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Three examples of intramicrobiome microbial communication

QS - Quorum sensing (N-acyl-homoserine lactones or peptides) Phenotype adaptation/Biofilm formation

DIET Direct Interspecies Electron Transfer (DIET) important in anaerobic communties

VOCs - Volatile Organic Compounds: long term, long distance, cross kingdom

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Modern Definition of Microbiome

Characteristic microbial community occupying a defined habitat with distinct physico-chemical properties. Consist of Microbiota + theater of activity and forms an ecological niche.

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Viruses and Phages are Part of

Microbiome

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Name three interaction types of microbial interaction

Positive (commensalism, mutualism, symbiotic)
Negative (amensalism, predation, parasitism, antagonism and competition)
Neutral.

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Three methods used for community fingerprinting

DGGE/TGGE Denaturing/Temperatur Gradient Gel Electrophoressis

T-RFLP Terminal Restriction Fragments Length Polymorphism

SSCP PCR-Single Strand Conformation Polymorphism

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Name Characteristics associated with Eubiosis and Dysbiosis

Eubiosis: high diversity, high abundance, tight network, low presence of potential pathogens
Dysbiosis: low diversity, low abundance, loose network, high presence of potential pathogens

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The cleaning regimen in a constricted environment like a hospital has what effect on the Microbiom?

Reduction of diversity, increase in abundance of antibiotic resistance. Shift from Gram+->Gram+.

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5 Steps in the Workflow from Sample to (Meta)Genome or Amplicon.

1 Sampling (Sampling, Storing, Enrichment)
2 Processing (Extraction, Library prepartion)
3 Sequencing (Illumina, Pacbio, Oxford Nanopore)
4 Bioinformatics (Quality fitering, Clustering, Taxonomic/Functional Profiling, Comparative analysis, Visualisation
5 Publishing/Storing

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What markers are commonly used for Amplicon Sequencing?

16S rRNA, 18S rRNA and ITS Internal trancribed spacers

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Name 4 Omic methods that complement each other in microbiome research

Genomics (DNA)
Transcriptomics (RNA)
Proteomics (Proteins)
Metabolomics (Metabolites)

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What are the differences between Top Down, Middle down, Bottom up approaches in Proteomics

Size of Protein/Peptide. Top-Down single Proteins are analyzed.
Middle down: Proteinmix is digested first, separated and peptides are analyzed
Bottom up: Proteinmix is digested into smaller fragments than middle down.

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Define core microbiota

The stable species (and or functions) within a microbiome.

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Mol.971UF Microbiome in Health and Environment at Technische Universität Graz

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human microbiome

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Mol.971UF Microbiome in Health and Environment at Technische Universität Graz

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