Unit 3 Flashcard Deck
(221 cards)
1
Q
What can microbes be thought of as?
A
independent, self-replicating factories that are great at bioconversion
2
Q
What is bioconversion?
A
The conversion of substance A to substance B through intracellular intermediates carried out by a biological entity
- biological entities can secrete enzymes into the environment that can carry out all steps of bioconversion outside of the cell
3
Q
What are polymicrobial communities?
A
- feeding networks
- cross-feeding
- syntrophism
- Microbes don’t live in a vacuum, so they are consistently subjected to living in environments with many different types of other microbes
4
Q
What is required to build the structures of microbes/
A
- carbon source
- nitrogen source
- sources of other elements (S, H, P, O, ions, other trace elements)
5
Q
What is required to make microbes perform their functions?
A
- enzymatic reactions
- transcription and translation
- transport molecules
- motility and directed movement (chemotaxis)
- nutrient acquisition
- cell wall synthesis and DNA replication
6
Q
What are the 4 main things needed to maintain the microbe in the environment?
A
1) replication
2) adaptation
3) repair mechanisms
4) power/energy
7
Q
What does metabolism do for microbes?
A
enables the processes required to maintain the cell
8
Q
What is metabolism?
A
- the sum of all chemical processes (reactions) in a living system
9
Q
What are the 4 chemical principles that make cellular metabolism possible?
A
1) Enzyme-mediated catalysis
2) reaction coupling
3) energy harvesting by redox reactions
4) use of membranes to form gradients of charge and chemical concentration
10
Q
What is enzyme-mediated catalysis?
A
catalysts that accelerate chemical reactions
11
Q
What is reaction coupling?
A
- when a conversion step is energetically unfavorable, it can be driven by coupling the reaction to a highly favorable one
12
Q
What is energy harvesting by redox reactions?
A
- oxidation is used to accumulate energy in a metabolically usable form, such as a proton pool or ATP
13
Q
What do gradients of charge and chemical concentration of membranes do for the cell?
A
biological membranes make it possible to transduce energy into metabolically useful forms
14
Q
What does replication do for microbes?
A
- self-replication with DNA as the blueprint
- builds the physical components of a cell
- helps to make or acquire the building blocks
15
Q
How do microbes adapt?
A
-adjust RNA profiles (transcriptome)
- modify the DNA
- change physical structures
- motility
- endospore formation/encystment
16
Q
What does repair do in microbes?
A
Damage to DNA, membranes, and proteins can occur from:
- free radicals
- UV light
- chemical reactions, etc
- exogenous substances and toxins
17
Q
What does cellular power do for microbes?
A
drives enzymes, facilitated membrane transport, nanomotors
18
Q
what can microbes generate energy from?
A
- charge differentials across a membrane
- electron transfer
- storage in high energy bonds of chemical intermediates
19
Q
Can concentration and charge gradients be involved in transportation simultaneously?
A
yes, commonly referred to as electrochemical gradient
20
Q
What is the concentration gradient?
A
Works in diffusion and is based off of the concentrations of uncharged/charged solutes
21
Q
What is the charge/chemical gradient?
A
Typically known as the membrane potential: a differential charge across the membrane layers
- used in the proton motive force
- H+ ions are used to be transported back into the cell, down the concentration gradient, and it tied to driving certain cellular processes
22
Q
What is special about oxygen when trying to create energy for the cell?
A
- oxygen is the strongest electron acceptor in nature
- is the terminal electron acceptor
- movement of electrons down the concentration gradient/ ETC is coupled with pumping of protons through the membrane = powering ADP phosphorylation
23
Q
What is the electron donor?
A
the substance oxidized in a redox reaction
24
Q
What is the electron acceptor?
A
the substance reduced in a redox reaction
25
What is special about NAD+ and NADH?
facilitate redox reactions without being consumed; they are recycled
26
What stores energy for bacterial metabolism?
