The cross talk occurring between bifidobacteria in the mammalian’s gut microbiota [ATCC15697]

We describe the molecular cross talk established under in vivo conditions between a set of human gut bifidobacterial commensals. Eleven groups of five conventional female 8-wk-old BALB/c mice taking a standard polysaccharide-rich Chow diet were administered a single daily dose of 109 CFU of either B. bifidum PRL2010, B. breve 12L , B. adolescentis 22L , B. longum subsp. infantis ATCC15697, or bifidobacterial couples, i.e., PRL2010-12L, PRL2010-22L, PRL2010-ATCC15696, 12L-22L, 12L-ATCC15697, 22L-ATCC15697, or a combination of all bifidobacterial strains. The transcriptome of bifidobacterial strains under in vivo conditions was analyzed. The transcripts expressed in B. bifidum PRL2010, B. breve 12L, B. adolescentis 22L and B. longum subsp. infantis ATCC15697 were profiled using a custom-made PRL2010-12L-22L-ATCC15697 (multibifido)-array representing 100%, 99%, 96%, 99% of the identified genes of these organisms, respectively.The observed functional changes in the trascriptomes of bifidobacteria might be caused by the possible shifts of the mice cecum microbiota upon colonization with bifidobacteria. Thus, we assessed if the presence of B. bifidum PRL2010, B. breve 12L, B. adolescentis 22L and B. longum subsp. infantis ATCC15697 on mono-, bi- or multi-association in the cecum of mice affects the overall composition of the microbiota of this environment. Microarray analysis was performed with an oligonucleotide array based on the B. adolescentis 22L, B. bifidum PRL2010, B. breve 12L and B. longum subsp. infantis ATCC15697 genomes for a total of 45220 oligonucleotide probes of 60 bp in length were designed on 7679 ORFs using eArray5.0 (Agilent Technologies). 5 Oligos were designed for each gene on a 4x44k Agilent Microarrays (Agilent Technologies, Santa Clara, CA, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 152 negative control probes designed on phage and plant sequences were also included on the chip. Reverse transcription and amplification of 500 ng of total RNA was performed with ImProm-IITM Reverse Transcriptase (Promega, Madison, USA) according to the manufacturer’s instructions. Five µg of cDNA was then labeled with ULS Labeling kit with Cy5 or Cy3 (Kreatech, The Netherlands). Labeled cDNA was hybridized using the Agilent Gene Transcription hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Transcription Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent's standard procedures.