Target
Primer
Bacteria
Bacteria
Universal
Bacteria
Bacteria
Archaea
Bacteria
Universal
Universal
Bacteria
Sequence
Region
B8F
AGAGTTTGATCCTGGCTCAG
B533R
TTACCGCGGCTGCTGGCAC
U341F
CCTACGGGRSGCAGCAG
B785R
TACNVGGGTATCTAATCC
U341F
CCTAYGGGRBGCASCAG
U806R
GGACTACNNGGGTATCTAAT
U341F
CCTAYGGGRBGCASCAG
B907R
CCGTCAATTCMTTTGAGTTT
B343F
TACGGRAGGCAGCAG
B534R
ATTACCGCGGCTGCTGGC
A344F
ACGGGGYGCAGCAGGCGCGA
A915R
GTGCTCCCCCGCCAATTCCT
U347F
GGAGGCAGCAGTRRGGAAT
U803R
CTACCRGGGTATCTAATCC
U515F
GTGYCAGCMGCCGCGGTA
U806R
GGACTACHVGGGTWTCTAAT
U515F
GTGYCAGCMGCCGCGGTA
U909R
CCCCGYCAATTCMTTTRAGT
U519F
CAGCMGCCGCGGTAATWC
B926R
CCGTCAATTCMTTTRAGTT
V1-V3
Reference
(Wang and Qian, 2009)
V3-V4
(Klindworth et al., 2013)
V3-V4
(Zakrzewski et al., 2012)
V3-V5
(Wang and Qian, 2009; Sogin et al., 2
006)
V3
(Liu et al., 2007)
V3-V5
(Teske and Sorensen, 2008)
V3-V4
(Nossa et al., 2010)
V4-V5
(Caporaso et al., 2011)
V4-V5
(Tamaki et al., 2011)
V4-V5
(Mao et al., 2011)
References
1.
Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J.,
Fierer, N., Knight, R., 2011. Global patterns of 16S rRNA diversity at a depth of millions of
sequences per sample. Proceedings of the National Academy of Sciences of the United States of
America 108 Suppl 1, 4516-4522.
2.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., Glockner, F.O., 2013.
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation
sequencing-based diversity studies. Nucleic Acids Research 41,e1.
3.
Liu, Z., Lozupone, C., Hamady, M., Bushman, F.D., Knight, R., 2007. Short pyrosequencing reads
suffice for accurate microbial community analysis. Nucleic Acids Research 35, e120.
4.
Mao, Y., Yannarell, A.C., Mackie, R.I., 2011. Changes in N-transforming archaea and bacteria in
soil during the establishment of bioenergy crops. PloS One 6, e24750.
5.
Nossa, C.W., Oberdorf, W.E., Yang, L., Aas, J.A., Paster, B.J., Desantis, T.Z., Brodie, E.L.,
Malamud, D., Poles, M.A., Pei, Z., 2010. Design of 16S rRNA gene primers for 454
pyrosequencing of the human foregut microbiome. World Journal of Gastroenterology 16,
4135-4144.
6.
Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., Arrieta, J.M.,
Herndl, G.J., 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere".
Proceedings of the National Academy of Sciences of the United States of America 103,
12115-12120.
7.
Tamaki, H., Wright, C.L., Li, X., Lin, Q., Hwang, C., Wang, S., Thimmapuram, J., Kamagata, Y.,
Liu, W.T., 2011. Analysis of 16S rRNA amplicon sequencing options on the Roche/454
next-generation titanium sequencing platform. PloS One 6, e25263.
8.
Teske, A., Sorensen, K.B., 2008. Uncultured archaea in deep marine subsurface sediments: have
we caught them all? The ISME journal 2, 3-18.
9.
Wang, Y., Qian, P.Y., 2009. Conservative Fragments in Bacterial 16S rRNA Genes and Primer
Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies. PLoS One 4(10):e7401.
10. Zakrzewski, M., Goesmann, A., Jaenicke, S., Junemann, S., Eikmeyer, F., Szczepanowski, R.,
Al-Soud, W.A., Sorensen, S., Puhler, A., Schluter, A., 2012. Profiling of the metabolically active
community from a production-scale biogas plant by means of high-throughput metatranscriptome
sequencing. Journal of Biotechnology 158, 248-258.