The phosphate bonds in ATP
27
What are the reactants and products of glycolysis?
Reactants: Glucose
Products: electron acceptor (pyruvate)
28
What are the reactants and products of the pentose phosphate pathway?
reactants: Glucose-6-phosphate
products: Ribose-5-phosphate sugar and NADPH
29
What are the reactants and products of the citric acid cycle?
reactants: acetyl-CoA
products: new electron carriers, new oxygen reducers (NADH, FADH2, ATP, CO2)
30
What are some characteristics of the electron transport systems/
- membrane-associated
- mediate transfer of electrons
- conserve some of the energy released during transfer and use it to synthesize ATP
- Many redox enzymes are involved in ET
- NADH dehydrogenase
31
What is special about anaerobic respiration?
- depends on the availability of alternate electron receptors hat works with the specific electron carriers of that species
- generates less proton motive force and ATP
32
What is the terminal electron acceptor in Anaerobic respiration?
nitrate
33
What is the stepwise process of nitrate reductions called?
denitrification
- main biological source of gaseous N2
34
What are the enzymes of the anaerobic respiration pathway repressed by?
oxygen
35
What happens when there is no oxygen or alternate electron acceptor for the ETS?
- after a few cycles all of the reducing power in the cell is used up because they can not deliver their electrons since their shuttles are shut down
- TCA cycle stops and pyruvate builds up
- Fermentation occurs to use up the pyruvate and regenerates reducing power of the cell
- electron donor and acceptor are the same compound
-substrate-level phosphorylation
36
What are the end products of fermentation?
it depends on the microbe
37
What are genomics?
discipline of mapping, sequencing, analyzing, and comparing genomes
38
What is the genome?
entire complement of genetic information
- includes genes regulatory sequences, and noncoding DNA
39
True or false: each electron donor may use alternative enzymes, depending on the environmental conditions
true
40
What must the bacterial cell do in response to changes in availability of electron donors or terminal electron acceptors?
must encode the appropriate oxioreductases and change its transcriptional profile
41
What are the 3 stages of genetic information flow?
1) replication
2) transcription
3) translation
42
What can be used to predict some level of bacterial function/phenotype?
- DNA sequences (Genome)
- RNA Sequences and copy numbers (transcriptome)
- Protein sequences and copy numbers (proteome)
43
What is the relationship between genome size and gene content?
the larger the genome size, the more amount of genes that are present
44
What type of organisms have the smallest genomes?
parasites and endosymbiotic microbes
45
What is the estimated minimum number of genes for a viable free-living cell?
250-300 genes
46
True or false: If two prokaryotic genes have identical sequences, the enzymes they encode will have the same enzymatic activity?
- True for genes without introns; true for mature mRNA sequences
- prokaryotic cells typically lack introns
- False for eukaryotic cells and for prokaryotes with introns because splicing variants of a gene can alter enzymatic activity
47
What is the DNA sequence like for two enzymes that catalyze the same reaction?
- the DNA sequences of the two can be different
48
What is a function of genome size?
the percentage of an organism's genes devoted to a specific cell function
49
What are the 5 sources and chemical variations of glycans in the gut?
- plant saccharides
- mucus glycans
- mammalian tissue
- microbial glycans
- milk ogliosaccharides
50
True or false: there are species-level differences in their pathway functions?
True
- Example: there are variations in functional complexity among starch utilization system (Sus)-like systems
51
What is microbial ecology?
the study of microbes in their environment and their interactions with each other
52
What are microbiota?
the microorganism of a particular site, environment/habitat, or geological period
53
What is the microbiome?
the collection of microorganisms and their genes that inhabit a particular environment
54
What is the Metagenome?
the genomes of whole biological communities from a particular habitat
55
What is the metatranscriptome?
the total content of gene transcripts (RNA copies of the gene) in a community
56
What is the order of (bacterial) classification?
