recipient with disease associated w gut microbiota dysbiosis

used to treat c diff

factors that influence fecal microbial transplants success

having a healthy donor with a good diet, stage of life and environoment

personalized responses to dietary composition trail (predict)

a series of studies that aims to predict individual metabolic responses to food, such as glucose, insulin and fat levels

overall goal of PREDICT

to design personalized interventions focused on key health outcomes

predict 1

associations between microbes and nutrients

they were driven by the presence and diversity of healthy and plant based foods