Review 1: "Nasopharyngeal Microbiome Composition and Its Clinical Correlates in Children Hospitalized With Severe Pneumonia in East Africa"

Review: This paper describes the nasopharyngeal (NP) microbiome composition (measured through 16S rRNA sequencing) in a cohort of infants and children (N=867; age range 28 days -12 years) admitted to hospitals in Kenya and Uganda with severe pneumonia.The article reports an association between Corynebacterium relative abundance in the NP microbiome of children with severe pneumonia and mortality.While the article contains interesting data, we have concerns about the study design, statistical methods used in investigating the association between the NP composition and clinical variables, and the interpretation of findings which should be considered if the paper were to be published.Overall, given concerns about the rationale for the study and the statistical methods, our recommendation is that the paper should be rejected or the authors asked to make major revisions. Major concerns:Potentially informative.The main claims made are not strongly justified by the methods and data, but may yield some insight.The results and conclusions of the study may resemble those from the hypothetical ideal study, but there is substantial room for doubt.Decision-makers should consider this evidence only with a thorough understanding of its weaknesses, alongside other evidence and theory.Decision-makers should not consider this actionable, unless the weaknesses are clearly understood and there is other theory and evidence to further support it.