In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea

Table 1 Flowchart on the computational search of articles in PubMed and their analysis using text-mining techniques

Purpose 1. To find 16S rRNA gene primers used to identify bacteria or archaea
Step	Description	Bacteria	Archaea
1	No. of computational searches in PubMed performed:	2940	5796
2	No. of abstracts and metadata of papers downloaded:	3245	6405
3	No. of papers processed by text-mining techniques:	2939	1687
4	No. of papers with oral score ≥1 and gene score ≥3 (partial reading):	576	44
5	No. of papers reviewed for full-text reading:	323+15^a	22+12^a
6	No. of papers with at least one different 16S rRNA gene primer:	129	16
Purpose 2. To create a list of oral-archaea species
Step	Description		Archaea
1	No. of computational searches in PubMed performed:		276
2	No. of abstracts and metadata of papers downloaded:		7548
3	No. of papers processed by text-mining techniques:		6734
4	No. of papers with oral score ≥1 and archaea score ≥3 (partial reading):		200
5	No. of papers reviewed for full-text reading:		60
6	No. of papers with at least one oral archaea species:		53

Papers from “purpose 1” received one score for the oral cavity words included in their abstracts and another for the terms associated with the 16S rRNA gene and its different regions; papers from “purpose 2” received an oral- and an archaeal-word score. In each score, for each different related term included in the abstract, we gave one point with repeated words only counted once (i.e., in a given abstract, the words “oral,” “mouth,” and “periodontitis” appear two, one, and three times so the oral cavity score is equal to three). The terms used to give the punctuations were those used to conduct the searches
^aAdditional publications on the study of the oral microbiota using sequencing were considered for full-text reading; these were previously reviewed for other reasons (n = 15) or were found during the search for the oral-archaea species (n= 12)

ISSN: 2049-2618