Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge

Enterococci, in particular vancomycin-resistant enterococci (VRE), are a leading cause of hospital-acquired infections. Promoting intestinal resistance against enterococci could reduce the risk of VRE infections. We investigated the effects of two Lactobacillus strains to prevent intestinal VRE. We used an intestinal colonisation mouse model based on an antibiotic-induced microbiota dysbiosis to mimic enterococci overgrowth and VRE persistence. Each Lactobacillus spp. was administered daily to mice starting one week before antibiotic treatment until two weeks after antibiotic and VRE inoculation. Of the two strains, Lactobacillus paracasei CNCM I-3689 decreased significantly VRE numbers in the feces demonstrating an improvement of the reduction of VRE. Longitudinal microbiota analysis showed that supplementation with L. paracasei CNCM I-3689 was associated with a better recovery of members of the phylum Bacteroidetes. Bile salt analysis and expression analysis of selected host genes revealed increased level of lithocholate and of ileal expression of camp (human LL-37) upon L. paracasei CNCM I-3689 supplementation. Although a direct effect of L. paracasei CNCM I-3689 on the VRE reduction was not ruled out, our data provide clues to possible anti-VRE mechanisms supporting an indirect anti-VRE effect through the gut microbiota. This work sustains non-antibiotic strategies against opportunistic enterococci after antibiotic-induced dysbiosis.

Dietary butyrate glycerides modulate intestinal microbiota composition and serum metabolites in broilers

Butyrate can modulate the immune response and energy expenditure of animals and enhance intestinal health. The present study investigated changes in the intestinal microbiota composition and serum metabolites of young broilers in response to 3,000 ppm butyrate in the form of butyrate glycerides (BG) via pyrosequencing of bacterial 16S rRNA genes and nuclear magnetic resonance (NMR). The dietary treatment did not affect the alpha diversity of intestinal microbiota, but altered its composition. Thirty-nine key operational taxonomic units (OTUs) in differentiating cecal microbiota community structures between BG treated and untreated chickens were also identified. Bifidobacterium was, in particular, affected by the dietary treatment significantly, showing an increase in not only the abundance (approximately 3 fold, P ≤ 0.05) but also the species diversity. The (NMR)-based analysis revealed an increase in serum concentrations of alanine, low-density and very low-density lipoproteins, and lipids (P ≤ 0.05) by BG. More interestingly, the dietary treatment also boosted (P ≤ 0.05) serum concentrations of bacterial metabolites, including choline, glycerophosphorylcholine, dimethylamine, trimethylamine, trimethylamine-N-oxide, lactate, and succinate. In conclusion, the data suggest the modulation of intestinal microbiota and serum metabolites by BG dietary treatment and potential contribution of intestinal bacteria to lipid metabolism/energy homeostasis in broilers.

Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier

BACKGROUND

Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbiome influences the gut-brain axis: modification of autonomic/sensorimotor connections, immune activation, and neuroendocrine pathway regulation. We hypothesised interactions between circulating gut-derived microbial metabolites, and the blood-brain barrier (BBB) also contribute to the gut-brain axis. Propionate, produced from dietary substrates by colonic bacteria, stimulates intestinal gluconeogenesis and is associated with reduced stress behaviours, but its potential endocrine role has not been addressed.

RESULTS

After demonstrating expression of the propionate receptor FFAR3 on human brain endothelium, we examined the impact of a physiologically relevant propionate concentration (1 μM) on BBB properties in vitro. Propionate inhibited pathways associated with non-specific microbial infections via a CD14-dependent mechanism, suppressed expression of LRP-1 and protected the BBB from oxidative stress via NRF2 (NFE2L2) signalling.

CONCLUSIONS

Together, these results suggest gut-derived microbial metabolites interact with the BBB, representing a fourth facet of the gut-brain axis that warrants further attention.

Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B12-Dependent and Glycyl Radical Enzymes

Propanediol dehydratase (PD), a recently characterized member of the glycyl radical enzyme (GRE) family, uses protein-based radicals to catalyze the chemically challenging dehydration of ( S)-1,2-propanediol. This transformation is also performed by the well-studied enzyme B₁₂-dependent propanediol dehydratase (B₁₂-PD) using an adenosylcobalamin cofactor. Despite the prominence of PD in anaerobic microorganisms, it remains unclear if the mechanism of this enzyme is similar to that of B₁₂-PD. Here we report ¹⁸O labeling experiments that suggest PD and B₁₂-PD employ distinct mechanisms. Unlike B₁₂-PD, PD appears to catalyze the direct elimination of a hydroxyl group from an initially formed substrate-based radical, avoiding the generation of a 1,1- gem diol intermediate. Our studies provide further insights into how GREs perform elimination chemistry and highlight how nature has evolved diverse strategies for catalyzing challenging reactions.

Effects of Blackcurrant and Dietary Fibers on Large Intestinal Health Biomarkers in Rats

This study examined the effects of anthocyanin-rich blackcurrant extract and dietary fibers individually and their combinations on biomarkers of large intestinal health in rats. After six weeks of feeding, rats fed diets with blackcurrant gained significantly less body weight and reduced their food intake resulting in a lower food efficiency compared with those rats fed control diets. Combining dietary fiber (apple or broccoli) with blackcurrant in the diet was more effective in reducing the body weight gain and food intake. Cecal bacterial populations and short-chain fatty acids differed between the experimental diets. Blackcurrants significantly altered the bacterial populations by increasing the abundance of Bacteroides-Prevotella-Porphyromonas group and Lactobacillus spp., while decreasing the abundance of Bifidobacterium spp. and Clostridium perfringens. Propionic acid concentrations were increased by the diets with blackcurrant. Butyric acid concentrations were increased by dietary fiber supplementation. Dietary fiber increased the number of goblet cells in the colon. Diets with blackcurrant were more effective in altering the biomarkers of large intestinal health than those without blackcurrant.

