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ost of the microbial diversity on our planet cannot be

cultivated and remains inaccessible. Getting access

to this ‘missing’ diversity is critical for both academia

and industry. The uncultivated species arguably represent the

largest source of unexplored biological and chemical diversity on

the planet.

Bridging the gap

Traditionally, a cultivation microbiologist would attempt to grow

novel species by manipulating the macronutrients and

micronutrients in the medium and changing cultivation conditions.

Whilst the success of this approach is undeniable, the rate of

microbial discovery it affords is low: just over 7,000 valid species

have been described to date out of perhaps millions that existed

in the samples used. The last 10-15 years have seen a

renaissance of novel cultivation approaches, all striving to bridge

the gap.

Our research group contributed to the effort by developing several

cultivation platforms that radically depart from conventional

cultivation. First, we developed a general method to cultivate at

least some uncultivated species (Fig. 1A).We reasoned that novel

species with unknown growth requirements could be grown if

provided with the growth components of their natural environment.

Following this logic, we placed environmental cells into a diffusion

chamber with 0.03μm pore-size membranes and returned the

chamber into the natural environment from where the cells were

collected so that diffusion would establish chemical

communication between the cells and Nature. A proof-of-concept

growth experiment showed a 300-fold higher recovery rate of

marine sediment micro-organisms over parallel cultures that

utilised traditional (standard Petri dish) techniques. Later, we

showed that the species composition of the grown material is also

markedly different between the chamber and Petri dish.

We further reasoned that the same device could be used in a very

different fashion and enrich different micro-organisms. The idea is

that, if a diffusion chamber is not inoculated with micro-organisms

and contains sterile agar, and if the pores of the membranes are

>0.2-0.4μm, then during this device’s environmental incubation

filamentous, chain-forming and mobile species should colonise

the inner space (Fig. 1B).We confirmed this in a proof-of-concept

study and isolated a number of novel Actinobacteria, fungi, and

other micro-organisms from soils. Note that the principal step,



enrichment, is a cornerstone of both the trap and diffusion

chamber approaches, but the resulting culture collections are

significantly different, making these methods complementary.

The ‘isolation chip’

The use of the diffusion chamber has a limitation: relatively low

throughput. To resolve this bottleneck, we designed a variant of the

diffusion chamber, the isolation chip, or ichip for short, which

consists of numerous micro-diffusion chambers containing single

cells. This modification enables the diffusion chamber-based

approach to grow and isolate environmental micro-organisms into

pure culture in a single step.

The ichip is an assembly of flat plates containing multiple

registered through-holes (Fig. 2).When the central plate is dipped

into a cell suspension in a gelling agent (left panel), each through-

hole captures a volume of suspension containing a certain

number of cells. If the suspension is appropriately diluted, this

number may be on average one cell per through-hole (central

panel). Upon solidification of the agent, the cells are immobilised

inside small gel plugs and become ‘trapped’ and isolated from

each other.

Sandwiching the plate between 0.03μm pore-size polycarbonate

filters effectively transforms the loaded plate into an array of many

diffusion mini-chambers (right panel). Subsequent

in situ

incubation in the cell’s original environmental habitat provides the

immobilised cells with their naturally occurring growth

components. Since most mini-chambers contain single cells, they

grow as pure cultures. In this way, cultivation/isolation of

uncultivated species is achieved in large numbers and in a single

Professor Slava Epstein outlines why getting access to ‘missing’ microbial diversity

could reveal a treasure trove for academia and industry

The lost treasure trove



H O R I Z O N 2 0 2 0 P R O J E C T S : P O R TA L


S O C I E TA L C H A L L E N G E S : H E A L T H & W E L L B E I N G

Fig. 1 Design and application of diffusion chamber (A) and microbial

trap (B)