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. 2021 Feb 28;13(3):793.
doi: 10.3390/nu13030793.

A Log Ratio-Based Analysis of Individual Changes in the Composition of the Oral Microbiota in Different Dietary Phases

Kirstin Vach  1   2 , Ali Al-Ahmad  2 , Annette Anderson  2 , Johan Peter Woelber  2 , Lamprini Karygianni  3 , Annette Wittmer  4 , Elmar Hellwig  2
Affiliations

A Log Ratio-Based Analysis of Individual Changes in the Composition of the Oral Microbiota in Different Dietary Phases

Kirstin Vach et al. Nutrients. .

Abstract

Background: Investigating the influence of nutrition on oral health has a long scientific history. Due to recent technical advances like sequencing techniques for the oral microbiota, this topic has gained scientific interest again. A basic challenge is to understand the influence of nutrition on the oral microbiota and on the interaction between the oral bacteria, which is also statistically challenging.

Methods: Log-transformed ratios of two bacteria concentrations are introduced as the basic analytic tool. The framework is illustrated by application in an experimental study exposing eleven participants to different nutrition schemes in five consecutive phases.

Results: The method could be sufficiently used to analyse the interrelation between the bacteria and to identify some bacterial groups with the same as well as different reactions to additional dietary components. It was found that the strongest changes in bacterial concentrations were achieved by the additional consumption of dairy products.

Conclusion: A log ratio-based analysis offers insights into the relation of different bacteria while taking specific features of compositional data into account. The presented methods allow becoming independent of the behaviour of other bacteria, which is a disadvantage of common analysis methods of compositions. The results indicate that modulations of the oral biofilm microbiota due to nutrition change can be attained.

Keywords: compositional data; microbiome; nutrition; oral health; ratio fractions.

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Conflict of interest statement

The authors report no conflicts of interest.

Figures

Figure 1
Figure 1
Bacterial groups and colour scheme for all figures.
Figure 2
Figure 2
Fractions of the bacterial groups on the total concentration per participant (column) and phase (row) based on mean values per phase.
Figure 3
Figure 3
Fractions of the bacterial groups on the total concentration per phase based on mean values per phase.
Figure 4
Figure 4
Mean log ratios for all bacterial pairs of bacterial groups and phases. The values are centred around 0 for each bacterial pair. The bacterial pairs are ordered according to the range of the mean values.
Figure 5
Figure 5
Standard deviations (sd) for phase-specific log ratios for all bacterial pairs of bacterial groups and phases based on empirical estimates. The pairs are sorted by the mean sd value over all phases.
Figure 6
Figure 6
Mean log ratio changes for all bacterial pairs for phases II–V with 95% confidence intervals.
Figure 7
Figure 7
Mean values for phase-based log ratios for changes for all pairs of bacteria and phases sorted by range (a) and mean (b).
Figure 8
Figure 8
Standard deviation (sd) for phase-based log ratios for changes for all pairs of bacteria and phases estimated empirical and sorted by mean of sd over the phases.
Figure 9
Figure 9
Mean values of average log ratio changes with 95% CI for bacterial groups 1 to 10 for phase II (top) to phase V (bottom). For colour scheme, see Figure 1.
Figure 10
Figure 10
Mean values of average log ratio changes sorted for bacterial groups 1 to 10 for phase II (top) to phase V (bottom). For colour scheme, see Figure 1.
Figure 11
Figure 11
Scatter plots of the mean values of bacterial groups’ specific average log ratio changes. Half-matrix right top: mean value for each bacterial group in one phase against the other phases. Half-matrix left bottom: mean value for each bacterial pair in one phase against the other phases.
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