Estimating Microbial Population Data from Optical Density

Mira, Portia; Yeh, Pamela J.; Hall, Barry G.

doi:10.1101/2021.12.22.473948

Cited by 3 publications

(3 citation statements)

References 19 publications

(23 reference statements)

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“…The difference between the mean OD was significant (p<0.05). OD values are an indirect measurement of bacterial growth and activity within a microenvironment (Mira et al, 2022) and as such, directly corresponded with the bacterial counts reported for the bacterial isolates during the shakeflask experiment. The axenic Bacillus sp.…”

Section: Growth Profile Studymentioning

confidence: 76%

Biodegradation potentials of edaphic bacterial isolates cultured on Haloxyfop R Methyl ester herbicide-mineral salt medium

Obayagbona,

Dunkwu-Okafor,

Odigie

et al. 2024

Nig. J. Biotechnol

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The heterotrophic and haloxyfop-R methyl ester utilizing bacterial counts associated with top soil samples was evaluated. Three (3) bacterial isolates; Bacillus sp., Micrococcus sp. and Staphylococcus sp. were cultured and screened for their ability to utilize haloxyfop-R methyl ester as sole source of carbon and energy using the turbidimeteric procedure. The growth profiles of two axenic cultures; Bacillus sp. and Micrococcus sp. were determined using the shake flask test. Parameters which included pH, mean viable bacterial counts, optical density and dissolved CO2 were determined during growth profiling using relevant procedures and equipment. The pH of the soil samples was 5.08 ± 0.02 for sample A and 4.62 ± 0.02 for sample B. The total heterotrophic bacterial count was 2.8 × 104 cfu/g ± 849 for A and 4.62 × 104 cfu/g ± 989 for B. The mean dissolved CO2 data for Micrococcus sp. during the growth profile study ranged from 1.1 mg/l ± 0.1 to 6.8 mg/l ± 0.2. Axenic Micrococcus sp. was the most effective amongst the growth profile cultures in mineralizing the herbicide content of the culture medium.

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Section: Growth Profile Studymentioning

confidence: 76%

Biodegradation potentials of edaphic bacterial isolates cultured on Haloxyfop R Methyl ester herbicide-mineral salt medium

Obayagbona,

Dunkwu-Okafor,

Odigie

et al. 2024

Nig. J. Biotechnol

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“…Fitness as a measure of reproductive potential is primarily evaluated using bacterial growth rates 70,71,72 . The density of the microbial culture is directly proportional to the optical density (OD), however, this is only true for a limited OD range, above which measuring culture density with high precision can be demanding 73 . Additionally, external factors affecting the morphology of bacterial cells, like filamentation, elongation or clumping of cells can interfere with OD measurements, thereby affecting growth rate measurements 74,75 .…”

Section: Discussionmentioning

confidence: 99%

Evolutionary barriers to horizontal gene transfer in macrophage associated Salmonella

Bhatia

Kirit

Bollback

2022

Preprint

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Horizontal Gene Transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from E. coli to S. Typhimurium strain 4/74 in four infection relevant environments and estimated the distribution of fitness effects (DFE) in each environment. Roughly half of the genes, 40-50%, had significant fitness effects in at least one environment, with most genes showing significant gene by environment (G x E) interactions. We further identified 12 genes with dosage-dependent effects across the four environments, indicating that intolerance of the recipient strain to high protein dosage is a significant barrier to HGT. We also found longer genes had stronger fitness detriments than shorter ones, showing that gene length can significantly hinder HGT. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment providing barriers to HGT.

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“…However, most require coding skills, such as GrowthCurver 1 , Grofit 2 or growthrates 3 and some are closed-source commercial software (e.g. GrowthRates 4 ). To streamline the process of growth curve analysis and make it more accessible, we developed Dashing Growth Curves, an easy-to-use open-source web application.…”

Section: Introductionmentioning

confidence: 99%

Dashing Growth Curves – a web application for rapid and interactive analysis of microbial growth curves

Reiter

Vorholt

2022

Preprint

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Background: Recording and analyzing microbial growth is a routine task in the life sciences. Microplate readers that record dozens to hundreds of growth curves simultaneously are increasingly used for this task, raising the demand for their rapid and reliable analysis. Results: Here, we present Dashing Growth Curves, an interactive web application (http://dashing-growth-curves.ethz.ch/) that enables researchers to quickly visualize and analyze growth curves without coding knowledge and independent of operating system. Growth curves can be fitted with Logistic or Gompertz growth models, or manually by selecting the linear growth phase in a logarithmic plot. Furthermore, Dashing Growth Curves automatically groups replicate samples and generates downloadable plots for extracted growth parameters such as growth rate or lag time. Conclusions: Dashing Growth Curves is an open-source web application that reduces the time required to analyze microbial growth curves from hours to minutes.

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Estimating Microbial Population Data from Optical Density

Cited by 3 publications

References 19 publications

Biodegradation potentials of edaphic bacterial isolates cultured on Haloxyfop R Methyl ester herbicide-mineral salt medium

Biodegradation potentials of edaphic bacterial isolates cultured on Haloxyfop R Methyl ester herbicide-mineral salt medium

Evolutionary barriers to horizontal gene transfer in macrophage associated Salmonella

Dashing Growth Curves – a web application for rapid and interactive analysis of microbial growth curves

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