In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing-A Proof-of-Principle Study

A low-cost, easy-to-use prototype bioreactor model for the investigation of human gut microbiota: validation using a prebiotic treatment

In vitro gut models allow for the study of the impact of molecules on human gut microbiota composition and function without the implication of the host. However, current models, such as the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), are expensive, time-consuming, and require specialized personnel. Homemade in vitro models that lessen these issues have limited evidence of their humanlike functionality. In this study, we present the development of a low-cost and easy-to-use bioreactor with the proven functionality of human microbiota. In our model, we evaluated the capability of replicating human gut microbiota growth and the response of the human bacterial community to a prebiotic, resistant starch, particularly resistant starch type 2 (RS2). Our bioreactor produced an environment that was stable for pH, temperature, and anaerobic conditions. The bioreactor consistently cultivated bacterial communities over a 48 h time period, replicating the composition of the gut microbiota and the associated metabolite production response to RS2, in line with prior human studies. In response to the RS2 prebiotic, we observed an increase in Bifidobacterium adolescentis and Bifidobacterium faecale and an increase in the production of the short-chain fatty acids such as acetate, propionate, and isobutyrate. Taken together, these data demonstrate that our low-cost and user-friendly prototype bioreactor model provides a favorable environment for the growth of human gut microbiota and can mimic its response to a prebiotic.

The Influence of Polysaccharides on Lipid Metabolism: Insights from Gut Microbiota

SCOPE

Polysaccharides are complex molecules of more than ten monosaccharide residues interconnected through glycosidic linkages formed via condensation reactions. Polysaccharides are widely distributed in various food resources and have gained considerable attention due to their diverse biological activities. This review presented a critical analysis of the existing research literature on anti-obesity polysaccharides and investigates the complex interplay between their lipid-lowering activity and the gut microbiota, aiming to provide a comprehensive overview of the lipid-lowering properties of polysaccharides and the underlying mechanisms of action.

METHODS AND RESULTS

In this review, the study summarized the roles of polysaccharides in improving lipid metabolism via gut microbiota, including the remodeling of the intestinal barrier, reduction of inflammation, inhibition of pathogenic bacteria, reduction of trimethylamine N-oxide (TMAO) production, and regulation of the metabolism of short-chain fatty acids (SCFAs) and bile acids (BAs).

CONCLUSION

These mechanisms collectively contributed to the beneficial effects of polysaccharides on lipid metabolism and overall metabolic health. Furthermore, polysaccharide-based nanocarriers combined with gut microbiota have broad prospects for developing targeted and personalized therapies for hyperlipidemia and obesity.

Effects of secretin gene knockout on the diversity, composition, and function of gut microbiota in adult male mice

The gut microbiota plays a vital role in maintaining gastrointestinal homeostasis, however, whether it is influenced by gut hormones remains unknown. Secretin is a well-known gastrointestinal hormone produced by enteroendocrine S cells. This study utilized 16S rRNA amplicon sequencing to characterize the effect of SCT deficiency on the gut microbiota. Our results show that systemic SCT knockout alters the composition and abundance of the mouse gut microbiota but does not affect fecal short-chain fatty acids and lipids concentrations. At the genus level, the abundance of Turicibacter, Bacteroides, Ruminococcu, Romboutsia, Asaccharobacter, and Parasutterella increased in SCT-/- mice, whereas the abundance of Akkermansia and Escherichia decreased. Functional prediction results showed that lack of SCT reduced the abundance of carbohydrate metabolism-related pathways but increased the abundance of linoleic acid metabolism and branched-chain amino acid degradation. Overall, systemic SCT knockout had only minor effects on gut microbiota composition and function in adult male mice fed a standard chow diet.

