J. P. Newson, et al., Salmonella effectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways.
Mol. Cell. Proteomics 2019 Mar 22; mcp.RA118.001093. doi: 10.1074/mcp.RA118.001093. PubMed
Summary and comments: The authors used mass spectrometry-based proteomics to identify host proteins modified by enzymes injected by the pathogenic bacteria Salmonella. Previous studies had identified various targets of the bacterial enzymes, SseK1 and SseK3. These enzymes are arginine glycosyltransferases that add a sugar molecule called N-acetyl glucosamine (GlcNAc) onto specific proteins at arginine residues. For this study, the cells were infected with bacteria engineered to have only either SseK1 or SseK3 active so that the proteins modified by each enzyme could be determined. A small number of host proteins were modified in the infected cells. The authors focused on the modification of proteins involved in activating cell death pathways. By modifying these proteins, the bacteria can prevent the infected cells from dying. In the infected cells, SseK1 added GlcNAc onto TRADD, a protein that functions as an adaptor in a cell death pathway. SseK3 added GlcNAc to two receptors, TNFR1 and TRAILR, both of which activate cell death pathways. To perform these proteomic studies, the authors used a procedure involving immunoprecipitation of proteins with arginine residues modified with GlcNAc and mass spectrometry analysis that detected peptides with GlcNAc modifications at arginine residues. Various biochemical assays supported their proteomic findings. Analysis of mice deficient in TRAILR or TNFR1 showed that only those deficient in TNFR1 were more susceptible to Salmonella infection, suggesting that this receptor is the more important target for SseK3. This study represents an example of how mass spectrometry-based proteomics can be used to detect posttranslationally modified proteins (Arg-GlcNAc) relevant for understanding mechanisms of pathogenicity of bacterial infections.
The version I read is a “preview” version of the accepted manuscript before copyediting and compilation.
L. Cortes, et al., Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome. Int. J. Mol. Sci. 2019 Mar 21;20(6): E1430. doi: 10.3390/ijms20061430. PubMed
Summary and comments: To understand how the microbes that live within our bodies influence health and contribute to disease, we need to understand the composition of these microbial communities and the proteins and metabolites that they produce. This study reports the analysis of the proteins from fecal samples from 8 infants (2 to 5 months old) in The Netherlands. The authors are careful not to overinterpret their findings from such a small sample size. A comparison of bacterial species identified through proteomic analysis versus those identified by DNA sequencing indicated that proteomic analysis revealed more the microbiome in more detail, identifying more genera and revealing species and strain differences between the samples. Because of the high variation between individuals, the authors clustered the equivalent proteins from different species and then grouped the proteins into metaclusters to perform comparisons between the microbiomes from each infant. The metaclusters were then classified into biochemical pathways using the KEGG Pathway database. One of infants had been treated with antibiotics; thus activity of the microbiome biochemical pathways (represented by the abundance of the proteins in the metaclusters) from the other seven were compared the microbiome of the single antibiotic-treated individual. This study adds to the growing knowledge regarding the gut microbiome in infants and shows that metaproteomics can reveal more details than DNA analysis. Large versions of the figures when viewed through the full text view resulted in a page not found error. However, the figures were legible in the PDF version.
Z. Liu, et al., The intestinal microbiota associated with cardiac valve calcification differs from that of coronary artery disease.
Atherosclerosis. 2018 Dec 4;284:121-128. doi: 10.1016/j.atherosclerosis.2018.11.038. PubMed
Summary and comments: There is growing evidence that gut dysbiosis, as unhealthy alterations in the gut microbiome are called, contributes to many different diseases and health conditions. This study examined the gut microbiome using DNA sequencing to determine if there were differences between patients with two different types of cardiovascular disease. They compared healthy subjects and patients with cardiac valve calcification (19 patients) or coronary artery disease (46 patients) or both (21 patients). A mathematical approach called principle component analysis showed that the gut microbiome data partially clustered the patients with only coronary artery disease with the healthy group, whereas the gut microbiome data clustered the patients with either valve calcification alone or valve calcification and cardiac artery disease away from the healthy group. The microbiomes from the valve calcification patients were the most different from the microbiomes of healthy controls. The 3 types of patients with the different cardiovascular diseases could be distinctly identified by principle component analysis of their gut microbiomes. Analysis of specific bacterial groups revealed distinct populations were higher in patients with either valve calcification or coronary artery disease and identified an association between specific bacterial populations and dyslipidemia, which is a major factor in cardiovascular disease. Understanding the differences in the gut microbiome in patients with different forms of heart disease may help clinicians determine who is most at risk for developing these different conditions and whether a patient with one condition is likely to develop the second.
M. Rostok, et al., Potential vaginal probiotics: safety, tolerability and preliminary effectiveness. Benef. Microbes. 2019 Mar 18; 1-10. doi: 10.3920/BM2016.0123. PubMed
Summary and comments: I could only access the abstract and supplementary materials for this article. The authors performed a small trial with 8 or 9 healthy women in each group. The trial design was a randomized double-blind, placebo crossover, meaning that the subjects were randomly assigned into the groups. One group was the placebo group. The others received one of two different oral preparations of probiotics with either a period of placebo treatment before or after the probiotic treatment (the crossover part of the study). The probiotic preparations contained 3 strains of a beneficial vaginal bacteria Lactobacillus crispatus. Significant reductions in the Nugent score and in the number of pathogenic bacteria (Garnerella vaginalis) occurred in the group receiving one of the probiotic preparations. A low Nugent score (<3) is an indication of a healthy vaginal bacterial composition. I find it difficult to understand how orally administered bacteria changed the vaginal microbiome, although it is possible that changing the gut microbiome alters the immune system to enable beneficial microbes to dominate in the vagina.
Cite as: N. R. Gough, A Closer Look: Microbes and Microbiomes. BioSerendipity (9 April 2019) https://www.bioserendipity.com/a-closer-look-microbes-and-microbiomes/