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis

Epidemiological studies propose a protective role for dietary fiber in colon cancer (CRC). One possible mechanism of fiber is its fermentation property in the gut and ability to change microbiota composition and function. Here, we investigate the role of a dietary fiber mixture in polyposis and elucidate potential mechanisms using TS4Cre × cAPC^l°^x468 mice. Stool microbiota profiling was performed, while functional prediction was done using PICRUSt. Stool short-chain fatty acid (SCFA) metabolites were measured. Histone acetylation and expression of SCFA butyrate receptor were assessed. We found that SCFA-producing bacteria were lower in the polyposis mice, suggesting a decline in the fermentation product of dietary fibers with polyposis. Next, a high fiber diet was given to polyposis mice, which significantly increased SCFA-producing bacteria as well as SCFA levels. This was associated with an increase in SCFA butyrate receptor and a significant decrease in polyposis. In conclusion, we found polyposis to be associated with dysbiotic microbiota characterized by a decline in SCFA-producing bacteria, which was targetable by high fiber treatment, leading to an increase in SCFA levels and amelioration of polyposis. The prebiotic activity of fiber, promoting beneficial bacteria, could be the key mechanism for the protective effects of fiber on colon carcinogenesis. SCFA-promoting fermentable fibers are a promising dietary intervention to prevent CRC.

Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study

Despite clinical findings suggesting that the form (liquid versus solid) of the sugars may significantly affect the development of metabolic diseases, no experimental data are available on the impact of their formulations on gut microbiota, integrity and hepatic outcomes. In the present sudy, C57Bl/6j mice were fed a standard diet plus water (SD), a standard diet plus 60% fructose syrup (L-Fr) or a 60% fructose solid diet plus water (S-Fr) for 12 weeks. Gut microbiota was characterized through 16S rRNA phylogenetic profiling and shotgun sequencing of microbial genes in ileum content and related volatilome profiling. Fructose feeding led to alterations of the gut microbiota depending on the fructose formulation, with increased colonization by Clostridium, Oscillospira and Clostridiales phyla in the S-Fr group and Bacteroides, Lactobacillus, Lachnospiraceae and Dorea in the L-Fr. S-Fr evoked the highest accumulation of advanced glycation end products and barrier injury in the ileum intestinal mucosa. These effects were associated to a stronger activation of the lipopolysaccharide-dependent proinflammatory TLR4/NLRP3 inflammasome pathway in the liver of S-Fr mice than of L-Fr mice. In contrast, L-Fr intake induced higher levels of hepatosteatosis and markers of fibrosis than S-Fr. Fructose-induced ex novo lipogenesis with production of SCFA and MCFA was confirmed by metagenomic analysis. These results suggest that consumption of fructose under different forms, liquid or solid, may differently affect gut microbiota, thus leading to impairment in intestinal mucosa integrity and liver homeostasis.

Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients

BACKGROUND

Hashimoto's thyroiditis (HT) is an organ-specific autoimmune disease in which both genetic predisposition and environmental factors serve as disease triggers. Many studies have indicated that alterations in the gut microbiota are important environmental factors in the development of inflammatory and autoimmune diseases. A comparative analysis was systematically performed of the gut microbiota in HT patients and healthy controls.

METHODS

First, a cross-sectional study of 28 HT patients and 16 matched healthy controls was conducted. Fecal samples were collected, and microbiota were analyzed using 16S ribosomal RNA gene sequencing. Second, an independent cohort of 22 HT patients and 11 healthy controls was used to evaluate the diagnostic potential of the selected biomarkers.

RESULTS

Similar levels of bacterial richness and diversity were found in the gut microbiota of HT patients and healthy controls (p = 0.11). A detailed fecal microbiota Mann-Whitney U-test (Q value <0.05) revealed that the abundance levels of Blautia, Roseburia, Ruminococcus_torques_group, Romboutsia, Dorea, Fusicatenibacter, and Eubacterium_hallii_group genera were increased in HT patients, whereas the abundance levels of Fecalibacterium, Bacteroides, Prevotella_9, and Lachnoclostridium genera were decreased. A correlation matrix based on the Spearman correlation distance confirmed correlations among seven clinical parameters. Additionally, the linear discriminant analysis effect size method showed significant differences in 27 genera between the two groups that were strongly correlated with clinical parameters. The linear discriminant analysis value was used to select the first 10 species from the 27 different genera as biomarkers, achieving area under the curve values of 0.91 and 0.88 for exploration and validation data, respectively.

CONCLUSIONS

Characterization of the gut microbiota in HT patients confirmed that HT patients have altered gut microbiota and that gut microbiota are correlated with clinical parameters, suggesting that microbiome composition data could be used for disease diagnosis. Further investigation is required to understand better the role of the gut microbiota in the pathogenesis of HT.

The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer

Metabolism regulation is crucial in colorectal cancer (CRC) and has emerged as a remarkable field currently. The cellular metabolism of glucose, amino acids and lipids in CRC are all reprogrammed. Each of them changes tumour microenvironment, modulates bacterial composition and activity, and eventually promotes CRC development. Metabolites such as short chain fatty acids, secondary bile acids, N-nitroso compounds, hydrogen sulphide, polyphenols and toxins like fragilysin, FadA, cytolethal distending toxin and colibactin play a dual role in CRC. The relationship of gut microbe-metabolite is essential in remodelling intestinal microbial ecology composition and metabolic activity. It regulates the metabolism of colonic epithelial cells and changes the tumour microenvironment in CRC. Microbial metabolism manipulation has been considered to be potentially preventive in CRC, but more large-scale clinical trials are required before their application in clinical practice in the near future.

Modulation of the Fecal Microbiota in Sprague-Dawley Rats Using Genetically Modified and Isogenic Corn Lines

This study investigated the composition and proportions of fecal microbiota in Sprague-Dawley rats after consuming two genetically modified (GM) corn lines in comparison with the isogenic corn and the AIN93G standard feed for 10 weeks using bar-coded 16S rRNA gene sequencing. As a result, GM corn did not significantly alter the overall health and alpha-diversity of fecal microbiota. Fecal microbiota structures could be separated into noncorn and corn but not non-GM and GM corn subgroups. Both non-GM and GM corn caused the increase in bacterial populations related to carbohydrates utilization, such as Lactobacillus, Barnesiella, and Bifidobacterium, and the reduction in potentially pathogenic populations, such as Tannerella and Moraxellaceae. In conclusion, similar effects on the fecal microbiota were observed after consuming a GM- and non-GM-corn-based diet for long periods. Further studies are warranted to elucidate the functional relevance of the changes in the proportions of bacterial populations in these diets.

Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation

Human milk (HM) is the golden standard for nutrition of newborn infants. Human milk oligosaccharides (HMOs) are abundantly present in HM and exert multiple beneficial functions, such as support of colonization of the gut microbiota, reduction of pathogenic infections and support of immune development. HMO-composition is during lactation continuously adapted by the mother to accommodate the needs of the neonate. Unfortunately, for many valid reasons not all neonates can be fed with HM and are either totally or partly fed with cow-milk derived infant formulas, which do not contain HMOs. These cow-milk formulas are supplemented with non-digestible carbohydrates (NDCs) that have functional effects similar to that of some HMOs, since production of synthetic HMOs is challenging and still very expensive. However, NDCs cannot substitute all HMO functions. More efficacious NDCs may be developed and customized for specific groups of neonates such as pre-matures and allergy prone infants. Here current knowledge of HMO functions in the neonate in view of possible replacement of HMOs by NDCs in infant formulas is reviewed. Furthermore, methods to expedite identification of suitable NDCs and structure/function relationships are reviewed as in vivo studies in babies are impossible.

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure

This study investigated the effect of various prebiotics (indigestible dextrin, α-cyclodextrin, and dextran) on human colonic microbiota at a dosage corresponding to a daily intake of 6 g of prebiotics per person (0.2% of dietary intake). We used an in vitro human colonic microbiota model based on batch fermentation starting from a faecal inoculum. Bacterial 16S rRNA gene sequence analysis showed that addition of 0.2% prebiotics did not change the diversity and composition of colonic microbiota. This finding coincided with results from a clinical study showing that the microbiota composition of human faecal samples remained unchanged following administration of 6 g of prebiotics over seven days. However, compared to absence of prebiotics, their addition reduced the pH and increased the generation of acetate and propionate in the in vitro system. Thus, even at such relatively low amounts, prebiotics appear capable of activating the metabolism of colonic microbiota.

Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation

The intestinal microbiota have emerged as a central regulator of host metabolism and immune function, mediating the effects of diet on host health. However, the large diversity and individuality of the gut microbiota have made it difficult to draw conclusions about microbiota responses to dietary interventions. In the light of recent research, certain general patterns are emerging, revealing how the ecology of the gut microbiota profoundly depends on the quality and quantity of dietary carbohydrates and proteins. In this review, I provide an overview of the dependence of microbial ecology in the human colon on diet and how the effects of diet on host health depend partially on the microbiota. Understanding how the individual-specific microbiota respond to short- and long-term dietary changes and how they influence host energy homeostasis will enable targeted interventions to achieve specific outcomes, such as weight loss in obesity or weight gain in malnutrition.

Porcine Small and Large Intestinal Microbiota Rapidly Hydrolyze the Masked Mycotoxin Deoxynivalenol-3-Glucoside and Release Deoxynivalenol in Spiked Batch Cultures In Vitro

Mycotoxin contamination of cereal grains causes well-recognized toxicities in animals and humans, but the fate of plant-bound masked mycotoxins in the gut is less well understood. Masked mycotoxins have been found to be stable under conditions prevailing in the small intestine but are rapidly hydrolyzed by fecal microbiota. This study aims to assess the hydrolysis of the masked mycotoxin deoxynivalenol-3-glucoside (DON3Glc) by the microbiota of different regions of the porcine intestinal tract. Intestinal digesta samples were collected from the jejunum, ileum, cecum, colon, and feces of 5 pigs and immediately frozen under anaerobic conditions. Sample slurries were prepared in M2 culture medium, spiked with DON3Glc or free deoxynivalenol (DON; 2 nmol/ml), and incubated anaerobically for up to 72 h. Mycotoxin concentrations were determined using liquid chromatography-tandem mass spectrometry, and the microbiota composition was determined using a quantitative PCR methodology. The jejunal microbiota hydrolyzed DON3Glc very slowly, while samples from the ileum, cecum, colon, and feces rapidly and efficiently hydrolyzed DON3Glc. No further metabolism of DON was observed in any sample. The microbial load and microbiota composition in the ileum were significantly different from those in the distal intestinal regions, whereas those in the cecum, colon and feces did not differ.IMPORTANCE Results from this study clearly demonstrate that the masked mycotoxin DON3Glc is hydrolyzed efficiently in the distal small intestine and large intestine of pigs. Once DON is released, toxicity and absorption in the distal intestinal tract likely occur in vivo This study further supports the need to include masked metabolites in mycotoxin risk assessments and regulatory actions for feed and food.

Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii

Mucus production is initiated before birth and provides mucin glycans to the infant gut microbiota. Bifidobacteria are the major bacterial group in the feces of vaginally delivered and breast milk-fed infants. Among the bifidobacteria, only Bifidobacterium bifidum is able to degrade mucin and to release monosaccharides which can be used by other gut microbes colonizing the infant gut. Eubacterium hallii is an early occurring commensal that produces butyrate and propionate from fermentation metabolites but that cannot degrade complex oligo- and polysaccharides. We aimed to demonstrate that mucin cross-feeding initiated by B. bifidum enables growth and metabolite formation of E. hallii leading to short-chain fatty acid (SCFA) formation. Growth and metabolite formation of co-cultures of B. bifidum, of Bifidobacterium breve or Bifidobacterium infantis, which use mucin-derived hexoses and fucose, and of E. hallii were determined. Growth of E. hallii in the presence of lactose and mucin monosaccharides was tested. In co-culture fermentations, the presence of B. bifidum enabled growth of the other strains. B. bifidum/B. infantis co-cultures yielded acetate, formate, and lactate while co-cultures of B. bifidum and E. hallii formed acetate, formate, and butyrate. In three-strain co-cultures, B. bifidum, E. hallii, and B. breve or B. infantis produced up to 16 mM acetate, 5 mM formate, and 4 mM butyrate. The formation of propionate (approximately 1 mM) indicated cross-feeding on fucose. Lactose, galactose, and GlcNAc were identified as substrates of E. hallii. This study shows that trophic interactions of bifidobacteria and E. hallii lead to the formation of acetate, butyrate, propionate, and formate, potentially contributing to intestinal SCFA formation with potential benefits for the host and for microbial colonization of the infant gut. The ratios of SCFA formed differed depending on the microbial species involved in mucin cross-feeding.

