Effects of Adding Lean Red Meat to a U.S.-Style Healthy Vegetarian Dietary Pattern on Gut Microbiota and Cardiovascular Risk Factors in Young Adults: a Crossover Randomized Controlled Trial.

BACKGROUND: Limited research evidence exists on the effects of red meat on gut microbiota in human adults. OBJECTIVE: We aim to assess the effects of consuming a Healthy U.S.-Style Dietary Pattern (HDP), without or with unprocessed or processed lean red meats, on gut microbiota and fecal short-chain fatty acid (SCFA) levels in healthy young adults. Secondary outcomes are cardiovascular disease risk factors. METHODS: We conducted a randomized, controlled, crossover trial with 3 3-wk dietary interventions, each separated by a 5-wk washout period with habitual dietary intake. Nineteen participants (8 females, age 26 ± 4 y old, BMI 23 ± 3 kg/m2) consumed 3 study diets in random order: 1) healthy lacto-ovo vegetarian diet (LOV); 2) LOV plus 3 ounces/d of cooked unprocessed lean red meat (URM); and 3) LOV plus 3 ounces/d of cooked processed lean red meat (PRM). Fecal and fasting blood samples were collected before and during the last 2 wk of each intervention. We measured fecal bacterial community structure using 16S rRNA amplicon sequencing (V4 region, primers 515F-806R). Community diversity, structure, and taxonomic composition were computed using Mothur v.1.44.3. RESULTS: The addition of unprocessed or processed lean red meats to a LOV HDP did not influence short-term changes in bacterial taxonomic composition. Independent of red meat intake, the HDP led to changes in 23 bacteria; reductions in serum total cholesterol (TC) and LDL-C concentrations; but no changes in fecal SCFA, serum triglycerides, HDL-C concentrations, TC/HDL-C ratio, or blood pressures. With data from all 3 diet interventions combined, changes in some bacteria were associated with improvements in TC, LDL-C, triglycerides, and HDL-C concentrations, and TC/HDL-C ratio. CONCLUSIONS: Healthy young adults who adopt an HDP that may be vegetarian or omnivorous, including lean red meat, experience short-term changes in gut microbial composition, which associate with improvements in multiple lipid-related cardiovascular risk factors. NCT03885544, https://clinicaltrials.gov/ct2/show/NCT03885544?cond=NCT03885544&draw=2&rank=1.

Development of a novel model of cholecystectomy in subsequently ovariectomized mice and characterization of metabolic and gastrointestinal phenotypes: a pilot study.

BACKGROUND: Cholecystectomy (XGB) is the most common abdominal surgery performed in the United States and is associated with an increased post-surgery incidence of metabolic and gastrointestinal (GI) diseases. Two main risk factors for XGB are sex (female) and age (40-50 yr), corresponding with onset of menopause. Post-menopausal estrogen loss alone facilitates metabolic dysfunction, but the effects of XGB on metabolic and GI health have yet to be investigated in this population. Study objectives were to (1) identify possible short-term effects of XGB and (2) develop a novel murine model of XGB in human menopause via subsequent ovariectomy (OVX) and assess longitudinal effects of OVX on metabolism, GI physiology, and GI microbiota in XGB mice. METHODS: Female C57BL/6 mice were utilized in two parallel studies (S1&S2). In S1, XGB mice were compared to a non-XGB baseline group after six wk. In S2, mice were XGB at wk0, either sham (SHM) or OVX at wk6, and sacrificed at wk12, wk18, and wk24. Body composition assessment and fresh fecal collections were conducted periodically. Serum and tissues were collected at sacrifice for metabolic and GI health endpoints. RESULTS: Compared to baseline, XGB increased hepatic CYP7A1 and decreased HMGCR relative expression, but did not influence BW, fat mass, or hepatic triglycerides after six wk. In S2, XGB/OVX mice had greater BW and fat mass than XGB/SHM. Cecal microbiota alpha diversity metrics were lower in XGB/OVX mice at wk24 compared the XGB/SHM. No consistent longitudinal patterns in fasting serum lipids, fecal microbial diversity, and GI gene expression were observed between S2 groups. CONCLUSIONS: In addition to developing a novel, clinically-representative model of XGB and subsequent OVX, our results suggest that OVX resulted in the expected phenotype to some extent, but that XGB may modify or mask some responses and requires further investigation.

