The Controversial Role of Human Gut Lachnospiraceae

In vitro fecal fermentation characteristics of bamboo insoluble dietary fiber and its impacts on human gut microbiota

Whole grain rice is a rich source of fiber, nutrients, and phytochemicals that may promote gastrointestinal health, but such beneficial components are typically removed with the bran during polishing. Soluble feruloylated arabinoxylan oligosaccharides (FAXO) and polyphenols (RBPP) isolated from rice bran are hypothesized to have positive impacts on human gut microbiota through a prebiotic function. Using an in vitro human fecal fermentation bioassay, FAXO and RBPP treatments were assessed for short-chain fatty acids (SCFA) production patterns and by evaluating their impacts on the phylogentic composition of human gut microbiota by 16S rRNA gene sequencing. Fresh fecal samples collected from healthy adults (n = 10, 5 males, 5 females) were diluted with anaerobic medium. Each sample received five treatments: CTRL (no substrates), FOS (fructooligosaccharides), FAXO, RBPP, and MIX (FAXO with RBPP). Samples were incubated at 37 °C and an aliquot was withdrawn at 0, 4, 8, 12, and 24 h Results showed that SCFA production was significantly increased with FAXO and was comparable to fermentation with FOS, a well-established prebiotic. RBPP did not increase SCFA productions, and no significant differences in total SCFA production were observed between FAXO and MIX, indicating that RBPP does not modify FAXO fermentation. Changes in microbiota population were found in FAXO treatment, especially in Bacteroides, Prevotella, and Dorea populations, indicating that FAXO might modulate microbiota profiles. RBPP and MIX increased Faecalibacterium, specifically F. prausnitzii. Combined FAXO and RBPP fermentation increased abundance of butyrogenic bacteria, Coprococcus and Roseburia, suggesting some interactive activity. Results from this study support the potential for FAXO and RBPP from rice bran to promote colon health through a prebiotic function.

Gut Microbiota and Its Possible Relationship With Obesity

Effects of host gut-derived probiotic bacteria on gut morphology, microbiota composition and volatile short chain fatty acids production of Malaysian Mahseer Tor tambroides

Statins, a class of drugs that can effectively remove cholesterol from serum, are used to regulate plasma total cholesterol and reduce the risk of cardiovascular diseases, but it is still unclear whether the drug are modulated by gut microbiota or the structures of gut microbiota are shaped by statins. We investigated the interactions between statins and the human gut microbiota during the in vitro fermentation process by 16S rRNA gene sequencing, gas chromatography (GC), and high-performance liquid chromatography (HPLC) analyses. The presence of fluvastatin (FLU2) specifically promoted the growth of Escherichia/Shigella, Ruminococcaceae UCG 014, and Sutterella. However, the composition of the gut bacterial microbiota remained relatively static in samples treated with rosuvastatin (ROS), simvastatin (SIM), and atorvastatin (ATO). The PICRUSt program predicted moderate differences in the functional categories related to the biosynthesis of other secondary metabolites, cellular processes and signaling, and signal transduction in the FLU2 fermentation samples. Our study revealed substantial variation in the structure and function of microbiomes from the FLU2-treated samples. In addition, short-chain fatty acids (SCFAs) were also significantly decreased in FLU2-treated samples compared with the samples treated with other stains. Statins can be degraded by the human gut microbiota in vitro, and the degradation rate was approximately 7%–30% and 19%–48% after fermentation was allowed to proceed for 24 h and 48 h, respectively. Generally, FLU2 could largely shape the composition and function of human gut microbiota, which resulted in changes in the production of SCFAs. In turn, all statins could be degraded or modified by the gut microbiota. Our study paves the way for elucidating statin-gut microbiota interactions in vitro towards the improvement of the host health and personalized medicine.