Diallyl trisulfide ameliorates bone loss and alters specific gut microbiota and serum metabolites in natural aging mice

Aging is a major cause of bone loss and osteoporosis. Diallyl trisulfide (DATS), one of the main organic sulfides in garlic oil, has been shown to alleviate arthritis in mice. However, further research is still needed to determine how DATS affects bone formation and bone loss in aging mice. Here, we established a mouse model of natural aging for dietary DATS intervention. DATS treatment improved the bone microstructure, including the disorganized arrangement of bone trabeculae and promoted collagen synthesis, as confirmed by micro-CT and histological analyses. The abundance of beneficial bacteria for bone formation, such as Clostridiaceae and Erysipelotrichaceae, and the microbial diversity and community richness were all altered by DATS, according to 16S rRNA sequencing data. 14 potential biomarkers and 9 important metabolic pathways were examined using serum metabolomics analysis. Additionally, there has been a significant reduction in sphingosine, which is directly associated with bone metabolism. The level of sphingosine and relative abundance of Clostridium were found to be negatively correlated by correlation analysis, indicating that bacteria may regulate bone reconstruction via influencing metabolites. Furthermore, Runx2 and β-catenin gene expression levels increased in bones, which may be related to the ameliorative mechanism of DATS. Our results suggested that DATS may prevent age-related bone loss by upregulating osteogenic gene expression through altering gut microbes and serum metabolism.

Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota

Short-chain fatty acids (SCFAs) play a key role in health and disease, as they regulate gut homeostasis and their deficiency is involved in the pathogenesis of several disorders, including inflammatory bowel diseases, colorectal cancer, and cardiometabolic disorders. SCFAs are metabolites of specific bacterial taxa of the human gut microbiota, and their production is influenced by specific foods or food supplements, mainly prebiotics, by the direct fostering of these taxa. This Review provides an overview of SCFAs' roles and functions, and of SCFA-producing bacteria, from their microbiological characteristics and taxonomy to the biochemical process that lead to the release of SCFAs. Moreover, we will describe the potential therapeutic approaches to boost the levels of SCFAs in the human gut and treat different related diseases.

In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet

BACKGROUND

Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.

RESULTS

Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24 h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.

CONCLUSIONS

These findings suggest that consuming MRE for 21 days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.

Stable Isotope Probing-RNA Strategy to Study Plant/Fungus Interactions

The use of stable-isotope probing (SIP) allows tracing specific labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permits the linkage of diversity and function. Here, we describe two methods designed to investigate the interactions between plants and their associated mycorrhizal compartment by tracing carbon flux from the host plant to its symbionts.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

RNA-based stable isotope probing provides no indication for rapid α-synuclein assimilation by murine gut bacteria

In Parkinson’s disease (PD), α-synuclein is a key protein in the process of neurodegeneration. Besides motor symptoms, most PD patients additionally suffer from gastrointestinal tract (GIT) dysfunctions, even several years before the onset of motor disabilities. Studies have reported a dysbiosis of gut bacteria in PD patients compared to healthy controls and have suggested that the enteric nervous system (ENS) can be involved in the development of the disease. As α-synuclein was found to be secreted by neurons of the ENS, we used RNA-based stable isotope probing (RNA-SIP) to identify gut bacteria that might be able to assimilate this protein. The gut contents of 24 mice were pooled and incubated with isotopically labelled (¹³C) and unlabelled (¹²C) α-synuclein. After incubation for 0, 4 and 24 h, RNA was extracted from the incubations and separated by density gradient centrifugation. However, RNA quantification of density-resolved fractions revealed no incorporation of the ¹³C isotope into the extracted RNA, suggesting that α-synuclein was not assimilated by the murine gut bacteria. Potential reasons and consequences for follow-up-studies are discussed.

The effect of sodium carboxymethyl starch with high degree of substitution on defecation

Sodium carboxymethyl starch (CMS-Na), a kind of food additive with high degree of substitution, is also known as a prebiotic. The aim of this study was to determine the effect of CMS-Na on defecation. Constipated mouse model was prepared by loperamide. Normal rats were also used in the study. Short-chain fatty acids in rat feces were detected by gas chromatography. The bacterial communities in rat feces were identified by 16S rDNA gene sequencing. 5-hydroxytryptamine (5-HT) and tryptophan hydroxylase 1 (Tph1) were measured by ELISA. The results showed that CMS-Na increased the fecal granule counts and intestinal propulsion rate in constipated mice. The contents of water, acetic acid, propionic acid and n-butyrate in feces, Tph1 in colon and 5-HT in serum of rats were increased. In addition, CMS-Na shortened the colonic transport time in rats. The 16S rDNA gene sequencing results indicated that CMS-Na increased the relative abundance of Alloprevotella and decreased the proportion of Lactobacillus. However, the biodiversity of the normal intestinal flora was not altered. In conclusion, CMS-Na can promote defecation in constipated mice. The mechanism may be related to the regulation of Alloprevotella and Lactobacillus in colon, the increase of short-chain fatty acids, and the promotion of the synthesis of Tph1 and 5-HT.