- Domain
- Kingdom
- Phylum
- Class
-Order
- Family
- Species
- Strain (for bacteria)
Each level has genetic differences
57
What are bacterial strains vs bacterial isolates?
- bacterial strains are of the same species but different in their genetic sequences, even by 1 nucleotide
- bacterial isolates may be of the same strain of different = may or may not be different in their genetic sequences
58
What allows for the different types of microbial activities in an ecosystem?
The following features of the microorganisms in each habitat
- the species present
- their population sizes
- the physiological state
59
What are the rates of microbial activity controlled by?
the nutrients and growth conditions that prevail
60
What are abiotic factors?
Non-living components like chemicals and physical structures of the environment that affect living organisms
61
True of False: every species has an optimal environment that it performs particularly well in.
True
62
What do the combination of abiotic factors present in an environment determine?
Whether or not a species can persist there
- all species have limits to the abiotic conditions that they can tolerate
63
What is the fundamental niche?
the range of environmental conditions under which an organism can survive, metabolize, and grow/reproduce
64
What happens as organisms are forced to experienced conditions outside of their fundamental niche?
- rates of reproduction decreases/stops
- as conditions become more extreme, an organism's sole function is to try and survive, rates of growth decrease/stops
65
What is a realized niche?
the conditions in which microbes are most successful, but can still inhabit other niches in which they are less ecologically successful = can still compete, metabolize and reproduce
66
What makes up the realized niche for microbes?
-metabolism/nutrients, environment (abiotic factors)
- ecologic/symbiotic factors
67
What is the realized niche in comparison to the fundamental niche?
the realized niche is a subset of the fundamental niche
68
What are characteristics of populations?
- derived from a single cell (clones)
- all cells of the same genetic strain
- populations can grow up as micro colonies
- populations interact to form communities
69
What are micro colonies?
aggregates of a few dozen to a few thousand cells
70
What are characteristics/definitions of communities/
- unified assemblage of multiple populations that coexist and interact at a given location (habitat)
71
What is a functional self-supporting system?
- ecosystem
- the combination of a community and habitat
72
What percentage of microbes are disease-causing/ human pathogenic?
much less than 1%
73
What is symbiosis?
close, prolonged physical or metabolic interactions between two or more populations
74
What is mutualism?
- both partner species benefit and may fail to grow independently
ex: lichens
75
What is synergism?
- two-way relationship where both partner species benefit through growth, but can still live independently as well
ex: mycorrhizae, rhizosphere: (plants and bacteria), microbiome of animals, bioluminescent bacteria and marine animals
76
What do mycorrhizae do for plants?
mycorrhizae uses the plants for a source of carbs/sugar in exchange for helping plants to fix nitrogen and extends the volume of soil accessible to the plants
77
What are the positive impacts of relationships between populations?
- enhances survival capacity of the interacting populations
- more efficient use of available resources than by an individual population
- populations can co-exist in habitats where neither could survive alone
- benefits and costs may not be equal across the relationship
78
What are benefits to bacterial mutualism?
- bacterial populations can complement each other so they can grow on minimal media
- mutualism is based on cross feeding of essential growth factors
79
What is commensalism?
A one-way relationship where one population benefits and the other is unaffected
- typically the unaffected population chemically or physically modifies a habitat so that the second population benefits
80
What is amensalism?
A one-way relationships where one population produces a substance that is inhibitory to another population
- first population gains a competitive edge as a result of its ability to inhibit the growth of competitive populations
81
What are the impacts of negative interactions between populations?
- limit population densities
- may eliminate a population that is not well adapted within the community of a given habitat
- colonization resistance
- maintain community stability in an ecosystem
82
How do resources typically enter an ecosystem?
- intermittently: large amount of nutrients may be followed by a period of nutrient deprivation
- produce intracellular storage polymers as a reserve materials when resources are abundant and use these sources when in a starvation period
83
When does competition occur?
