5-Shotgun, genome-centric metagenomics and metabolic flux balance

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Considering taxonomic analysis, do you think you need more reads.

For marker gene-based analysis

For metagenomics

Roughly you need the same amounth of reads

Don't know.

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Do you think that host DNA contamination is more difficult to mange.

In shotgun metagenomics because sequencing random.

In amplicon sequencing because primers cannot discriminate microbial from host DNA

It creates the same problems to the two approaches.

Don't know.

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Activity of the microbes can be identified more easily.

Using shotgun DNA sequencing.

Using marker genes and amplicon sequencing on DNA.

None of the two approaches can really identify activity.

Don't know.

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In CENTRIFUGE there is a procedure to reduce the size of the database used for calculating abundance of different taxa.

Yes, it is an approach based on kmers indexing.

No, this specific reduction approach is used in KRAKEN.

Yes, it is an approach removing very similar genomic portion in different species.

Don't know.

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Which one of these software use marker genes to calculate abundance of different taxa?

Kraken

MetaPhlAn2

CENTRIFUGE

Don't know

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Considering different samples collected from human gut, which one of these considerations is correct.

Taxonomy is more conserved than functions.

Functions are more conserved than taxonomy.

The level of conservation is strictly related to the taxonomy level and the functional classification approach.

Taxonomy and functions are equally conserved among samples.

Don't know.

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The main target of the metagenomic binning approach performed on scaffolds.

Is to obtain a taxonomic assignment of the scaffolds obtained from the assembly.

It is to cluster scaffolds belonging to the same species/strain.

It is to calculate the abundance level of the scaffolds recovered from assembly.

Don't know

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In the genome-centric metagenomic approach scaffolds can be clustered considering:

Their lenght

Their coverage profile, GC content, tetranucleotidic composition and taxonomy

Only using coverage profile in different samples.

Only using tetranucleotidic composition and taxonomy.

Don't know.

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Which environment do you think will host the more diverse and complex microbial community?

Marine samples.

Soil samples.

Gut samples.

Skin samples.

Don't know.

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What are two of the most relevant databases used in metabolic flux balance?

KEGG and ecoCYC

RAST and CARD

Bigg and Virtual Metabolic Human

don't know

Other:

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