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms

Strategies to combat microbiota-associated health problems are of high interest in pig production. Successful intervention strategies with beneficial long-term effects are still missing. Most studies on pig microbiota have been conducted under standardized experimental conditions, but the situation in commercial farms differs dramatically. This study describes the fecal microbiota in German commercial pig farms under practical conditions. The study is part of the larger project "Optibiom" that aims to use bacterial composition and farm metadata to formulate tailor-made solutions for farm-specific health maintenance strategies. Special consideration is given to the sow-piglet relationship. Fecal samples from sows and their piglets were collected at two time points each in 20 different farms (sows ante- and postpartum and piglets before and after weaning). The extracted DNA was sequenced with Illumina 16S rDNA sequencing. For data analysis and visualization, differential abundance analyses, as well as hierarchical clustering and nonmetric multidimensional scaling (NMDS) were performed. A new "family unit" was implemented to compare farms based on the association between the microbiota in sows and their offspring. There are distinct changes in the microbial communities in sows before and after birth as well as in suckling and post-weaning piglets. The suckling pig microbiota is particularly different from all other groups and shows a lower bacterial diversity. While dominant genera in antepartum sows further displace the abundance of non-dominant genera postpartum, the opposite was true for piglets, where non-dominant bacteria in the suckling phase became dominant after weaning. The family unit for sows and their piglets led to separate cluster formation for some farms. The results indicate that the sow-piglet relationship is one driving force for the observed differences of the pig farms. The next step in the analysis will be the combination of metadata (feeding, housing and management practices) to find farm-specific differences that can be exploited to formulate a farm-specific health maintenance strategy.

Processing Matters in Nutrient-Matched Laboratory Diets for Mice-Microbiome

The composition of the microbiome is subject to the host's diet. In commercial laboratory mouse diets, different physical forms of the same diets are available, containing-according to their labels-identical ingredients and nutrient compositions. However, variations in nutrient composition and starch gelatinization due to production processes and their impact on digestibility have been described. In this study, a total of 48 C57BL/J6 mice were assigned to two equal groups and were fed diets (produced with different processes-extruded vs. pelleted) for eight weeks in two biological replicates. At the end of the experiment, samples were collected from five different gastrointestinal regions, including the stomach, small intestine, cecum, large intestine, and an extracorporeal region (feces), and the microbiome was analyzed with 16S rRNA gene amplicon sequencing. The replicates in both experiments differed significantly in their relative abundances of Muribaculaceae species. Furthermore, the gastrointestinal content of pellet-fed mice contained larger numbers of Lactobacillus species. These results indicate that starch gelatinization and ingredient composition significantly influence microbial makeup. In conclusion, different feed processing methods may affect fundamental digestive and metabolic processes, impacting animal experiments and biasing microbiome data.

Dietary resistant starch preserved through mild extrusion of grain alters fecal microbiome metabolism of dietary macronutrients while increasing immunoglobulin A in the cat

