Mining Microbial Diversity

Gwynneth Matcher

Department of Biochemistry and Microbiology

What are microorganisms?

Bacteria (Size range : 700µm - 0.2 µm)

Algae (Unicellular, filamentous)

Fungi (Unicellular, filamentous)

Protists (e.g. amoeba, Plasmodium)

Viruses

• Estimated 100 000 to 10 000 000 000 bacteria per gram of soil

• Microorganisms produce more oxygen than trees

• Marine Viruses - ~ 1013 particles per litre of seawater

Microbial Abundance

“Imagine walking out in the countryside and not being able to

tell a snake from a cow from a mouse from a blade of grass. That has been our level of ignorance”

~Carl Woese

With reference to microbes :

Hug et al., 2016

• 92 bacterial phyla

• CPR phyla (purple)

- No isolated representative

- Still in the process of definition at lower taxonomic levels

Microbial component of ecosystem functioning

• Ubiquitous

• Play key roles in biogeochemical processes

• Integral part of all ecosystems

• Identification through 16S rRNA, 18S rRNA, ITS genes

Example of ecological studies : Eastern Cape estuaries

(Matcher et al. 2011)

Eastern Cape estuaries

Cyanobacterium Synechococcus sp.

Pelagibacter ubique

Variovovax paradoxus Acidovorax valerianellae Caenimonas koreensis

(Matcher et al. 2011)

Whole genome sequencing

Fragment &

sequence

A single next gen sequencing run (Miseq platform)

20-25 million sequences (13-15 Gb of data)

generates

Sequence results

Find overlapping sequences

Build contiguous sequences

Final contigs

Elucidation of biosynthetic pathways

Predicted structure

Structural homologue

Siderophore

(Jiwaji et al. 2017)

Metagenomics

• Extract DNA from all the cells in the community

Metagenomics

• Extract DNA from all the cells in the community

• Use NGS technology to sequence the community DNA

• Bioinformatics to re-assemble the sequences from overlapping reads

Metagenomics

• Extract DNA from all the cells in the community

• Use NGS technology to sequence the community DNA

• Bioinformatics to re-assemble the sequences from overlapping reads

Reassembling microbial genomes from metagenomics sequence datasets

Bioinformatic identification of biosynthetic gene clusters

Example of commercial application :

Marine natural products research

• ~3500 km of coastline, 5 Bioregions • 12,914 recorded species (excluding microbiota) • 346 sponge and 227 tunicate species

Griffiths et al., 2010

Sponge-microbe interactions

• Sessile marine invertebrates (Phylum: Poriphera)

• Up to 50 % of sponge body mass made up by bacteria

• Bacterial symbionts provide nutrients e.g. nitrogen, phosphates

• Bacterial symbionts produce bioactive secondary metabolites used by the sponge for chemical defence

Phorbas clathrata Tsitsikamma pedunculata Aaptos sp Tsitsikamma favus

MARINE DRUG DISCOVERY From chemical defence to anti-cancer therapies

Tsitsikamma pedunculata Tsitsikamma favus

Mandelalides • Purified from the ascidian

Lissoclinum mandelalii (Algoa Bay) • Potent anti-cancer activity • Secondary metabolites likely

produced by microbial symbiont

Pyrroloiminoquinones • Topoisomerase

inhibitor • Anti-malarial, anti-TB

activity • Likely produced by

bacterial symbiont Tsitsikammamine A

Sikorska et al., 2012