As a by-product of citrus processing, ponkan (Citrus reticulata Blanco, cv. Ponkan) peel residue is a source of high quality dietary fiber (DF). To make a full utilization of this resource and give a better understanding on the probiotic function of its DF, soluble dietary fiber (SDF) and insoluble dietary fiber (IDF) were extracted from ponkan peel residue (after flavonoids were extracted) using an alkaline method, followed by modifications using a composite physical-enzymatic treatment. The in vitro fermentation properties of the modified SDF and IDF (namely, MSDF and MIDF) and their effects on short-chain fatty acids (SCFA) production and changes in the composition of human gut microbiota were investigated. Results showed that MSDF and MIDF both significantly lowered the pH value and enhanced total SCFA content in the broths after fermented for 24 h by fecal inocula (p < 0.05) with better effects found in MSDF. Both MSDF and MIDF significantly reduced the diversity, with more in the latter than the former, and influenced the composition of human gut microbiota, especially increasing the relative abundance of Bacteroidetes and decreasing the ratio of Firmicutes to Bacteroidetes (F/B) value. The more influential microbiota by MSDF were g-Collinsella, p-Actinobacteria and g-Dialister, while those by MIDF were f-Veillonellaceae, c-Negativicutes and f-Prevotellacese. These results suggested that the modified ponkan peel residue DF can be utilized by specific bacteria in the human gut as a good source of fermentable fiber, providing a basis for the exploitation of the citrus by-product.

Red beetroots, rich in betanin, may act as prebiotics and impact gut microbiota. Because the human gut microbiota is unique to each person, the effectiveness of prebiotics varies with the enterotype. In this study, we hypothesized that the effects of red beetroot powder (RP) and betanin pigment (BP) would differ depending on the enterotype. Fecal samples from 30 subjects were analyzed and categorized into three enterotypes: Phocaeicola, Prevotella, and Bifidobacterium. Feces were collected from one representative subject from each enterotype cluster for fermentation. Results showed that RP and BP affected microbiota composition and short-chain fatty acid (SCFA) production differently across enterotypes. The Bifidobacterium cluster showed significantly reduced alpha diversity, with the direction of change in the gut microbiota composition being different from that of other subjects. Additionally, SCFAs significantly increased, with the highest increase in the Bifidobacterium cluster. In this cluster, metabolic pathways related to SCFAs (i.e., starch and sucrose metabolism and glycolysis/gluconeogenesis) were altered. Conversely, Prevotella-dominant feces exhibited fewer changes in SCFAs and a lower increase in Bifidobacterium abundance than the others. These findings highlight that RP and BP elicit enterotype-specific responses in the gut microbiota composition and SCFA production, emphasizing the importance of enterotypes in personalized nutrition.

Background Gut microbiota development and composition can be influenced by an existing dynamic balance between host physiology and lifestyle. This systematic review aims to assess the impact of physical activity on human gut microbiota. Methods PubMed, Scopus and Web of Science were searched until May 2019. Full-text in English were recruited if focused on gut microbiota in healthy athletes or active people, without age or gender restrictions, collected on faecal samples and analysed with genome sequencing of rRNA 16S. All types of study design were included as long as they performed a comparison with a sedentary control group. No specific time frame for the publication date was applied. Quality assessment was performed using the JBI Critical Appraisal Checklist for Analytical Cross Sectional Studies (2017) and Cochrane Risk of Bias Tool for Randomized Controlled Trials. Results The analysis yielded 7/985 articles: five cross-sectional studies and two clinical trials, published from 2014 to 2019. The overall methodological assessment was of fair quality. Types of exercise included in the studies were: rugby, running, aerobic exercise, bodybuilding. More in detail, regarding the exercise load, some studies were conducted on elite professional athletes, such as rugby players, marathon runners or bodybuilders, with rigorous training, while other studies included a few weeks of aerobic and resistance training at a moderate intensity. Shannon diversity index increased in three studies. Concerning phyla, Firmicutes were increased in five studies and three studies described a significant decrease in Bacteroides. Conclusions This systematic review confirms the direct correlation between microbiota composition and physical activity, but further studies are needed to establish the possible presence of a causal link between the two factors. Key messages Exercise can play an important role as an environmental factor in determining gut microbiota composition. Further studies are needed to gain robust evidence of physical activity influence on gut microbiota variability.