Effect of Dietary Inulin Supplementation on the Gut Microbiota Composition and Derived Metabolites of Individuals Undergoing Hemodialysis: A Pilot Study.

OBJECTIVE: The prebiotic fiber inulin has been studied in individuals undergoing hemodialysis (HD) due to its ability to reduce gut microbiota-derived uremic toxins. However, studies examining the effects of inulin on the gut microbiota and derived metabolites are limited in these patients. We aimed to assess the impact of a 4-week supplementation of inulin on the gut microbiota composition and microbial metabolites of patients on HD. DESIGN AND METHODS: In a randomized, double-blind, placebo-controlled, crossover study, twelve HD patients (55 ± 10 y, 50% male, 58% Black American, BMI 31.6 ± 8.9 kg/m2, 33% diabetes mellitus) were randomized to consume inulin [10 g/d for females; 15 g/d for males] or maltodextrin [6 g/d for females; 9 g/d for males] for 4 weeks, with a 4-week washout period. We assessed the fecal microbiota composition, fecal metabolites (short-chain fatty acids (SCFA), phenols, and indoles), and plasma indoxyl sulfate and p-cresyl sulfate. RESULTS: At baseline, factors that explained the gut microbiota variability included BMI category and type of phosphate binder prescribed. Inulin increased the relative abundance of the phylum Verrucomicrobia and its genus Akkermansia (P interaction = 0.045). Inulin and maltodextrin resulted in an increased relative abundance of the phylum Bacteroidetes and its genus Bacteroides (P time = 0.04 and 0.03, respectively). Both treatments increased the fecal acetate and propionate (P time = 0.032 and 0.027, respectively), and there was a trend toward increased fecal butyrate (P time = 0.06). Inulin did not reduce fecal p-cresol or indoles, or plasma concentrations of p-cresyl sulfate or indoxyl sulfate. CONCLUSIONS: A 4-week supplementation of inulin did not lead to major shifts in the fecal microbiota and gut microbiota-derived metabolites. This may be due to high variability among participants and an unexpected increase in fecal excretion of SCFA with maltodextrin. Larger studies are needed to determine the effects of prebiotic fibers on the gut microbiota and clinical outcomes to justify their use in patients on HD.

Integrated Label-Free and 10-Plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome.

Gut microbiota can regulate host physiological and pathological status through gut-brain communications or pathways. However, the impact of the gut microbiome on neuropeptides and proteins involved in regulating brain functions and behaviors is still not clearly understood. To address the problem, integrated label-free and 10-plex DiLeu isobaric tag-based quantitative methods were implemented to compare the profiling of neuropeptides and proteins in the hypothalamus of germ-free (GF)- vs conventionally raised (ConvR)-mice. A total of 2943 endogenous peptides from 63 neuropeptide precursors and 3971 proteins in the mouse hypothalamus were identified. Among these 368 significantly changed peptides (fold changes over 1.5 and a p-value of <0.05), 73.6% of the peptides showed higher levels in GF-mice than in ConvR-mice, and 26.4% of the peptides had higher levels in ConvR-mice than in GF-mice. These peptides were mainly from secretogranin-2, phosphatidylethanolamine-binding protein-1, ProSAAS, and proenkephalin-A. A quantitative proteomic analysis employing DiLeu isobaric tags revealed that 282 proteins were significantly up- or down-regulated (fold changes over 1.2 and a p-value of <0.05) among the 3277 quantified proteins. These neuropeptides and proteins were mainly involved in regulating behaviors, transmitter release, signaling pathways, and synapses. Interestingly, pathways including long-term potentiation, long-term depression, and circadian entrainment were involved. In the present study, a combined label-free and 10-plex DiLeu-based quantitative method enabled a comprehensive profiling of gut microbiome-induced dynamic changes of neuropeptides and proteins in the hypothalamus, suggesting that the gut microbiome might mediate a range of behavioral changes, brain development, and learning and memory through these neuropeptides and proteins.

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs.

