scholarly journals Inferring mixed-culture growth from total biomass data in a wavelet approach

2006 ◽  
Vol 370 (2) ◽  
pp. 777-792 ◽  
Author(s):  
V. Ibarra-Junquera ◽  
P. Escalante-Minakata ◽  
J.S. Murguía ◽  
H.C. Rosu
Keyword(s):  
Mixed Culture ◽  
Total Biomass ◽  
Culture Growth

scholarly journals Detection of mixed-culture growth in the total biomass data by wavelet transforms

2010 ◽  
Vol 8 (02) ◽  
Author(s):  
H.C. Rosu ◽  
J.S. Murguía ◽  
V. Ibarra-Junquera
Keyword(s):  
Wavelet Transform ◽  
Mixed Culture ◽  
Microbial Growth ◽  
Physical Parameters ◽  
Logarithmic Scale ◽  
Total Biomass ◽  
Growth Processes ◽  
Microbial Species ◽  
Hölder Exponents ◽  
Culture Growth

We have shown elsewhere that the presence of mixed-culture growth of microbial species in fermentation processes can be detected with high accuracy by employing the wavelet transform. This is achieved because the crosses in the different growth processes contributing to the total biomass signal appear as singularities that are very well evidenced through their singularity cones in the wavelet transform; however, we used very simple two-species cases.In this work, we extend the wavelet method to a more complicated illustrative fermentation case of three microbial species for which we employ several wavelets of different number of vanishing moments in order to eliminate possible numerical artifacts. Working in this way allows filtering in a more precise way the numerical values of the Hölder exponents; therefore, we were able to determine the characteristic Hölder exponents for the corresponding crossing singularities of the microbial growth processes and their stability logarithmic scale ranges up to the first decimal in the value of the characteristic exponents. Since calibrating the mixed microbial growth by means of their Hölder exponents could have potential industrial applications, the dependence of the Hölder exponents on the kinetic and physical parameters of the growth models remains as a future experimental task.

scholarly journals Predicting microbial growth in a mixed culture from growth curve data

2019 ◽  
Vol 116 (29) ◽  
pp. 14698-14707 ◽  
Author(s):  
Yoav Ram ◽  
Eynat Dellus-Gur ◽  
Maayan Bibi ◽  
Kedar Karkare ◽  
Uri Obolski ◽  
...  
Keyword(s):  
Mixed Culture ◽  
Microbial Growth ◽  
Growth Curves ◽  
Growth Cycle ◽  
Relative Fitness ◽  
Accurate Estimation ◽  
Environmental Perturbations ◽  
Fitness Consequence ◽  
Culture Growth ◽  
Growth Differences

Determining the fitness of specific microbial genotypes has extensive application in microbial genetics, evolution, and biotechnology. While estimates from growth curves are simple and allow high throughput, they are inaccurate and do not account for interactions between costs and benefits accruing over different parts of a growth cycle. For this reason, pairwise competition experiments are the current “gold standard” for accurate estimation of fitness. However, competition experiments require distinct markers, making them difficult to perform between isolates derived from a common ancestor or between isolates of nonmodel organisms. In addition, competition experiments require that competing strains be grown in the same environment, so they cannot be used to infer the fitness consequence of different environmental perturbations on the same genotype. Finally, competition experiments typically consider only the end-points of a period of competition so that they do not readily provide information on the growth differences that underlie competitive ability. Here, we describe a computational approach for predicting density-dependent microbial growth in a mixed culture utilizing data from monoculture and mixed-culture growth curves. We validate this approach using 2 different experiments withEscherichia coliand demonstrate its application for estimating relative fitness. Our approach provides an effective way to predict growth and infer relative fitness in mixed cultures.

Commensalism and Competition in Mixed Cultures of Lactobacillus bulgaricus and Streptococcus thermophilus1

1976 ◽  
Vol 39 (5) ◽  
pp. 337-341 ◽  
Author(s):  
NANCY J. MOON ◽  
G. W. REINBOLD
Keyword(s):  
Mixed Culture ◽  
Rapid Growth ◽  
Acid Production ◽  
Stationary Phases ◽  
Exponential Phase ◽  
Mixed Cultures ◽  
Lactobacillus Bulgaricus ◽  
Single Strain ◽  
Limiting Nutrients ◽  
Culture Growth

Cultures of Streptococcus thermophilis and Lactobacillus bulgaricus produced more acid in mixed than in single strain culture. Growth of S. thermophilus in mixed culture was enhanced during the exponential phase and reached higher numbers in the stationary phase than when grown alone. L. bulgaricus was inhibited in the exponential and stationary phases of growth in mixed culture. L. bulgaricus liberated Seitz-filterable compounds during its growth that stimulated growth and acid production of S. thermophilus. These compounds are believed to be responsible for the commensal response observed in mixed cultures. Because of its rapid growth, S. thermophilus was a better competitor than L. bulgaricus for limiting nutrients in the medium. This resulted in inhibition of the growth of L. bulgaricus. The competitive and commensal response was optimal at 37 C and at a ratio of numbers of lactobacilli to streptococci of 2:1 at inoculation.

scholarly journals Indole Production Promotes Escherichia coli Mixed-Culture Growth with Pseudomonas aeruginosa by Inhibiting Quorum Signaling

2011 ◽  
Vol 78 (2) ◽  
pp. 411-419 ◽  
Author(s):  
Weihua Chu ◽  
Tesfalem R. Zere ◽  
Mary M. Weber ◽  
Thomas K. Wood ◽  
Marvin Whiteley ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Mixed Culture ◽  
Receptor Gene ◽  
Enteric Bacteria ◽  
Wild Type ◽  
Content Type ◽  
E Coli ◽  
Culture Growth ◽  
Indole Production

