The best practice for microbiome analysis using R

Wen, Tao; Niu, Guoqing; Chen, Tong; Shen, Qirong; Yuan, Jun; Liu, Yong‐Xin

doi:10.1093/procel/pwad024

Cited by 48 publications

(26 citation statements)

References 64 publications

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“…Sequenced reads underwent analysis utilizing R (v4.3.1) and DADA2 (v1.26.0) ( Callahan et al, 2016 ; Wen et al, 2023 ). Initial preprocessing involved the removal of 20 base pairs from both the beginning and the end of each read to eliminate low-quality regions flanking the reads.…”

Section: Methodsmentioning

confidence: 99%

Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity

Zaparte,

Dore,

White

et al. 2024

Front. Neurosci.

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Alcohol use disorder (AUD) is a complex and widespread disease with limited pharmacotherapies. Preclinical animal models of AUD use a variety of voluntary alcohol consumption procedures to recapitulate different phases of AUD, including binge alcohol consumption and dependence. However, voluntary alcohol consumption in mice is widely variable, making it difficult to reproduce results across labs. Accumulating evidence indicates that different brands of commercially available rodent chow can profoundly influence alcohol intake. In this study, we investigated the effects of three commercially available and widely used rodent diet formulations on alcohol consumption and preference in C57BL/6 J mice using the 24 h intermittent access procedure. The three brands of chow tested were LabDiet 5,001 (LD5001), LabDiet 5,053 (LD5053), and Teklad 2019S (TL2019S) from two companies (Research Diets and Envigo, respectively). Mice fed LD5001 and LD5053 displayed higher levels of alcohol consumption and preference compared to mice fed TL2019S. We also found that alcohol consumption and preference could be rapidly switched by changing the diet 48 h prior to alcohol administration. Sucrose, saccharin, and quinine preferences were not altered, suggesting that the diets did not alter sweet and bitter taste perception. We also found that mice fed LD5001 displayed increased quinine-resistant alcohol intake compared to mice fed TL2019S, suggesting that diets could influence the development of compulsive behaviors such as alcohol consumption. We profiled the gut microbiome of water- and alcohol-drinking mice that were maintained on different diets and found significant differences in bacterial alpha- and beta-diversities, which could impact the gut–brain axis signaling and alcohol consumption.

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Section: Methodsmentioning

confidence: 99%

Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity

Zaparte,

Dore,

White

et al. 2024

Front. Neurosci.

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“…Unless otherwise specified, statistical analysis and data visualization were performed in R software. The bioinformatics analysis followed the methods of previous research with slight modification (Wen et al., 2023 ), and the main steps are listed below. Prior to alpha‐diversity analyses, we used the R phyloseq (v1.44.0) package to control potential sequencing depth influences by subsampling all samples to 17,098 sequences (McMurdie & Holmes, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas

Yan,

Lei,

Zhao

et al. 2024

Ecology and Evolution

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The issue of poor sexual performance of some male giant pandas seriously impairs the growth and the genetic diversity of the captive population, yet there is still no clear understanding of the cause of the loss of this ability and its underlying mechanism. In this study, we analyzed the gut microbiota and its function in 72 fecal samples obtained from 20 captive male giant pandas, with an equal allocation between individuals capable and incapable of natural mating. Additionally, we investigated fecal hormone levels and behavioral differences between the two groups. A correlation analysis was then conducted among these factors to explore the influencing factors of their natural mating ability. The results showed significant differences in the composition of gut microbiota between the two groups of male pandas. The capable group had significantly higher abundance of Clostridium sensu stricto 1 (padjusted = .0021, GLMM), which was positively correlated with fatty acid degradation and two‐component system functions (Spearman, padjusted < .05). Additionally, the capable group showed higher gene abundance in gut microbiota function including purine and pyrimidine metabolism and galactose metabolism, as well as pathways related to biological processes such as ribosome and homologous recombination (DEseq2, padjusted < .05). We found no significant differences in fecal cortisol and testosterone levels between the two groups, and no difference was found in their behavior either. Our study provides a theoretical and practical basis for further studying the behavioral degradation mechanisms of giant pandas and other endangered mammal species.

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“…In this study, the methods described in references [ 17 , 18 , 19 , 20 , 21 ] were employed for the processing and analysis of sequencing data. This involved merging pair-end reads, trimming primers and barcodes, clustering OTUs (Operational Taxonomic Units), de-replication sequences, reducing abundance noise, removing chimeras, and generating the feature table.…”

Section: Methodsmentioning

confidence: 99%

Changes in Gut Microbiota Associated with Parity in Large White Sows

Bu,

Feng,

et al. 2023

Animals

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As one of the most critical economic traits, the litter performance of sows is influenced by their parity. Some studies have indicated a connection between the gut microbiota and the litter performance of animals. In this study, we examined litter performance in 1363 records of different parities of Large White sows. We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) among sows with parity 7 or higher. To gain a deeper understanding of the potential role of gut microbiota in this phenomenon, we conducted 16S rRNA amplicon sequencing of fecal DNA from 263 Large White sows at different parities and compared the changes in their gut microbiota with increasing parity. The results revealed that in comparison to sows with a parity from one to six, sows with a parity of seven or higher exhibited decreased alpha diversity in their gut microbiota. There was an increased proportion of pathogenic bacteria (such as Enterobacteriaceae, Streptococcus, and Escherichia–Shigella) and a reduced proportion of SCFA-producing families (such as Ruminococcaceae), indicating signs of inflammatory aging. The decline in sow function may be one of the primary reasons for the reduction in their litter performance.

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The best practice for microbiome analysis using R

Cited by 48 publications

References 64 publications

Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity

Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity

Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas

Changes in Gut Microbiota Associated with Parity in Large White Sows

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