Dataset Information

Transcriptome Analysis of the Clostridioides difficile Response to Different Doses of Bifidobacterium breve.

ABSTRACT: Probiotics are widely used in the prevention of Clostridioides difficile infection (CDI). The precise dosage of probiotics is a challenge. In this study, Clostridioides difficile ATCC 9689 (CD) was exposed to different doses of Bifidobacterium breve (YH68). A transcriptomic analysis was performed on CD cells that were separately exposed to low or high doses of YH68 cell-free culture supernatant (CFCS; CDL; or CDH, respectively). The results showed that the inhibitory effect of YH68 (cell pellets or CFCS) on the growth and the damage to the cell membrane integrity of CD exhibited a dose-response relationship at the physiological level. At the transcriptional level, a large number of differentially expressed genes (DEGs) were concentrated in amino acid, carbohydrate, energy metabolism and membrane transport in CDL and CDH cells, suggesting that both doses of YH68-CFCS triggered a significant change in activities in these metabolic pathways. Importantly, a significant stimulation or suppression was found in the pathogenic pathways (quorum sensing, signal transduction, flagellar assembly, biofilm formation, and drug resistance) of CDL and CDH cells, whereas there were some differences between the two doses. For example, the expression levels of genes related to quorum sensing and signal transduction in CDH cells were suppressed significantly, whereas genes encoding toxin production and sporulation factors were enhanced; in CDL cells, the expression levels of genes associated with flagellar assembly and biofilm formation were suppressed, whereas genes associated with drug resistance were upregulated significantly. These results indicated that the inhibitory effect of YH68-CFCS against CD, especially in pathogenic and metabolic aspects, did not demonstrate a dose-response relationship at the transcriptional level.

SUBMITTER: Yang J

PROVIDER: S-EPMC7411088 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Transcriptome Analysis of the Clostridioides difficile Response to Different Doses of Bifidobacterium breve.

Yang Jingpeng J Yang Hong H

Frontiers in microbiology 20200731

Probiotics are widely used in the prevention of Clostridioides difficile infection (CDI). The precise dosage of probiotics is a challenge. In this study, Clostridioides difficile ATCC 9689 (CD) was exposed to different doses of Bifidobacterium breve (YH68). A transcriptomic analysis was performed on CD cells that were separately exposed to low or high doses of YH68 cell-free culture supernatant (CFCS; CDL; or CDH, respectively). The results showed that the inhibitory effect ...[more]

PMID: 32849451

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Project description:The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (760 g/l) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron transporters were found induced by Fur regulation during low iron (11 g/l) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were found significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some initial intermediates (phenylpyruvate, oxo-isocaproate, 3-hydroxy-butanoyl-CoA, crotonyl-CoA) were found accumulated, while some end product like isocaproate and butanoate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were found enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB,) of the F0F1-type was found induced while the formation of a V-type, mostly proton-pumping, ATP-consuming ATPase (atpDBAFCEKI, was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. An intensive remodeling of the cell wall was observed most likely to increase antibiotic resistance. Polyamine biosynthesis (spe) was found induced leading to an accumulation of spermine, spermidine and putrescine. The fur mutant lost most of its flagella. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, significant decrease in metabolic iron utilization and protection during the complex transition.

Dataset Information

Transcriptome Analysis of the Clostridioides difficile Response to Different Doses of Bifidobacterium breve.

Publications

Transcriptome Analysis of the <i>Clostridioides difficile</i> Response to Different Doses of <i>Bifidobacterium breve</i>.

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