Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities.

Heating and cooking vegetables not only enhances their palatability but also modifies their chemical structure, which in turn might affect their fermentation by resident gut microbes. Three commonly consumed vegetables that are known to undergo chemical browning, also known as Maillard reaction, during cooking - eggplant, garlic, and onion - were each fried, grilled, or roasted. The cooked vegetables were then subjected to an in vitro digestion-fermentation process aimed to simulate the passage of food through the human oro-gastro-intestinal tract. In the last step, the undigested fractions of these foods were anaerobically fermented by the complex human gut microbiota. We assessed the structure of microbial communities maintained on each cooked vegetable by high-throughput 16S rRNA gene amplicon sequencing, measured the levels of furosine, a chemical marker of the Maillard browning reaction, by HPLC, and determined the antioxidant capacities in all samples with ABTS and FRAP methods. Overall, vegetable type had the largest, statistically significant, effect on the microbiota structure followed by the cooking method. Onion fermentation supported a more beneficial community including an expansion of Bifidobacterium members and inhibition of Enterobacteriaceae. Fermentation of cooked garlic promoted Faecalibacterium growth. Among cooking methods, roasting led to a much higher ratio of beneficial-to-detrimental microbes in comparison with grilling and frying, possibly due to the exclusion of any cooking oil in the cooking process.

Gut Microbiota Fermentation of Digested Almond-Psyllium-Flax Seed-Based Artisan Bread Promotes Mediterranean Diet-Resembling Microbial Community.

Different modifications of the standard bread recipe have been proposed to improve its nutritional and health benefits. Here, we utilized the in vitro Human Gut Simulator (HGS) to assess the fermentation of one such artisan bread by human gut microbiota. Dried and milled bread, composed of almond flour, psyllium husks, and flax seeds as its three main ingredients, was first subjected to an in vitro protocol designed to mimic human oro-gastro-intestinal digestion. The bread digest was then supplied to complex human gut microbial communities, replacing the typical Western diet-based medium (WM) of the GHS system. Switching the medium from WM to bread digest resulted in statistically significant alterations in the community structure, encoded functions, produced short-chain fatty acids, and available antioxidants. The abundances of dietary fiber degraders Enterocloster, Mitsuokella, and Prevotella increased; levels of Gemmiger, Faecalibacterium, and Blautia decreased. These community alterations resembled the previously revealed differences in the distal gut microbiota of healthy human subjects consuming typical Mediterranean vs. Western-pattern diets. Therefore, the consumption of bread high in dietary fiber and unsaturated fatty acids might recapitulate the beneficial effects of the Mediterranean diet on the gut microbiota.

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants.

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

Growth of Bifidobacterium species is inhibited by free fatty acids and bile salts but not by glycerides.

High-fat diets have been associated with lower gut and fecal abundances of genus Bifidobacterium. Here, we investigated whether commonly consumed dietary free fatty acids have any detrimental effect on the growth of B. adolescentis, B. bifidum, and B. longum. We found that the presence of free fatty acids in the medium inhibits the growth of Bifidobacterium species to a varying degree, with capric (C10:0), oleic (C18:1), and linoleic (C18:2) acids displaying the largest effect. In comparison, free fatty acids did not affect the growth of Escherichia coli. When fats were added as a mixture of mono- and diacylglycerols, the inhibitory effect on Bifidobacterium growth was abolished.

Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota.

Melanoidins are the products of the Maillard reaction between carbonyl and amino groups of macromolecules and are readily formed in foods, especially during heat treatment. In this study we utilized the three-stage Human Gut Simulator system to assess the effect of providing melanoidins extracted from either biscuits or bread crust to the human gut microbiota. Addition of melanoidins to the growth medium led to statistically significant alterations in the microbial community composition, and it increased short-chain fatty acid and antioxidant production by the microbiota. The magnitude of these changes was much higher for cultures grown with biscuit melanoidins. Several lines of evidence indicate that such differences between these melanoidin sources might be due to the presence of lipid components in biscuit melanoidin structures. Because melanoidins are largely not degraded by human gastrointestinal enzymes, they provide an additional source of microbiota-accessible nutrients to our gut microbes.

Bioactivity of food melanoidins is mediated by gut microbiota.

Melanoidins are an important component of the human diet (average consumption 10 g/day), which escape gastrointestinal digestion and are fermented by the gut microbiota. In this study melanoidins from different food sources (coffee, bread, beer, balsamic vinegar, sweet wine, biscuit, chocolate, and breakfast cereals) were submitted to an in vitro digestion and fermentation process, and their bioactivity was assessed. Some melanoidins were extensively used by gut microbes, increasing production of short chain fatty acids (mainly acetate and lactate) and favoring growth of the beneficial genera Bifidobacterium (bread crust, pilsner and black beers, chocolate and sweet wine melanoidins) and Faecalibacterium (biscuit melanoidins). Quantification of individual phenolic compounds after in vitro fermentation allowed their identification as microbial metabolites or phenolics released from the melanoidins backbone (specially pyrogallol, 2-(3,4-dihydroxyphenyl)acetic and 3-(3,4-dihydroxyphenyl)propionic acids). Our results also showed that antioxidant capacity of melanoidins is affected by gut microbiota fermentation.

Differential MicroRNA Signatures in the Pathogenesis of Barrett's Esophagus.

OBJECTIVES: Barrett's esophagus (BE) is the precursor lesion and a major risk factor for esophageal adenocarcinoma (EAC). Although patients with BE undergo routine endoscopic surveillance, current screening methodologies have proven ineffective at identifying individuals at risk of EAC. Since microRNAs (miRNAs) have potential diagnostic and prognostic value as disease biomarkers, we sought to identify an miRNA signature of BE and EAC. METHODS: High-throughput sequencing of miRNAs was performed on serum and tissue biopsies from 31 patients identified either as normal, gastroesophageal reflux disease (GERD), BE, BE with low-grade dysplasia (LGD), or EAC. Logistic regression modeling of miRNA profiles with Lasso regularization was used to identify discriminating miRNA. Quantitative reverse transcription polymerase chain reaction was used to validate changes in miRNA expression using 46 formalin-fixed, paraffin-embedded specimens obtained from normal, GERD, BE, BE with LGD or HGD, and EAC subjects. RESULTS: A 3-class predictive model was able to classify tissue samples into normal, GERD/BE, or LGD/EAC classes with an accuracy of 80%. Sixteen miRNAs were identified that predicted 1 of the 3 classes. Our analysis confirmed previous reports indicating that miR-29c-3p and miR-193b-5p expressions are altered in BE and EAC and identified miR-4485-5p as a novel biomarker of esophageal dysplasia. Quantitative reverse transcription polymerase chain reaction validated 11 of 16 discriminating miRNAs. DISCUSSION: Our data provide an miRNA signature of normal, precancerous, and cancerous tissue that may stratify patients at risk of progressing to EAC. We found that serum miRNAs have a limited ability to distinguish between disease states, thus limiting their potential utility in early disease detection.