Hi B.N. Wong,

For identifying bacteria from pure culture, we always prefer to use primer pair that can amplify entire 16S region i.e. 1.5 Kb. However this culture dependent approach is applicable when you have few number of samples. For this purpose we use universal 16S primer set such as 27F and 1492R (Article Identification and characterization of endophytic bacteria i...

But if we have more number of samples (say 100 or more) basically environmental samples like soil, plant then culture independent approach is best

using illumina sequencing method for getting bacterial composition . In this case, for 16S sequencing, you can use primers pair (515F-806R) for targeting V4 region or 515F-926R for targeting V4-V5 region. You can see numerous papers using these primers for studying bacterial diversity. I would suggest you to go through this link (https://earthmicrobiome.org/protocols-and-standards/16s/ ) for getting more idea.

Best wishes

The best way now is to use NGS. Anyway the universal primers like 27F and 515R can help to determine genus, but not species

there are now further publications describing applications and benchmarking resolution and performance of different 16S regions by application:

DOI: 10.1186/s12864-015-2194-9

Hi, see this article

Isolation, identification and characterization of endophytic bacteria antagonistic to Phytophthora palmivora causing black pod of cocoa in Malaysia

Thanks all for yours answers. They are all very useful！

for DNA extract from endophytic bacteria, probably you can find Chen et al., 2016 from my profile. : )