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Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

Francis C Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai, Daryi Wang
2010 BMC Bioinformatics  
Conclusions: Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing.  ...  In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.  ...  Acknowledgements We wish to thank the reviewers for their valuable comments and suggestions, which helped us to improve our analysis.  ... 
doi:10.1186/1471-2105-11-565 pmid:21083935 pmcid:PMC3098102 fatcat:5lq36kyopbakta45nk7rfmx5cq

Next-Generation Environmental Diversity Surveys of Foraminifera: Preparing the Future

J. Pawlowski, F. Lejzerowicz, P. Esling
2014 The Biological Bulletin  
Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation.  ...  In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach.  ...  Some of the unpublished data reported here were obtained with help of the Biodiversity of Marine euKaryotes (BioMarKs, consortium, which was funded by the European Union ERANet  ... 
doi:10.1086/bblv227n2p93 pmid:25411369 fatcat:vuor2qangvb7laszhsxpeyomiy

Ecological and evolutionary drivers of microbial community structure in termite guts

Carsten Dietrich, Brune, Andreas (Prof. Dr.)
This dissertation includes studies examining the archaeal and bacterial diversity of the gut microbiota over a wide range of termites using high-throughput sequencing of the 16S rRNA genes.  ...  Since these observations are based on highly limited samplings of hosts, it is uncertain if these differences reflect important evolutionary patterns.  ...  Hao Zheng is a doctoral student in the International Max Planck Research School for Environmental, Cellular and Molecular Microbiology (IMPRS-MIC), Marburg.  ... 
doi:10.17192/z2015.0344 fatcat:hbtsobobcbaqpikslagnott3y4

Genetic diversity in V. vinifera and its impact on hosted microbiota

Murad K. Awad
The impact of Vitis cultivars, environment and agronomic management on the bacterial microbiome inhabiting those cultivars was performed using next-generation sequencing (NGS) in a metagenomics approach  ...  targeting the 16S rRNA gene.  ...  There has been some ambiguity in the use of this term in the past; where marker gene sequencing has also been referred to as metagenomics.  ... 
doi:10.26262/ fatcat:gww64eco4rfmbjugmovkzzhlqm