Because obesity is associated with many co-morbidities, including diabetes mellitus, this study evaluated the second-meal effect of a commercial prebiotic, inulin-type fructans, and the effects of the prebiotic on faecal microbiota, metabolites and bile acids (BA). Nine overweight beagles were used in a replicated 3×3 Latin square design to test a non-prebiotic control (cellulose) against a low (equivalent to 0·5 % diet) and high dose (equivalent to 1·0 % diet) of prebiotic over 14-d treatments. All dogs were fed the same diet twice daily, with treatments provided orally via gelatin capsules before meals. On days 13 or 14 of each period, fresh faecal samples were collected, dogs were fed at 08.00 hours and then challenged with 1 g/kg body weight of maltodextrin in place of the 16.00 hours meal. Repeated blood samples were analysed for glucose and hormone concentrations to determine postprandial incremental AUC (IAUC) data. Baseline glucose, insulin and active glucagon-like peptide-1 levels were similar between all groups (P>0·10). Glucose and insulin IAUC after glucose challenge appeared lower following the high dose, but did not reach statistical relevance. Prebiotic intervention resulted in an increase in relative abundance of some Firmicutes and a decrease in the relative abundance of some Proteobacteria. Individual and total faecal SCFA were significantly increased (P<0·05) following prebiotic supplementation. Total concentration of excreted faecal BA tended to increase in dogs fed the prebiotic (P=0·06). Our results indicate that higher doses of inulin-type prebiotics may serve as modulators of gut microbiota, metabolites and BA pool in overweight dogs.

Race-dependent association of sulfidogenic bacteria with colorectal cancer.

OBJECTIVE: Colorectal cancer (CRC) incidence is higher in African Americans (AAs) compared with non-Hispanic whites (NHWs). A diet high in animal protein and fat is an environmental risk factor for CRC development. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC. Hydrogen sulfide, produced by autochthonous sulfidogenic bacteria, triggers proinflammatory pathways and hyperproliferation, and is genotoxic. We hypothesised that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AA and NHW. DESIGN: Colonic biopsies from uninvolved or healthy mucosa from CRC cases and tumour-free controls were collected prospectively from five medical centres in Chicago for association studies. Sulfidogenic bacterial abundance in uninvolved colonic mucosa of AA and NHW CRC cases was compared with normal mucosa of AA and NHW controls. In addition, 16S rDNA sequencing was performed in AA cases and controls. Correlations were examined among bacterial targets, race, disease status and dietary intake. RESULTS: AAs harboured a greater abundance of sulfidogenic bacteria compared with NHWs regardless of disease status. Bilophila wadsworthia-specific dsrA was more abundant in AA cases than controls. Linear discriminant analysis of 16S rRNA gene sequences revealed five sulfidogenic genera that were more abundant in AA cases. Fat and protein intake and daily servings of meat were significantly higher in AAs compared with NHWs, and multiple dietary components correlated with a higher abundance of sulfidogenic bacteria. CONCLUSIONS: These results implicate sulfidogenic bacteria as a potential environmental risk factor contributing to CRC development in AAs.

A Gnotobiotic Mouse Model with Divergent Equol-Producing Phenotypes: Potential for Determining Microbial-Driven Health Impacts of Soy Isoflavone Daidzein.

The implications of soy consumption on human health have been a subject of debate, largely due to the mixed evidence regarding its benefits and potential risks. The variability in responses to soy has been partly attributed to differences in the metabolism of soy isoflavones, compounds with structural similarities to estrogen. Approximately one-third of humans possess gut bacteria capable of converting soy isoflavone daidzein into equol, a metabolite produced exclusively by gut microbiota with significant estrogenic potency. In contrast, lab-raised rodents are efficient equol producers, except for those raised germ-free. This discrepancy raises concerns about the applicability of traditional rodent models to humans. Herein, we designed a gnotobiotic mouse model to differentiate between equol producers and non-producers by introducing synthetic bacterial communities with and without the equol-producing capacity into female and male germ-free mice. These gnotobiotic mice display equol-producing phenotypes consistent with the capacity of the gut microbiota received. Our findings confirm the model's efficacy in mimicking human equol production capacity, offering a promising tool for future studies to explore the relationship between endogenous equol production and health outcomes like cardiometabolic health and fertility. This approach aims to refine dietary guidelines by considering individual microbiome differences.

Effects of xylo-oligosaccharide on gut microbiota, brain protein expression, and lipid profile induced by high-fat diet.

