Metataxonomic Analysis of Milk Samples From SARS-CoV-2-Positive and SARS-CoV-2-Negative Women

Abstract

Objective: To assess the impact of SARS-CoV-2 viral infection on the metataxonomic profile and its evolution during the first month of lactation.

Methods: Milk samples from 37 women with full-term pregnancies and mild SARS-CoV-2 infection and from 63 controls, collected in the first and fifth postpartum weeks, have been analyzed. SARS-CoV-2 RNA was assessed by reverse transcription polymerase chain reaction (RT-PCR) both in cases and controls. After DNA extraction, the V3-V4 hypervariable region of the gene 16S rRNA was amplified and sequenced using the MiSeq system of Illumina. Data were submitted for statistical and bioinformatics analyses after quality control.

Results: All the 1st week and 5th week postpartum milk samples were negative for SARS-CoV-2 RNA. Alpha diversity showed no differences between milk samples from the study and control group, and this condition was maintained along the observation time. Analysis of the beta-diversity also indicated that the study and control groups did not show distinct bacterial profiles. Staphyloccus and Streptococcus were the most abundant genera and the only ones that were detected in all the milk samples provided. Disease state (symptomatic or asymptomatic infection) did not affect the metataxonomic profile in breast milk.

Conclusion: These results support that in the non-severe SARS-CoV-2 pregnant woman infection the structure of the bacterial population is preserved and does not negatively impact on the human milk microbiota.

Keywords: SARS-CoV-2; human milk; infant gut colonization; metataxonomic analysis; microbiota.

FIGURE 1

Flow diagram of the study participants. IC, informed consent. Invalid samples: non-availability, inadequate patient identification or inadequate handling or storage.

FIGURE 2

PCoA plots of bacterial profiles (at the ASVs level) of milk samples according to SARS-CoV-2 status (study and control group) and study time point, based on the Bray-Curtis similarity analysis (relative abundance) (A), and Jaccard’s coefficient for binary data (presence/absence) (B). Where blue circles (T1_Neg) refer to 1st week samples from the control group, yellow triangles (T1_Pos) to 1st week samples from the study group, purple crosses (T2_Neg) to 5th week samples from the control group, and orange × s (T2_Pos) to 5th week samples from the study group. The value given on each axis label represents the percentage of the total variance explained by that axis.

FIGURE 3

PCoA plots of bacterial profiles (at the ASVs level) of pooled (study and control group) milk samples according to time, based on the Bray-Curtis similarity (relative abundance) (A) and Jaccard’s coefficient for binary data (presence/absence) (B) analyses. Where blue circles (T1) refer to 1st week samples, and yellow triangles (T2), to 5th week samples. The value given on each axis label represents the percentage of the total variance explained by that axis.

FIGURE 4

PCoA plots of bacterial profiles (at the ASVs level) of milk samples according to mode of labor completion, based on the Bray-Curtis similarity analysis (relative abundance) (A) and Jaccard’s coefficient for binary data (presence/absence) (B). Where orange circles refer to samples from women who had cesarean section, and purple triangles, to those who had vaginal delivery. The value given on each axis label represents the percentage of the total variance explained by that axis.