The fecal bifidobacterial transcriptome of adults: A microarray approach

Abstract

Bifidobacteria are a predominant group present among adult human intestinal microbiota and are considered to be beneficial to host health. Both the dynamics and functional activity of bifidobacteria from the intestinal tract of four adults, following ingestion of a mix consisting of short chain galactooligosaccharides, long chain fructooligosaccharides and acidic oligosaccharides from pectin hydrolysate (GFP), was investigated. The percentage of total bifidobacteria, monitored by quantitative real time PCR, was not significantly altered but marked species-specific changes occurred in all individuals over time, indicating a dynamic bifidobacterial community. Insight into the functional activity of the bifidobacteria was acquired using a clone library-based microarray comprising the genomes of various bifidobacteria to reveal the bifidobacterial transcriptome within the fecal community. Total RNA from the fecal microbial community was hybridized to the microarray and 310 clones were selected for sequencing which revealed genes belonging to a wide range of functional groups demonstrating substantial metabolic activity. While the intake of GFP did not have a significant effect on the overall change in gene expression, 82 genes showed a significant change. Most of the predicted genes were involved in metabolism of carbohydrates of plant origin, house keeping functions such as DNA replication and transcription, followed by membrane transport of a wide variety of substrates including sugars and metals and amino acid metabolism. Other genes were involved in transport, nucleotide metabolism, amino acid metabolism, environmental information processing and cellular processes and signalling. A smaller number of genes were involved in general metabolism, glycan metabolism, energy metabolism, lipid metabolism and cell surface. These results support the notion that bifidobacteria utilize mainly indigestible polysaccharides as their main source of energy and biosynthesis of cellular components.

The function of our microbiota: who is out there and what do they do?

“…Metatranscriptome analysis of fecal samples from two healthy volunteers found that most expressed genes (26% of all sequenced and annotated transcripts) were involved in the metabolism of carbohydrate (Booijink et al, 2010). Recently the majority of bifidobacterial transcripts within the fecal community of adults were also reported to be involved in metabolism of carbohydrates of plant origin (Klaassens et al, 2011). …”

Gut microbiota, the pharmabiotics they produce and host health

“…The genetic pathway responsible for the de novo synthesis of vitamin B 12 by L. reuteri has previously been described for two L. reuteri strains (103) . More recently, the presence of bifidobacterial genes, predicted to be involved in the biosynthesis of several B vitamins has been identified in bifidobacteria residing in faecal samples of adult subjects (104)(105)(106) .…”

Dynamics of Gut Microbiota in Autoimmune Lupus

“…Comparing the predicted gut microbiome of lupus-prone mice to that of the control, categories representing genes important for genetic information processing (e.g., DNA replication and repair, protein synthesis) and nucleotide metabolism were significantly lower in MRL/lpr microbiome (Fig. 4A), indicating reduced turnover of bacterial DNA, RNA, and protein synthesis (58). This was accompanied by a significant increase in cell motility genes (e.g., bacterial chemotaxis and flagellar assembly) in the gut microbiome of lupus-prone mice healthy control treated with canola oil; vehicle, lupus-prone MRL/lpr treated with canola oil; RA, MRL/lpr treated with retinoic acid (6 mg/kg of body weight); VARA, MRL/lpr treated with retinol (6 mg retinol/kg of body weight) and retinoic acid (0.6 mg/kg of body weight, which facilitates retinol storage).…”