A transcriptomic analysis to understand this unique phenotype showed a change in expression of some σ B -controlled genes along with several non-σ B controlled genes. Δ rsbW was defective in spore and biofilm formation, adhered better to human gut epithelia and was less virulent in a Galleria mellonella infection model. Δ rsbW did not have deleterious fitness defects but tolerated acidic environments and detoxified reactive oxygen and nitrogen species better. difficile physiology, a rsbW mutant (Δ rsbW ) where σ B is ‘always on’, was generated. To cope with environmental stresses, it uses the alternative sigma factor B (σ B ) to modulate gene transcription, which is regulated by an anti-sigma factor, RsbW. The anaerobic pathogen Clostridioides difficile, a primary cause of antibiotic-associated diarrhoea, faces a variety of stresses in the environment and in the mammalian gut. Our data demonstrate that HFHPD altered the community structure of lactase bacteria in the intestinal mucosa, decreased the abundance of the critical lactase bacteria, and promoted the occurrence of diarrhea. Compared to NM, the abundance of Bifidobacterium were lower in MD, while MD added sources for lactase bacteria of Rhizobium, Amycolatopsis, and Cedecea. At the genus level, Bifidobacterium was the dominant genus (over 90% of the total). Where Actinobacteria were higher in NM, and Proteobacteria were higher in MD. In taxonomic composition, lactase bacteria on the intestinal mucosa were sourced from Actinobacteria and Proteobacteria. Meanwhile, the Principal coordinate analysis (PCoA) and Adonis test showed that the community structures of lactase bacteria in NM and MD were significantly different (P < 0.05). The Chao1 and Observed specie indexes in the MD were higher than those in the NM, but this was not significant (P > 0.05). Operational Taxonomic Units (OTUs) were 23 and 31 in the normal group (NM) and model group (MD), respectively, and 11 of these were identical. Therefore, we reconnoiter the relationship between diarrhea induced by a high-fat and high-protein diet (HFHPD) and intestinal mucosal lactase bacteria from the perspective of functional genes. Lactase is a functional enzyme strongly associated with diarrhea, while lactase bacteria in the intestine are an important source of microbial lactase. Message me if you'd like to see some codes I've used or have any other questions.Excessive fat and protein in food can cause diarrhea by disturbing the intestinal microecology. I would encourage you to seek further support in your research community and start fiddling around with RStudio and these various packages. I feel publishing with these types of R packages are more credible in the literature as well. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Many others have stood where you're standing, resulting in a lot of blog posts etc. Although, command line analysis is quite difficult at times to learn and incredibly frustrating, it's not impossible. Therefore, I would advise to use CLC as more of a preliminary analysis tool. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). Hi Cristina, I previously used CLC for RNA-Seq analysis and fiddled with lots of parameters, my final output delivered a low number of differentially expressed genes (DEG) that were uninformative. Message me if you'd like to see some codes I've used or have any other questions.
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