- when two populations are striving for the same resource
- often it's a single nutrient present in limiting concentrations
- competition can also be for space, terminal electron acceptors, and other factors
- both populations achieve Lower densities than what they would alone
84
What do competitive interactions typically result in?
exclusion of a closely related population
85
What can competitive exclusion prevent?
two populations from occupying the same ecological niche
- the populations with a higher growth rate in the habitat will succeed over the one with lower growth rate
86
How do gut microbes prevent the invasion of pathogenic species?
- through colonization resistance = competitive exclusion via amensalism
87
What is neutralism?
low population densities and low metabolic activity permit microorganisms to co-exist without competing for the same available resources in the habitat
88
What do low rates of metabolic activity characterize?
the resting stages of microbes
- favors a lack of interaction
89
Why is neutralism more likely to occur at low population densities?
microbes are less likely to come in contact with each other
90
Why are actively growing vegetative cells less likely to exhibit neutralism toward other microbial populations?
because they are actively growing and thus competing
91
What is parasitism?
A one-way relationship where one population benefits and the other is harmed
- parasite derives its nutritional needs from the host cell or organism and damages the host
92
What is the difference between predation and parasitism?
- parasitism is a relatively long period of contact between organisms and the parasite is smaller than the host
93
When is the intensity of interactions between populations the greatest?
at high population densities and when populations are actively growing
94
A given species typically have an effect on what?
small number of other species, but not the entire community
95
True/False: the extinction of a single species does not have a long term effect on the viability of the community
True - other species in the community can usually provide the missing physical, chemical or metabolic elements to the community
- sometimes though, the loss of one species can have a disproportionate large effect on the entire community
96
The loss of what type of species can have a disproportionately large effect on the community?
- a keystone species
- exists in lower numbers
- may be predators, sources of food, synergistic species, or providers of some other essential factor for the community
97
True/False: the most abundant species or the major energy producers of the community are typically not the keystone species.
True
98
What is the order of species to recover in a damaged environment?
1) typically antibiotics are pretty resistant
2) primary/pioneer species
3) secondary/intermediate species
4) tertiary/climax species
99
What can environmental succession occur on?
- environments that are devoid of any pre-existing communities
- in environments where there has been big community disturbances but not complete elimination of some communities
100
What do the initial colonizers (pioneer/primary species) do in ecological succession/environmental recovery?
- alter the physical and chemical environment = allowing subsequent colonization of additional species
- each additional species alters the biotic and abiotic factors of the environment = allowing more and more additional species
101
What stops ecological colonization/succession?
- until a dynamic equilibrium is reached in the community between the populations, their biochemical and biologic activities, and the abiotic factors (climax community)
102
What is an indicator species?
- a species where their presence, absence, pr abundance can reflect a specific trait or characteristic of the ecosystem
- used as a proxy to indicate a change in the ecosystem
-reflect changes in a unique set of environmental qualities or characteristics found in a specific place, such as a unique microenvironment
103
What bacteria is used as an indicator organism for water quality?
- coliform bacteria
- potable and recreational water tested, its presence signals a potential for disease
104
What media type is most commonly used to detect coliform bacteria in water?
- medias that contain lactose as the primary fermentable sugar
105
What type of coliform is used mainly in water testing?
- fecal coliform, not all coliforms are fecal
106
What is a key bacteria in fecal coliform?
E. coli
107
What is a benefit for bacterial microbiota to use humans as a host?
Because humans have multiple cell types, there a many different relationships between a human host and microbes
108
What is a benefit to ecosystems with a higher species diversity?
they tend to be more resilient
- species are not all likely to be affected by a disturbance in the same way
109
What contributes to community richness?
What types of species is there
110
What contributes to community evenness?
how many of different species there are
111
what is Alpha diversity?
the diversity within a particular area or ecosystem
112
What is beta diversity?
a comparison of diversity between ecosystems, measured as the amount of species change between the ecosystems
113
What are the metrics used to make Beta Diversity comparisons between pairs of ecosystems/sites?
