Published in Metagenomics
Owing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis.We review here the contribution of machine learning techniques for the field of metagenomics, by presenting known successful approac...
Published in Metagenomics
Intestinal bacteria play an important role in animal health. They extract and process nutrients present in their host's diet, help to develop their host's immune system, and recycle organic compounds, water, and minerals. The gut bacterial diversity is poorly known in wild animals. This study is the first description of the diversity of bacteria al...
Published in Metagenomics
Study of the human microbiota in relation to human health and disease is a rapidly expanding field. To fully understand this complex relationship using low-coverage Illumina short reads, we develop a profiling method, microbial nucleotide signatures (MNSs), to characterize the human microbiota. By calculating the nucleotide diversities along the se...
Published in Metagenomics
Relatively few studies have been conducted on the effect of diet on the intestinal microbiota. We followed the response of the fecal microbiota to a carbohydrate-restricted diet in an obese volunteer. The community composition was estimated through 16S rRNA gene sequence analysis. Bacteria of the Prevotella genus dominated the microbiota. Eliminati...
Published in Metagenomics
Diversity of microorganisms involved in the biogeochemi-cal N cycle is of fundamental interest in microbial ecology. Denitrifica-tion is a key step in the cycle by which nitrate is reduced to dinitrogen gas via the soluble nitrite and the gaseous compounds nitric oxide and nitrous oxide. The process is carried out by the sequential activity of the ...
Published in Metagenomics
The rumen bacterial composition of both pre-ruminant dairy calves and cows and beef steers was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent and-independent clustering methods. The core rumen microbiome, regardless of the rumen developmental status or breeds, consisted of 8 phyla, 11 classes, 1...
Published in Metagenomics
The RDP Classifier is a widely used bioinfor-matic program that performs taxonomic classification of 16S rRNA gene sequences. However, the accuracy of the program is not clear when it is applied to common PCR products of the 16S rRNA variable regions, which are heavily used in microbiome projects. In this study, full-length 16S rRNA gene alignments...
