Deck 17: Metagenomes: Genome Analysis of Communities

Question 1

What is a metagenome?

A) All the bacterial genomes in a niche
B) All the genomes of all the individuals of a species
C) The genomes of an individual and all their close relatives
D) The genomes of all the organisms in an environmental sample

Answer 1

The genomes of all the organisms in an environmental sample

Question 2

Match the missing words in the following phrase. The majority of species considered in metagenomics are [A], including bacteria, [B], and microscopic [C] organisms. An ecosystem comprising these organisms is called a [D].

Answer 2

a. A = microbial
b. B = viruses
c. C = eukaryotic
d. D = microbiome

Question 3

Fill in the blank. A ______ is a host organism plus its associated microbes

Answer 3

holobiont

Question 4

Match each of the Five Great Ideas of Biology with the corresponding aspects of metagenomics.

-Identification of individual organisms in a microbiome

A) The cell is the fundamental unit of life
B) The gene as the unit of heredity
C) Evolution by natural selection
D) Life is chemistry
E) Biology as an organized system

Question 5

Match each of the Five Great Ideas of Biology with the corresponding aspects of metagenomics.

-Species identification using rRNA sequencing

A) The cell is the fundamental unit of life
B) The gene as the unit of heredity
C) Evolution by natural selection
D) Life is chemistry
E) Biology as an organized system

Question 6

Match each of the Five Great Ideas of Biology with the corresponding aspects of metagenomics.

-Organisms in a community co-evolve

A) The cell is the fundamental unit of life
B) The gene as the unit of heredity
C) Evolution by natural selection
D) Life is chemistry
E) Biology as an organized system

Question 7

Match each of the Five Great Ideas of Biology with the corresponding aspects of metagenomics.

-Organisms in a community are nutritionally co-dependent

A) The cell is the fundamental unit of life
B) The gene as the unit of heredity
C) Evolution by natural selection
D) Life is chemistry
E) Biology as an organized system

Question 8

Match each of the Five Great Ideas of Biology with the corresponding aspects of metagenomics.

-Transcriptional analysis of a microbiome

A) The cell is the fundamental unit of life
B) The gene as the unit of heredity
C) Evolution by natural selection
D) Life is chemistry
E) Biology as an organized system

Question 9

Prochlorococcus cyanobacteria are very highly abundant in sea water. Why was Prochlorococcus not discovered until the 1980s? Please select all that apply.

A) Metagenome sequencing was not available until the 1980s
B) Prochlorococcus species are photosynthetic
C) Prochlorococcus cells are hard to distinguish by light microscopy
D) Prochlorococcus cells were not easily cultured

Question 10

Analysis of microbial communities by direct sequencing has numerous advantages over culture-dependent analysis. Which of the following are advantages of culture-based methods over culture-independent analysis? Please select all that apply.

A) Culture-dependent methods capture
More species than culture-independent methods
B) Cultured organisms can provide reference genomes
C) Culture-based methods are less biased than direct sequencing
D) Cultivation is better at identifying low-abundance organisms than direct sequencing

Question 11

rRNA sequencing allows the identification and quantification of eukaryotic and bacterial species within a microbial sample.

Question 12

Which of the following is not an advantage of rRNA sequencing for microbial species identification?

A) All cellular organisms have ribosomes
B) rRNA sequences have conserved and variable regions
C) rRNA phylogenies correlate to other phylogenies
D) rRNA sequencing can detect horizontal gene transfer

Question 13

Different Prochlorococcus ecotypes cannot be distinguished using rRNA sequencing.

Question 14

Researchers determine species diversity in a sample by examining DNA sequences and assigning organisms to bins according to sequence similarity. What name is used for the binned groups?

A) phylotype
B) microbiome
C) clade
D) genus

Question 15

Match the missing words in the following phrase. Bacterial and archaeal species are difficult to define because the [A] definition of production of viable offspring by sexual reproduction does not apply to asexual organisms. [B] is very common among bacteria and archaea, which further confuses the species concept. Some ways that researchers have used to classify [C] species are: definition based on morphological and biochemical similarity, DNA [D] capacity, frequency of natural DNA [E], and DNA [F] within a defined range.

Question 16

What does a rarefaction curve show?

A) Whether sampling bias has occurred
B) Species abundance in a population
C) The number of individuals in a population
D) Species richness in a population

Question 17

α-diversity refers to diversity within a sample and β-diversity refers to diversity between samples.

Question 18

Metagenomic data can be clustered to determine which criteria are diagnostic for a group and which characteristics are less important. This analysis is called _______ _______ analysis

Question 19

Which of the following characteristics are true of the human gut microbiome? Please select all that apply.