- Bray-Curtis dissimilarity
- Jaccard Distance
- Unweighted UniFrac
114
What is the Bray-Curtis dissimilarity Beta Diversity metric?
- examines abundance of certain microbes shared between two samples and the number of microbes found in each
- ranges from 0 to 1
- if both samples share the same number of microbes and the same abundance, the dissimilarity will be 0
- if absolutely nothing is shared, the value = 1
115
What is the Jaccard Distance metric of Beta Diversity?
- bounded between 0 and 1
- does not take abundances into account, only the presence of microbes in one or both samples
116
What is the unweighted UniFrac metric of beta diversity?
- considers the phylogenetic relationships between the microbes found in two samples
- the weighted version takes abundance into account
117
What is the matrix in biofilms?
a mixture of polysaccharides, proteins and nucleic acids
- the matrix binds cells together
-traps nutrients for microbial growth and help prevent detachment of cells in flowing systems
118
What are biofilms important for medically?
- implantable medical devices
- Wound-healing
- Dental health
- hospital acquired infections
- tissues
119
What are the benefits to enrichment culturing methods?
- obtain microbes from a natural sample
- can isolate organisms from a mixed community by manipulating growth conditions (media/temp) to select for a specific organisms
- can prove that a microbe lives in a habitat
120
What are the disadvantages to enrichment culture methods?
- cannot prove that a microbe doesn't live in a habitat
- requires you to know the nutrient needs of your organism of interest
- ability to culture an organism tells us nothing about their ecological significance interactions
121
What is culture media?
nutrient solutions used to grow microbes in the lab
122
What is defined media?
media that you know the exact chemical composition of
123
What is complex media?
composed of digests of chemical unknown substances
(yeast and meat extracts)
124
What is nutrient-rich media?
media containing many nutrients that allows a variety of microbes to grow (non-specific)
125
What is selective media?
Contains compounds that selectively inhibit growth of some microbes but not others
126
What are the pros and cons of enrichment cultures?
Pros: can price the presence of an organism, can isolate and organism from an environment
- cons: cannot prove that an organism does not inhabit an environment, says nothing about an organism's ecological significance
127
What is required for a successful microbe cultivation?
to know the nutritional requirements and supply them in proper forms and proportions in a culture medium
128
What is the "great plate count anomaly"?
only a minority of bacterial species have been cultures from all environments
129
How do we study microbes without growing them in the lab?
Via DNA
- all microbes have DNA
- organism specific
- predict functional capability
- if we know the DNA, we can predict the RNA and the proteins
130
What is capillary gel electrophoresis?
The process used in Sanger sequencing that separates DNA fragments based on size and run them through a thin, long tube containing a gel matrix
131
What are the ingredients needed for PCR?
- DNA template
- primers
- DNA polymerase (thermotolerant - often Taq)
- Heat and cool cycles
- buffer with nucleotides
132
What 4 methods constitute next generation/second generation sequencing?
- Pyrosequencing
- Sequencing by Synthesis (Illumina)
- Sequencing by Ligation
- Ion semiconductor sequencing
133
What are some characteristics of next gen/second generation sequencing?
- performing many sequencing reactions at the same time (parallelizing)
- outputs are short reads (5--50bps) at high accuracy
- most studies today use the illumination platform
- faster and more accurate
134
What constitutes first generation sequencing?
-Sanger sequencing
- Maxam and Gilbert Sanger chain-termination
135
What are characteristics of first generation sequencing?
- infer identity using dNTPs then visualize with electrophoresis
- 500-1000bps
- relatively slow and expensive
136
What is third generation sequencing?
PacBio, Oxford Nanopore
137
What are the characteristics of Third generation sequencing?
