Instruct: Identify the main category of Medrxiv papers based on the titles and abstracts
Query: Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n=58) and lower (n=35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We found that time in the intensive care unit and the type of oxygen support, both of which are associated to additional treatments such as antibiotic usage, explained the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load had a reduced impact. Specifically, mechanical ventilation was linked to altered community structure, lower species- and higher strain-level diversity, and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomic analysis of the lower respiratory tract of mechanically ventilated COVID-19 patients identified specific oral bacteria, different to those observed in controls. These oral taxa were found physically associated with proinflammatory immune cells, which showed higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
45
The categories of this paper are: pharmacology
33
The categories of this paper are: physical
41
The categories of this paper are: nephrology
16
The categories of this paper are: immunology
7
The categories of this paper are: emergency
22
The categories of this paper are: clinical
31
The categories of this paper are: imaging
49
The categories of this paper are: intensive
30
The categories of this paper are: radiology
72
The categories of this paper are: urology
13
The categories of this paper are: genetic
5
The categories of this paper are: health
15
The categories of this paper are: allergy
46
The categories of this paper are: therapeutics
39
The categories of this paper are: rheumatology
47
The categories of this paper are: care