Hi Gail,

Luo et al. (2015; https://linkinghub.elsevier.com/retrieve/pii/S0043135414007507) used following primers:

"To characterize the bacterial and archaea diversity and temporal evolution, automated ribosomal intergenic spacer analyses (ARISA) were conducted. The extracted DNA was amplified with primer set 1389F (50-ACG GGC GGT GTG TGC AAG-30) and 71R (50-TCG GYG CCG AGC CGA GCC ATC C-30) for archaea (Qu et al., 2009) and with primer set ITSF (50-GTC GTA ACA AGG TAG CCG TA-30) and ITSReub (50-GCC AAG GCA TCC ACC-30) for bacteria (Cardinale et al., 2004)."

Hope this helps?

Robert Thomas Bachmann Thank you so much. I used the universal 16S primers

16S Amplicon PCR Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG 16S Amplicon PCR Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC

and it did not give me the desired base pair.

Hi Gail, have you included a positive control in your protocol?

specific bacterial primers:

357Wf: CCTACGGGNGGCWGCAG and 785R: GACTACHVGGGTATCTAATCC, Archaeal primer:

517F: GCYTAAAGSRNCCGTAGC and 909R: TTTCAGYCTTGCGRCCGTAC to target 16S rRNA gene. 

You can follow my recent article for microbiome study in the anaerobic digestion reactors:

"Enhanced methanogenic co-degradation of propionate and butyrate by anaerobic microbiome enriched on conductive carbon fibers"

Gail Joseph You did not get desired band size, what does that mean?

Hi Gail Joseph

were you able to study the microbial communities?

Robert Thomas Bachmann , Sorry for not replying earlier. I was able to run the analysis, I called the company (Illumina) and they guided me through the process and also helped in ordering the right primers.

Abhijeet Singh, As per the Illumina protocol the library size was expected to 630 bp, but when we ran our libraries it was only 350 bp. We got new primers and got the desired library size now.

Gail Joseph Kindly share the new primers that worked.