- sequence native DNA in real time with single-molecule resolution
- lower accuracy than NGS (~15% error rate)
- tens of kb fragments on average
- very fast
- long reads helpful for genome assembly
- read 10,000 bases in less than 2 hours
138
What sequencing types are short-read sequencing?
-First generation
- Next generation/ second generation
139
What sequencing types are long-read sequencing?
Third generation
140
What are characteristics of PacBio Third generation sequencing?
- read single DNA molecule in real time
- DNA polymerase at the bottom of the well with florescent tags
141
What are characteristics of Oxford Nanopore Third generation sequencing?
- Passes DNA through protein pores embedded in a synthetic membrane
- detector measures change in electric current
- generates extremely long reads of DNA seqs
142
How do you identify bacteria only by sequencing?
- small subunit ribosomal RNA genes
- found in all domains of life
- 16S rRNA in prokaryotes vs. 18S rRNA in eukaryotes
- functionally constant
143
What did rRNA do for phylogenetic studies?
established the presence of three domains of life
- provided a unified phylogenetic framework
144
What do differences in 16S rRNA do?
- the variability at some nucleotide positions allows for identification of uncultured bacteria
145
What areas of 16S rRNA are slow to change (sufficiently conserved) between species/strains?
stems with intramolecular basepairing
146
What structures of 16S rRNA is quicker to change (less conserved) between prokaryotic species?
loops
147
How do you identify bacteria using sequencing only?
- performs PCR reaction using primers form highly conserved regions that flank highly variable regions of 16S rRNA
148
What is comparative rRNA sequencing?
- used to build molecular phylogeny by:
- obtain cultures of pure bacteria
- amplification of the the 16S rRNA
- sequencing of the amplified gene
- Analysis of sequence in reference to other sequences
149
What is a phylogenetic tree?
- a graphic illustration of the relationships among sequences
- composed of nodes and branches
150
What do branches symbolize in a phylogenetic tree?
- define the order of descent and ancestry of the nodes (nodes demonstrate similarity)
- branch lengths represent the relative differences that have occurred along that branch from the last node
151
What is metagenomics?
total DNA from a microbial community is isolated and sequences without culture or enrichment
152
When can we use 16S rRNA sequencing?
to distinguish family, genus, and species levels
153
What do we use to differentiate/distinguish different strains?
shotgun metabolomics sequencing
154
What is the human microbiome?
the collection of microbes and their genes that inhabit the human body
155
what organisms constitute the human microbiome?
- bacteria
- viruses
- fungi
156
What is the ratio of human cells to microbial cells?
1:1
157
What are some characteristics of microbial cells in the human body?
- not evenly distributed
- not typically associated with disease
- often present in vastly diverse communities
158
What is the estimate of totally bacterial phyla that exist?
1300
159
What are the main 4 types of bacterial phyla that dominate humans?
- Majority are: bacteriodetes and firmicutes
- there are also Actinobacteria Proteobacteria
160
What is most commonly reported in studies?
The family, Genus, or Species levels
161
What is the scientific name rule at the Genus level?
- genus is written first and is capitalized
162
What is the scientific name rule at the species level?
- written in lower case
- written in latin
- italicized or underlined
163
What is a way to tell is a name is at the order level?
if the name ends in "ales"
- pronounced 'ay-lees'
164
What is a way to tell if a name is at the family level?
if the name ends in ceae
- pronounced 'see-ay'
165
What is special about each body site and their microbial communities?
- each body site is colonized predominately by only certain bacterial groups
166
What is special about the microbial types/taxa between sites and individuals?
the carriage of microbial taxa varies between these sites and individuals
167
What is special about metabolic pathways at each bacterial site?
- metabolic pathways for each site remain similar and stable within healthy populations
168
What's the debate of first contact in wombs?
- traditionally, wombs have been thought of as sterile, but some studies showed bacterial DNA in placenta and amniotic fluid.
- it is also believed in other studies that these findings are due to sample contamination
169
What happens at the time of birth?
