1
Q
what is the definition of altered microbial forensics
A
- discipline of characterizing microbio evidence
- to develop investigative leads
- in crim and civil cases
2
Q
who did the human microbiome project
A
- NIH USA
- 2007-2013
3
Q
what was the mission of the human microbiome project
A
to create tools that help us study the human microbiome and understand how it affects health and disease
4
Q
Originally thought that microbial cells outnumber human cells in the body ____ to 1
A
10
5
Q
we now know Originally microbial cells outnumber human cells in the body ____ to 1
A
1.3
6
Q
what are recent advances in human microbiome research
A
- investigating factors influencing the microbiome
- determining which factors influence changes in the human microbiome (dynamics)
- great deal of microbiome variation between individuals
7
Q
true/false great deal of microbiome variation between individuals
A
true
8
Q
what are some of the factors influencing the microbiome
A
- Human genetics
- Immune interactions in early
development - Body site
- Diet
- Antibiotics
- Lifestyle
9
Q
Organisms in the environment enter the body why
A
- to cause an immune response or
- to be added to the microbiota
10
Q
Understanding the relevance of differing microbiota between individuals is confounded by what
A
uniqueness of an individual’s microbiome
11
Q
how much of the human genome is identical
A
99.5%
12
Q
how much of human genomes are unique to an individual
A
0.5%
13
Q
true/false Current data suggests two individuals may show no overlap in the microbial species in their microbiome
A
true
14
Q
true/false the degree of personalization in the human microbiome is so high it might have forensic applications
A
true
15
Q
for translating knowledge of human microbiome functional applications, itll be critical to determine what
A
- strain level resolution (animal studies)
- disease relevant strains (population studies)
- identify biomarkers
16
Q
Prior to establishment of ______ analysis of microbes on a genome scale was expensive and time consuming
A
MPS technologies
17
Q
describe what analysis of microbes on a genome scale was like prior to MPS
A
- expensive
- time consuming
- no bioinformatic tools like databases
18
Q
what is metagenomics
A
- the direct genetic analysis of genomes contained in an environmental sample
- note: environmental means any environment like oceans or organs
19
Q
true/false advances in MPS and bioinformatics stimulated metagenomics
A
true
20
Q
what is problematic about what wikipedia thinks metagenomics is
A
- their figure focuses on sanger
- but really we use MPS
21
Q
a key resource for metagenomics are ____
A
databases
22
Q
how many microbial genomes were sequenced a decade ago vs now with MPS
A
- then ~300
- now ~74,400
23
Q
break down the microbial genomes that have been sequenced to some degree of completion with MPS
A
- 63,771 bacterial
- 1610 archaea
- 705 eukaryote
- 8,388 virus
24
Q
true/false some genomic databases are public
A
true
25
how many metagenome datasets at Integrated Microbial Genomes & Microbiome Samples (IMG/M) database
20,199
26
where does the skin microbiome habitate
on the outer layer of skin
27
describe the link between skin microbiome and forensics
- *using MPS tech, bioinformatics, and databases*
- researchers can use skin microbiome as a genetic signature
- to identify items they mightve contacted while committing a crime
28
why is it nearly impossible to get a genetic profile of human DNA following contact w an item
often LCN
29
how can LCN DNA be analysed
by increasing PCR cycles (stochastic effects)
30
how can LCN DNA be avoided
focus on hypervariable regions of mtDNA
31
how much bacteria can be collected by swabbing/scraping a cubic cm of skin
10-50k bacteria
32
why are researchers using AI to develop microbiome/ host association models
cause theres a massive amount of data obtained from microbiome analyses
33
are researchers using supervised or un-supervised machine learning
both/ either
34
the decision to use 16s rRNA vs WGS depends on what
- type of data required
- research question
- throughput requirements/ limitations
- cost
35
generally, if 16s rRNA or WGS better
- WGS is preferable cause it has better strain level info and higher resolution
- butttt note this requires higher throughput sequencing and more bioinformatic power
- *could maybe* use a hybrid of both
36
describe the hybrid approach of 16s rRNA and WGS
combines enrichment and sequencing of a small set of targeted, informative markers
37
what new method is being explored for human identification
using stable, universal clade-specific markers from skin microbiomes
38
what are some prominent genera found in the skin micobiome
- Proprionibacterium,
- Staphylococcus
- Corynebacterium
39
**true/false** there seems to be enough taxa in the skin microbiome to enable potential human identification
true
40
what is hid-SkinPlex
- a skin microbiome profiling assay for forensic human ID
- based on multiplexed targeted amplicon MPS
41
who developed hid-SkinPlex
Schmedes et al. (2017)
42
what is the accuracy of hid-SkinPlex identifying a person through samples from the foot, manubrium *(breast bone)*, and hand
- 92%
- 96%
- 100%
43
using hid-SkinPlex, how accurate was the prediction of the body site origin
86%
44
what issue was found during early hid-SkinPlex testing
- Some samples were misclassified
- repeated samples from the same hand sometimes differed more than samples from another person’s hand
45
What improvements are being worked on for the hid-SkinPlex assay
Adding new targets identified using the population-differentiation measure FST to improve accuracy.
