Paper - Review

DOI: 10.1038/s41522-021-00254-z

Abstract

The oral microbiome
→ has been connected ← with lung health
→ may be of significance ← in the progression of SARS-CoV-2 infection

Saliva-based SARS-CoV-2 test
→ provide the opportunity → to leverage stored samples
→ for assessing the oral microbiome

These collection kits
→ have NOT ❌ been tested
→ for their accuracy ← in measuring the oral microbiome

Saliva
→ is highly enriched ← with human DNA
Reducing it → prior to shotgun sequencing
→ may increase → the depth of bacterial reads

Examined
→ both 1⃣ the effect of saliva collection method 2⃣ sequence processing
← on measurement of microbiome 1⃣ depth 2⃣ diversity
← by 1⃣ 16S rRNA gene amplicon 2⃣ shotgun metagenomics

❗: collected 56 samples ← from 22 subjects

Each subject
→ provided saliva samples ← with & without preservative
A subset
→ provided → a second set of samples the following day

❗: 16s rRNA gene sequencing
→ was performed ← on all samples
❗: Shotgun metagenomics → was performed
← on a subset of samples ← collected 1⃣ with preservative 2⃣ without human DNA depletion
← before sequencing

❗: the beta diversity distances
← within subject over time
→ was smaller ← than between unrelated subjects
❗: distances ← within subjects
→ were smaller ← in samples collected with preservative

Samples
← collected with preservative
→ had higher alpha diversity ← measuring both 1⃣ richness 2⃣ evenness

Human DNA depletion
← before 1⃣ extraction 2⃣ shotgun sequencing
→ yielded higher total & relative reads
→ mapping to bacterial sequences

❗: collecting saliva ← with preservative
→ may provide more consistent measures ← of the oral microbiome
→ increases yield of bacterial sequences

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