Topic 7 - Diet, the gut microbiome, & human health (PART 1) Flashcards
Define microbiome
the collective genomes of the micro-organisms in a particular environment
The first meaning is an inclusive one that refers to an entire habitat where microorganisms dwell, and encompasses the microbes, their genomes, and the surrounding environment.
The second, narrower, meaning is “the collection of genes and genomes of members of a microbiota.”
Define microbiota
the community of micro-organisms themselves
Define microbiota diversity
a measure of how many different species, and dependent on the diversity indices, how evenly distributed they are in the community
lower diversity is considered a marker of dysbiosis (microbial imbalance) in the gut and has been found in autoimmune diseases & obesity and cardiometabolic conditions, as well as in elderly people
Define colonocytes
epithelial cells of the colon
Define germ-free animals
animals that have no micro-organisms living in or on them
Define short chain fatty acids
fatty acids with 2 or 6 carbon atoms that are produced by bacterial fermentation of dietary fibres
How were microbiomes studied in the ‘olden’ days?
- microscopes
- culture dependent methods (pure culture)
problem is that not everything can be cultured
What are the main challenges of new sequencing techniques used to study microbiomes?
- hard to distinguish them via morphology
- hard to grow
or is this culture-dependent technique challenges??? I think it might be
DNA to understand the taxonomy of microbes
- conserved regions are agreed upon to use as a barcode
- must be conserved for all microbes but different enough to tell species apart
- established protocols to extract DNA, amplify DNA, and determine barcode
What is the V4 region of ribosomes?
- the region in purple is the area that is amplified by DNA primers
- it is agreed upon as a way to taxonomically distinguish bacterial species
Why can’t the V4 region be used to classify fungi?
Because one of the differences b/w bacteria & eukaryotes (like fungi) is that we have different ribosomes & thus diff ribosomal subunits
a different subunit would have to be amplified for the fungi
How does sequencing occur?
- targeted regions are amplified (bioinformatic treatment)
- merge 2 together
- then we cluster them together based on similarity (OTU)
- when we put that through a data base to assign taxonomy, we can determine which species each sample belongs to
- the abundance can also be determined
What is alpha diversity?
a measure of species richness (number of taxa) within a single microbial environment
- how many different microbial species could be detected in a specific sample
What is beta diversity?
a measure of diversity in microbial community b/w different environments (difference in taxonomic abundance profiles from diff samples)
- how different is the microbial composition in one environment compared to another
How can we work out what the gut microbes are doing?
- diff techniques to amplify the DNA and assemble into WHOLE genomes (shotgun sequencing)
- gives the whole genome, and can link this to the microbiome
- can understand a pathway which is being expressed when RNA is used
“metagenome”
What are the 3 basic functions of microbes?
1) digest food components
2) produce vitamins
3) stimulate the immune system
If we transplant a stool sample from an obese mouse to a normal mouse, . . .
the normal mouse becomes obese
Low FODMAP diet
- increased actinobacteria
- high FODMAP diet decreased abundance of bacteria involved in gas consumption
- reduced IBS
Shown in human observational studies + human interventional studies
Fibre & prebiotics
- increased microbiota diversity & SCFA production
- reduced type 2 diabetes & cardiovascular disease
- human obs studies + human interventional studies
How is the microbiome distributed throughout the body of the baby?
newborn babies have similar microbiomes in all sections of their bodies
- vaginal delivery have vaginal-like microbiomes
- caesarian delivery have skin-like microbiomes
The developing gut microbiome - early gut colonization has 4 phases
- Phase 1: Sterile gut
- Phase 2: initial acquisition - vagina, feces, hospital
- Phase 3: breast-feeding or bottle-feeding (different)
- Phase 4: Start of solids; move to adult flora
(Bifidobacteria remain key flora into adutlhood)
What is the difference in microbiomes b/w breast-fed vs bottle-fed babies?
- Breast fed more bifidobacteria (up to 90% of flora)
- Bottle fed more diverse; more Bacteroides, and Clostridial species
What are HMOs good for?
- they help bifidobacteria to grow & proliferate
- it competitively excludes pathogens from binding
- decoy for other microbes to attach to so they can be removed
- macronutrient digestion
- development of mucus layer
- HMOs affect bifidobacteria and promote growth of SCFAs
What is the effect of SCFA?
