Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 region sequences
Violeta Larios Serrato,
Beatriz Meza,
Carolina Gonzalez-Torres,
Javier Gaytan-Cervantes,
Joaquín González Ibarra,
Clara Esperanza Santacruz Tinoco,
Yu-Mei Anguiano Hernández,
Bernardo Martínez Miguel,
Allison Cázarez Cortazar,
Brenda Sarquiz Martínez,
Julio Elias Alvarado Yaah,
Antonina Reyna Mendoza Pérez,
Juan José Palma Herrera,
Leticia Margarita García Soto,
Adriana Inés Chávez Rojas,
Guillermo Bravo Mateos,
Gabriel Samano Marquez,
Concepción Grajales Muñiz,
Javier Torres
Affiliations
Violeta Larios Serrato
Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional , México, Mexico
Beatriz Meza
Universidad Autónoma de Baja California Sur , La Paz, Baja California Sur, Mexico
Carolina Gonzalez-Torres
Laboratorio de Secuenciación, División de Desarrollo de la Investigación, IMSS , Torreón, Mexico
Javier Gaytan-Cervantes
Laboratorio de Secuenciación, División de Desarrollo de la Investigación, IMSS , Torreón, Mexico
Joaquín González Ibarra
División de Desarrollo de la Investigación en Salud, Coordinación de Investigación en Salud, IMSS , Torreón, Mexico
Clara Esperanza Santacruz Tinoco
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Yu-Mei Anguiano Hernández
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Bernardo Martínez Miguel
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Allison Cázarez Cortazar
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Brenda Sarquiz Martínez
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Julio Elias Alvarado Yaah
División de Laboratorios Especializados, Coordinación de Calidad de Insumos y Laboratorios Especializados, IMSS , Torreón, Mexico
Antonina Reyna Mendoza Pérez
Coordinación de Vigilancia Epidemiológica, Dirección de Prestaciones Médicas, IMSS , Torreón, Mexico
Juan José Palma Herrera
Hospital General de Zona No. 27, Ciudad de México Norte, IMSS , México, Mexico
Leticia Margarita García Soto
Hospital General de Zona No. 27, Ciudad de México Norte, IMSS , México, Mexico
Adriana Inés Chávez Rojas
Coordinadora de Información y Análisis Estratégicos, OOAD Cd de México , México, Mexico
Guillermo Bravo Mateos
Hospital General de Zona con Medicina Familiar No. 8 Cd de México, IMSS , México, Mexico
Gabriel Samano Marquez
Hospital General de Zona con Medicina Familiar No. 8 Cd de México, IMSS , México, Mexico
Concepción Grajales Muñiz
Departamento de Vigilancia Epidemiológica, IMSS Bienestar , México, Mexico
Javier Torres
Unidad de Investigación Médica en Enfermedades Infecciosas, UMAE Pediatría, Centro Médico Nacional SXXI, IMSS , Torreón, Mexico
ABSTRACT Studies on the role of the oral microbiome in SARS-CoV-2 infection and severity of the disease are limited. We aimed to characterize the bacterial communities present in the saliva of patients with varied COVID-19 severity to learn if there are differences in the characteristics of the microbiome among the clinical groups. We included 31 asymptomatic subjects with no previous COVID-19 infection or vaccination; 176 patients with mild respiratory symptoms, positive or negative for SARS-CoV-2 infection; 57 patients that required hospitalization because of severe COVID-19 with oxygen saturation below 92%, and 18 fatal cases of COVID-19. Saliva samples collected before any treatment were tested for SARS-CoV-2 by PCR. Oral microbiota in saliva was studied by amplification and sequencing of the V1-V3 variable regions of 16S gene using an Illumina MiSeq platform. We found significant changes in diversity, composition, and networking in saliva microbiota of patients with COVID-19, as well as patterns associated with severity of disease. The presence or abundance of several commensal species and opportunistic pathogens were associated with each clinical stage. Patterns of networking were also found associated with severity of disease: a highly regulated bacterial community (normonetting) was found in healthy people whereas poorly regulated populations (disnetting) were characteristic of severe cases. Characterization of microbiota in saliva may offer important clues in the pathogenesis of COVID-19 and may also identify potential markers for prognosis in the severity of the disease. IMPORTANCE SARS-CoV-2 infection is the most severe pandemic of humankind in the last hundred years. The outcome of the infection ranges from asymptomatic or mild to severe and even fatal cases, but reasons for this remain unknown. Microbes normally colonizing the respiratory tract form communities that may mitigate the transmission, symptoms, and severity of viral infections, but very little is known on the role of these microbial communities in the severity of COVID-19. We aimed to characterize the bacterial communities in saliva of patients with different severity of COVID-19 disease, from mild to fatal cases. Our results revealed clear differences in the composition and in the nature of interactions (networking) of the bacterial species present in the different clinical groups and show community-patterns associated with disease severity. Characterization of the microbial communities in saliva may offer important clues to learn ways COVID-19 patients may suffer from different disease severities.