Midlife overweight and obesity are risk factors of cognitive decline and Alzheimer' s disease (AD) in late life. In addition to increasing risk of obesity and cognitive dysfunction, diets rich in fats also contributes to an imbalance of gut microbiota. Xylo-oligosaccharides (XOS) are a kind of prebiotic with several biological advantages, and can selectively promote the growth of beneficial microorganisms in the gut. To explore whether XOS can alleviate cognitive decline induced by high-fat diet (HFD) through improving gut microbiota composition, mice were fed with normal control or 60% HFD for 9 weeks to induce obesity. After that, mice were supplemented with XOS (30 g or 60 g/kg-diet) or without, respectively, for 12 weeks. The results showed that XOS inhibited weight gain, decreased epidydimal fat weight, and improved fasting blood sugar and blood lipids in mice. Additionally, XOS elevated spatial learning and memory function, decreased amyloid plaques accumulation, increased brain-derived neurotrophic factor levels, and improved neuroinflammation status in hippocampus. Changes in glycerolipids metabolism-associated lipid compounds caused by HFD in hippocampus were reversed after XOS intervention. On the other hand, after XOS intervention, increase in immune-mediated bacteria, Faecalibacterium was observed. In conclusion, XOS improved gut dysbiosis and ameliorated spatial learning and memory dysfunction caused by HFD by decreasing cognitive decline-associated biomarkers and changing lipid composition in hippocampus.

Gut microbiome responds to alteration in female sex hormone status and exacerbates metabolic dysfunction.

Women are at significantly greater risk of metabolic dysfunction after menopause, which subsequently leads to numerous chronic illnesses. The gut microbiome is associated with obesity and metabolic dysfunction, but its interaction with female sex hormone status and the resulting impact on host metabolism remains unclear. Herein, we characterized inflammatory and metabolic phenotypes as well as the gut microbiome associated with ovariectomy and high-fat diet feeding, compared to gonadal intact and low-fat diet controls. We then performed fecal microbiota transplantation (FMT) using gnotobiotic mice to identify the impact of ovariectomy-associated gut microbiome on inflammatory and metabolic outcomes. We demonstrated that ovariectomy led to greater gastrointestinal permeability and inflammation of the gut and metabolic organs, and that a high-fat diet exacerbated these phenotypes. Ovariectomy also led to alteration of the gut microbiome, including greater fecal ß-glucuronidase activity. However, differential changes in the gut microbiome only occurred when fed a low-fat diet, not the high-fat diet. Gnotobiotic mice that received the gut microbiome from ovariectomized mice fed the low-fat diet had greater weight gain and hepatic gene expression related to metabolic dysfunction and inflammation than those that received intact sham control-associated microbiome. These results indicate that the gut microbiome responds to alterations in female sex hormone status and contributes to metabolic dysfunction. Identifying and developing gut microbiome-targeted modulators to regulate sex hormones may be useful therapeutically in remediating menopause-related diseases.

Gut microbiota and diet matrix modulate the effects of the flavonoid quercetin on atherosclerosis.

Gut bacterial metabolism of dietary flavonoids results in the production of a variety of phenolic acids, whose contributions to health remain poorly understood. Here, we show that supplementation with the commonly consumed flavonoid quercetin impacted gut microbiome composition and resulted in a significant reduction in atherosclerosis burden in conventionally-raised (ConvR) Apolipoprotein E (ApoE) knockout (KO) mice fed a high-MAC (microbiota-accessible carbohydrates) diet. However, this effect was not observed in animals consuming a defined diet containing low levels of MAC. Furthermore, we found that the effect of quercetin on atherosclerosis required gut microbes, as supplementation of this flavonoid to germ-free (GF) ApoE KO mice consuming the high-MAC diet did not affect the development of atherosclerosis. Metabolomic analysis revealed that consumption of quercetin significantly increased plasma levels of benzoylglutamic acid and protocatechuic acid in ConvR mice exposed to the high-MAC diet, while these increases were not observed in GF mice or conventional animals consuming the low-MAC diet supplemented with the flavonoid. Furthermore, levels of these metabolites were negatively associated with atherosclerosis burden. Altogether, these results suggest that the beneficial effects of quercetin on atherosclerosis are influenced by gut microbes and dietary MAC.

Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities.

