Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner

Abstract

Understanding how viral infections impact and are modulated by the microbiome is an important problem in basic research but is also of high clinical relevance under the current pandemic. To facilitate the study of interactions between microbial communities and pathogenic viruses under safe conditions, the infectious agent is generally inactivated prior to processing samples.

Two dimensions of chemical variation of the human microbiome across body sites and in COVID-19 patients

“…The 16S rRNA dataset of Boix-Amorós et al [36] includes samples from four body sites (nasal, skin, oral, and fecal communities); furthermore, community DNA from each body site was sequenced before and after treatment with viral inactivation by ethanol, formaldehyde, heat, psoralen, or trizol. Considering reference proteomes for untreated communities, oral and nasal sites exhibit the lowest and highest ranges of Z C compared to other body sites, and the skin and gut have intermediate Z C whereas the gut has lower than other body sites (Fig.…”

“…Chemical variation of microbial proteins across body sites, after viral inactivation treatment, and multi-omics comparison. ( A – B ) Z C and of community reference proteomes for body sites, based on 16S rRNA gene sequences from [36]. (A) Chemical metrics for nasal, oral, skin, and gut sites.…”

“…Skin and gut communities have intermediate n O2 whereas gut communities have lower n H2 O than other body sites (Figure 3A). Furthermore, Boix-Amorós et al (2021) performed viral inactivation experiments by treating samples with ethanol, formaldehyde, heat, psoralen, or trizol. Treatment with ethanol, and to a lesser extent heat or trizol, results in lower n H2 O of community reference proteomes; no systematic change in n O2 was observed here (Figure 3–figure supplement 1).…”

“…Multi-omics comparison of chemical metrics for microbiomes in human body sites. ( A ) n O2 and n H2O of community reference proteomes for nasal, oral, skin, and gut sites, based on 16S rRNA gene sequences from Boix-Amorós et al (2021). ( B ) Community reference proteomes based on 16S rRNA data for controls in COVID-19 studies (Table 1).…”

“…The dataset of 16S rRNA gene sequences reported by Boix-Amorós et al (2021) 3A). Furthermore, Boix-Amorós et al (2021) performed viral inactivation experiments by treating samples with ethanol, formaldehyde, heat, psoralen, or trizol.…”