CleanBSequences: an efficient curator of biological sequences in R

Pozzi, Florencia Ileana; Green, Gisela Y.; Barbona, Ivana; Rodríguez, Gustavo; Felitti, Silvina Andrea

doi:10.1007/s00438-020-01671-z

Cited by 2 publications

(1 citation statement)

References 19 publications

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“…According to the number of sequences for each OTU in each sample, an abundance matrix of the OTUs in each sample (otu_table.biom) was constructed. Based on sequence comparison, the phylogeny of the representative sequences of the OTUs was constructed with PyNAST (v0.1) software [ 18 ] and a phylogenetic tree file (rep_phylo.tre) was obtained. According to the principle of minimum depth, all the samples were randomly selected to obtain an OTU table (otu_table_even.biom).…”

Section: Methodsmentioning

confidence: 99%

Informatic analysis of the pulmonary microecology in non-cystic fibrosis bronchiectasis at three different stages

Wang

Chen

et al. 2022

Open Life Sciences

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This study explored the impact of pulmonary microecological changes on disease progression in non-cystic fibrosis bronchiectasis (nCFB). A careful search of the NCBI BioProject database revealed the 16S rRNA-based microbiological testing results of 441 pulmonary sputum samples from patients in the relatively stable (baseline), acute exacerbation, or recovery stage. After preliminary analysis and screening, we selected 152 samples for further analyses, including determination of the operational taxonomic unit (OTU) distribution at the phylum, class, order, family and genus levels, community structure, alpha diversity, beta diversity, microbial multivariables, correlations, and community structure after the abundances of intragroup samples were averaged. The recovery group showed significant differences in pulmonary microbiological changes (P < 0.05) compared with the other groups. There were 30 differentially abundant OTUs, with 27 and 7 at the genus and phylum levels, respectively. The Chao1 value of the recovery group was comparable to that of the baseline group, and the Shannon and Simpson values of the recovery group were the highest. Rhodococcus in Actinobacteria was positively correlated with Ochrobactrum in Firmicutes. The differences in pulmonary microecological changes at different nCFB stages may serve as a biologically predictive indicator of nCFB progression.

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Section: Methodsmentioning

confidence: 99%