As research into gut microbiota deepens, the impact of diet on the composition of human gut microbiota and their metabolites has gradually become a focal point. This paper reviews recent advancements in understanding how diet influences gut microbiota composition and their metabolic products. Firstly, it introduces the basic concepts of gut microbiota and their role in maintaining health. Next, it explores the effects of different types of diets (such as high-fiber, high-fat, high-protein, and refined sugar diets) on the composition of gut microbiota and analyzes their impact on microbiota diversity. Then, it discusses the influence of diet on gut microbiota metabolites, including short-chain fatty acids, amino acid metabolites, and gases. Further, it examines the practical applications of dietary interventions on health, especially their potential impact on chronic diseases. Finally, the paper summarizes the limitations of current research and suggests future research directions and challenges. Overall, the influence of diet on gut microbiota and their metabolites holds profound health significance and provides important evidence for formulating scientific dietary recommendations.

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model

Composition of the gut microbiota, and related short chain fatty acids (SCFAs) production can influence allergic status. Extensively hydrolysed casein (eHC) infant formulas are used for management of cow's milk protein (CMP) allergy; however, effects of eHC on gut microbiota as a potential mechanism contributing to benefits of eHC for infants with allergy are not well understood. This exploratory study aimed to assess the in vitro effects of eHC on infant gut microbial composition and metabolism. Two batches of a specific eHC preparation, along with a mixture of individual amino acids (AA), were first digested in the in vitro TNO Intestinal Model-1 (TIM-1) simulating infant upper gastrointestinal digestion conditions followed by an in vitro colon fermentation model inoculated with faeces from healthy, formula-fed infants. Peptide profile after digestion of the test compounds, as well as effects of the compounds on microbiota community structure and SCFA production were assessed. Overall peptide profiles of the eHC preparations (qualitative, based on liquid chromatography-mass spectrometry) remained largely unaffected by simulated upper gastrointestinal digestion. Faecal fermentation of the specific eHC preparations influenced microbiota composition, with a major impact on Bacteroides abundance. SCFA production was increased beyond control conditions by eHC but not AA. The impact of the AA mixture differed considerably from that of the eHC containing specific peptides. Results suggest that eHC formulas can impact microbiota composition and SCFA production in an in vitro colon fermentation model. While the descriptive results of this study require future confirmation under a more extensive experimental setup, it can be hypothesised that mechanisms modulating microbiota composition and metabolism occurring in infants fed with eHC formula for the management of CMP allergy might contribute to clinical observations related to allergy and tolerance development.

In the human gut, millions of bacteria contribute to the microbiota, whose composition is specific for every individual. Although we are just at the very beginning of understanding the microbiota concept, we already know that the composition of the microbiota has a profound impact on human health. A key factor in determining gut microbiota composition is diet. Preliminary evidence suggests that dietary patterns are associated with distinct combinations of bacteria in the intestine, also called enterotypes. Western diets result in significantly different microbiota compositions than traditional diets. It is currently unknown which food constituents specifically promote growth and functionality of beneficial bacteria in the intestine. The aim of this review is to summarize the recently published evidence from human in vivo studies on the gut microbiota-modulating effects of diet. It includes sections on dietary patterns (e.g. Western diet), whole foods, food constituents, as wells as food-associated microbes and their influence on the composition of human gut microbiota. The conclusions highlight the problems faced by scientists in this fast-developing field of research, and the need for high-quality, large-scale human dietary intervention studies.

Although iron is an essential nutrient for humans, as well as for almost all other organisms, it is poorly absorbed (~15%) from the diet such that most passes through the upper gut into the large intestine. The colonic microbiota is thus exposed to, and potentially influenced by, such residual iron which could have an impact on human health. The aim of the research described here is to determine how the major forms of dietary iron (inorganic iron and haem) influence metabolic activity and composition of the human gut microbiota by utilizing an in vitro parallel, pH-controlled anaerobic batch culture approach. Controlled iron provision was enabled by the design of a ‘modified’ low-iron gut-model medium whereby background iron content was reduced from 28 to 5 μM. Thus, the impact of both low and high levels of inorganic and haem iron (18–180 μM and 7.7–77 μM, respectively) could be explored. Gut-microbiota composition was determined using next generation sequencing (NGS) based community profiling (16S rRNA gene sequencing) and flow-fluorescent in situ hybridization (FISH). Metabolic-end products (organic acids) were quantified using gas chromatography (GC) and iron incorporation was estimated by inductively coupled plasma optical emission spectroscopy (ICP-OES). Results showed that differences in iron regime induced significant changes in microbiota composition when low (0.1% w/v) fecal inoculation levels were employed. An increase in haem levels from 7.7 to 77 μM (standard levels employed in gut culture studies) resulted in reduced microbial diversity, a significant increase in Enterobacteriaceae and lower short chain fatty acid (SCFA) production. These effects were countered when 18 μM inorganic iron was also included into the growth medium. The results therefore suggest that high-dietary haem may have a detrimental effect on health since the resulting changes in microbiota composition and SCFA production are indicators of an unhealthy gut. The results also demonstrate that employing a low inoculum together with a low-iron gut-model medium facilitated in vitro investigation of the relationship between iron and the gut microbiota.