Dietary digestion-resistant starch (RS) provides health benefits to the host via gut microbiome-mediated metabolism. The degree to which cats manifest beneficial changes in response to RS intake was examined. Healthy cats (N = 36) were fed identically formulated foods processed under high (n = 17) or low (n = 19) shear extrusion conditions (low and high RS levels [LRS and HRS], respectively). Fecal samples collected after 3 and 6 weeks' feeding were assayed for stool firmness score, short-chain fatty acids, ammonia, and changes to the global metabolome and microbiome; fecal immunoglobulin A (IgA) was analyzed at week 6. Few differences were seen in proximate analyses of the foods; stool firmness scores did not differ. In cats consuming HRS food, concentrations of fecal butyrate and the straight chain:branched chain fatty acid ratio were significantly greater in feces at both weeks 3 and 6, while fecal ammonia was reduced at week 6 relative to feces from LRS-fed cats. Fecal IgA concentrations were significantly higher at week 6 with HRS food. RS consumption altered 47% of the fecal metabolome; RS-derived sugars and metabolites associated with greater gut health, including indoles and polyamines, increased in the cats consuming HRS food relative to those fed the LS food, while endocannabinoid N-acylethanolamines decreased. Consumption of HRS food increased concentrations of the ketone body 3-hydroxybutyrate in feces and elevated concentrations of reduced members of NADH-coupled redox congeners and NADH precursors. At the microbiome genus-level, 21% of operational taxonomic units were significantly different between food types; many involved taxa with known saccharolytic or proteolytic proclivities. Microbiome taxa richness and Shannon and Simpson alpha diversity were significantly higher in the HRS group at both weeks. These data show that feline consumption of grain-derived RS produces potentially beneficial shifts in microbiota-mediated metabolism and increases IgA production.

Consumption of identically formulated foods extruded under low and high shear force reveals that microbiome redox ratios accompany canine immunoglobulin A production

Digestion-resistant starch (RS) can provide health benefits to the host via gut microbiome-mediated metabolism. This study tested the physiological effects on healthy dogs of identically formulated foods processed under high (n = 16) or low (n = 16) shear extrusion conditions resulting in respective lower and higher levels of RS. Faecal samples collected at weeks 3 and 6 were assayed for stool score, proximate analysis, short-chain fatty acids (SCFA), immunoglobulin A (IgA) and microbiome; faecal metabolome was characterized at week 6. Proximate and digestibility analyses of the foods and stool scores and stool proximate analysis showed few differences between the two shear methods except for increased apparent fibre digestibility in the low shear food. In contrast, levels of butyrate (p = .030) and total SCFA (p = .043) were significantly greater in faeces at week 6 from dogs who consumed the low versus high shear food. Faecal IgA levels were significantly higher at week 3 (p = .001) but not week 6 (p = .110) in the low shear food. Significant differences in 166 metabolites between consumption of the two foods were identified via faecal metabolomic analysis, with changes in sugars, bile acids, advanced glycation end products and few amino acids. Strikingly, consumption of the low shear food resulted in elevated levels of the reduced members of redox couples derived from metabolized sugars and branched-chain and phenyl amino acids. Alpha diversity of the microbiome showed significantly higher species richness in faeces from the low shear group at week 6, though other measures of diversity were similar for both foods. Twelve genus-level operational taxonomic units (OTU; half Firmicutes) significantly differed between the food types. Six OTU significantly correlated with RS-derived sugars and ratios of the redox couples. Taken together, these data show that RS impacts microbiome-mediated metabolism in the gut, resulting in changes in the reducing state.

Conserved and variable responses of the gut microbiome to resistant starch type 2

Resistant starch type 2 (RS2), a dietary fiber comprised solely of glucose, has been extensively studied in clinical trials and animal models for its capacity to improve metabolic and systemic health. Because the health modulatory effects of RS2 and other dietary fibers are thought to occur through modification of the gut microbiome, those studies frequently include assessments of RS2-mediated changes to intestinal microbial composition and function. In this review, we identify the conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies. Consistent outcomes of RS2 interventions include reductions in bacterial α-diversity; increased production of lumenal short-chain fatty acids; and enrichment of Ruminococcus bromii, Bifidobacterium adolescentis, and other gut taxa. Different taxa are usually responsive in animal models, and many RS2-mediated changes to the gut microbiome vary within and between studies. The root causes for this variation are examined with regard to methodological and analytical differences, host genetics and age, species differences (eg, human, animal), health status, intervention dose and duration, and baseline microbial composition. The significant variation found for this single dietary compound highlights the challenges in targeting the gut microbiome to improve health with dietary interventions. This knowledge on RS2 also provides opportunities to improve the design of nutrition studies targeting the gut microbiome and to ultimately identify the precise mechanisms via which dietary fiber benefits human health.

Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota

Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.

High-Amylose Maize, Potato, and Butyrylated Starch Modulate Large Intestinal Fermentation, Microbial Composition, and Oncogenic miRNA Expression in Rats Fed A High-Protein Meat Diet

High red meat intake is associated with the risk of colorectal cancer (CRC), whereas dietary fibers, such as resistant starch (RS) seemed to protect against CRC. The aim of this study was to determine whether high-amylose potato starch (HAPS), high-amylose maize starch (HAMS), and butyrylated high-amylose maize starch (HAMSB)—produced by an organocatalytic route—could oppose the negative effects of a high-protein meat diet (HPM), in terms of fermentation pattern, cecal microbial composition, and colonic biomarkers of CRC. Rats were fed a HPM diet or an HPM diet where 10% of the maize starch was substituted with either HAPS, HAMS, or HAMSB, for 4 weeks. Feces, cecum digesta, and colonic tissue were obtained for biochemical, microbial, gene expression (oncogenic microRNA), and immuno-histochemical (O⁶-methyl-2-deoxyguanosine (O⁶MeG) adduct) analysis. The HAMS and HAMSB diets shifted the fecal fermentation pattern from protein towards carbohydrate metabolism. The HAMSB diet also substantially increased fecal butyrate concentration and the pool, compared with the other diets. All three RS treatments altered the cecal microbial composition in a diet specific manner. HAPS and HAMSB showed CRC preventive effects, based on the reduced colonic oncogenic miR17-92 cluster miRNA expression, but there was no significant diet-induced differences in the colonic O⁶MeG adduct levels. Overall, HAMSB consumption showed the most potential for limiting the negative effects of a high-meat diet.

RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment

The RNA-SIP technology allows for linking the structure and function of complex microbial communities, that is, the identification of microbial key players involved in distinct degradation and assimilation processes under in situ conditions. Being dependent on RNA, this technique is particularly suited for environments with high numbers of very active, that is, significantly RNA-expressing microorganisms, such as intestinal tract samples. We use RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in order to better understand the functionality of these medically and economically important nutrients in human and animal intestinal environments.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease

AIM

Bacteroides vulgatus and B. dorei have a protective effect against atherosclerosis, suggesting that expansion of these species in the gut microbiota could help patients with coronary artery disease (CAD). This study aimed to investigate the effect of resistant starch (RS) on the gut microbiota and its metabolites in fecal sample cultures from patients with CAD and individuals without CAD, using a single-batch fermentation system.

METHODS

Fecal samples from 11 patients with CAD and 10 individuals without CAD were fermented for 30 h with or without RS in the Kobe University Human Intestinal Microbiota Model (KUHIMM). Gut microbiota and the abundance of B. vulgatus and B. dorei were analyzed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing and the quantitative polymerase chain reaction. Short-chain fatty acids were analyzed using high-performance liquid chromatography.

RESULTS

Gut microbial analysis showed significantly lower levels of B. vulgatus and B. dorei in the original fecal samples from patients with CAD, which was simulated after 30 h of fermentation in the KUHIMM. Although RS significantly increased the absolute numbers of B. vulgatus and B. dorei, and butyrate levels in CAD fecal sample cultures, the numbers varied among each patient.

CONCLUSIONS

The effect of RS on gut microbiota and its metabolites in the KUHIMM varied between CAD and non-CAD fecal sample cultures. The KUHIMM may be useful for preclinical evaluations of the effects of RS on the gut microbiota and its metabolites.

