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Human Gut Microbiota–Transplanted Gn Pig Models for HRV Infection
Published in Lijuan Yuan, Vaccine Efficacy Evaluation, 2022
A total of 5,616,353 non-chimeric high-quality sequences from the feces of the human donor and the recipient pigs were analyzed with QIIME. We analyzed the sequences at the operational taxonomic unit (OTU) level (Schloss and Handelsman, 2005). The recipient pigs carried microbiota that is similar to the human donor's microbiota (Figure 11.1A), despite that all pigs had received the attenuated HRV vaccine. Two bacterial phyla, Firmicutes and Proteobacteria, representing over 98% of total bacterial sequences in each subject, dominated the microbiota of both the human donor (delivered by C-section) and the recipient pigs. The most abundant genera within Firmicutes were Streptococcus, Enterococcus, Veillonella, and Staphylococcus (Figure 11.1A). The rank abundance curve showed that the gut microbiota of the human donor and pigs had a long tail of rare OTUs (data not shown). For example, around 900 OTUs (species rank from 100 to 1,000) each accounted only 0.01% (10–4) to well below 0.001% (10–5) of total bacteria.
Aeroallergen sampling
Published in Richard F. Lockey, Dennis K. Ledford, Allergens and Allergen Immunotherapy, 2020
Estelle Levetin, Josh D. McLoud
NGS is frequently used for metagenomic analysis—the study of the genetic material of all organisms from an environmental sample [81]. The aim of metagenomics is to characterize the microbial diversity and ecology of a specific environment, including atmospheric samples. NGS results yield operational taxonomic units (OTUs), clusters of similar DNA sequences for a particular marker gene, generally the 16S rRNA gene for bacteria, ITS gene for fungi, and 18S rRNA gene for other eukaryotes. The sequence similarity is commonly defined at 97%, and OTUs may designate a species, a genus, or other taxonomic level. Unlike qPCR, prior knowledge of the organisms present and prior development of species-specific primers are not needed.
Assessing the Microbiome—Current and Future Technologies and Applications
Published in David Perlmutter, The Microbiome and the Brain, 2019
Thomas Gurry, Shrish Budree, Alim Ladha, Bharat Ramakrishna, Zain Kassam
The processed OTU table contains the absolute abundance of the individual OTUs and accompanying taxonomic classification in the sequenced sample. It is a common practice for researchers to normalize the OTU count and report the relative abundance of organisms present in samples at various taxonomic levels, including the phylum level to genus level, with 16S data and species level with shotgun metagenomic data (Jovel et al. 2016 and Olsen 2016). Relative abundances are usually represented using graphical plots, including heat maps, bar-plots, and circular phylogenetic trees. Heatmaps utilize color-coding to represent numerical values, like OTU abundance, and are particularly common and a useful method of representing large-scale data graphically as they are visually appealing.
Changes in the oral and nasal microbiota in pediatric obstructive sleep apnea
Published in Journal of Oral Microbiology, 2023
Xiaoman Zhang, Xinyi Li, Huajun Xu, Zhihui Fu, Fan Wang, Weijun Huang, Kejia Wu, Chenyang Li, Yupu Liu, Jianyin Zou, Huaming Zhu, Hongliang Yi, Su Kaiming, Meizhen Gu, Jian Guan, Shankai Yin
Analysis of the oral and nasal microbiota was performed as described previously [21]. The raw 16S rRNA gene amplicon sequences were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME) platform [22]. The operational taxonomic units (OTUs) (≥97% identity) were created in the Quantitative Insights into Microbial Ecology (QIIME; http://qiime.org/scripts/pick_otus.html) database. The taxonomy of OTUs was annotated according to the Greengenes database [23]. First, the sequences were demultiplexed based on the barcodes assigned to each sample. Then, the demultiplexed pair-end sequences from each sample were quality-controlled (stitched, filtered, trimmed, and de-noised, with ambiguous/chimeric sequences being removed) using DADA2 in QIIME2 and clustered to generate an amplicon sequence variant table [24].
Integration of network pharmacology and intestinal flora to investigate the mechanism of action of Chinese herbal Cichorium intybus formula in attenuating adenine and ethambutol hydrochloride-induced hyperuricemic nephropathy in rats
Published in Pharmaceutical Biology, 2022
Na Li, Mukaram Amatjan, Pengke He, Boheng Zhang, Xianyan Mai, Qianle Jiang, Haochen Xie, Xiaoni Shao
Operational taxonomic units (OTUs) are hypothetical taxa for sequence clustering that facilitate the study of sample species composition and diversity information. In general, OTU clustering analysis is usually performed at a 97% similarity level, with each OTU representing a set of similar sequences. The representative sequences of OTUs are annotated taxonomically by the UCLUST classification (Edgar 2010). The evolutionary tree composed of the top 50 OTUs in abundance was performed in Figure 6A, primarily for the calculation of subsequent α-diversity and β-diversity analyses. Venn diagrams (Figure 6B) visualize the similarity of OTUs composition between groups. The overlapping part of the petal is the OTUs shared by adjacent groups, and each colour represents a group. A total of 4851 OTUs were generated from the five groups, and there were 615 unique OTUs in CG, 205 in HNG, 536 in AG, 245 in FHG and 183 in FLG, five groups with 1008 OTUs in common.
Efficacy of Yougui pill combined with Buzhong Yiqi decoction in alleviating the sexual dysfunction in female rats through modulation of the gut microbiota
Published in Pharmaceutical Biology, 2022
Yangyun Wang, Chaoliang Shi, Wandong Yu, Wei Jiao, Guowei Shi
After sequencing, the paired raw data were merged using Trimmomatic (Bolger et al. 2014). Quality control of raw data was performed; then, the data were filtered into clean reads using the Quantitative Insights Into Microbial Ecology software (http://qiime.org/). Based on the similarity level, the sequences were divided into different operational taxonomic units (OTUs); OTUs with ≥97% similarity level were selected for bioinformatics analysis using USEARCH (version 7.1, http://drive5.com/uparse/). Taxonomic analysis of OTUs with a similarity level of greater than 97% was performed using RDP classifier (http://sourceforge.net/projects/rdp-classifier/) to obtain the community composition of each sample. The rank abundance curve and rarefaction curve were plotted to determine the species abundance and species uniformity.