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Cecum digesta microbial analysis using 16 S rRNA next-generation sequencing indicated no significant community-level changes in the microbiota.
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Sequences were then used for microbial diversity analysis using QIIME.
The microbial population analysis using FISH showed that also the population did not change when changing from nitrate to nitrite as electron acceptor in the system (Fig. 2).
Microbial community analysis using fluorescence in situ hybridization (FISH) technique revealed that granules were enriched with SOB contributing to autotrophic denitrification.
To gain a more in-depth understanding of the changes in the fecal microbiota of CD patients undergoing EEN therapy and to confirm our findings using HTS on the 16S rRNA gene, microbial community analysis using metagenomics was performed on a subset of the samples.
The prepared DNA samples were quantified using a Nanodrop 1000 Micro-Volume UV-vis Spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA) and stored at -80°C until used for the real-time PCR analysis using microbial rDNA primers, as described later.
This comparison was achieved by sequence analysis using the Comprehensive Microbial Resources (CRM) database from JCVI (http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi), and confirmed by BLAST searches.
Comparative genome analysis using macro-arrays provides insights into microbial evolution and genetic diversity in microbial populations [20], [27].
Both Mothur and QIIME focus on microbial analysis and so, due to the potential of large numbers of OTUs, perform phylogenetic analysis using neighbour-joining or distance methods.
To identify the dominant microbial species in enriched SRB cultures responsible for the thiolation of MMAV, we performed molecular analysis using the enriched and nonenriched SRB cultures.
Further multi-allelic analysis using genes coding for the ribosomal proteins (rMLST, 51-loci) has been used to integrate microbial genealogy and typing [ 2].
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