Transcriptional regulation and adaptation to a high-fiber environment in Bacillus subtilis HH2 isolated from feces of the giant panda

Abstract

In the giant panda, adaptation to a high-fiber environment is a first step for the adequate functioning of intestinal bacteria, as the high cellulose content of the gut due to the panda's vegetarian appetite results in a harsh environment. As an excellent producer of several enzymes and vitamins, Bacillus subtilis imparts various advantages to animals. In our previous study, we determined that several strains of B. subtilis isolated from pandas exhibited good cellulose decomposition ability, and we hypothesized that this bacterial species can survive in and adapt well to a high-fiber environment. To evaluate this hypothesis, we employed RNA-Seq technology to analyze the differentially expressed genes of the selected strain B. subtilis HH2, which demonstrates significant cellulose hydrolysis of different carbon sources (cellulose and glucose). In addition, we used bioinformatics software and resources to analyze the functions and pathways of differentially expressed genes. Interestingly, comparison of the cellulose and glucose groups revealed that the up-regulated genes were involved in amino acid and lipid metabolism or transmembrane transport, both of which are involved in cellulose utilization. Conversely, the down-regulated genes were involved in non-essential functions for bacterial life, such as toxin and bacteriocin secretion, possibly to conserve energy for environmental adaptation. The results indicate that B. subtilis HH2 triggered a series of adaptive mechanisms at the transcriptional level, which suggests that this bacterium could act as a probiotic for pandas fed a high-fiber diet, despite the fact that cellulose is not a very suitable carbon source for this bacterial species. In this study, we present a model to understand the dynamic organization of and interactions between various functional and regulatory networks for unicellular organisms in a high-fiber environment.

Fig 1. The growth curves of B. subtilis HH2 exposed to different carbon sources.

B. subtilis HH2 was cultured in cellulose or glucose medium following 1% inoculation at 37°C in a shaker at 150 rpm; the OD₆₀₀ was measured every hour. Each graph represents the mean of three independent biological replicates grown on three different days. The error bars represent the standard deviations (SDs) of the optical density at each time point.

Fig 2. Bacteria under the light microscope.

(A) B. subtilis HH2 was cultured in glucose medium until OD₆₀₀~1. (B) B. subtilis HH2 was cultured in cellulose medium until OD₆₀₀~1.

Fig 3. KEGG analysis of flagellar assembly (bsu02040) in B. subtilis.

Yellow boxes indicate significantly down-regulated genes in the cellulose group, and gray boxes indicate up-regulated genes (none in this figure). Green indicates a group of proteins.