46
what is FST
- A measure of population differentiation based on genetic structure
- calculated by comparing pairwise differences within a population to those between populations.
47
describe the mock case study comparing hid-SkinPlex to human STR/SNP profiling using skin swabs
- **Human STR/SNP profiles**: 32-52% complete *sooo lots of missing data*
* **hid-SkinPlex**: associated samples to human host w 100% efficiency *but this one is better so theres good potential*
48
what did tozzo et al 2020 do
- did a meta-analysis
- on state of the art for skin microbiome analysis
- found that there are lots of pieces of a puzzle, but not yet complete
49
what can PMI help us w
- validting or refuting alibis
- identifying suspects and witnesses
- reconstructing the death scene
50
**true/false** Estimating PMI to the hour of death is often impossible
true
51
why is estimating PMI to the hour of death often impossible
since this level of precision based on physical evidence alone is virtually nonexistent
52
when can using insect activity associated w a corpse be useful for PMI
- if the remains have been decomposing for days to weeks
- if theres insect activity *so not winter and less so indoors*
53
**true/false** microbial communities have been shown to change in a predictable, clock-like manner, during decomp
true
54
what is decomposition
The return of a cadaver to its chemical constituents through chemical decomposition and the action of organisms that consume tissues
55
in decomp, do organisms work inside-out or outside-in
both/either
56
what influences the decomposition processes
- climate
- weather
- geography
57
investigators determining PMI work ____ *(backwards/forwards)*
backwards
58
what are the stages of decomp
- fresh
- early-decomp
- advanced-decomp
- skeletonization
59
what types of changes happen during the fresh stage of decomp
- *some outwards signs of change butttt*
- cellular and biochemical level *mostly*
- initiated by oxygen deprivation
60
what are the diff elements within the fresh stage of decomp
- algor mortis
- rigor mortis
- liver mortis
61
what is algor mortis
the body equilibrates to ambient temperatures
62
what is rigor mortis
the entire body stiffen ultimately due to the locking of actin and myosin proteins
63
what is livor mortis
areas of the body in contact with a surface discolor because of pooling of blood (due to gravity)
64
what ends rigor mortis
autolysis
65
what is autolysis
destruction of cells/tissues by their own enzymes
66
describe the bacteria during the fresh stage of decomp
- those that dont require a living host
- and those not restricted in growth cause immune system
67
describe insect evidence in the fresh stage of decomp
- blow flies (calliphoridae)
- may lay eggs in protected areas
- like eyes, ears, nose, body, thicker hair
68
describe what happens in early decomp
- rapid changes at biochem and microbial levels
- skin begins to slip off in large sheets
- hair falls out
- remains turn gray/green then black
- active putrefactiom w fermentation and proteolysis
69
describe the bacteria during early decomp
- gut decomposes so bacteria enters in and moves through circulatory system
- metabolizing blood and making black residue
- anaerobic bacteria proliferate and produce gases causing the remains in bloat
- thennn the pressure of the gases forces fluids out *purge*
70
describe the insects during early decomp
- eggs hatch
- adult flies lay more eggs that hatch
- maggot masses travel around the body
- spread digestive enzymes and bacteria
- necrophagous beetles and parasitic insects may also colonize the body now
71
when does advanced decomp initiate
- caving of the flesh of the eyes, throat, and abdominal cavity
- orrr post-purge
- *diff people say diff times*
72
**true/false** advanced decomp is wet
- **false**
- a drier stage
73
what is putrefication
anaerobic decomp of organic matter by bacteria/fungi
74
describe insects activity in advanced decomp
- fly activity declines
- coleoptera that like drier substrates may continue
75
describe skeletonization
- all soft tissues are eliminated, leaving dry bone
- may last months-years
76
describe insect activity during skeletonization
none
77
describe scavenging activity during skeletonization
- mostly gone
- except those that use bone
78
