Dataset Information

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing.

ABSTRACT: The gut microbiota play important roles in the degradation of chemical compounds of herbal medicines (HMs). However, little information regarding the interplay between HMs and the gut microbiota is available. Thus, the aim of this study was to investigate the composition of the fecal microbiota of young (age, 11 weeks) hens fed a conventional diet containing a crude Astragalus (0.5%) additive for 21 days (group A) vs. controls (group B) that were fed only conventional feed. The fecal contents of 14-week-old hens were collected for DNA extraction, and then the V3 and V4 hyper-variable regions of the 16S rRNA gene were amplified and analyzed using high-throughput sequencing technology. A distinctive difference in microbial diversity was observed between the two groups. The microbial composition of hens fed a diet supplemented with Astragalus was greater than that of the control group. At the genus level, Lactobacillus was more abundant in group A than group B (p?

SUBMITTER: Qiao H

PROVIDER: S-EPMC5928015 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing.

Qiao Hongxing H Zhang Liheng L Shi Hongtao H Song Yuzhen Y Bian Chuanzhou C

AMB Express 20180430 1

The gut microbiota play important roles in the degradation of chemical compounds of herbal medicines (HMs). However, little information regarding the interplay between HMs and the gut microbiota is available. Thus, the aim of this study was to investigate the composition of the fecal microbiota of young (age, 11 weeks) hens fed a conventional diet containing a crude Astragalus (0.5%) additive for 21 days (group A) vs. controls (group B) that were fed only conventional feed. The fecal contents of ...[more]

PMID: 29713833

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Project description:As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner - with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.

Dataset Information

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing.

Publications

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing.

Similar Datasets

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