Dietary fiber consumption has been linked with improved cardiometabolic health, however, human studies have reported large interindividual variations in the observed benefits. We tested whether the effects of dietary fiber on atherosclerosis are influenced by the gut microbiome. We colonized germ-free ApoE-/- mice with fecal samples from three human donors (DonA, DonB, and DonC) and fed them diets supplemented with either a mix of 5 fermentable fibers (FF) or non-fermentable cellulose control (CC) diet. We found that DonA-colonized mice had reduced atherosclerosis burden with FF feeding compared to their CC-fed counterparts, whereas the type of fiber did not affect atherosclerosis in mice colonized with microbiota from the other donors. Microbial shifts associated with FF feeding in DonA mice were characterized by higher relative abundances of butyrate-producing taxa, higher butyrate levels, and enrichment of genes involved in synthesis of B vitamins. Our results suggest that atheroprotection in response to FF is not universal and is influenced by the gut microbiome.

Meat Consumption and Gut Microbiota: a Scoping Review of Literature and Systematic Review of Randomized Controlled Trials in Adults.

Emerging research indicates the importance of gut microbiota in mediating the relationship between meat intake and human health outcomes. We aimed to assess the state of available scientific literature on meat intake and gut microbiota in humans (PROSPERO, International Prospective Register of Systematic Reviews, CRD42020135649). We first conducted a scoping review to identify observational and interventional studies on this topic. Searches were performed for English language articles using PubMed, Cochrane Library, Scopus, and CINAHL (Cumulated Index to Nursing and Allied Health Literature) databases from inception to August 2021 and using keywords related to meat (inclusive of mammalian, avian, and aquatic subtypes) and gut microbiota. Of 14,680 records, 85 eligible articles were included in the scoping review, comprising 57 observational and 28 interventional studies. One prospective observational study and 13 randomized controlled trials (RCTs) were identified in adults without diagnosed disease. We included the 13 RCTs, comprising 18 comparisons, in the systematic review to assess the effects of higher and lower intakes of total meat and meat subtypes on the gut microbiota composition. The bacterial composition was differentially affected by consuming diets with and without meat or with varied meat subtypes. For example, higher meat intake tended to decrease population sizes of genera Anerostipes and Faecalibacterium, but it increased the population size of Roseburia across studies. However, the magnitude and directionality of most microbial responses varied, with inconsistent patterns of responses across studies. The data were insufficient for comparison within or between meat subtypes. The paucity of research, especially among meat subtypes, and heterogeneity of findings underscore the need for more well-designed prospective studies and full-feeding RCTs to address the relationships between and effects of consuming total meat and meat subtypes on gut microbiota, respectively.

Maximizing the Estrogenic Potential of Soy Isoflavones through the Gut Microbiome: Implication for Cardiometabolic Health in Postmenopausal Women.

Soy isoflavones have been suggested as an alternative treatment for managing postmenopausal symptoms and promoting long-term health due to their structural similarity to mammalian estrogen and ability to bind to estrogen receptors. Among all soy isoflavones and their metabolites, (S)-equol is known for having the strongest estrogenic activity. Equol is a metabolite of the soy isoflavone daidzein produced through intestinal bacterial metabolism. However, more than half of the human population is not able to produce equol due to the lack of equol-producing bacteria in their gastrointestinal tract. The interpersonal variations in the gut microbiome complicate the interpretation of data collected from humans. Furthermore, because rodents are efficient equol-producers, translatability between rodent models and humans is challenging. Herein, we first summarized the current knowledge of the microbial conversion of daidzein to equol, its relation to health, and proposed the need for developing model systems by which equol production can be manipulated while controlling other known confounding factors. Determining the necessity of equol-producing capacity within a gut microbial community when consuming soy as a functional ingredient, and identifying strategies to maximize equol production by modulating the gut microbiome, may provide future therapeutic approaches to improve the health of postmenopausal women.

Quercetin Increases Mitochondrial Biogenesis and Reduces Free Radicals in Neuronal SH-SY5Y Cells.

