Clinical data description of enrolled patients.

Normal distributions are represented as mean土 SD while non normal distributions are represented by median and interquartile range. Categorical variables are represented with percentage. Groups with different letters statistically differ (p < 0.05).

Nasopharyngeal and gut microbiota composition is modified depending on the severity of COVID-19 symptoms.

(A) Alpha diversity analysis of nasopharyngeal swab samples microbiota. (B) Alpha diversity analysis of stool samples microbiota. (C) PCoA for Bray-Curtis index of nasopharyngeal swab microbiota. (D) PCoA for Bray-Curtis index of stool samples microbiota. Values are represented as mean ± SD. Significant differences are represented as * = p < 0.05.

Microbiota composition of nasopharyngeal and stool samples at phylum level is slightly modified by COVID-19 symptoms severity. In contrast, at genus level, severity increases the total amount of detected bacteria in nasopharyngeal swabs while in stool samples it is reduced.

(A) Representation of the most abundant phyla in nasopharyngeal swab samples. (B) Representation of the most abundant phyla in stool samples. (C) Taxa identification of the most abundant genera in nasopharyngeal swab samples. (D) Taxa identification of the most abundant genera in stool samples.

Differential analysis expression of microbiota composition from nasopharyngeal and stool samples revealed the presence of specific bacteria related to COVID-19 severity index.

(A) Venn diagram showing ASVs distribution in nasopharyngeal swab samples. (B) Venn diagram showing ASVs distribution in stool samples. (C) LEfSe plot of taxonomic biomarkers present in nasopharyngeal swab samples (p value = 0.01 and LDA value = 4). (D) LEfSe plot of taxonomic biomarkers present in stool samples (p value = 0.01 and LDA value =4).

Whereas mild biomarkers showed negative correlations towards clinical variables, severe biomarkers presented positive correlations.

(A) Correlation plot of nasopharyngeal swab biomarkers and clinical variables. (B) Correlation plot of stool samples biomarkers and clinical variables. RR: respiratory rate; HR: heart rate; GI: gastrointestinal alterations.

The existence of a relationship between the abundance of nasopharyngeal severe biomarkers and stool severe biomarkers allow the employment of an abundance ratio between them as a new tool for predicting COVID-19 severity.

(A) Correlation plot among biomarkers found in nasopharyngeal swab and stool samples in each condition (mild, moderate and severe from left to right) (B) Ratio of the abundance between P. timonensis (stool) and M. salivarium and P.dentalis (nasopharyngeal swab) biomarkers. Groups with different letters statistically differ (p < 0.05).