Microbes Pt3: Lec 9-11 Flashcards
(22 cards)
What is microbiota?
members of a community of microbes in a specific environment
What is a microbiome?
all genes contained within the microbiota members
Explain dysbiosis:
condition of unbalanced microbiota and microbiome structure caused by external factors (medication or disease)
What are the main functions of gut microbiome?
- Breakdown food into material:
“Digestible” food broken by stomach and small intestine enzymes
“Non-digestible” food broken down by large intestine microbes (e.g. fiber)
SI → LI (Oxygen↓, Nutrient levels↓, pH↑, Bacteria↑) - Pathogen Resistance - fill these ecological niches with symbionts and commensals
- Stimulate Immune System - prime the immune system for later infections
What are the main bacterial phytes in the human gut?
Main Bacterial Phytes: Firmicutes and Bacteriodates
What is the main archaeon in the human gut?
Main Archaeon: Methanobrevibacter
Explain IBD and how it realtes to the human gut:
IBD (Inflamed Bowel disease) - chronic gut inflammation - most prevalent in industrial countries
Clinical and Experimental data suggests dysbiosis is major to IBD: as patients showed decreased microbiota diversity compared to healthy guts
List 3 ways we can manipulate the human microbiota, how it helps, waht methods are used for each step, and where it might go wrong:
- Manipulating Diet (Biophilia) - animal diets showed increased Biophilia bacteria linked to IBD symptoms
Tracked through stool - but diet it very easy to manipulate (yay!)
Prebiotics - food ingredients that help species changes to microbiota leading to beneficial results - Introducing Beneficial Bacteria
Faecal microbiota transplantation (FMT or FTT) - oral capsules taken to transfer whole microbial communities from one person to another
Very successful to treat Clostridioides difficile infection (CDI) - pathogen that releases toxins in gut causing colitis and diarrhoea.
Probiotics - “good” living microbes - Eliminate Undesired Bacteria
Phage therapy - targets specific undesired microbiota members
Antibiotics - modifies microbiota (could cause good bacteria to die off and cause CDI)
define the two types of cultivation of microbes:
Pure cultivation - when only one strain is studied in a cultivation
Co-culture - when two or more strains are cultured together
Explain shotgun metagenomics:
untargeted sequences of extracted DNA (all genes) enables to determine functional potential of community
Define metatransciptomics:
untargeted sequences of extracted RNA that tell us what is being expressed. Tells us the actual activity
waht is metaproteomics?
proteins produced of microbes used to understand the function and potential of said proteins
What is metametabolimics?
metabolism of the microbe community and how ti realtes to the function and drive of the microbe
What is functional redundancy and why it is important?
multiple species that have the same ecological niche - if one dies, there’s another to replace it
More redundancy allows for ecosystems to stay stable, avoids species going extinct
Explain the Bromeliad Microbiome case:
prokaryotic community vary greatly between leaves
Functional gene groups are highly consistent between bromeliads - even thought prokaryotic identity species varied greatly
Explain the difference between potatial and expression of genomes in microbes and give an example
genomes contain lots of information that’s never expressed - these expressions change by environment
(Expression - mRNA turned to proteins) mRNA fragmented → reverse transcription to cDNA → sequenced cDNA to original sequencing → alignment and genome sequencing)
Example: Antibiotic resistance genes in microbes (ARGs)
No consistent relationship between number of genes and number of transcriptions expressed - the expression depends on the growth conditions!
*This is why metatranscriptomics is so important!
Waht is biogeography?
the study of distribution of biodiversity ove space and time to reveal where organisms live, their abundance, and why
What si the first argument about microbe biogeography placement and explain?
Microbes are Everywhere (Cosmopolitan distribution): First arguement
Microbes can disperse anywhere, the only thing stopping them is the environmental conditions
Supported by the fact the microbes are extremely abundance and are extremely small and can thus travel far distances by natural means very easily
Even on local scale with humans - human microbes are fully dispersed within hours
supporting case study: Priest Pot: Fenlay group: studied free-living protists and found that 43/50 species were present in the one pond.
Explain why smaller organism distribution supports the cosmopolitan distribution of microbe biogeography dispersal:
Smaller the organism the easier it is for global distribution:
The larger it is → less likely the are able to successfully disperse
Ubiquitous dispersal → mean lower global species diversity as richness would be high but diversity would be lower (risk of extinction would be lower)
Seen in protists and insects
What si the second arguement of microbe biogeography?
Microbes are non-uniformly distributed: Second arguement
Based on dispersal limits = exist for larger organisms → evidence this is true for microbes
Dispersal of Fungi: show geography endemism is a key feature for fungle communities
Show a relationships between distance and species but appears to have limits
More distant → more different
Explain tuatara gut microbiology (background info, results, and health)
Background info: gut microbiomes can influence a lot about its host, tuatara are genetically unique coming from an extinct lineage of reptilian species, and are geographically isolated
Data collected from different groups of tuatara to see if bacterial microbes, parasitism are different (testing bacteria through 16S rRNA)
Results: Bacterial communities shifted by sanctuary and had lots of overlap
Bacterial influenced by health - and many bacteria shared but very different from other reptiles
Explain the 1000 Hot springs - Matt Scott Case Study
Measured bacterial and archaeal community compositions (16S rrNA) and 46 physicochemical parameters from NZ hot springs
Study had a large temp and pH range
Microbial diversity driven mostly by pH, not temperature (except 70*)
