Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities.

Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.

Walnut consumption and gut microbial metabolism: Results of an exploratory analysis from a randomized, crossover, controlled-feeding study.

BACKGROUND & AIMS: The effect of walnut-related modulation of gut microbiota composition on microbiota functionality is unknown. The aim was to characterize the effect of a walnut-enriched diet (WD), compared to a fatty acid-matched diet devoid of walnuts (WFMD) and a diet where oleic acid replaces alpha-linolenic acid (ORAD), on bacterial gene expression. METHODS: A 3-period, randomized, crossover, controlled-feeding study was conducted. Participants were provided a 2-week run-in standard western diet (SWD; 50% kcal carbohydrate, 16% protein, 34% fat, 12% SFA). Following the SWD in random sequence order, participants were provided the WD, WFMD, and ORAD (48% carbohydrate; 17% protein; fat 35%; 7% SFA). The WD contained 18% of energy from walnuts (57 g/d/2100 kcal). The WFMD and ORAD were devoid of walnuts; liquid non-tropical plant oils were included in these diets. Metatranscriptomic analyses were performed as an exploratory outcome. RESULTS: The analytical sample included 35 participants (40% female) with a mean ± SD age of 43 ± 10 y and BMI of 30.3 ± 4.9 kg/m2. The ⍺-diversity of taxa actively expressing genes, assessed by observed species (p = 0.27) and Pielou's Evenness (p = 0.09), did not differ among the diets. The ⍺-diversity of actively expressed genes was greater following the WD compared to the WFMD and ORAD as assessed by the observed genes and Pielou's Evenness metrics (p < 0.05). ß-Diversity of the actively expressed genes differed following the WD compared to the WFMD (p = 0.001) and ORAD (p = 0.001); ß-diversity did not differ between the WFMD and ORAD. Active composition analyses showed increased Gordonibacter (p < 0.001) activity following the WD vs. the ORAD. Greater expression of many genes was observed following the WD compared to the WFMD and ORAD. Following the WD, greater expression of metabolism-related genes encoding glycine amidinotransferase (GATM; K00613) and arginine deiminase (K01478) was observed compared to the WFMD. Greater expression of glycine amidinotransferase (GATM; K00613) by Gordonibacter was also observed following the WD vs. the WFMD and ORAD. CONCLUSION: Our results suggest walnut intake may increase endogenous production of homoarginine through gut microbiota-mediated upregulation of GATM, which is a novel mechanism by which walnuts may lower cardiovascular disease risk. However, given the exploratory nature replication is needed. CLINICAL TRIAL REGISTRATION: Clinicaltrials.gov (NCT02210767).

Herbs and Spices Modulate Gut Bacterial Composition in Adults at Risk for CVD: Results of a Prespecified Exploratory Analysis from a Randomized, Crossover, Controlled-Feeding Study.

BACKGROUND: Herbs and spices are rich in polyphenolic compounds that may influence gut bacterial composition. The effect of culinary doses of herbs and spices consumed as part of a well-defined dietary pattern on gut bacterial composition has not been previously studied. OBJECTIVES: The aim of this prespecified exploratory analysis was to examine gut bacterial composition following an average American diet (carbohydrate: 50% kcal; protein: 17%; total fat: 33%; saturated fat: 11%) containing herbs and spices at 0.5, 3.3, and 6.6 g.d-1.2100 kcal-1 [low-, moderate-, and high-spice diets, respectively (LSD, MSD, and HSD)] in adults at risk for CVD. METHODS: Fifty-four adults (57% female; mean ± SD age: 45 ± 11 y; BMI: 29.8 ± 2.9 kg/m2; waist circumference: 102.8 ± 7.1 cm) were included in this 3-period, randomized, crossover, controlled-feeding study. Each diet was provided for 4 wk with a minimum 2-wk washout period. At baseline and the end of each diet period, participants provided a fecal sample for 16S rRNA gene (V4 region) sequencing. QIIME2 was used for data filtration, sequence clustering, taxonomy assignment, and statistical analysis. RESULTS: α-diversity assessed by the observed features metric ( P = 0.046) was significantly greater following the MSD as compared with the LSD; no other between-diet differences in α-diversity were detected. Differences in ß-diversity were not observed between the diets ( P = 0.45). Compared with baseline, ß-diversity differed following all diets ( P < .02). Enrichment of the Ruminococcaceae family was observed following the HSD as compared with the MSD (relative abundance = 22.14%, linear discriminant analysis = 4.22, P = 0.03) and the LSD (relative abundance = 24.90%, linear discriminant analysis = 4.47, P = 0.004). CONCLUSIONS: The addition of herbs and spices to an average American diet induced shifts in gut bacterial composition after 4 wk in adults at risk for CVD. The metabolic implications of these changes merit further investigation. This trial was registered at clinicaltrials.gov as NCT03064932.