Alzheimer's disease (AD) is a common neurodegenerative disorder that causes dementia and affects millions of people worldwide. The mechanism underlying AD is unclear; however, oxidative stress and mitochondrial biogenesis have been reported to be involved in AD progression. Previous research has also reported the reduction in mitochondrial biogenesis in the brains of patients with AD. Quercetin (QE), a type of polyphenol, has been found to be capable of increasing mitochondrial biogenesis in the body. Accordingly, we explored whether QE could reduce amyloid beta (Aß) accumulation caused by hydrogen peroxide (H2O2)-induced oxidative stress in SH-SY5Y cells. Our results revealed that QE stimulated the expression of mitochondrial-related proteins such as SIRT1, PGC-1α, and TFAM and subsequently activated mitochondrial biogenesis. Additionally, QE increased ADAM10 expression but reduced H2O2-induced reactive oxygen species production, apoptosis, ß-site amyloid precursor protein cleaving enzyme 1 expression, and Aß accumulation in the SH-SY5Y cells. These findings indicate that QE can effectively elevate mitochondrial biogenesis-related proteins and reduce the damage caused by oxidative stress, making it a promising option for protecting neuronal cells.

Impact of administration route on nanocarrier biodistribution in a murine colitis model.

The incidence of inflammatory bowel disease (IBD) is increasing worldwide. Although current diagnostic and disease monitoring tests for IBD sensitively detect gut inflammation, they lack the molecular and cellular specificity of positron emission tomography (PET). In this proof-of-concept study, we use a radiolabeled macrophage-targeted nanocarrier probe (64Cu-NOTA-D500) administered by oral, enema, and intraperitoneal routes to evaluate the delivery route dependence of biodistribution across healthy and diseased tissues in a murine model of dextran sodium sulfate (DSS)-induced colitis. High inter-subject variability of probe uptake in intestinal tissue was reduced by normalization to uptake in liver or total intestines. Differences in normalized uptake between healthy and DSS colitis animal intestines were highest for oral and IP routes. Differences in absolute liver uptake reflected a possible secondary diagnostic metric of IBD pathology. These results should inform the preclinical development of inflammation-targeted contrast agents for IBD and related gut disorders to improve diagnostic accuracy.

Graded dietary resistant starch concentrations on apparent total tract macronutrient digestibility and fecal fermentative end products and microbial populations of healthy adult dogs.

Resistant starch (RS) is fermentable by gut microbiota and effectively modulates fecal short-chain fatty acid concentrations in pigs, mice, and humans. RS may have similar beneficial effects on the canine gut but has not been well studied. The objective of this study was to evaluate the effects of 0%, 1%, 2%, 3%, and 4% dietary RS (Hi-maize 260) on apparent total tract macronutrient digestibility, fecal characteristics, fermentative end-product concentrations, and microbiota of healthy adult dogs. An incomplete 5 × 5 Latin square design with seven dogs and five experimental periods was used, with each treatment period lasting 21 d (days 0 to 17 adaptation; days 18 to 21 fresh and total fecal collection) and each dog serving as its own control. Seven dogs (mean age = 5.3 yr; mean body weight = 20 kg) were randomly allotted to one of five treatments formulated to be iso-energetic and consisting of graded amounts of 100% amylopectin cornstarch, RS, and cellulose and fed as a top dressing on the food each day. All dogs were fed the same amount of a basal diet throughout the study, and fresh water was offered ad libitum. The basal diet contained 6.25% RS (dry matter [DM] basis), contributing approximately 18.3 g of RS/d based on their daily food intake (292.5 g DM/d). Data were evaluated for linear and quadratic effects using SAS. The treatments included 0%, 1%, 2%, 3%, and 4% of an additional RS source. Because Hi-maize 260 is approximately 40% digestible and 60% indigestible starch, the dogs received the following amounts of RS daily: 0% = 18.3 g (18.3 + 0 g), 1% = 20.1 g (18.3 + 1.8 g), 2% = 21.9 g (18.3 + 3.6 g), 3% = 23.7 g (18.3 + 5.4 g), and 4% = 25.5 g (18.3 + 7.2 g). Apparent total tract DM, organic matter, crude protein, fat, and gross energy digestibilities and fecal pH were linearly decreased (P < 0.05) with increased RS consumption. Fecal output was linearly increased (P < 0.05) with increased RS consumption. Fecal scores and fecal fermentative end-product concentrations were not affected by RS consumption. Although most of the fecal microbial taxa were not altered, Faecalibacterium were increased (P < 0.05) with increased RS consumption. The decrease in fecal pH and increase in fecal Faecalibacterium would be viewed as being beneficial to gastrointestinal health. Although our results seem to indicate that RS is poorly and/or slowly fermentable in dogs, the lack of observed change may have been due to the rather high level of RS contained in the basal diet.

