Taxonomical analysis of the suspended bacterial fraction in the dromedary rumen fluid

Abstract

An analysis of the dominant microbial taxa present in suspension within the rumen fluid from slaughtered one-humped camel (Camelus dromedarius) in Algeria was carried out using cultureindependent molecular techniques. The rumen fluid of freshly eviscerated animals was sampled by a syringe and filtered through 0.22 μm filters in sterile conditions. Lyophilized filters were subsequently used as starting material for bacterial lysis and total DNA extraction procedures using DNA purification kits and suitably adapted protocols. The gene corresponding to the small subunit of ribosomal RNA (16S rDNA) was PCR-amplified from the bulk of DNA using eubacterial primers, and the pool of amplicons was ligated to plasmids and cloned in Escherichia coli, generating a clone bank of several hundred individuals representative of the rumen bacterial community. A preliminary analysis of 86 clones, sorted by amplified ribosomal DNA restriction analysis (ARDRA), and sequenced by Applied Biosystems automated sequencing using fluorescent terminators yielded the following results. The most abundant amplicon belonged to the Pseudomonas genus encompassing over 65% of the clones. Pseudomonas lutea appeared the most frequent homology hit in a BLAST GenBank comparison. The remaining flora featured taxa include (in order of deceasing abundance): Synechococcus sp., Moraxella osloensis, Sphingomonas sp., Diaphorobacter nitroreducens, Acinetobacter sp., Ruminococcus albus, Propionibacterium acnes and Comamonas sp. The data constitute the baseline for a comparison of the results with those that will be obtained by further metagenomic approaches to compare the fluid associated bacterial community with those attached to the solid particulate fraction.

Key words: Camelus dromedarius, dromedary camel, rumen fluid, rumen bacteria.