Objective

Pseudomonas aeruginosa is a gram-negative bacterium, which can produce endotoxin, exotoxin, proteolytic enzyme and other substances and infect human and other organisms [1, 2]. At present, macrolide and aminoglycoside antibiotics are commonly used for curing the clinical infection of P. aeruginosa. However, with the emergence of drug resistance, P. aeruginosa are difficult to treat by common antibiotics. Thus, we are seeking for effective antimicrobial agents from traditional Chinese medicine to treat infection of P. aeruginosa. Previously, our research group have proved that sodium houttuyfonate (SH) can effectively inhibit the P. aeruginosa [3, 4]. Here, our aim is to investigate possible antimicrobial mechanism of SH by comparing the transcriptomic differences between SH drug and blank control groups.

The assemble transcriptome contains thousands of transcripts. Thus this study provides transcriptomic comparison between SH medication group and blank control group rather than comparisons of expression of several certain genes such as algD, algR, lasI, phzM, lasA and bdlA, in previous studies [4,5,6]. The difference of these transcriptome can be used as the basis for studying gene expression changes in SH treatment and control groups.

Data description

We cultured P. aeruginosa under two conditions, with 4 biological replications which were cultured independently under each condition:

  1. 1.

    ATCC 27853 was inoculated into LB liquid medium and cultured overnight at 37 °C. The culture were centrifuged for 1 min at 12,000 r/min, and pour out the supernatant, diluted with sterile water to 0.5 Maxwell colorimetric tube, and diluted to 107 times for later use. The SH was prepared according to our previous research [6]. The prepared SH samples in LB medium with 1 MIC (minimum inhibitory concentration) SH of 512 μg/ml were cultured for 24 h at 37 °C until OD600 was 0.6–0.8, and collected by centrifugation of 1 min at 12,000 r/min, and then rinsed with sterile water for 3 times. Then we placed the collected bacterial samples in the centrifuge tube, sealed it with sealing film, and sent the sample for RNA-seq with dry ice.

  2. 2.

    The samples of blank control were collected similarly as SH treatment samples except without drug treatment.

Totally 170.53 MB of transcriptome sequencing data is obtained after RNA-seq applying BGISEQ-500 platform. The original data of sequencing includes reads with low quality, linker contamination and high content of unknown base N are removed before data analysis to ensure the reliability of the results. This project used SOAPnuke [7], a filtering software independently developed by Huada Corporation, to make statistics and trimmomatic [8] to filter. Firstly, readers including connectors are removed. Then the reads with unknown base N content more than 5% are wiped off. Finally, the low-quality reads are removed (we define reads with a mass value of less than 10 and a proportion of more than 20% of the total number of bases in the reads as low-quality reads). The filtered “Clean Reads” are saved in FASTQ format. The file format corresponding to each sample is FASTQ format (Table 1).

Table 1 Overview of transcriptome data files
Full size table

The original sequencing sequence data (fastq file), including reference genome information, can be obtained on NCBI. After the quality control of the original data, we used Bowtie2 [9] to compare clean reads to the reference gene sequence (Table S1), and then RSEM [10] was used to calculate the expression levels of genes and transcripts. After completion, totally 5938 genes are assembled from sequencing data.

In order to reflect the correlation of gene expression between samples, Pearson correlation coefficients of all gene expression amounts between every samples are calculated, and expression amount distribution analysis are performed. The obtained results are shown in Fig. S1A [13]. According to the gene expression level of each sample, a total of 2047 differentially expressed genes are detected by the threshold of fold changes > 2, Q value < 0.001, including 368 up-regulated genes and 1679 down-regulated genes. The results are shown in volcanic map of Fig. S1B [13].

Limitations

The limitations of this data is that there is not a gradient comparison under multiple different concentrations of SH, and the transcriptome expression of P. aeruginosa under 24 h of culture is selected in this study, which may make the results inconsistent with other research results. In addition, in our previous studies [4, 5], the qRT-PCR results showed that genes of lasA, algD, algR are down regulated by SH treatment in P. aeruginosa. However, these genes are found to be below the detection threshold in this study. This may be due to the different technologies used in determination of the gene expression.