- help the growth of enterocytes and use them for energy harvest
- also involved with anti-inflammatory cytokines
- involved in immune modulation
Adult microbiome
- both genetic and environmental factors
- increasing diversity of flora as awe age
- in some newer PCR studies, up to 92% of the flora in adults were “novel” species
- serial stool collections show remarkable stability by an individual
Who first discovered microorganisms in the body?
Leeuwenhoek
- made a simple microscope
- found them in dental plaque and a stool sample
What challenge did Robert Koch find during the “golden age of bacteriology”?
- He required a solid medium that would support bacterial growth (to obtain pure cultures)
- his associate’s wife eventually suggested agar
- he impact on medical microbiology was immediate
What was the great plate count anomaly?
most of the microscopically observable microorganisms in an environmental sample could not be cultured in the lab
Usually, between 1.0% and 0.1% of the total bacteria could be accounted for by the standard plating method.
What amazing discovery did Woese make?
- he used a molecular phylogenetic approach for tracing human history
- he couldn’t use fossils bc most microbes can’t be fossilized
- he took cellular
ribosomes and undertook a comparative analysis of the sequences of one component: the
small subunit ribosomal RNAs or SSU rRNAs. - Woese reasoned that the
similarities and differences between these sequences (i.e., the order of
the four chemical bases—adenine, uracil (or thymine in DNA), cytosine,
and guanine) would reflect the phylogenetic relationships of the organisms from which they were obtained.
Based on the SSU rRNAs, what did Woese find?
he found that there are 3 domains of life, 2 prokaryotic (bacteria, archae), and 1 eukaryotic
- eukaryotic cells have 18S rRNas
- prokaryotic cells have 16S rRNAs
The SSU rRNA sequences not only contained unique short sequences that defined the three domains but also contained unique sequences that permitted assignment of cells to specific phyla
Which 2 primary inventions expended the range of applications for SSu rRNA analysis?
- Sanger sequencing in 1977
- polymerase chain reaction (1980)
permitted the cloning and sequencing of SSU
rRNA genes from DNA samples extracted directly from environmental
samples
What is metagenomics?
sequencing of entire genomes
What happens in whole-genome shotgun sequencing?
DNA sequences are randomly broken up (shot-gunned) into smaller DNA fragments; computer programs reassemble the complete sequence by taking these fragments and looking for regions of overlap
What do metagenome sequences provide info about?
they provide info about which bacteria exist in a microbial population and at least a partial prediction of what functions are encoded by its genes
Proportion of microbes in / on the body
- 1% to 3% of body mass
- bacteria vastly outnumber the other kinds of microorganisms
- ratio of bacterial cells to human cells is about 1.3 to 1 (NOT 10 to 1)
What was the goal of the Human Microbiome Project?
to catalog the bacterial taxa associated with different body habitats on the healthy human
What were the main findings of the Human Microbiome Project?
- there is substantial variation in microbial community composition & diversity at diff body habitats
- oral & intestinal communities were very diverse, vaginal communities less so
- no taxa were universally present in all body
habitats and individuals - there is a high degree of stability in microbiome variety within an individual
What was the goal of the Metagenomics of the Human Intestinal Tract?
to link the genes of the human intestinal microbiota to a broad range of states of both health + disease
focused on IBD and obesity
What were the key findings of MetaHIT?
- each individual carries over 536,000 unique genes, indicating that most of the gene pool of 3.3 million (non-redundant genes) was shared by the entire cohort of humans
- Almost 40% of the genes from each individual
were shared with at least half of the individuals of the cohort. - most of the genes cataloged were of bacterial origin (only a tiny percentage were archaeal & eukaryotic)
- bacteroidetes + firmicutes are most prevalent
The integrated gene catalog (IGC) contains. . .
the most comprehensive intercontinental catalog of reference genes for the gut microbiota discovered to date
What is the Human Oral Microbiome Database?
a web-accessible collection of info on the ~700 prokaryote species detected in the human oral cavity
- created from 16S rRNA gene sequence
data
- aimed to determine the relative abundance of taxa in the oral cavity and identify new candidate taxa
What are OTUs (operational taxonomic units)?
when researchers sample a community, they take bacterial sequence data and cluster together members that probably belong to the same taxonomic groups - they define “UTOs”
UTOs are similar bacterial individuals, which could be phyla or species
What is richness?
the number of species in a biological community, not taking into account the abundance of each one
What is evenness?
the number of individuals from each species in the community - the distribution of OTU abundance
How is diversity usually represented?
by the Shannon index
Taking into account the number of species and how individual bacteria are distributed among those species, the index measures how statistically difficult it would be to predict the identity of the next bacterial
individual sampled, given what is already known about the community.
