The effects of diets supplemented with either chickpea or its main oligosaccharide raffinose on the composition of the faecal microbial community were examined in 12 healthy adults (18-65 years) in a randomised crossover intervention study. Subjects consumed their usual diet supplemented with soups and desserts that were unfortified, or fortified with either 200 g/d of canned chickpeas or 5 g/d of raffinose for 3 week periods. Changes in faecal bacterial populations of subjects were examined using 16S rRNA-based terminal restriction fragment length polymorphisms (T-RFLP) and clone libraries generated from the diet pools. Classification of the clone libraries and T-RFLP analysis revealed that Faecalibacterium prausnitzii, reported to be an efficient butyrate producer and a highly metabolically active bacterium in the human intestinal microbiota, was more abundant in the raffinose diet and the chickpea diet compared to the control diet. However, no significant difference was observed in the faecal total short chain fatty acid concentration or in the levels of the components (butyrate, acetate and propionate) with the chickpea diet or the raffinose diet compared to the control diet. Bifidobacterium species were detected by T-RFLP in all three diet groups and quantitative real-time PCR (qPCR) analysis showed a marginal increase in 16S rRNA gene copies of Bifidobacterium with the raffinose diet compared to control (P>0.05). The number of individuals showing TRFs for the Clostridium histolyticum - Clostridum lituseburense groups, which include pathogenic bacteria species and putrefactive bacteria, were lower in the chickpea diet compared to the other two treatments. Diet appeared to affect colonisation by a high ammonia-producing bacterial isolate which was detected in 83%, 92% and 42% of individuals in the control, raffinose and chickpea groups, respectively. Our results indicate that chickpea and raffinose have the potential to modulate the intestinal microbial composition to promote intestinal health in humans.

Actinobacteria, particularly bifidobacteria, are widely observed to be underrepresented in metagenomic studies of microbial communities. We have compared human fecal microbiota clone libraries based on 16S rRNA and cpn60 PCR products. Taxonomic profiles were similar except that the cpn60 libraries contained large numbers of bifidobacterial sequences.

Sub-therapeutic doses of antibiotics are added to animal feed to treat and prevent infections and to improve growth and production. Intensive animal breeding for food production has led to a substantial increase in the use of antibiotics in the recent decades. Exposing bacteria to low doses of antimicrobial agents over a long period of time lead to selection of antimicrobial resistant genes in bacteria. This overuse of sub-therapeutic antibiotics in animal feeds can contribute to antibiotic resistance development in bacteria creating health dangers to human. It has been shown that the antibiotic avoparcin, when removed from animal feeds in Sweden, resulted in a significant reduction in vancomycin resistance in human clinical isolates. The European Union has banned all in-feed use of antibiotics from 2006 and the use of antibiotics in feed is being considered for elimination (or intense regulation) in other parts of the world. Moreover consumer requests for antibiotic free meat products are increasing and countries exporting meat to the European Union are required to follow suit. It is also clear that the complete withdrawal of feed antibiotics has a detrimental effect on production and animal health to the extent that more antibiotics may ultimately be subscribed for therapeutics purposes to control disease conditions. The removal of antibiotics from animal feed will also lead to an increase in the proportions of harmful microbes like E. coli, Salmonella and Campylobacter in the gut microflora of farm animals challenging human food safety. Therefore alternatives to sub-therapeutic antibiotics are urgently needed, but to make this transition, a better understanding and a more fundamental knowledge about the role of microorganism in gut function is required. This report will outline how the native intestinal microbial population can be harnessed to improve animal health and performance. Moreover the recent findings in the search for alternatives to in-feed antibiotics that hold potential to successfully manipulate this ecosystem will be discussed.