Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection

Crovetto, F.; Selma‐Royo, Marta; Crispi, F.; Carbonetto, Belén; Pascal, R.; Larroya, Marta; Casas, Irene; Tortajada, Marta; Escudero, Nuria; Muñoz‐Almagro, Carmen; Gómez-Roig, María Dolores; González-Torres, Pedro; Collado, María Carmen; Gratacós, E.

doi:10.1038/s41598-022-17542-z

Cited by 12 publications

(24 citation statements)

References 48 publications

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“…In the MRS+ samples, members of the Bifidobacteriaceae and Oscillospiraceae families were enriched, while Microbacteriaceae was decreased with a significant difference, suggesting an alteration in the intestinal microbiota due to the presence of the SARS-CoV-2 virus in infected pregnant women. A previous study of nasopharyngeal swab samples taken from Spanish pregnant women with COVID-19 reported a bacterial diversity at the phylum level similar to that in our work, where the Prevotellacea family had the highest abundance [ 31 ]. In another comparative study in the Italian population carried out using rectal swab samples from healthy individuals versus COVID-19 patients at different phases of the disease, the comparison of the microbial composition pointed out significant changes in the bacterial communities during progressive phases of the disease [ 29 ].…”

Section: Discussionsupporting

confidence: 84%

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2

Juárez-Castelán

Vélez-Ixta

Corona-Cervantes

et al. 2022

IJMS

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COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother–neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.

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Section: Discussionsupporting

confidence: 84%

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2

Juárez-Castelán

Vélez-Ixta

Corona-Cervantes

et al. 2022

IJMS

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“…Irrespective of COVID-19 disease status, the nasopharyngeal microbiota of the symptomatic patients, i.e., Irrespective of the disease status, the nasopharyngeal microbiota in Indian samples was found to be dominated by the phylum Firmicutes, Proteobacteria, and Actinobacteriota and the family Staphylococcaceae and Corynebacteriaceae. This is in line with the reports presented in earlier studies inspecting nasopharyngeal microbiota in other geographies [27], [28], [29].…”

Section: Association Of Inferred Functions With Microbiota Samples Du...supporting

confidence: 93%

“…[27], [23] barring a few exceptions [29]. Our findings also indicate a lower diversity associated with COVID-19, concurring with these findings.…”

Section: Association Of Inferred Functions With Microbiota Samples Du...supporting

confidence: 91%

Composition of nasopharyngeal microbiota in individuals with SARS-CoV-2 infection across three COVID-19 waves in India

Bose

Wasimuddin

Acharya

et al. 2023

Preprint

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Background: SARS-COV-2 is an enveloped RNA virus that is responsible for the global pandemic COVID-19. The virus is reported to cause dysbiosis of the Human Nasopharyngeal microbiota, consequently regulating the host immunity and infection pathophysiology. The compositional change in microbial diversity due to the virus has been reported by independent authors in smaller cohorts and different geographical regions, with a few correlating with fungal and bacterial co-infections. Here, we study for the first time, the nasopharyngeal microbial diversity in the COVID-19 patients, across the three waves in India and explore its correlation with the causative virus variant (and/or the severity of symptoms, if any). Methods: We profiled the nasopharyngeal microbiota of 589 Indian subjects, across the three waves (First; n=181, Second; n=217, Third; n=191), which were further categorized as COVID-19 positives and COVID-19 negatives. These respective groups were further divided into subgroups based on the symptoms as Asymptomatic and Symptomatic. The nasopharyngeal swabs were collected from subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India. Using high throughput 16S rRNA gene amplicon-based sequencing, we sequenced and profiled the nasopharyngeal DNA microbiome prior to subjecting them to diversity, composition and network analyses. Results: Patients infected with SARS-COV-2 showed a reduced microbial alpha diversity compared to the COVID-19 negatives, in a wave-dependent manner, as implicated by measuring the alpha diversity indices. Furthermore, the compositional change in the community was found to be significantly associated with the viral load as well as the severity of the symptoms observed in the patients. Preliminary taxonomic analysis indicated that, overall, Firmicutes, Proteobacteria, and Actinobacteriota were amongst the dominating Phyla, while Staphylococcaceae and Corynebacteriaceae were the most abundant Families. Also, the microbiota signatures of the first and third wave were more similar to each other at the phylum level compared to the second wave. However, the abundance of microbes varied greatly between the major groups i.e COVID-19 positives and the negatives at the family level, in the respective waves. A similar observation was made where both the commensals and pathobionts differed in abundance between the patient subgroups. Interestingly, the change in microbial network architecture from first to second wave was driven by opportunistic pathogens such as Paenibacillus, Peptostreptococcus, and Solobacterium while Leptotrichia and Actinomyces were noted to be taxonomic groups driving the changes during the third wave when compared to the second wave. Conclusion: In the Indian cohort examined, SARS-COV-2 infection perturbs the nasopharyngeal microbiome, resulting in lower & varied diversity in the niche, irrespective of the virus variant (& thus, the COVID wave) and the disease severity. Whether these changes assist in COVID-19 disease onset & progression, would be interesting to explore in the future.

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“…A recent study from Spain reported that the overall composition of the nasopharyngeal microbiota differs in pregnant women with SARS-CoV-2 infection compared to healthy controls ( 37 ). Specifically, the authors observed a higher abundance of Prevotellaceae family (Bacteroidales order) in pregnant women with active SARS-CoV-2 infection.…”

Section: Discussionmentioning

confidence: 99%

“…Most studies exploring the impact of SARS-CoV-2 infection on the microbiota have focused on the lung (32), gut (33)(34)(35), and nasopharyngeal mucosa (36) in non-pregnant adults. Two studies to our knowledge, have characterized the gut and nasopharyngeal microbiotas at the time of delivery and post-partum colostrum of pregnant women with SARS-CoV-2 infection (37,38). The first study conducted in Spain, reports an increased abundance of Bacteroidales in the nasopharyngeal swabs of pregnant women with active SARS-CoV-2 infection compared to healthy controls.…”

Section: Introductionmentioning

confidence: 99%

Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

Leftwich

Vargas-Robles

Rojas-Correa

et al. 2022

Preprint

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The microbiome inherited at birth exerts marked effects on immune programming with long-term health consequences. Here, we demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition compared to healthy controls at the time of delivery. Accordingly, infants born to pregnant women with early SARS-CoV-2 infection exhibit a unique oral microbiota dominated by Streptococcus species. Together, we demonstrated that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant's microbiome-dependent immune programming.

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Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection

Cited by 12 publications

References 48 publications

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2

Composition of nasopharyngeal microbiota in individuals with SARS-CoV-2 infection across three COVID-19 waves in India

Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

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