The more rare species there are in the sample, the higher the value.
The Shannon
index positively correlates with both richness and evenness.
What is the holobiont?
the host along with all its associated microorganisms
What is the hologenome model?
considers the host genome and microbiome together as a unit of evolution that undergoes selection
How many bacterial cells can we find in and on our body in comparison to the number of human cells?
similar
How can the 16S rRNA gene be used to identify bacterial species?
It has a conserved and variable region. The variable region can be used to identify species.
What is community profiling?
It is a method to find out what microbes are present in a sample and it is done by using 16S rRNA gene sequences.
The FUNCTION of microbes is NOT described by either. . .
shotgun sequencing OR 16SrRNA gene sequencing
What does 16S rRNA gene sequencing tell us?
16S rRNA gene sequences tell you something about community diversity i.e. what microbes are found in the sample?
What does shotgun sequencing describe?
It describes the gene content i.e. the long stretch of the nucleotides A, C, G, T
What would be the benefit of knowing a causative link between the gut microbiota and disease?
When a causative link has been proved, we might be able to modulate the gut microbiota to diagnose, prevent or cure diseases.
What does “human microbiome” refer to?
the collective genes of the microbial community associated with humans
The beneficial role of dietary fibre in the large intestine has been proposed to be:
Both as a substrate for gut microbes to degrade and by production of short chain fatty acids from bacterial digestion.
What are the major trends we see in the human microbiome?
Different body sites generally host different communities of microbes (e.g. the gut has more Firmicutes than the skin on average).
What can we say about the number of microbial genes compared to the human genome?
The number of microbial genes is about 100 times larger than that of the human genome.
What approximate percentage of the gut microbiota has been cultured so far?
About 30% of our gut microbiota has been cultured. Culturing means that we grow them in a specific medium to study them separately under controlled conditions. So about 30% of our gut has been cultured, which may not seem like much. However, for example in soils only <1% has been cultured.
What kinds of vitamins can microbes produce?
vitamin K
B12
How are gut microbes in involved in immune development?
- Induction, training and function of the immune system is done by a meet and greet with microbes.
- This helps the immune system to figure out which microbes keeps the body healthy and which causes disease.
- If the immune system does not work properly food allergies and auto-immune disease can develop.
What are some processes that microbes are involved in?
a) The production of vitamins that we can absorb and use.
b) The digestion of food.
c) The influencing of our weight gain and weight loss.
Indicate if the following statement is true of false.
To find out what microbial species we are dealing with we use a microscope.
FALSE
Compare the gut microbiome in the first few weeks of life vs later on
The gut microbiome is dynamic in the first weeks of life, with lower
diversity and higher variability; a transition to higher diversity and lower
variability occurs as development proceeds.
What can lead to disruptions in gut microbiota?
infections, antibiotics, and drastic changes in diet can lead to disruptions
In older adulthood, the composition of the gut microbiota begins to shift toward. . .
LESS diversity & more pro-inflammatory species
Does the placenta contain any bacteria?
- Was initially believed to be sterile
- Now found to contain a set of culturable bacteria
- Prior to this, the presence of bacteria was diagnostic for adverse pregnancy outcomes
- The TYPE of bacterial taxa present (not the mere occurrence of bacteria in the placenta) may be what initiates intrauterine infection & leads to adverse pregnancy outcomes
Where does the placenta likely get its bacteria from?
- Most likely from the oral microbiome
What types of bacteria are found in the placenta?
- nonpathogenic commensal microbiota
- Firmicutes, Tenericutes Proteobacteria, Bacteroidetes, & Fusobacteria
How does the baby acquire most of its microbiota?
The act of passing through the birth canal in a vaginal delivery and thus coming into contact with the maternal feces and vaginal microbiota influences the infant’s gut microbiota composition at birth
The first colonizers of the infant gut in vaginal birth are
Facultative anaerobic bacteria, such as Staphylococcus
How is the bacterial composition different in C-section babies?
