Assessment of stool collection and storage conditions for in vitro human gut model studies

Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota

BACKGROUND

Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies.

METHODS AND RESULTS

Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80 °C or 4 °C) significantly influenced either microbial composition at 16 h of anaerobic culture or the principal components of the metabolome at 8 or 16 h. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2'-fucosyllactose or dextrose).

CONCLUSIONS

These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16 hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota.

An outlook on fluorescent in situ hybridization coupled to flow cytometry as a versatile technique to evaluate the effects of foods and dietary interventions on gut microbiota

The increasing interest in the effects of the gut microbiota on host health has stimulated the investigation of the composition of this microbial community and the factors affecting these microorganisms. This review discusses the recent advances and progress applications in the use of the fluorescent in situ hybridization (FISH) coupled to flow cytometry (FC) technique (FISH-FC) in studies evaluating the gut microbiota published in the last 10 years, with particular emphasis on the effects of foods and dietary interventions. These studies have shown that FISH-FC technique is capable of detecting and quantifying several groups of bacteria found as part of the gut microbiota. FISH-FC can be considered an effective, versatile, and rapid technique to evaluate alterations in gut microbiota composition caused by different foods as assessed in studies in vitro, in vivo, and in clinical trials. Some specific probes have been most used to represent the general gut microbiota, such as those specific to Lactobacillus spp./Enterococcus spp., Bacteroidaceae/Prevotellaceae, Clostridium histolyticum, and Bifidobacterium spp. FISH-FC technique could have an important opportunity for application in studies with next-generation probiotics belonging to the gut microbiota. Optimizations of FISH-FC protocols could allow more discoveries about the gut microbiota, including the development of new probes targeting microorganisms still not explored, the analysis of individual portions of the intestine, and the proposition of novel quantitative approaches.

Physical Activity and Dietary Composition Relate to Differences in Gut Microbial Patterns in a Multi-Ethnic Cohort-The HELIUS Study

Physical activity (PA) at recommended levels contributes to the prevention of non-communicable diseases, such as atherosclerotic cardiovascular disease (asCVD) and type 2 diabetes mellitus (T2DM). Since the composition of the gut microbiota is strongly intertwined with dietary intake, the specific effect of exercise on the gut microbiota is not known. Moreover, multiple other factors, such as ethnicity, influence the composition of the gut microbiota, and this may be derived by distinct diet as well as PA patterns. Here we aim to untangle the associations between PA and the gut microbiota in a sample (n = 1334) from the Healthy Life In an Urban Setting (HELIUS) multi-ethnic cohort. The associations of different food groups and gut microbiota were also analyzed. PA was monitored using subjective (n = 1309) and objective (n = 162) methods, and dietary intake was assessed with ethnic-specific food frequency questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing, and the functional composition was generated with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Associations were assessed using multivariable and machine learning models. In this cohort, a distinct gut microbiota composition was associated with meeting the Dutch PA norm as well as with dietary intake, e.g., grains. PA related parameters such as muscle strength and calf circumference correlated with gut microbiota diversity. Furthermore, gut microbial functionality differed between active and sedentary groups. Differential representation of ethnicities in active and sedentary groups in both monitor methods hampered the detection of ethnic-specific effects. In conclusion, both PA and dietary intake were associated with gut microbiota composition in our multi-ethnic cohort. Future studies should further elucidate the role of ethnicity and diet in this association.