Nature - USA (2020-08-20)

Article

Schematic of the microfluidic device

inlet outlet

Mother-Machine chip

media flow

mother cell

preshift

glucose

postshift

acetate

filtration / wash

Experiment

Lag time distribution

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Lag time after acetate switch (h)

0

20

40

60

80

100

120

Counts

mean = 3.80 h

std = 0.93

mean (adj) = 2.69 h

Batch optical density

Time (h)

log(OD

/ODt

) 0

Derivative

x10-3

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0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

-1

0

1

2

3

4

5

growth rate (acetate) = 0.51 h-1

batch lag time = 4.14 h

Time after switch (h)

-0.2-2 024681012

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

Growth rate (h

-1)

Instantaneous growth rate

ab

cde

Extended Data Fig. 3 | Single-cell behaviour during a glucose-to-acetate
shift in microf luidics. a, Diagram showing the microf luidic device (mother
machine) in which bacterial cells are grown. The cells are loaded in narrow
trenches (inset), where they are diffusively fed from the medium f lowing
through the feeding lane. As cells grow out of the trenches, they are washed
away by the medium f low. We focused solely on the cells at the closed end of
each trench, also called ‘mother cells’, as they are kept for the duration of the
experiment. b, Diagram outlining the experimental protocol. Cells were
recovered from the mother machine using glucose medium, and then
connected to a f lask with culture growing in the same medium^43. The medium
was switched as for batch cultures, and the f low was restarted towards the
mother machine. Cells continued growing for a short time after filtration both
in batch and in the mother machine, presumably because of residual glucose in
the system; therefore the experiment resembles a diauxic shift. c,
Instantaneous single-cell growth rates determined from cell length. Length
traces from individual cells were used to compute instantaneous growth rates;
the blue points and blue shaded area represent population averages and
standard deviations. The orange trace is the instantaneous growth rate trace of
an example cell. d, Single-cell lag-time distribution. The lag time is defined as
the time delay in growth after the switch compared with instantaneous growth
at the maximum postshift growth rate. Instantaneous growth-rate traces were
used to compute single-cell lag times (Methods). The red dashed line shows the
mean of the lag-time distribution of the tracked cells. Cells tracked in the
mother machine introduce a bias towards long lag times, because growing cells

are washed away instead of being amplified, as happens in batch culture.

Therefore, we also calculated the expected batch lag time (2.69 h; grey dashed

line), taking into account cell growth (Methods). e, The postshift growth curve

(grey) of the batch culture connected to the microf luidic chamber was used to

determine the batch lag time (4.14 h). The maximum growth rate along the

growth curve corresponds to the approximately linear part of the log(OD(t))

(grey dotted line), for a growth rate of 0.51 h−1. The red dotted line shows the

time derivative of log(OD(t)). The quantitative agreement between the

microf luidics and the batch is not perfect. Nevertheless, the single-cell

distribution of lag times shows that the response of individual cells after the

shift is unimodal, and that the lag time is not governed by a small subpopulation

of cells that grows immediately on acetate, as expected in ref.^12. We see no

reason why this cell population should not be present in the microf luidics if it

were present in the batch. Our data also showed no evidence for the

prediction^12 that most cells would never recover and grow after the shift.

However, because the cells were grown in a microf luidic chip, our experiment

cannot definitively rule out the possibility that the recovery of growth

observed here is due to differences in the conditions. To determine whether

such a nongrowing population exists in the batch culture, we performed

another experiment (Extended Data Fig. 4). n = 681 cells. We carried out the

growth-curve experiment once, with two independent lanes (one with YFE44,

one with the wild-type strain); the plots are relative to results obtained from the

f lask inoculated with YFE44.