- critical microbial exposure happens at birth
- maternal microbes + early-life microbiota leaves a lasting imprint on the biology of the offspring
170
What constitutes maternal microbiota and how is it introduced?
- vaginal, intestinal/fecal, breastmilk, and skin sources
- vaginal and fecal microbes are undergo vertical transmission
- intestinal sources are introduced via transplacentally
171
What is a major source in structuring the microbiome composition during early life?
- birth mode
- feeding mode
172
What adapts during the different stages of pregnancy?
- maternal microbiota and the immune system
173
What play key roles in fetal immunity?
- maternal microbiota and by products
ex: DNA, cell fragments, and metabolites
174
What constitutes the main source of microorganisms for neonatal microbial assembly?
- during vaginal birth
- maternal gut and vaginal microbiota
175
What is the main postnatal source of microorganisms and immune- modulating compounds?
- breastmilk
- drives neonatal microbiota and immune system development
176
What is special about breastmilk?
composition and complex and unique to each person
177
How is the needs of infants tailored through information in the breast milk?
during breastfeeding, there is a reverse flow of milk back into the breast = may serve as information
178
What occurs within the first 1,000 days of birth?
- parallel microbial-immune development in early life
179
What is Atopic March?
common progression of allergic symptoms from infancy to adulthood
180
What the order of allergic symptoms to develop and when do they occur?
1) dry skin: begins at birth
2) Eczema/atopic dermatitis: first few weeks or months of life - infancy
3) food allergies: first few months or years of life - infancy
4) Rhinitis/ nasal allergies: after age 3 - childhood
5) asthma: first few months to years of life - childhood
181
What are some causes of the atopic march?
- skin barrier damage
- microbiome alteration
- interferences of predicted genes
- social dysfunction of cells and molecules
- epigenetic factors
182
What types of people have lower rates of asthma and allergies?
- amish people/ people who live on farms
183
Why do people who live on farms tend to see lower rates of allergies?
- increased tolerance to microbial antigens due to widespread exposure from lifestyle factors
184
What is the hygiene hypothesis?
- early childhood exposure to particular microorganisms protects against allergies by strengthening the immune system.
- a lack of such exposure is thought to lead to poor immune tolerance
185
What happens in the small intestine/
- mucus, oxygen, and antimicrobial peptides regulate bacterial colonization and organization near the epithelium
- bacterial contact at Peters patches facilitates immune sampling of the microbiota
186
What happens in the large intestine?
- denser inner mucus layer protects epithelium
- outer mucus layer is colonized by many bacteria, phages, and immune factors
- in the lumen, microbes can attach to food particles and debris
- oxygen is highest towards the crypt
187
What are characteristics of Gut inflammation and inflammatory bowel disease?
loss of the protective mucus layer and uncontrolled bacterial contact
188
What are the 3 types of skin microenvironments?
- dry skin
- moist skin
- sebaceous skin
189
What effects chemical and bacterial composition of the skin?
- environmental factors (weather)
- host factors (personal hygiene, age)
190
What do microbes interact with on the skin?
- skin surface
- skin structures
191
What happens in a synergistic host-microbe relationship?
- host provides nutrients to the microbes
- microbes promotes epithelial and immune homeostasis and pathogen resistance via their products and occupation of metabolic niches
192
What does the microbe do in a pathogenic relationship?
- invades through the epithelium, causing inflammation and sometimes benefiting from the inflammatory response
193
What is special about the oral microbiome?
- the oral cavity has different habitats = different structures colonized by different subgroups of bacteria
194
What is a common bacteria among all structures in the oral microbiome?
streptococcus
195
How does the oral microbiome affect the rest f the body?
Bacteria can leave their place in the oral structure and get logded in other parts of the body like plaque buildup in the cardiovascular system
196
What are some characteristics of the lung microbiome?
