No abstract

Background: Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited or certified reference materials available to the wider community. In this study, we describe the development of the first reference reagents produced by the National Institute for Biological Standards and Control (NIBSC) for microbiome analysis by next-generation sequencing. These can act as global working standards and will be evaluated as candidate World Health Organization International Reference Reagents. Results: We developed the NIBSC DNA reference reagents Gut-Mix-RR and Gut-HiLo-RR and a four-measure framework for evaluation of bioinformatics tool and pipeline bias. Using these reagents and reporting system, we performed an independent evaluation of a variety of bioinformatics tools by analysing shotgun sequencing and 16S rRNA sequencing data generated from the Gut-Mix-RR and Gut-HiLo-RR. We demonstrate that key measures of microbiome health, such as diversity estimates, are largely inflated by the majority of bioinformatics tools. Across all tested tools, biases were present, with a clear trade-off occurring between sensitivity and the relative abundance of false positives in the final dataset. Using commercially available mock communities, we investigated how the composition of reference reagents may impact benchmarking studies. Reporting measures consistently changed when the same bioinformatics tools were used on different community compositions. This was influenced by both community complexity and taxonomy of species present. Both NIBSC reference reagents, which consisted of gut commensal species, proved to be the most challenging for the majority of bioinformatics tools tested. Going forward, we recommend the field uses site-specific reagents of a high complexity to ensure pipeline benchmarking is fit for purpose. Conclusions: If a consensus of acceptable levels of error can be agreed on, widespread adoption of these reference reagents will standardise downstream gut microbiome analyses. We propose to do this through a large open-invite collaborative study for multiple laboratories in 2020.

Ice cream is a popular dairy product among consumers of all ages. Textural attributes of ice are the key factors determining the market success of the product. Ice cream is a dairy aerated dessert that is frozen prior to consumption. It is a microcrystalline network of liquid and solid phases. It contains air cells entrapped in liquid phase and various other components like proteins, fat globules, stabilizers, sugar, soluble and insoluble salts are also present in this phase. It is a complex physicochemical and colloidal system consisting on many complex ingredients that affect ice cream structure both in positive and defective functionality. Both stabilizers and emulsifiers improve the texture of ice cream by enhancing its viscosity and limiting the movement of free water molecules but their excess may cause the lower melting and less whip ability. As sugar provides sweet taste, improves thickness as well as bulkiness but on other hand its excessive use can turn ice cream into soggy structure above solid contents of about 42%. One of its compositional contents, fat, also exerts good effects on body, texture, palatability, flavor intensity, emulsion formation and maintenance of melting point. If fat contents exceed a specific usage concentration they cause faster meltdown of ice cream along with destabilization and agglomeration of fat droplets. Higher overrun results in collapsing of air cells ultimately shrinkage of structure occurs. Hardness might also reduced as a result of smaller ice crystals due to high overrun values. Fiber addition causes the binding of free water hence flow rate get reduced and consistency coefficient as well as viscosity enhanced. Binding of water results in less availability of its molecules; freezing point rises and melting point decreases. It is much critical to control the balance ice cream properties by maintaining its structure, texture and body. It is a best carrier for fruit fiber, chunks, purees, paste, concentrates; milk and whey isolates and concentrates; egg, egg yolks and their products; different flavorings, nuts, chocolate, probiotics and yogurt. So far, it is important to maintain its solid contents and structure with balanced proportion of ingredients.

A novel series of oxy-diester-functionalized gemini surfactants (Cm-E2O-Cm) were synthesized and a comprehensive analysis of their biophysicochemical properties was carried out.

Spores of Clostridium difficile carry a chitinase enzyme whose function is to bind to mucin, leading to its degradation. We show in vivo that this is potentially an important element of colonization and virulence.