Berberine Ameliorates Periodontal Bone Loss by Regulating Gut Microbiota

Postmenopausal osteoporosis (PMO) is a risk factor for periodontitis, and current therapeutics against PMO prevent the aggravated alveolar bone loss of periodontitis in estrogen-deficient women. Gut microbiota is recognized as a promising therapeutic target for PMO. Berberine extracted from Chinese medicinal plants has shown its effectiveness in the treatment of metabolic diseases such as obesity and diabetes via regulating gut microbiota. Here, we hypothesize that berberine ameliorates periodontal bone loss by improving the intestinal barriers by regulating gut microbiota under an estrogen-deficient condition. Experimental periodontitis was established in ovariectomized (OVX) rats, and the OVX-periodontitis rats were treated with berberine for 7 wk before sacrifice for analyses. Micro–computed tomography and histologic analyses showed that berberine treatment significantly reduced alveolar bone loss and improved bone metabolism of OVX-periodontitis rats as compared with the vehicle-treated OVX-periodontitis rats. In parallel, berberine-treated OVX-periodontitis rats harbored a higher abundance of butyrate-producing gut microbiota with elevated butyrate generation, as demonstrated by 16S rRNA sequencing and high-performance liquid chromatography analysis. Berberine-treated OVX-periodontitis rats consistently showed improved intestinal barrier integrity and decreased intestinal paracellular permeability with a lower level of serum endotoxin. In parallel, IL-17A-related immune responses were attenuated in berberine-treated OVX-periodontitis rats with a lower serum level of proinflammatory cytokines and reduced IL-17A+ cells in alveolar bone as compared with vehicle-treated OVX-periodontitis rats. Our data indicate that gut microbiota is a potential target for the treatment of estrogen deficiency–aggravated periodontal bone loss, and berberine represents a promising adjuvant therapeutic by modulating gut microbiota.

The Effect of Digestion and Digestibility on Allergenicity of Food

Food allergy prevalence numbers are still on the rise. Apart from environmental influences, dietary habits, food availability and life-style factors, medication could also play a role. For immune tolerance of food, several contributing factors ensure that dietary compounds are immunologically ignored and serve only as source for energy and nutrient supply. Functional digestion along the gastrointestinal tract is essential for the molecular breakdown and a prerequisite for appropriate uptake in the intestine. Digestion and digestibility of carbohydrates and proteins thus critically affect the risk of food allergy development. In this review, we highlight the influence of amylases, gastric acid- and trypsin-inhibitors, as well as of food processing in the context of food allergenicity.

Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors

An increasing body of literature suggests that both individual and collections of bacteria are associated with the progression of colorectal cancer. As the number of studies investigating these associations increases and the number of subjects in each study increases, a meta-analysis to identify the associations that are the most predictive of disease progression is warranted. We analyzed previously published 16S rRNA gene sequencing data collected from feces and colon tissue. We quantified the odds ratios (ORs) for individual bacterial taxa that were associated with an individual having tumors relative to a normal colon. Among the fecal samples, there were no taxa that had significant ORs associated with adenoma and there were 8 taxa with significant ORs associated with carcinoma. Similarly, among the tissue samples, there were no taxa that had a significant OR associated with adenoma and there were 3 taxa with significant ORs associated with carcinoma. Among the significant ORs, the association between individual taxa and tumor diagnosis was equal to or below 7.11. Because individual taxa had limited association with tumor diagnosis, we trained Random Forest classification models using only the taxa that had significant ORs, using the entire collection of taxa found in each study, and using operational taxonomic units defined based on a 97% similarity threshold. All training approaches yielded similar classification success as measured using the area under the curve. The ability to correctly classify individuals with adenomas was poor, and the ability to classify individuals with carcinomas was considerably better using sequences from feces or tissue.IMPORTANCE Colorectal cancer is a significant and growing health problem in which animal models and epidemiological data suggest that the colonic microbiota have a role in tumorigenesis. These observations indicate that the colonic microbiota is a reservoir of biomarkers that may improve our ability to detect colonic tumors using noninvasive approaches. This meta-analysis identifies and validates a set of 8 bacterial taxa that can be used within a Random Forest modeling framework to differentiate individuals as having normal colons or carcinomas. When models trained using one data set were tested on other data sets, the models performed well. These results lend support to the use of fecal biomarkers for the detection of tumors. Furthermore, these biomarkers are plausible candidates for further mechanistic studies into the role of the gut microbiota in tumorigenesis.

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions

The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.