ABSTRACTIndole production byEscherichia coli, discovered in the early 20th century, has been used as a diagnostic marker for distinguishingE. colifrom other enteric bacteria. By using transcriptional profiling and competition studies with defined mutants, we show that cyclic AMP (cAMP)-regulated indole formation is a major factor that enablesE. coligrowth in mixed biofilm and planktonic populations withPseudomonas aeruginosa. Mutants deficient in cAMP production (cyaA) or the cAMP receptor gene (crp), as well as indole production (tnaA), were not competitive in coculture withP. aeruginosabut could be restored to wild-type competitiveness by supplementation with a physiologically relevant indole concentration.E. colisdiAmutants, which lacked the receptor for both indole andN-acyl-homoserine lactones (AHLs), showed no change in competitive fitness, suggesting that indole acted directly onP. aeruginosa. AnE. colitnaAmutant strain regained wild-type competiveness if grown withP. aeruginosaAHL synthase (rhlIandrhlI lasI) mutants. In contrast to the wild type,P. aeruginosaAHL synthase mutants were unable to degrade indole. Indole produced during mixed-culture growth inhibited pyocyanin production and other AHL-regulated virulence factors inP. aeruginosa. Mixed-culture growth withP. aeruginosastimulated indole formation inE. colicpdA, which is unable to regulate cAMP levels, suggesting the potential for mixed-culture gene activation via cAMP. These findings illustrate how indole, an early described feature ofE. colicentral metabolism, can play a significant role in mixed-culture survival by inhibiting quorum-regulated competition factors inP. aeruginosa.

scholarly journals Predicting microbial relative growth in a mixed culture from growth curve data

2015 ◽  
Author(s):  
Yoav Ram ◽  
Eynat Dellus-Gur ◽  
Maayan Bibi ◽  
Uri Obolski ◽  
Judith Berman ◽  
...  
Keyword(s):  
Mixed Culture ◽  
Growth Curve ◽  
Growth Curves ◽  
Relative Fitness ◽  
Model Organisms ◽  
Accurate Estimation ◽  
Relative Growth ◽  
E Coli ◽  
Culture Growth ◽  
Unique Markers

AbstractEstimates of microbial fitness from growth curves are inaccurate. Rather, competition experiments are necessary for accurate estimation. But competition experiments require unique markers and are difficult to perform with isolates derived from a common ancestor or non-model organisms. Here we describe a new approach for predicting relative growth of microbes in a mixed culture utilizing mono- and mixed culture growth curve data. We validated this approach using growth curve and competition experiments withE. coli. Our approach provides an effective way to predict growth in a mixed culture and infer relative fitness. Furthermore, by integrating several growth phases, it provides an ecological interpretation for microbial fitness.

scholarly journals Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in Streptococcus thermophilus and Lactobacillus bulgaricus

2010 ◽  
Vol 76 (23) ◽  
pp. 7775-7784 ◽  
Author(s):  
Sander Sieuwerts ◽  
Douwe Molenaar ◽  
Sacha A. F. T. van Hijum ◽  
Marke Beerthuyzen ◽  
Marc J. A. Stevens ◽  
...  
Keyword(s):  
Amino Acids ◽  
Folic Acid ◽  
Mixed Culture ◽  
Transcriptome Profiling ◽  
Streptococcus Thermophilus ◽  
Lactobacillus Delbrueckii ◽  
Lactobacillus Bulgaricus ◽  
Systematic Analysis ◽  
Culture Growth ◽  
Branched Chain

ABSTRACT Many food fermentations are performed using mixed cultures of lactic acid bacteria. Interactions between strains are of key importance for the performance of these fermentations. Yogurt fermentation by Streptococcus thermophilus and Lactobacillus bulgaricus (basonym, Lactobacillus delbrueckii subsp. bulgaricus) is one of the best-described mixed-culture fermentations. These species are believed to stimulate each other's growth by the exchange of metabolites such as folic acid and carbon dioxide. Recently, postgenomic studies revealed that an upregulation of biosynthesis pathways for nucleotides and sulfur-containing amino acids is part of the global physiological response to mixed-culture growth in S. thermophilus, but an in-depth molecular analysis of mixed-culture growth of both strains remains to be established. We report here the application of mixed-culture transcriptome profiling and a systematic analysis of the effect of interaction-related compounds on growth, which allowed us to unravel the molecular responses associated with batch mixed-culture growth in milk of S. thermophilus CNRZ1066 and L. bulgaricus ATCC BAA-365. The results indicate that interactions between these bacteria are primarily related to purine, amino acid, and long-chain fatty acid metabolism. The results support a model in which formic acid, folic acid, and fatty acids are provided by S. thermophilus. Proteolysis by L. bulgaricus supplies both strains with amino acids but is insufficient to meet the biosynthetic demands for sulfur and branched-chain amino acids, as becomes clear from the upregulation of genes associated with these amino acids in mixed culture. Moreover, genes involved in iron uptake in S. thermophilus are affected by mixed-culture growth, and genes coding for exopolysaccharide production were upregulated in both organisms in mixed culture compared to monocultures. The confirmation of previously identified responses in S. thermophilus using a different strain combination demonstrates their generic value. In addition, the postgenomic analysis of the responses of L. bulgaricus to mixed-culture growth allows a deeper understanding of the ecology and interactions of this important industrial food fermentation process.

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