- infants born by C-section harbor bacterial communities similar to those found on the skin surface and in the
hospital environment - The gut microbiota of infants delivered by C-section appears to be less diverse
- a substantial absence of Bifidobacterium and Bacteroides species, accompanied by an increase in the presence of Clostridium difficile
Elective vs Emergency C-section
- Colonization of the infant gut is also affected by elective versus emergency Cesarean delivery, as bacterial richness and diversity is lowest among infants born by elective C-section and highest among those born by emergency C-section
- Researchers speculate that during emergency C-section, the infant is still exposed to many species from its mother’s microbiome before surgery is initiated, which may account for the differences
Other ways babies can be exposed to microbes
feeding, kissing, caressing, diet
Children born by C-section are at an increased risk of . . .
allergies and asthma
also associated with higher body mass + childhood obesity
One study found that microbiota of babies born via C-section vs vaginal birth is similar after 6 weeks. They found that _______ was the strongest determinant of bacterial community composition & function
body size
4 factors that are known to alter the guy microbiome are associated with a higher rate of Cesarean surgery
1) diet
2) antibiotic exposure
3) gestational age
4) host genetics
Maternal high-fat diet during gestation & lactation is associated with. . .
a distinct microbiome in the newborn’s stool, with a notable depletion of Bacteroides
Preterm infant
- displays increased occurrence of potential pathogens
- high interindividual variability
- reduced microbial diversity
- harbor increased levels of facultative anaerobic microorganisms (e.g. Lacobacillus)
What are some of the health problems experienced by preterm infants?
- delayed maturation of immune system - can increase risk of infection
- have reduced levels of Bifidobacterium
- Necrotitizing enterocolitis (NEC) is a serious gastrointestinal disease occurring in preterm infants
- cause and effect not clear
increase in proeobacteria, decrease in firmicutes before diagnosis of NEC
Mode of feeding on babies
- The gut microbiota of breastfed infants is dominated by Actinobacteria: in particular, beneficial species of Bifidobacterium
and Lactobacillus - The formula-fed
infant develops a more diverse microbiota, with fewer bifidobacteria and
more pathogens - Human breast milk contains, in addition to live bacteria, a great variety of
complex carbohydrates called human milk oligosaccharides
Are HMOs digestible by infants?
No
Instead, these sugars are digested by selected bacteria in the infant GI tract that
are genetically equipped to break them down: specifically Bifidobacterium infantis
modulate the intestinal microbiota of breastfed infants and act as prebiotics by enriching certain beneficial bacteria
and promoting the release of short-chain fatty acids that feed the infant gut.
What are some other benefits of breastfeeding?
- long-term benefits as well as short-term benefits (lowered risk of infectious diseases in childhood)
- long term: a lower prevalence of
overweight/obesity, protection against type 2 diabetes, and even increased
performance on intelligence tests
What is the most significant factor shifting the microbiota toward a more diverse and stable adult-like composition?
weaning
How does gut microbiota change after introduction of solid foods?
- more complex microbiota
- bifidobacteria proportions drop as mirobiota diversifies
- facultative anerobes decrease
- strictly anaerobic clostridia increase
- proportions of bacteroides remain unchanged & are one of the most PREDOMINANT groups in infant after weaning
- higher prevalence of butyrate-producing bacteria
their ability to easily metabolize the complex carbohydrates
that have been introduced into the diet
In contrast with adults, the average healthy child has a gut community with significantly ______ abundances of Bacteroidetes & significantly _______ Firmicutes & Actinobacteria
lower
greater abundances
with age comes diversity
Although the reasons for
lower microbial diversity in children are not clear, they are likely related to
children’s more limited environmental and dietary exposures.
How do the functions of the microbiota differ in children vs adults?
Compared with adults, children have gut microbial communities that are enriched in functions that may support ongoing physical development
the microbiota of adults
is enriched in functions associated with inflammation and increased risk of
adiposity (or obesity)
also, kids (DNA, replication, repair, growth, development); adults (synthesis of vitamin B12, folate)
Kids have higher than adults
Bifidobacterium
Besides early diet, other
factors that may influence the early colonization process in children include
antibiotic exposure, farm exposure, place of birth, and the presence of siblings and
household pets
What are the main external factors that can affect the composition of the microbiota in healthy adults?
infection, major dietary changes, antibiotic therapy, other medications
Old age and gut microbiota
Increases in the relative abundance
of Bacteroidetes (over Firmicutes) and Proteobacteria are observed, with reductions in Actinobacteria, including important Bifidobacterium strains, as aging proceeds.
A centenarian’s microbiota is characterized by. . .
an increase in pathobionts with a decrease in the numbers of butyrate-producing bacteria
lower microbial diversity is associated with increased FRAILTY and INFLAMMATION
Which kind of elderly person has the highest diversity in gut microbiota?
- an older adult living in a community setting who consumes a low fat / higher fibre diet that includes a variety of foods
The majority of viruses in the gut are . . .
bacteriophages
but the virome is mostly unexplored
