16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only a few platforms offer a user-friendly interface and none comprehensively covers the whole analysis pipeline from raw data processing down to complex analysis. We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namco’s capabilities by studying the association between a rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention. Namco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available at https://exbio.wzw.tum.de/namco/.

Context Cold exposure (CE) has been shown to enhance energy expenditure by activating brown adipose tissue thermogenesis and metabolism in humans. However, it remains to be elucidated if there are gender-specific differences in cold-induced thermogenesis and metabolism. Objective To study the impact of mild CE on resting energy expenditure (REE) and metabolism in males compared with females. Setting A cross-sectional study. Participants 117 healthy young Caucasians participated in this study (58 males). Mean age was 25.1 ± 3.6 years and mean body mass index 22.3 ± 1.7 kg/m². Intervention Participants underwent a short-term CE using water perfused mattresses to activate nonshivering thermogenesis. Main Outcome Measures REE was assessed before and 2 hours after CE followed by blood sampling. Selected metabolites and hormones were measured. Skin temperatures were monitored at various sites throughout the experiment. Results Participants showed a significant increase in REE after CE (6.5%, P < .001). This increase did not differ between genders (P = .908). However, there were differences between males and females in changes of plasma glucose (–5.1% versus –7.4%, P = .024), leptin (–14.3% versus –30.1%, P < .001) and adiponectin (5.4% versus 12.8%, P = .018) after CE. We observed a significant decrease of the supraclavicular skin temperature in men (–0.3%, P = .034), but not in women (0.3%, P = .326)(P = .019 between genders). Conclusions We did not observe a difference in the thermogenic response, measured as change of REE, to CE in women compared with men. However, we found that some metabolic and hormonal changes were more pronounced in women than in men suggesting a gender-specific response to cold.

Background/Objectives: The gut-microbiota-dependent metabolite trimethylamine-N-oxide (TMAO) has been linked to cardiovascular disease (CVD) risk, while dietary fiber is associated with reduced CVD risk and improved gut health. Considering these associations, we conducted a randomized, double-blind, pilot study to investigate the influence of fiber supplementation on intestinal TMAO formation after beef consumption. Subjects/Methods: 13 volunteers underwent a two-week dietary fiber and placebo intervention. We assessed the effect of fiber supplementation on the gut microbiota and gene abundance of the enzyme cutC, a key enzyme for microbial TMA formation, a precursor for TMAO. We measured the TMAO response following beef consumption after the two-week intervention. We also examined the role of hepatic enzyme FMO3 on TMAO plasma levels. Results: Although overall TMAO production did not change between the dietary fiber and placebo group (p-value = 0.26, 95% CI), subgroup analysis revealed that fiber supplementation attenuated TMAO formation following beef intake in participants with lower habitual meat consumption ( <3 times/week, p-value = 0.029, 95% CI). Furthermore, fiber intervention significantly downregulated microbial cutC gene abundance (p = 0.034, 95% CI), suggesting a mechanism by which fiber might reduce plasma TMAO levels. While dietary fiber intervention did not alter TMAO production across all participants, it showed a potential effect in individuals with lower habitual meat intake. The observed downregulation of cutC gene abundance suggests a mechanism for the beneficial impact of fiber on TMAO formation. Conclusion: These findings support the role of a high-fiber, low-meat diet as a promising strategy to mitigate TMAO-related CVD risk.