Selected publications about amplicon sequencing

2015

Amplicon analysis (MiSeq): Lange, A., Schilling E., Strittmatter A. et al., AmpliconDuo: A split-sample filtering protocol for high-throughput amplicon sequencing of microbial communities. PLOS One 10(11)

Amplicon analysis (MiSeq): Köberl, M. et al., Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America. Frontiers in microbiology 6

Amplicon analysis: Tambadou, F. et al., Characterization of the colistin (polymyxin E1 and E2) biosynthetic gene cluster. Archives of Microbiology

2014

Amplicon analysis: Schiml, S. et al., The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J. 80 (6)

Amplicon analysis: Zozomová-Lihová, J. et al., When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine schulzii trigenomic allopolyploid. New Phytologist

Amplicon analysis: Schmidt, R. et al., Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants. Frontiers in microbiology 5

Fish-Project: Roche 454 & MiSeq: Haase et al. Species identification by DNA sequencing (Application of Next Generation Sequencing on Food and Feed Analysis). eFOOD-Lab International (2)

Amplicon analysis: Chaillou et al. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. The ISME Journal

Amplicon analysis: Holler et al. Metagenomic analysis of the stool microbiome in patients receiving allogeneic SCT: Loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal GvHD. BBMT 01.030

Amplicon analysis: Wunderlin et al. Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments. Environ. Microbio. Reports

Amplicon analysis: Herlemann et al. Uncoupling of bacterial and terrigenous dissolved organic matter dynamics in decomposition experiments. PLOS One 9(4)

Amplicon analysis: Fauser et al. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. The Plant Journal, 79 (2)

Amplicon analysis: Gomathi et al. Screening of Indigenous Oxalate Degrading Lactic Acid Bacteria from Human Faeces and South Indian Fermented Foods: Assessment of Probiotic Potential. The Scientific World Journal, 648059

Amplicon analysis: Sugiyama et al. Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field. PLOS One 9(6)

2013

Amplicon analysis: Wunderlin et al. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. environmental microbiology reports 10.1111

Amplicon analysis: Sauvain et al. Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria. Aquat Sci, 10.1007

Amplicon analysis: Bueche et al. Quantification of Endospore-Forming Firmingcutes by Quantitative PCR with the Functional Gene spo0A. Appl. Environ.Microbiol. 79(17)

Amplicon analysis: Sedlácek et al. Enterococcus ureilyticus sp. nov and Enterococcus rotai sp. nov., two urease-producing enterococci from the environment. IJSEM 63(Pt 2)

Amplicon analysis: Heinrichs et al. Analysis of Black Fungal Biofilms Occurring at Domestic Water Taps (I): Compositional Analysis Using Tag-Encoded FLX Amplicon Pyrosequencing. Mycopathologia 1-11

2012

Amplicon analysis: Matyasek R et al. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13:722

Amplicon analysis: Jacoby et al. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 7:12

Amplicon analysis: Håkansson Å et al. Blueberry Husks and Probiotics Attenuate Colorectal Inflammation and Oncogenesis, and Liver Injuries in Rats Exposed to Cycling DSS-Treatment. PLoS ONE 7(3)

2010

Amplicon analysis: Medinger, R., Ottenwälder, B. et al. Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of Eukaryotic microorganisms. Molecular Ecology, 19 Suppl. 1: 32-40

Amplicon analysis: Nolte, V., Ottenwälder, B. et al. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology; 19(14):2908-2915

Bold = Eurofins employee