what are the effects of temp, humidity, rainfall, and soil on decomp
- **change tempo and mode**
- may enter multiple stages of decomp at once
- may bypass a stage
- may prolong a stage
- *basically makes PMI inaccurate*
79
in first few days of decomp, estimating PMI is aided by what
knowledge of algor mortis, rigor mortis, and livor mortis
80
At 20°C rigor mortis sets in at ______h after death and persists for _____ h
- 2-6 h
- 24-84 h
81
Livor mortis begins between _____h after death and will continue to develop up to _____
- 30 min and 3 h
- 12 h
82
**true/false** temp affects PMI
trueee
83
what does ADH and ADD stand for
- accumulated degree hours
- accumulated degree days
84
what Two methods are used to assess PMI based on insect colonization
1. age of the maggot (short-term evaluation) and
2. the succession pattern of an insect community (long-term evaluation)
85
**true/false** studies on insects are location specific
often yes
86
**true/false** Succession of different microbial communities can indicate PMI
true
87
how does MPS allow microbial succession patterns to be characterized
cause thousands of microbial taxa can be profiles per sample
88
how do we collect microbial data from decomposing bodies for regression models
1. collect data from multiple decomposing individuals
2. to start processing: extract DNA
3. PCR amplify taxonomically informative DNA regions:
4. the **16S rRNA** amplicon to survey **bacterial and archeal** populations present in a microbial community
5. the **18S rRNA** amplicon for **eukaryotic** characterizations
6. the internal transcribed spacer (**ITS**) gene region is used for **fungi**
7. give data to AI so they can develop regression models so that later on w unknown PMI bodies, it can predict it
89
Animals smaller than humans enable the use of what
- larger sample sizes
- easier manipulation
- lower cost
- greater accessibility
- more rapid growth
- reproduction
90
using mice as a model system, they could predict PMI within a ____ day-window over ____ days of decomposition
- 3-day
- 48 days
91
microbes may not be informative for PMI on humans until after ____hours postmortem
48
92
When a mammalian corpse decomposes the nutrients released do what to the soil
- enable selective growth of specialized soil microbial communities
- these appear in consistent patterns
93
**true/false** the microbiome assessments of soils associated w decomposing carcasses for PMI had similar errors to the skin studies
true
94
what are grave soils
soils associated with decomposing carcasses
95
**true/false** similar microbial clocks of decomp are present across soil types
true
96
**true/false** seasons influence microbial communities
true
97
how do seasons influence microbial communities
diversity of bacteria and eukaryotes is higher in the summer
98
what variable helps PMI across seasons be more accurately predicted
using ADD
99
**true/false** Carcass mass had a significant impact on the succession of microbes
false
100
**true/false** Insect abundance influenced the pattern of microbe succession
false
101
what are the knowledge gaps in microbiome analysis
1. A complete understanding of whether nonhuman models are useful for development of microbial clocks
2. Time frame(s) for which microbes are most informative for building a microbial clock
3. Which environmental variables are most useful for model improvement
4. The effect of the initial condition of the remains on the microbial clock
5. Sample type that is most informative for estimating PMI
6. Robust methods and parameters for modeling
102
what are the steps needed for microbiome analysis to be adopted by the justice system
* Recognize a need
* Address through research
* Publish/communicate
* Validate prototype *(accepted by the FS community)*
* Adopt as new tool
103
Microbial
flashcards
Decks in class (15)
# Cards
-
Intro45
-
Pandemics and Epidemics23
-
Risk Assessment and Societal Infrastructure99
-
Disease and Microbial Forensics Investigations116
-
4: Organisms- Viruses183
-
5: Organisms: Fungi161
-
6: Organisms: Bacteria121
-
9: Food Security & Agricultural Attack109
-
10: Microbiome Analysis103
-
11: Toxin Analysis & Nucleic Acid Analysis153
-
Sequencing from Lab DNA21
-
12: DNA sequencing, genome assembly, DNA diagnostics84
-
13: Emerging Pathogens118
-
Maybe long answers3
-
Important i think149
