Oleg Paliy

We analyzed riverbed microbiota structure, gene expression, and fatty acid production across several sites along Little Miami River in Ohio, United States. The sites varied in stream width, shading, surrounding land use, and the size of the riparian zone. Within each site, we observed strong concordance among microbial community composition, functional gene expression, and fatty acid signature. All microbial communities were dominated by the members of phylum Proteobacteria, class Planctomycetacia, and by algal and cyanobacterial cells. The measured concentrations of chlorophyll a, dissolved oxygen, and soluble phosphorus were the main environmental determinants of microbial community structure. These were in turn dependent on the level of penetrating sunlight and, to a lesser degree, on the width of the riparian zone. The level of sunlight affected the expression of light-harvesting complexes, methanogenesis genes, anaerobic respiratory reductases and fermentation pathways, as well as functions of denitrification, ammonification, and sulfate reduction. The expression of phosphorus scavenging and antibiotic resistance genes was highest at the site lacking a riparian zone and surrounded by farmland. Overall, our findings demonstrate that riverbed microbiota exhibit consistent structural and functional responses to interacting geochemical and anthropogenic gradients. Our data also provide support for the hypothesis that phototrophic microorganisms act as central organizers of benthic community metabolism.

Pomegranate is a fruit that grows abundantly in the Middle East and Africa. It is rich in polyphenols, sugars, fiber, and vitamins, and has long been associated in traditional and alternative medicine with numerous health benefits, including the treatment of diarrhea and gut inflammation. We assessed how regular daily intake of fresh pomegranate can affect the distal gut microbiota of young healthy female students in Egypt, a region with abundant pomegranate production and frequent occurrence of gut dysbiosis. Interrogation of microbiota structure based on the sequencing of the 16S ribosomal RNA gene amplicons indicated that subject-to-subject variability was the main driver of microbiota community differences. Nevertheless, pomegranate consumption led to changes in the abundances of several genera including increased levels of Saccharofermentans, Enterococcus, and Prevotella. The relative counts of Dysosmobacter, Coprococcus, and Collinsella decreased after pomegranate intake. The magnitude of community structure shift after diet intervention correlated with the increase in the total polyphenol concentration measured in subjects’ urine. The overall ratio of presumed beneficial-to-detrimental microbes was also improved with pomegranate addition to the diet, supporting the advantageous effects of pomegranate eating.

We used the in vitro Human Gut Simulator system to assess the fermentation of oro-gastro-intestinally digested asparagus powder by the human gut microbiota.

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.

Eggplant, garlic, and onion were each fried, grilled, or roasted, and were subjected to an in vitro digestion-fermentation process. Vegetable type had the largest effect on the gut microbiota structure. Oonion supported a more beneficial community.

Almonds are a rich source of beneficial compounds for human health. In this work, we assessed the influence of almond cultivars and harvest time on their morphological (length, width and thickness) and nutritional (ash, moisture, proteins) profiles. We also evaluated the impact of an in vitro digestion and fermentation process on almonds’ antioxidant and phenolic content, as well as their support of gut microbiota community and functionality, including the production of short-chain fatty acids (SCFAs), lactic and succinic acids. The length, width, and thickness of almonds varied significantly among cultivars, with the latter two parameters also exhibiting significant changes over time. Moisture content decreased with maturity, while protein and ash increased significantly. Total antioxidant capacity released by almonds after digestion and fermentation had different trends depending on the antioxidant capacity method used. The fermentation step contributed more to the antioxidant capacity than the digestion step. Both cultivar and harvest time exerted a significant influence on the concentration of certain phenolic compounds, although the total content remained unaffected. Similarly, fecal microbiota modulation depended on the cultivar and maturity stage, with the Guara cultivar and late maturity showing the largest effects. Cultivar type also exerted a significant impact on the concentration of SCFAs, with the Guara cultivar displaying the highest total SCFAs concentration. Thus, we conclude that cultivar and harvest time are key factors in shaping the morphological and nutritional composition of almonds. In addition, taking into account all the results obtained, the Guara variety has the best nutritional profile.

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.

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.

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While a substantial amount of dietary fats escape absorption in the human small intestine and reach the colon, the ability of resident microbiota to utilize these dietary fats for growth has not been investigated in detail. In this study we used an in vitro multi-vessel simulator system of the human colon to reveal that human gut microbiota is able to utilize typically consumed dietary fatty acids to sustain growth. Gut microbiota adapted quickly to a macronutrient switch from a balanced Western diet type medium to its variant lacking carbohydrates and proteins. We defined specific genera that increased their abundance on the fats-only medium, including Alistipes, Bilophila, and several genera of class Gammaproteobacteria. In contrast, abundances of well-known glycan and protein degraders including Bacteroides, Clostridium, and Roseburia were reduced in such conditions. Predicted prevalences of microbial genes coding for fatty acid degradation enzymes and anaerobic respiratory reductases were significantly increased in the fats-only environment, whereas the abundance of glycan degradation genes was diminished. These changes also resulted in lower microbial production of short chain fatty acids and antioxidants. Our findings provide justification for the previously observed alterations in gut microbiota observed in human and animal studies of high-fat diets. Importance Increased intake of fats in many developed countries raised awareness of potentially harmful and beneficial effects of high fat consumption on human health. Some dietary fats escape digestion in the small intestine and reach the colon where they can be metabolized by gut microbiota. We show that human gut microbes are able to maintain a complex community when supplied with dietary fatty acids as the only nutrient and carbon sources. Such fatty acid based growth leads to lower production of short chain fatty acids and antioxidants by community members, which might potentially have negative health consequences on the host.