Secretory IgA (SIgA) is the dominant antibody class in mucosal secretions. The majority of plasma cells producing IgA are located within mucosal membranes lining the intestines. SIgA protects against the adhesion of pathogens and their penetration into the intestinal barrier. Moreover, SIgA regulates gut microbiota composition and provides intestinal homeostasis. In this review, we present mechanisms of SIgA generation: T cell-dependent and -independent; in different non-organized and organized lymphoid structures in intestinal lamina propria (i.e., Peyer’s patches and isolated lymphoid follicles). We also summarize recent advances in understanding of SIgA functions in intestinal mucosal secretions with focus on its role in regulating gut microbiota composition and generation of tolerogenic responses toward its members.

We identified a human orthologue of tRNA:m5C methyltransferase from Saccharomyces cerevisiae, which has been previously shown to catalyse the specific modification of C34 in the intron-containing yeast pre-tRNA Leu (CAA). Using transcripts of intron-less and intron-containing human pre-tRNA Leu (CAA) genes as substrates, we have shown that m5C34 is introduced only in the intron-containing tRNA precursors when the substrates were incubated in the HeLa extract. m5C34 formation depends on the nucleotide sequence surrounding the wobble cytidine and on the structure of the prolongated anticodon stem. Expression of the human Trm4 (hTrm4) cDNA in yeast partially complements the lack of the endogenous Trm4p enzyme. The yeast extract prepared from the strain deprived of the endogenous TRM4 gene and transformed with hTrm4 cDNA exhibits the same activity and substrate specificity toward human pre-tRNALeu transcripts as the HeLa extract. The hTrm4 MTase has a much narrower specificity against the yeast substrates than its yeast orthologue: human enzyme is not able to form m5C at positions 48 and 49 of human and yeast tRNA precursors. To our knowledge, this is the first report showing intron-dependent methylation of humanpre-tRNA Leu (CAA) and identification of human gene encoding tRNA methylase responsible for this reaction.

Providing safe products and compliance of legal requirements is still a great challenge for food manufacturers regarding microbiological safety, especially in the context of Listeria monocytogenes food contamination. L. monocytogenes is a human pathogen, which, due to the ability of survival and proliferation in preservation conditions such as high salinity, acidity and refrigeration temperatures, is a significant threat to the food industry. Novel methods of elimination of the bacterial pathogen in food products and food processing environments are required. Among emerging technologies, one of the very promising solutions is using bacteriophages as natural control agents. This review focus on the major aspects of phage-based inhibition of L. monocytogenes in aspects of food safety. We describe an overview of foods and technological factors influencing the efficacy of phage use in biocontrol of L. monocytogenes. The most noteworthy are food matrix properties, phage concentration and stability, the time of phage application and product storage temperature. The combined methods, phage immobilization (active packing), pathogen resistance to phages and legislation aspects of antilisterial bacteriophage use in the food industry are also discussed.

A range of interactions between gut microbiota and iron (Fe) metabolism is described. Oral probiotics ameliorate host’s iron status. However, this has been proven for single-strain probiotic supplements. Dose-dependence of beneficial probiotic supplementation effect on iron turnover remains unexplored. Our study aimed to investigate the effects of oral multispecies probiotic supplementation in two doses on iron status in rats. Thirty rats were randomized into three groups receiving multispecies probiotic supplement at a daily dose of 2.5 × 10⁹ CFU (PA group, n = 10) and 1 × 10¹⁰ CFU (PB group, n = 10) or placebo (KK group, n = 10). After 6 weeks, rats were sacrificed for analysis, blood samples, and organs (the liver, heart, kidneys, spleen, pancreas, femur, testicles, duodenum, and hair) were collected. The total fecal bacteria content was higher in the PB group vs. PA group. Unsaturated iron-binding capacity was higher in the PB group vs. KK group. Serum Fe was lower in both PA and PB vs. KK group. Iron content in the liver was higher in the PB group vs. KK group; in the pancreas, this was higher in the PB group vs. the KK and PA group, and in the duodenum, it was higher in both supplemented groups vs. the KK group. A range of alterations in zinc and copper status and correlations between analyzed parameters were found. Oral multispecies probiotic supplementation exerts dose-independent and beneficial effect on iron bioavailability and duodenal iron absorption in the rat model, induces a dose-independent iron shift from serum and intensifies dose-dependent pancreatic and liver iron uptake.

In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.