- previously thought that the lungs were free from bacteria, but this is wrong. there is a low microbial biomass however
- humans inhale between 8,000-11,000 liters per day
- the lung does not have a mucosal surface (lipid- covered) like the GI tract.
197
Why is the healthy lung a low biomass site for microbe?
- aerobic environment
- ciliated
- Lower surface temperatures in trachea and bronchi
- external surface
- surfactant (host-produced detergent) in alveoli
- surfactant proteins and anti-microbial peptides
- little mucin (food for microbes) in alveoli
- contain alveolar macrophages (bacterial predator)
198
What are some ways to sample the airway microbiome?
- induced sputum
- bronchoalveolar lavage (bronchoscopy)
- end-bronchial biopsy (bronchoscopy)
199
What allows for microbial elimination in the lungs to have the host to become healthy again?
- cough
- mucocillary clearance
- innate and adaptive host defense
200
What types of microbial immigration occur in the lung to cause disease?
- microaspiration
- inhalation of bacteria
- direct mucosal dispersion
201
What are some regional growth conditions of the lung that can contribute to disease?
- nutrient availability
- oxygen tension
- temperature
- pH
- concentration of inflammatory cells
- activation of inflammatory cells
- local microbial competition
- host epithelial cell interactions
202
What locations of microbes are linked to asthma?
- lung and gut microbes have been linked to asthma
203
What can happen to metabolites produced by the gut microbiota?
-can travel and impact other organ systems
- vagus nerve and enteric nervous system thought to link the gut with the brain
204
What maintains homeostasis in the vaginal microbiome?
- commensal bacteria by interacting with epithelial cells
- loss of commensal bacteria can lead to increased microbial diversity and changes in immune and epithelial homeostasis
205
What is bacterial vaginosis associated with?
- loss of lactobacillus bacteria and is replaced with increased microbial diversity of unrelated bacteria
206
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Vaginal bacteria may be a useful marker for what?
- in identifying risk of pre-term birth
208
What diseases can bacteria near or on the teeth cause?
- dental caries
- tooth abscess
209
What diseases can be caused by bacteria in or near the periodontist (gums)?
- gingivitis
- periodontitis
210
What diseases can be caused by microbes in the stomach?
- Gastro-esophageal reflux disease
- use of proton pump inhibitors and H2 blockers
- Gastroparesis
211
What diseases can be caused by microbes in the lung that contribute to lung dysbiosis?
impaired clearance mechanisms
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What diseases can be caused by microbes in the oropharynx that contribute to lung dysbiosis?
- oropharyngeal dysphagia
213
What diseases can be caused by microbes in the nasal cavity that contribute to lung dysbiosis?
- anatomic abnormalities
- cystic fibrosis
- irritants and pollutants
- immunodeficiancy
- viral infections
214
What diseases can be caused by microbes in the nasopharynx that contribute to lung dysbiosis?
- defects in mucosal immunity
- ciliary dyskinesia
215
What are the 2 major outstanding questions and needs in human microbiome research?
- How do the unique relationships between the microbiome and the immune system influence health outcomes
- Understanding the substantial structural variations in species and subspecies that influence microbiome functionality.
216
What is the influence of microbiomes in precision medicine?
- based on microbiome data of different groups, different respective treatments can be used that is tailored to help those groups the best
217
How does the gut microbiome impact the way we process drugs?
- directly breaks them down
- can produce products that influence drug kinetics and travel in the body
- interferes with host metabolism of the drug
- modify bioavailability of the drug
218
What can trigger asthma attacks?
- allergens (mold, dust mites)
- pollutants
- stress
- tobacco smoke
- pests
- cold air
219
What are some recognized challenges in asthma?
- it can manifest in different ways
- responses to available treatments vary
- limited knowledge of processes behind variability
- imprecise or nonexistent biomarkers for some subtypes of asthma
- unmet medical need
- limited knowledge of contributions of microbiome across lifespan
220
What group of people have the highest rates of death due to asthma?
- black women
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