A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

BACKGROUND

The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation.

RESULTS

The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many "polysaccharide utilization loci" (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species.

CONCLUSION

The analysis confirmed the camel rumen's microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries.

Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology

Interest in faecal microbiota transplantation (FMT) has increased as therapy for intestinal diseases, but safety issues limit its widespread use. Intestinal fermentation technology (IFT) can produce controlled, diverse and metabolically active 'artificial' colonic microbiota as potential alternative to common FMT. However, suitable processing technology to store this artificial microbiota is lacking. In this study, we evaluated the impact of the two cryoprotectives, glycerol (15% v/v) and inulin (5% w/v) alone and in combination, in preserving short-chain fatty acid formation and recovery of major butyrate-producing bacteria in three artificial microbiota during cryopreservation for 3 months at -80°C. After 24 h anaerobic fermentation of the preserved microbiota, butyrate and propionate production were maintained when glycerol was used as cryoprotectant, while acetate and butyrate were formed more rapidly with glycerol in combination with inulin. Glycerol supported cryopreservation of the Roseburia spp./Eubacterium rectale group, while inulin improved the recovery of Faecalibacterium prausnitzii. Eubacterium hallii growth was affected minimally by cryopreservation. Our data indicate that butyrate producers, which are key organisms for gut health, can be well preserved with glycerol and inulin during frozen storage. This is of high importance if artificially produced colonic microbiota is considered for therapeutic purposes.

Diet and microbiota linked in health and disease

Diet has shaped microbiota profiles through human evolution.

Microbiome in the Gut-Skin Axis in Atopic Dermatitis

The microbiome is vital for immune system development and homeostasis. Changes in microbial composition and function, termed dysbiosis, in the skin and the gut have recently been linked to alterations in immune responses and to the development of skin diseases, such as atopic dermatitis (AD). In this review, we summarize the recent findings on the gut and skin microbiome, highlighting the roles of major commensals in modulating skin and systemic immunity in AD. Although our understanding of the gut-skin axis is only beginning, emerging evidence indicates that the gut and skin microbiome could be manipulated to treat AD.

Propionibacterium spp.-source of propionic acid, vitamin B12, and other metabolites important for the industry

Bacteria from the Propionibacterium genus consists of two principal groups: cutaneous and classical. Cutaneous Propionibacterium are considered primary pathogens to humans, whereas classical Propionibacterium are widely used in the food and pharmaceutical industries. Bacteria from the Propionibacterium genus are capable of synthesizing numerous valuable compounds with a wide industrial usage. Biomass of the bacteria from the Propionibacterium genus constitutes sources of vitamins from the B group, including B12, trehalose, and numerous bacteriocins. These bacteria are also capable of synthesizing organic acids such as propionic acid and acetic acid. Because of GRAS status and their health-promoting characteristics, bacteria from the Propionibacterium genus and their metabolites (propionic acid, vitamin B12, and trehalose) are commonly used in the cosmetic, pharmaceutical, food, and other industries. They are also used as additives in fodders for livestock. In this review, we present the major species of Propionibacterium and their properties and provide an overview of their functions and applications. This review also presents current literature concerned with the possibilities of using Propionibacterium spp. to obtain valuable metabolites. It also presents the biosynthetic pathways as well as the impact of the genetic and environmental factors on the efficiency of their production.

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice

Three polysaccharides were extracted from purple sweet potatoes and then administered to normal and cyclophosphamide treated mice by gavage.

Microbial biotransformations in the human distal gut

The human distal gut is home to a rich and dense microbial community with representatives of all three domains of life which are intricately connected with our physiology and health. The combined genomes of these microbes, collectively called the human microbiome, vastly expand the metabolic capacities of our own genome, allowing us to break down and extract energy from dietary compounds that human enzymes cannot digest. In addition, the variable composition of these communities and their biotransformations might explain inter-individual differences in toxicities, tolerances and efficacies for certain drugs. Recent advances in sequencing technologies and bioinformatics have provided exciting new insights into the genomes of our microbial symbionts, their functional capacities and the interactions between these microbes and their human host. This review summarizes the metabolic conversions of dietary components and pharmaceuticals that take place in the human distal gut, as well as their implications for human health. LINKED ARTICLES: This article is part of a themed section on When Pharmacology Meets the Microbiome: New Targets for Therapeutics? To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.24/issuetoc.

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers

Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs. We observed that Prevotella and Bifidobacterium abundance were associated with HCs, whereas butyrate and propionate-producing bacteria like Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium were significantly enriched in TB patients. Functional analysis showed reduced biosynthesis of vitamins and amino acids in favour of enriched metabolism of butyrate and propionate in TB subjects. The TB subjects were also investigated during the course of treatment, to analyse the variation of GM. Although perturbation in microbial composition was still evident after a month's administration of anti-TB drugs, significant changes were observed in metagenome gene pool that pointed towards recovery in functional capacity. Therefore, the findings from this pilot study suggest that microbial dysbiosis may contribute to pathophysiology of TB by enhancing the anti-inflammatory milieu in the host.

Evaluation of inter-individual differences in gut bacterial isoflavone bioactivation in humans by PCR-based targeting of genes involved in equol formation

AIM

To identify human subjects harbouring intestinal bacteria that bioactivate daidzein to equol using a targeted PCR-based approach.