The proportion of different microbial populations in the human gut is an important factor that in recent years has been linked to obesity and numerous metabolic diseases. Because there are many factors that can affect the composition of human gut microbiota, it is of interest to have information about what is the composition of the gut microbiota in different populations in order to better understand the possibilities for improving nutritional management. A group of 31 volunteers were selected according to established inclusion and exclusion criteria and were asked about their diet history, lifestyle patterns, and adherence to the Southern European Atlantic Diet. Fecal samples were taken and subsequently analyzed by real-time PCR. The results indicated different dietary patterns for subjects who consumed a higher amount of fruits, vegetables, legumes, and fish and a lower amount of bakery foods and precooked foods and snacks compared to Spanish consumption data. Most participants showed intermediate or high adherence to Southern European Atlantic Diet, and an analysis of gut microbiota showed high numbers of total bacteria and Actinobacteria, as well as high amounts of bacteria belonging to the genera Lactobacillus spp. and Bifidobacterium spp. A subsequent statistical comparison also revealed differences in gut microbiota depending on the subject's body weight, age, or degree of adherence to the Southern European Atlantic Diet.

Polychlorinated biphenyls (PCBs) are ubiquitous environmental pollutants associated with a wide variety of adverse human health outcomes. PCB 126 and PCB 153 are among the most prevalent congeners associated with human exposure. Emerging studies have suggested that PCB exposure leads to lower gut microbial diversity although their effects on microbial production of health promoting short-chain fatty acids (SCFAs) has been scarcely studied. Blue potatoes are rich in anthocyanins (ACNs), which is a class of polyphenols that promote the growth of beneficial intestinal bacteria such as Bifidobacterium and Lactobacillus and increase the generation of SCFAs. A batch-culture, pH-controlled, stirred system containing human fecal microbial communities was utilized to assess whether human gut microbiota composition and SCFA production are affected by: (a) PCB 126 and PCB 153 exposure; and (b) ACN-rich digests in the presence and absence of the PCB congeners. Anthocyanin-rich blue potato meals (11.03 g) were digested over 12 h with and without PCB 126 (0.5 mM) and PCB 153 (0.5 mM) using an in vitro simulated gut digestion model involving upper gastrointestinal digestion followed by metabolism by human fecal microbiota. Fecal digests were collected for analysis of gut microbial and SCFA profiles. Polychlorinated biphenyl-exposed fecal samples showed a significant (p < 0.05) decrease in species richness and a significantly (p < 0.05) different microbial community structure. PCB treatment was associated with an increased (p < 0.05) relative abundance of Akkermansia, Eggerthella, and Bifidobacterium and a decreased (p < 0.05) relative abundance of Veillonella, Streptococcus, and Holdemanella. ACN digests counteracted the altered abundances of Akkermansia and Bifidobacterium seen with the PCB treatment. PCB exposure was associated with a significant (p < 0.05) decrease in total SCFA and acetate concentrations. ACN digests were associated with significantly (p < 0.05) higher SCFA and acetate concentrations in the presence and absence of PCBs. Human fecal matter exposed to PCB 126 and PCB 153 led to decreased abundance and altered gut microbiota profiles as well as lowered SCFA and acetate levels. Importantly, this study showed that prebiotic ACN-rich potatoes counteract PCB-mediated disruptions in human gut microbiota profiles and SCFA production.