2022
DOI: 10.7554/elife.78454
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Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Abstract: Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to o… Show more

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Cited by 18 publications
(52 citation statements)
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References 112 publications
(138 reference statements)
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“…However, this approach comes with a long list of caveats, including the following assumptions: (1) the relationship between absorbance and CFU/ml is unchanged after evolution (i.e., no evolved changes in cell size/shape); (2) the environment in which the growth curve is measured is analogous to the evolved environment; and (3) the growth parameters used as indirect measures of fitness directly translate to fitness (i.e., there are no evolved adversarial interactions between the lines) (Concepción-Acevedo et al 2015 ; Ram et al 2019 ). These assumptions are often erroneous as large-scale phenotyping can result in contradictory observations, such as the relationship between absorbance and CFU/ml not being affected by evolution (Lenski and Travisano 1994 ; Grant et al 2021 ; Marshall et al 2022 ; Smith et al 2022 ). Thus, for our first case, we compared three approaches for indirectly estimating fitness through a microbial growth curve.…”
Section: Resultsmentioning
confidence: 99%
“…However, this approach comes with a long list of caveats, including the following assumptions: (1) the relationship between absorbance and CFU/ml is unchanged after evolution (i.e., no evolved changes in cell size/shape); (2) the environment in which the growth curve is measured is analogous to the evolved environment; and (3) the growth parameters used as indirect measures of fitness directly translate to fitness (i.e., there are no evolved adversarial interactions between the lines) (Concepción-Acevedo et al 2015 ; Ram et al 2019 ). These assumptions are often erroneous as large-scale phenotyping can result in contradictory observations, such as the relationship between absorbance and CFU/ml not being affected by evolution (Lenski and Travisano 1994 ; Grant et al 2021 ; Marshall et al 2022 ; Smith et al 2022 ). Thus, for our first case, we compared three approaches for indirectly estimating fitness through a microbial growth curve.…”
Section: Resultsmentioning
confidence: 99%
“…We identified phenotypic changes during adaptation to biofilm growth including changes in cell morphology, increased extracellular matrix (ECM) production and alterations of growth rate. We also identified genetic changes accompanying enhanced biofilm growth that varied according to the genetic background of the population [ 17 ].…”
Section: Resultsmentioning
confidence: 99%
“…tb clinical isolates to biofilm growth, using an evolve and re-sequence approach. We discovered that the mutational pathway to enhanced biofilm growth varied between clinical isolates [ 17 ]. These results led us to hypothesize that the regulatory mechanisms underlying pellicle biofilm formation exhibit similar variation.…”
Section: Introductionmentioning
confidence: 99%
“…It included assemblies of over 300,000 genomes which had not previously been available (the raw data only had been available). The assemblies and search indexes allowed multiple other studies of plasmids[5, 6], bacterial adaptation[7, 8, 9, 10], and compression/indexing algorithms[11, 12, 13, 14, 15]. However, there were a few limitations.…”
Section: Introductionmentioning
confidence: 99%