METHODS AND RESULTS

In a pilot study including 17 human subjects, equol formation was determined in faecal slurries. In parallel, faecal DNA was amplified by PCR using degenerate primers that target highly conserved regions of dihydrodaidzein reductase and tetrahydrodaidzein reductase genes. PCR products of the expected size were observed for six of the eight subjects identified as equol producers. Analysis of clone libraries revealed the amplification of sequences exclusively related to Adlercreutzia equolifaciens in four of the subjects tested positive for equol formation, whereas in three of the equol producers, only sequences related to Slackia isoflavoniconvertens were observed. No amplicons were obtained for one equol-forming subject, thus suggesting the presence of nontargeted alternative genes. Amplicons were only sporadically observed in the nonequol producers.

CONCLUSION

The majority of human subjects who produced equol were also detected with the developed PCR-based approach.

SIGNIFICANCE AND IMPACT OF THE STUDY

The obtained results shed light on the distribution and the diversity of known equol-forming bacterial species in the study group and indicate the presence of as yet unknown equol-forming bacteria.

The response of canine faecal microbiota to increased dietary protein is influenced by body condition

Background

High protein diets shift the faecal microbiota into a more unfavourable composition in obese humans. In lean dogs, higher protein consumption is accompanied with increased production of putrefactive fermentation products, whereas obese dogs have a different gut microbiota compared to lean dogs. Still, the impact of high dietary protein on gut microbiota in obese dogs remains unclear. The aim of this study was to investigate faecal microbial changes in lean and obese dogs in response to two different levels of dietary protein.

Six healthy lean and six obese Beagles were fed a high protein diet (HP) and a low protein diet (LP) for 28 days each in a crossover design. Denaturing gradient gel electrophoresis and quantitative PCR were performed on faecal samples for microbial profiling. Plasma acylcarnitine and fermentation metabolites were measured.

Results

Dogs fed HP had higher concentrations of protein fermentation metabolites including faecal ammonia, isovalerate, isobutyrate, phenol, indole, serum indoxyl sulphate and plasma 3-OH isovalerylcarnitine compared to dogs fed LP, whereas no changes in faecal concentrations of acetate and butyrate were observed. The abundances of clostridial clusters IV and XIVa, covering the majority of butyrate-producing bacteria, and of the butyrate kinase gene, one of the terminal genes of the butyrate synthesis pathway were higher in dogs on HP compared to LP. Significant interactions between diet and body condition were found for the abundance of Firmicutes, Lactobacillus and clostridial cluster I. The similarity coefficient of faecal microbiota between the two diets was smaller in obese dogs than in lean dogs.

Conclusions

High protein diet increased the abundance and activity of butyrate-producing bacteria in Beagles independent of the body condition. In addition, increasing dietary protein content had a greater overall impact on faecal microbiota in obese compared to lean dogs.

Electronic supplementary material

The online version of this article (10.1186/s12917-017-1276-0) contains supplementary material, which is available to authorized users.

Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production

The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors. To investigate temporal stability and reproducibility, a further experiment was performed 1 year later with four of the carbohydrates. The lower pH (5.5) led to higher butyrate and the higher pH (6.5) to more propionate production. The strongest propionigenic effect was found with rhamnose, followed by galactomannans, whereas fructans and several α- and β-glucans led to higher butyrate production. 16S ribosomal RNA gene-based quantitative PCR analysis of 22 different microbial groups together with 454 sequencing revealed significant stimulation of specific bacteria in response to particular carbohydrates. Some changes were ascribed to metabolite cross-feeding, for example, utilisation by Eubacterium hallii of 1,2-propanediol produced from fermentation of rhamnose by Blautia spp. Despite marked inter-individual differences in microbiota composition, SCFA production was surprisingly reproducible for different carbohydrates, indicating a level of functional redundancy. Interestingly, butyrate formation was influenced not only by the overall % butyrate-producing bacteria in the community but also by the initial pH, consistent with a pH-dependent shift in the stoichiometry of butyrate production.

Lifestyle alters GUT-bacteria function: Linking immune response and host

Microbiota in human is a "mixture society" of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us ("from the beginning") in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- "mom" as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.

Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial

Recurrent hepatic encephalopathy (HE) is a leading cause of readmission despite standard of care (SOC) associated with microbial dysbiosis. Fecal microbiota transplantation (FMT) may improve dysbiosis; however, it has not been studied in HE. We aimed to define whether FMT using a rationally derived stool donor is safe in recurrent HE compared to SOC alone. An open-label, randomized clinical trial with a 5-month follow-up in outpatient men with cirrhosis with recurrent HE on SOC was conducted with 1:1 randomization. FMT-randomized patients received 5 days of broad-spectrum antibiotic pretreatment, then a single FMT enema from the same donor with the optimal microbiota deficient in HE. Follow-up occurred on days 5, 6, 12, 35, and 150 postrandomization. The primary outcome was safety of FMT compared to SOC using FMT-related serious adverse events (SAEs). Secondary outcomes were adverse events, cognition, microbiota, and metabolomic changes. Participants in both arms were similar on all baseline criteria and were followed until study end. FMT with antibiotic pretreatment was well tolerated. Eight (80%) SOC participants had a total of 11 SAEs compared to 2 (20%) FMT participants with SAEs (both FMT unrelated; P = 0.02). Five SOC and no FMT participants developed further HE (P = 0.03). Cognition improved in the FMT, but not the SOC, group. Model for End-Stage Liver Disease (MELD) score transiently worsened postantibiotics, but reverted to baseline post-FMT. Postantibiotics, beneficial taxa, and microbial diversity reduction occurred with Proteobacteria expansion. However, FMT increased diversity and beneficial taxa. SOC microbiota and MELD score remained similar throughout.

CONCLUSION

FMT from a rationally selected donor reduced hospitalizations, improved cognition, and dysbiosis in cirrhosis with recurrent HE. (Hepatology 2017;66:1727-1738).

