Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community. These results highlight the benefit of reconstructing complete genomes from metagenomic data and demonstrate methods for achieving this goal.

Novel research strategy for safe use of legume proteins in human nutrition

Earlier studies on protein antinutrients and allergens naturally present in legume seeds have shown that these compounds are responsible for the impaired performance of experimental animals when exposed for a long term. These reactions were characterized by lowered nutritional performance, reduced growth, pure digestion and absorption, changes in gut motility, structural damage in small intestine and diarrhoea. A lot of efforts were made for gathering data on heat stability and resistance to chemical or enzyme treatments of these compounds to reduce or eliminate these harmful effects.A novel research approach has described that these compounds have a special regulatory role in the gut metabolism and modulate hormone and immune responses which resulted in a novel concept of “nonnutritive biologically active compound”. These studies revealed that the chemical structure of these compounds was responsible for the induction of such physiological reactions as increased endogen N-loss, change in the plasma amino acid concentration or plasma lipid composition with reduction of total cholesterol level or developing of harmful immune responses to luminal antigens resistant to the gut digestion. Resent studies were therefore related to the description of their interaction with the gut metabolism and understanding of the modulation of gut immune responses to luminal antigens.This review was inspired to summarise the research efforts on the above field performed by the Nutritional and Biological Units of the Central Food Research Institute.

Food safety in focus

The review provides selected examples on the activities and main results of the research and development work after the re-organization of the Central Food Research Institute (Budapest) at the turn of the 21 st century.

Lactobacilli stimulate the innate immune response and modulate the TLR expression of HT29 intestinal epithelial cells in vitro

The potentially probiotic strain Lactobacillus plantarum BFE 1685 isolated from a child's faeces and the probiotic strain Lactobacillus rhamnosus GG were investigated for their capability to influence the innate immune response of HT29 intestinal epithelial cells towards Salmonella enterica serovar Typhimurium. Furthermore, their capacity to modulate toll-like receptor expression of HT29 cells was investigated at the mRNA and protein levels. TNF-alpha was used in cell culture with HT29 cells to mimic an inflammatory background, and in the presence of this chemokine HT29 cells were sensitised to respond to the Lactobacillus strains as evidenced by an increased response in IL-8 production. In addition, when HT29 cells were first treated with lactobacilli and then infected with S. Typhimurium, the IL-8 levels in response to S. Typhimurium were significantly higher, indicating that HT29 cells were sensitised by lactobacilli. Neither of the lactobacilli was able to stimulate TLR4 production at the mRNA level, however, TLR2 and TLR9 transcription levels measured by quantitative PCR were up-regulated when HT29 cells were incubated with lactobacilli, but not with S. Typhimurium. Up-regulation of TLR9 expression was higher for L. rhamnosus GG than for L. plantarum BFE 1685. Expression levels of TLR2 and TLR5 were enhanced also at the protein level as determined by flow cytometry after staining with the respective antibodies. In contrast, TLR9 expression was not significantly up-regulated, which may be explained by protein degradation, or possible down-stream regulatory effects. These findings show that stimulation of specific signaling pathways occurs in the cross-talk between probiotic bacteria and gut epithelium cells, which can help to explain the adjuvant properties of probiotic lactobacilli.