A) E. coli is the most abundant bacterial species in the human gut
B) Gut bacteria are largely parasitic
C) Gut bacteria are largely aerobic
D) Enzymes produced by gut bacteria help humans obtain more energy from food.

Question 20

Researchers analyzed the gut bacteria in obese and non-obese mice and found that the bacterial populations differed. Transplanting gut bacteria from obese mice into the non-obese mice resulted in the non-obese mice gaining weight. What do these results show? Please select all that apply.

A) Increased diversity of gut bacteria increases the risk of obesity
B) Increased abundance of gut bacteria increases the risk of obesity
C) The host can produce phenotypes in the microbiome
D) The microbiome can produce phenotypes in the host

Question 21

What do congruent phylogenies suggest?

A) That organisms are under the same selective pressures
B) That organisms are closely related
C) That natural selection acts at the level of the individual
D) That all members of a species have the same microbiome

Question 22

Ants of the Attine lineage cultivate fungal gardens in their colonies. The relationship between the ants and the fungus has co-evolved over millions of years. Match the descriptor of the ant-fungal relationship with its meaning

-Required for survival

A) Obligate
B) Mutualistic
C) Endosymbiotic
D) Symbiotic

Question 23

Ants of the Attine lineage cultivate fungal gardens in their colonies. The relationship between the ants and the fungus has co-evolved over millions of years. Match the descriptor of the ant-fungal relationship with its meaning

-Both species benefit from the partnership

A) Obligate
B) Mutualistic
C) Endosymbiotic
D) Symbiotic

Question 24

Ants of the Attine lineage cultivate fungal gardens in their colonies. The relationship between the ants and the fungus has co-evolved over millions of years. Match the descriptor of the ant-fungal relationship with its meaning

-This is not exhibited in the ant-fungus relationship

A) Obligate
B) Mutualistic
C) Endosymbiotic
D) Symbiotic

Question 25

Ants of the Attine lineage cultivate fungal gardens in their colonies. The relationship between the ants and the fungus has co-evolved over millions of years. Match the descriptor of the ant-fungal relationship with its meaning

-Interaction between species

A) Obligate
B) Mutualistic
C) Endosymbiotic
D) Symbiotic

Question 26

Escovopsis fungi are parasites of the fungal gardens cultivated by Attine ants. The cultivated fungi are passed vertically through the generations as each queen takes the cultivar to her new colony. By contrast, Escovopsis species transfer horizontally from one colony to another. Despite these different transfer methods, the phylogenies of the ants, their cultivated fungus, and the parasite species are very similar. Why does the Escovopsis phylogeny resemble the ant and cultivated fungi phylogenies?

A) Escovopsis fungi can undergo sexual reproduction with the cultivated fungal species
B) Transfer of Escovopsis to a new colony occurs only once the colony is well established
C) A small amount of Escovopsis is vertically transferred, so the phylogeny resembles the vertically transferred cultivated fungal species.
D) Escovopsis is subjected to selective pressure from the evolving ant and cultivated fungal species

Question 27

Match the missing words in the following phrase. The Red Queen Hypothesis suggests that the rate at which [A] mutations emerge in a [B] is higher if a parasite is exposed to a [C] that is [D] rather than one that is [E].

Question 28

Different communities of organisms tend to exhibit different biochemical capacities.

Question 29

Which of the following methods cannot be used to assess what the organisms in a metagenome are doing?

A) rRNA sequencing
B) Shotgun sequencing
C) Functional metagenomics
D) RNA-seq

Question 30

Researchers used a metagenomic approach to assess the presence of antibiotic resistance genes in the human microbiome. Which experimental step allowed the researchers to obtain only the gene sequences of interest?

A) Extraction of genomic DNA from fecal samples
B) Cloning fragmented DNA from fecal sample into a host strain
C) Sequencing DNA samples
D) Cultivation of host strain on media containing antibiotics

Question 31

Which technique did researchers use to examine the gene activity of Prochlorococcus and associated species during the daily cycle?

A) RNA-seq
B) Metagenome shotgun sequencing
C) Biochemical profiling
D) Cloning

Question 32

Experiments with marine samples containing Prochlorococcus and other microorganisms showed that gene expression in non-photosynthetic organisms mirrored the diurnal oscillation pattern exhibited by Prochlorococcus, which is photosynthetic. What explanations did the researchers suggest for the diurnal expression pattern in the non-photosynthetic members of the community? Please select all that apply.

A) Gene expression in regulated by salt in the environment
B) Gene expression is regulated by nutrient availability
C) Gene expression depends on photosynthesis in Prochlorococcus
D) Gene expression is temperature regulated