A review of metabolic potential of human gut microbiome in human nutrition

The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.

Functional properties of anti-inflammatory substances from quercetin-treated Bifidobacterium adolescentis

The genus Bifidobacterium is well known to have beneficial health effects. We discovered that quercetin and related polyphenols enhanced the secretion of anti-inflammatory substances by Bifidobacterium adolescentis. This study investigated characteristics of the anti-inflammatory substances secreted by B. adolescentis. The culture supernatant of B. adolescentis with quercetin reduced the levels of inflammatory mediators in activated macrophages. Spontaneous quercetin degradant failed to increase anti-inflammatory activity, while the enhancement of anti-inflammatory activity by quercetin was sustained after washout of quercetin. Physicochemical treatment of the culture supernatant indicated that its bioactive substances may be heat-stable, non-phenolic, and acidic biomolecules with molecular weights less than 3 kDa. Acetate and lactate have little or no effect on nitric oxide production. Taken together, the anti-inflammatory substances secreted by B. adolescentis may be small molecules but not short chain fatty acids. In agreement with these findings, stearic acid was tentatively identified as a bioactive candidate compound.

Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids

Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well-recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden-Meyerhof-Parnas pathway. This study shows that reconstruction of metabolic pathways - a common goal of omics studies - could be incorrect if well-recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically.

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota

Background: Preclinical research has shown that the gastrointestinal microbiota exhibits circadian rhythms and that the timing of food consumption can affect the composition and function of gut microbes. However, there is a dearth of knowledge on these relations in humans.Objective: We aimed to determine whether human gastrointestinal microbes and bacterial metabolites were associated with time of day or behavioral factors, including eating frequency, percentage of energy consumed early in the day, and overnight-fast duration.Design: We analyzed 77 fecal samples collected from 28 healthy men and women. Fecal DNA was extracted and sequenced to determine the relative abundances of bacterial operational taxonomic units (OTUs). Gas chromatography-mass spectroscopy was used to assess short-chain fatty acid concentrations. Eating frequency, percentage of energy consumed before 1400, and overnight-fast duration were determined from dietary records. Data were analyzed by linear mixed models or generalized linear mixed models, which controlled for fiber intake, sex, age, body mass index, and repeated sampling within each participant. Each OTU and metabolite were tested as the outcome in a separate model.Results: Acetate, propionate, and butyrate concentrations decreased throughout the day (P = 0.006, 0.04, and 0.002, respectively). Thirty-five percent of bacterial OTUs were associated with time. In addition, relations were observed between gut microbes and eating behaviors, including eating frequency, early energy consumption, and overnight-fast duration.Conclusions: These results indicate that the human gastrointestinal microbiota composition and function vary throughout the day, which may be related to the circadian biology of the human body, the microbial community itself, or human eating behaviors. Behavioral factors, including timing of eating and overnight-fast duration, were also predictive of bacterial abundances. Longitudinal intervention studies are needed to determine causality of these biological and behavioral relations. This trial was registered at clinicaltrials.gov as NCT01925560.

Whole cereal grains and potential health effects: Involvement of the gut microbiota

The intakes of whole cereal grains (WCGs) have long been linked to decreased risks of metabolic syndromes (MetS) and several chronic diseases. Owing to the complex range of components of cereals, which may show synergistic activities to mediate these protective effects, the mechanisms by which the benefits of whole cereals arise are not fully understood. The gut microbiota has recently become a new focus of research at the intersection of diet and metabolic health. Moreover, cereals contain various ingredients known as microbiota-accessible substrates that resist digestion in the upper gastrointestinal tract, including resistant starch and non-starch polysaccharides such as β-glucan and arabinoxylans, making them an important fuel for the microbiota. Thus, WCGs may manipulate the ecophysiology of gut microbiota. In this review, the scientific evidence supporting the hypothesis that WCGs prevent MetS by modulating gut microbiota composition and functions are discussed, with focuses on cereal intake-related mechanisms by which gut microbiota contributes to human health and scientific evidences for the effects of WCGs on modulating gut microbiota. Once strong support for the association among WCGs, gut microbiota and host metabolic health can be demonstrated, particular cereals, their processing technologies, or cereal-based foods might be better utilized to prevent and possibly even treat metabolic disease.

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology

Commensal and beneficial microbes secrete myriad products which target the mammalian host and other microbes. These secreted substances aid in bacterial niche development, and select compounds beneficially modulate the host and promote health. Microbes produce unique compounds which can serve as signaling factors to the host, such as biogenic amine neuromodulators, or quorum-sensing molecules to facilitate inter-bacterial communication. Bacterial metabolites can also participate in functional enhancement of host metabolic capabilities, immunoregulation, and improvement of intestinal barrier function. Secreted products such as lactic acid, hydrogen peroxide, bacteriocins, and bacteriocin-like substances can also target the microbiome. Microbes differ greatly in their metabolic potential and subsequent host effects. As a result, knowledge about microbial metabolites will facilitate selection of next-generation probiotics and therapeutic compounds derived from the mammalian microbiome. In this article we describe prominent examples of microbial metabolites and their effects on microbial communities and the mammalian host.

Gut microbiome, metabolome, and allergic diseases

The number of patients with allergic and inflammatory disorders has been increasing during the past several decades. Accumulating evidence has refined our understanding of the relationship between allergic diseases and the gut microbiome. In addition, the gut microbiome is now known to produce both useful and harmful metabolites from dietary materials. These metabolites and bacterial components help to regulate host immune responses and potentially affect the development of allergic diseases. Here, we describe recent findings regarding the immunologic crosstalk between commensal bacteria and dietary components in the regulation of host immunity and the influence of this relationship on the development of allergic diseases.

