Early melanoma invasivity correlates with gut fungal and bacterial profiles.

BACKGROUND: The microbiome is emerging as a crucial player of the immune checkpoint in cancer. Melanoma is a highly immunogenic tumour, and the composition of the gut microbiome has been correlated to prognosis and evolution of advanced melanoma and proposed as a biomarker for immune checkpoint therapy. OBJECTIVES: We investigated the gut fungal and bacterial compositions in early-stage melanoma and correlated microbial profiles with histopathological features. METHODS: Sequencing of bacterial 16S rRNA and the fungal internal transcribed spacer region was performed on faecal samples of patients with stage I and II melanoma, and healthy controls. A meta-analysis with gut microbiota data from patients with metastatic melanoma was also carried out. RESULTS: We found a combination of gut fungal and bacterial profiles significantly discriminating patients with melanoma from controls. In patients with melanoma, we observed an abundance of Prevotella copri and yeasts belonging to the order Saccharomycetales. We found that the bacterial and fungal community correlated to melanoma invasiveness, whereas the specific fungal profile correlated to melanoma regression. Bacteroides was identified as general marker of immunogenicity, being shared by regressive and invasive melanoma. In addition, the bacterial communities in patients with stage I and II melanoma were different in structure and richer than those from patients with metastatic melanoma. CONCLUSIONS: The composition of the gut microbiota in early-stage melanoma changes along the gradient from in situ to invasive (and metastatic) melanoma. Changes in the microbiota and mycobiota are correlated to the histological features of early-stage melanoma, and to the clinical course and response to immune therapies of advanced-stage melanoma, through direct or indirect immunomodulation.

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells.

Nucleotide-binding Oligomerization Domain-2 (NOD2) mutations are associated with an increased risk to develop Crohn's Disease. In previous studies, we have shown that Nod2-/- mice manifest increased proportion of Lamina Propria (LP) CD4+ LAP+ Foxp3- regulatory cells, when compared with Nod2+/+ mice, while CD4+ Foxp3 + regulatory cells were not affected. Here, we investigated the Nod2 gut microbiota, by 16S rRNA pyrosequencing, at steady state and after TNBS-colitis induction in mice reared separately or in cohousing, correlating the microbial profiles with LP regulatory T cells proportion and tissue cytokines content. We found that enrichment of Rikenella and Alistipes (Rikenellaceae) in Nod2-/- mice at 8 weeks of age reared separately was associated with increased proportion of CD4+ LAP+ Foxp3- cells and less severe TNBS-colitis. In co-housed mice the acquisition of Rickenellaceae by Nod2+/+ mice was associated with increased CD4+ LAP+ Foxp3- proportion and less severe colitis. Severe colitis was associated with enrichment of gram-negative pathobionts (Escherichia and Enterococcus), while less severe colitis with protective bacteria (Barnesiella, Odoribacter and Clostridium IV). Environmental factors acting on genetic background with different outcomes according to their impact on microbiota, predispose in different ways to inflammation. These results open a new scenario for therapeutic attempt to re-establish eubiosis in Inflammatory Bowel Disease patients with NOD2 polymorphisms.

The Root of Flowering Plants and Total Evidence.

Support for Amborella as the sole survivor of an evolutionary lineage that is sister to all other angiosperms comes from positions in DNA multiple-sequence alignments that have a poor fit to time-reversible substitution models. These sites exhibit significant levels of homoplasy, compositional heterogeneity, and strong heterotachy. We report phylogenetic analyses with observed, randomized, and simulated data which show there is little or no expectation that these sites provide useful information for understanding relationships among basal angiosperms. Their inclusion in phylogenetic analyses leads to a long-branch attraction artifact that favors Amborella as sister to other angiosperms in reconstructed phylogenies. Using parametric simulations, we show that sites in chloroplast sequences that exhibit less homoplasy between angiosperms and gymnosperms provide more reliable information for inferring basal angiosperm relationships. We confirm our earlier findings that the basal angiosperm Amborella is most closely related to aquatic herbs. Our current and previously reported (Goremykin et al. 2013) analyses highlight an essential aspect of the total evidence approach to phylogenetic inference. They suggest that data partitioning aimed at identifying components of the data that better fit evolutionary models is a more reliable approach to phylogeny reconstruction at deep taxonomic levels.

Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.

Expressed sequence tags (ESTs) are providing a valuable approach to sampling organism-expressed genomes, especially when studying large genomes such as those of many plants. We report on the comparison of 8,647 ESTs generated from six different grape (Vitis vinifera L.) organs: berry, root, leaf, bud, shoot and inflorescence. Clustering and assembly of these ESTs resulted in 4,203 unique sequences and revealed that at this level of EST sampling, each organ shares a low percentage of transcripts with the others. To define organ relationships based on EST counts, we calculated a distance matrix of pairwise correlation coefficients between the libraries which indicated bud, inflorescence and shoot as a group distinct from the other organs considered in this study. A putative function was identified for about 85% of the unique sequences. By assigning them to specific functional classes, we were able to highlight strong differences between organs in the metabolism, protein biosynthesis and photosynthesis categories. This grape EST collection has also proven to be a valuable source for the development of 'functional' simple sequence repeats (SSRs) markers: a total of 405 SSRs have been identified. EST sequences and annotation results have been organised in the IASMA-grape database, freely available at the address http://genomics.iasma.it.