The Gut Microbiota: A Promising Target in the Relation between Complementary Feeding and Child Undernutrition.

Child undernutrition is a major public health challenge that is persistent and disproportionately prevalent in low- and middle-income countries. Undernourished children face adverse health, economic, and social consequences that can be intergenerational. The first 1000 days of life, from conception until the child's second birthday, constitute the period of greatest vulnerability to undernutrition. The transition process from milk-based diets to solid, semi-solid, and soft food and liquids other than milk, referred to as complementary feeding (CF), occurs between the age of 6 mo and 2 y. CF practices that do not meet the WHO's guiding principles and are lacking in both quality and quantity increase susceptibility to undernutrition, restrict growth, and jeopardize child development and survival. The gut microbiota develops toward an adult-like configuration within the first 2-3 y of life. Recent studies suggest that significant changes in the gut microbial composition and functional capacity occur during the CF period, but these studies were conducted in high-income countries. Research in low- and middle-income countries, on the other hand, has implicated a disrupted gut microbiota in child undernutrition, and animal experiments reveal the potential for a causal relation. Given the growing body of evidence for a plausible role of the gut microbiota in the link between CF and undernutrition, microbiota-targeted complementary food may be a promising treatment modality for undernutrition management. The aims of this paper are to review the evidence for the relation between CF and undernutrition and to highlight the potential of the gut microbiota to be a promising target in this relation. Our summary of the current state of the knowledge in this area provides a foundation for future research and helps inform the design of interventions targeting the gut microbiota to combat child undernutrition and promote healthy growth.

Extraction optimization for combined metabolomics, peptidomics, and proteomics analysis of gut microbiota samples.

Multiomic studies are increasingly performed to gain a deeper understanding of molecular processes occurring in a biological system, such as the complex microbial communities (i.e., microbiota) that reside the distal gut. While a combination of metabolomics and proteomics is more commonly used, multiomics studies including peptidomcis characterization are less frequently undertaken. Here, we investigated three different extraction methods, chosen for their previous use in extracting metabolites, peptides, and proteins, and compared their ability to perform metabolomic, peptidomic, and proteomic analysis of mouse cecum content. The methanol/chloroform/water extraction performed the best for metabolomic and peptidomic analysis as it detected the largest number of small molecules and identified the largest number of peptides, but the acidified methanol extraction performed best for proteomics analysis as it had the highest number of protein identifications. The methanol/chloroform/water extraction was further analyzed by identifying metabolites with tandem mass spectrometry (MS/MS) analysis and by gene ontology analysis for the peptide and protein results to provide a multiomics analysis of the gut microbiota.

Gut microbiome variation modulates the effects of dietary fiber on host metabolism.

BACKGROUND: There is general consensus that consumption of dietary fermentable fiber improves cardiometabolic health, in part by promoting mutualistic microbes and by increasing production of beneficial metabolites in the distal gut. However, human studies have reported variations in the observed benefits among individuals consuming the same fiber. Several factors likely contribute to this variation, including host genetic and gut microbial differences. We hypothesized that gut microbial metabolism of dietary fiber represents an important and differential factor that modulates how dietary fiber impacts the host. RESULTS: We examined genetically identical gnotobiotic mice harboring two distinct complex gut microbial communities and exposed to four isocaloric diets, each containing different fibers: (i) cellulose, (ii) inulin, (iii) pectin, (iv) a mix of 5 fermentable fibers (assorted fiber). Gut microbiome analysis showed that each transplanted community preserved a core of common taxa across diets that differentiated it from the other community, but there were variations in richness and bacterial taxa abundance within each community among the different diet treatments. Host epigenetic, transcriptional, and metabolomic analyses revealed diet-directed differences between animals colonized with the two communities, including variation in amino acids and lipid pathways that were associated with divergent health outcomes. CONCLUSION: This study demonstrates that interindividual variation in the gut microbiome is causally linked to differential effects of dietary fiber on host metabolic phenotypes and suggests that a one-fits-all fiber supplementation approach to promote health is unlikely to elicit consistent effects across individuals. Overall, the presented results underscore the importance of microbe-diet interactions on host metabolism and suggest that gut microbes modulate dietary fiber efficacy. Video abstract.

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet.

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600-1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.