Microbial Interactions and Interventions in Colorectal Cancer

Recently, several lines of evidence that indicate a strong link between the development of colorectal cancer (CRC) and aspects of the gut microbiota have become apparent. However, it remains unclear how changes in the gut microbiota might influence carcinogenesis or how regional organization of the gut might influence the microbiota. In this review, we discuss several leading theories that connect gut microbial dysbiosis with CRC and set this against a backdrop of what is known about proximal-distal gut physiology and the pathways of CRC development and progression. Finally, we discuss the potential for gut microbial modulation therapies, for example, probiotics, antibiotics, and others, to target and improve gut microbial dysbiosis as a strategy for the prevention or treatment of CRC.

Propionate metabolism and diversity of relevant functional genes by in silico analysis and detection in subsurface petroleum reservoirs

Propionate is a common metabolic intermediate occurring in environmental samples including petroleum reservoirs. Available microbial genomes were obtained from the NCBI database and analyzed in silico by hmmscan to check three metabolic pathways of propionate production in petroleum reservoir systems. The succinate pathway was the dominant one while the other two (lactate and 1,2-propanediol pathways) contributed less to the formation of propionate according to the Hidden Markov Model calculation. The mmdA gene encoding methylmalonyl-CoA decarboxylase was used as a biomarker gene to detect the diversity of microbes involved in the propionate formation in Jiangsu oil reservoirs. The mmdA gene clone library showed that microbes affiliated within the genus of Archaeoglobus, Thermococcus, Anaerobaculum, as well as more than ten other genera were the potential microorganisms involved in the production of propionate. Meanwhile, as the biomarker genes involved in the other two propionate-producing pathways, the functional genes of lcdA and pduP were tested with PCR amplification, but no positive results were observed in Jiangsu oil reservoirs.

A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline

The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.

How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers

The composition of the gut microbiota of mammals is greatly influenced by diet. Therefore, evaluation of different food ingredients that may promote changes in the gut microbiota composition is an attractive approach to treat microbiota disturbances. In this study, three dietary fibers, such as inulin (I, 10%), resistant starch (RS, 10%), and citrus pectin (3%), were employed as supplements to normal chow diet of adult male rats for 2 weeks. Fecal microbiota composition and corresponding metabolite profiles were assessed before and after prebiotics supplementation. A general increase in the Bacteroidetes phylum was detected with a concurrent reduction in Firmicutes, in particular for I and RS experiments, while additional changes in the microbiota composition were evident at lower taxonomic levels for all the three substrates. Such modifications in the microbiota composition were correlated with changes in metabolic profiles of animals, in particular changes in acetate and succinate levels. This study represents a first attempt to modulate selectively the abundance and/or metabolic activity of various members of the gut microbiota by means of dietary fiber.

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

BACKGROUND

The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.

METHODS

The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.

RESULTS

We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.

DISCUSSION

This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.

Regulation of inflammation by microbiota interactions with the host

The study of the intestinal microbiota has begun to shift from cataloging individual members of the commensal community to understanding their contributions to the physiology of the host organism in health and disease. Here, we review the effects of the microbiome on innate and adaptive immunological players from epithelial cells and antigen-presenting cells to innate lymphoid cells and regulatory T cells. We discuss recent studies that have identified diverse microbiota-derived bioactive molecules and their effects on inflammation within the intestine and distally at sites as anatomically remote as the brain. Finally, we highlight new insights into how the microbiome influences the host response to infection, vaccination and cancer, as well as susceptibility to autoimmune and neurodegenerative disorders.

Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle

The composition and activity of the microbiota in the human gastrointestinal tract are primarily shaped by nutrients derived from either food or the host. Bacteria colonizing the mucus layer have evolved to use mucin as a carbon and energy source. One of the members of the mucosa-associated microbiota is Akkermansia muciniphila, which is capable of producing an extensive repertoire of mucin-degrading enzymes. To further study the substrate utilization abilities of A. muciniphila, we constructed a genome-scale metabolic model to test amino acid auxotrophy, vitamin biosynthesis, and sugar-degrading capacities. The model-supported predictions were validated by in vitro experiments, which showed A. muciniphila to be able to utilize the mucin-derived monosaccharides fucose, galactose, and N-acetylglucosamine. Growth was also observed on N-acetylgalactosamine, even though the metabolic model did not predict this. The uptake of these sugars, as well as the nonmucin sugar glucose, was enhanced in the presence of mucin, indicating that additional mucin-derived components are needed for optimal growth. An analysis of whole-transcriptome sequencing (RNA-Seq) comparing the gene expression of A. muciniphila grown on mucin with that of the same bacterium grown on glucose confirmed the activity of the genes involved in mucin degradation and revealed most of these to be upregulated in the presence of mucin. The transcriptional response was confirmed by a proteome analysis, altogether revealing a hierarchy in the use of sugars and reflecting the adaptation of A. muciniphila to the mucosal environment. In conclusion, these findings provide molecular insights into the lifestyle of A. muciniphila and further confirm its role as a mucin specialist in the gut.IMPORTANCEAkkermansia muciniphila is among the most abundant mucosal bacteria in humans and in a wide range of other animals. Recently, A. muciniphila has attracted considerable attention because of its capacity to protect against diet-induced obesity in mouse models. However, the physiology of A. muciniphila has not been studied in detail. Hence, we constructed a genome-scale model and describe its validation by transcriptomic and proteomic approaches on bacterial cells grown on mucus and glucose, a nonmucus sugar. The results provide detailed molecular insight into the mucus-degrading lifestyle of A. muciniphila and further confirm the role of this mucin specialist in producing propionate and acetate under conditions of the intestinal tract.

Linseed Oil Supplementation of Lambs' Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure

Diet has been shown to have a significant impact on microbial community composition in the rumen and could potentially be used to manipulate rumen microbiome structure to achieve specific outcomes. There is some evidence that a window may exist in early life, while the microbiome is being established, where manipulation through diet could lead to long-lasting results. The aim of this study was to test the hypothesis that dietary supplementation in early life will have an effect on rumen microbial composition that will persist even once supplementation is ceased. Twenty-seven new-born lambs were allocated to one of three dietary treatments; a control group receiving standard lamb meal, a group receiving lamb meal supplemented with 40 g kg^-1 DM of linseed oil and a group receiving the supplement pre-weaning and standard lamb meal post-weaning. The supplement had no effect on average daily feed intake or average daily weight gain of lambs. Bacterial and archaeal community composition was significantly (p = 0.033 and 0.005, respectively) different in lambs fed linseed oil throughout the study compared to lambs on the control diet. Succinivibrionaceae, succinate producers, and Veillonellaceae, propionate producers, were in a higher relative abundance in the lambs fed linseed oil while Ruminococcaceae, a family linked with high CH₄ emitters, were in a higher relative abundance in the control group. The relative abundance of Methanobrevibacter was reduced in the lambs receiving linseed compared to those that didn’t. In contrast, the relative abundance of Methanosphaera was significantly higher in the animals receiving the supplement compared to animals receiving no supplement (40.82 and 26.67%, respectively). Furthermore, lambs fed linseed oil only in the pre-weaning period had a bacterial community composition significantly (p = 0.015) different to that of the control group, though archaeal diversity and community structure did not differ. Again, Succinivibrionaceae and Veillonellaceae were in a higher relative abundance in the group fed linseed oil pre-weaning while Ruminococcaceae were in a higher relative abundance in the control group. This study shows that lambs fed the dietary supplement short-term had a rumen microbiome that remained altered even after supplementation had ceased.

Alterations of the Gut Microbiome in Hypertension

Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner.

Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing.

Results: Hypertension implicated a remarkable gut dysbiosis with significant reduction in within-sample diversity and shift in microbial composition. Metagenome-wide association study (MGWAS) revealed 53,953 microbial genes that differ in distribution between the patients and healthy controls (false discovery rate, 0.05) and can be grouped into 68 clusters representing bacterial species. Opportunistic pathogenic taxa, such as, Klebsiella spp., Streptococcus spp., and Parabacteroides merdae were frequently distributed in hypertensive gut microbiome, whereas the short-chain fatty acid producer, such as, Roseburia spp. and Faecalibacterium prausnitzii, were higher in controls. The number of hypertension-associated species also showed stronger correlation to the severity of disease. Functionally, the hypertensive gut microbiome exhibited higher membrane transport, lipopolysaccharide biosynthesis and steroid degradation, while in controls the metabolism of amino acid, cofactors and vitamins was found to be higher. We further provided the microbial markers for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.78, demonstrating the potential of gut microbiota in prediction of hypertension.

Conclusion: These findings represent specific alterations in microbial diversity, genes, species and functions of the hypertensive gut microbiome. Further studies on the causality relationship between hypertension and gut microbiota will offer new prospects for treating and preventing the hypertension and its associated diseases.

Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles

Recently, a "human gut microbial gene catalogue," which ranks the dominance of microbe genus/species in human fecal samples, was published. Most of the bacteria ranked in the catalog are currently publicly available; however, the growth media recommended by the distributors vary among species, hampering physiological comparisons among the bacteria. To address this problem, we evaluated Gifu anaerobic medium (GAM) as a standard medium. Forty-four publicly available species of the top 56 species listed in the "human gut microbial gene catalogue" were cultured in GAM, and out of these, 32 (72%) were successfully cultured. Short-chain fatty acids from the bacterial culture supernatants were then quantified, and bacterial metabolic pathways were predicted based on in silico genomic sequence analysis. Our system provides a useful platform for assessing growth properties and analyzing metabolites of dominant human gut bacteria grown in GAM and supplemented with compounds of interest.

Beef, Chicken, and Soy Proteins in Diets Induce Different Gut Microbiota and Metabolites in Rats

Previous studies have paid much attention to the associations between high intake of meat and host health. Our previous study showed that the intake of meat proteins can maintain a more balanced composition of gut bacteria as compared to soy protein diet. However, the associations between dietary protein source, gut bacteria, and host health were still unclear. In this study, we collected colonic contents from the growing rats fed with casein, beef, chicken or soy proteins for 90 days, and analyzed the compositions of gut microbiota and metabolites. Compared to the casein group (control), the chicken protein group showed the highest relative abundance of Lactobacillus and the highest levels of organic acids, including lactate, which can in turn promote the growth of Lactobacillus. The soy protein group had the highest relative abundance of Ruminococcus but the lowest relative abundance of Lactobacillus. Long-term intake of soy protein led to the up-regulation of transcription factor CD14 receptor and lipopolysaccharide-binding protein (LBP) in liver, an indicator for elevated bacterial endotoxins. In addition, the intake of soy protein also increased the levels of glutathione S-transferases in liver, which implicates elevated defense and stress responses. These results confirmed that meat protein intake may maintain a more balanced composition of gut bacteria and reduce the antigen load and inflammatory response from gut bacteria to the host.

Structure of protein emulsion in food impacts intestinal microbiota, caecal luminal content composition and distal intestine characteristics in rats

SCOPE

Few studies have evaluated in vivo the impact of food structure on digestion, absorption of nutrients and on microbiota composition and metabolism. In this study we evaluated in rat the impact of two structures of protein emulsion in food on gut microbiota, luminal content composition, and intestinal characteristics.

METHODS AND RESULTS

Rats received for 3 weeks two diets of identical composition but based on lipid-protein matrices of liquid fine (LFE) or gelled coarse (GCE) emulsion. LFE diet led to higher abundance, when compared to the GCE, of Lactobacillaceae (Lactobacillus reuteri) in the ileum, higher β-diversity of the caecum mucus-associated bacteria. In contrast, the LFE diet led to a decrease in Akkermansia municiphila in the caecum. This coincided with heavier caecum content and higher amount of isovalerate in the LFE group. LFE diet induced an increased expression of (i) amino acid transporters in the ileum (ii) glucagon in the caecum, together with an elevated level of GLP-1 in portal plasma. However, these intestinal effects were not associated with modification of food intake or body weight gain.

CONCLUSION

Overall, the structure of protein emulsion in food affects the expression of amino acid transporters and gut peptides concomitantly with modification of the gut microbiota composition and activity. Our data suggest that these effects of the emulsion structure are the result of a modification of protein digestion properties.