Changes of Mouse Gut Microbiota Diversity and Composition by Modulating Dietary Protein and Carbohydrate Contents: A Pilot Study

Dietary Milk or Isolated Legume Proteins Modulate Intestinal Microbiota Composition in Rats

Shifts toward increased proteolytic fermentation, such as, for example, in athlete and high-protein weight loss diets, may alter the relative abundance of microbial species in the gut and generate bioactive, potentially deleterious metabolic products. In the current investigation, intestinal (caecal) microbiota composition was studied in rats fed diets differing only in their constituent proteins: milk (casein (CAS), lactalbumin (LA)) or legume (Cicer arietinum, Lupinus angustifolius) protein isolates (chickpea protein isolate (CPI), lupin protein isolate (LI)). ANOSIM and Discriminant Analysis showed significant (p < 0.05) differences at both family and genus levels in both microbiota composition and functionality as a consequence of feeding the different proteins. Differences were also significant (p < 0.05) for predicted functionality parameters as determined by PICRUSt analysis. LA induced a generally healthier microbiota composition than CAS, and higher amounts of Methanobrevibacter spp. and Methanogenic_PWY were found in the LI group. LEfSe analysis of bacterial composition and functional activities revealed a number of groups/functions able to explain the different effects found with milk and legume protein isolates. In conclusion, the mostly beneficial modulation of intestinal microbiota generally found with legume-based diets is likely to be due, at least in part, to their constituent proteins.

Faecal metabolome responses to an altered dietary protein:carbohydrate ratio in adult dogs

High-protein diets may aid weight loss and weight maintenance programs in both humans and dogs, although the effect of dietary protein levels on gut metabolism and functionality has not been studied in depth. The current study aimed to investigate the effect of an altered dietary protein:carbohydrate ratio on gut function in adult dogs by means of faecal metabolomic fingerprinting. More specifically, functional metabolic differences in dogs fed a high-protein/low-carbohydrate (HPLC) vs. low-protein/high-carbohydrate (LPHC) diet were studied by equally allocating twelve clinically healthy (6 lean and 6 obese) Beagles into two groups in a cross-over design, with each group receiving two isocaloric diets for four weeks. The faecal metabolome revealed that different protein:carbohydrate ratio can influence host and/or gut microbiome metabolism and function, while no effect was observed on the body condition. Targeted analysis demonstrated that the HPLC diet significantly increased the concentration of indole, spermidine, and pipecolinic acid and decreased the concentration of azelaic acid, D-fructose, mannose, and galactose (p < 0.05). Multivariate modelling (OPLS-DA) of the untargeted faecal metabolome revealed distinctly different metabolomic profiles following the HPLC vs. LPHC diet, with 18 altered pathways. The HPLC diet influenced amino acid and lipid metabolism, potentially promoting weight loss and immune function, whereas the LPHC diet affected carbohydrate fermentation and may promote anti-oxidative function.

Effect of Consumption of Animal Products on the Gut Microbiome Composition and Gut Health

The gut microbiome is critical in human health, and various dietary factors influence its composition and function. Among these factors, animal products, such as meat, dairy, and eggs, represent crucial sources of essential nutrients for the gut microbiome. However, the correlation and characteristics of livestock consumption with the gut microbiome remain poorly understood. This review aimed to delineate the distinct effects of meat, dairy, and egg products on gut microbiome composition and function. Based on the previous reports, the impact of red meat, white meat, and processed meat consumption on the gut microbiome differs from that of milk, yogurt, cheese, or egg products. In particular, we have focused on animal-originated proteins, a significant nutrient in each livestock product, and revealed that the major proteins in each food elicit diverse effects on the gut microbiome. Collectively, this review highlights the need for further insights into the interactions and mechanisms underlying the impact of animal products on the gut microbiome. A deeper understanding of these interactions would be beneficial in elucidating the development of dietary interventions to prevent and treat diseases linked to the gut microbiome.

Dietary Protein, Chronic Salt-Sensitive Hypertension, and Kidney Damage

It has been estimated that over a fifth of deaths worldwide can be attributed to dietary risk factors. A particularly serious condition is salt-sensitive (SS) hypertension and renal damage, participants of which demonstrate increased morbidity and mortality. Notably, a large amount of evidence from humans and animals has demonstrated that other components of the diet can also modulate hypertension and associated end-organ damage. Evidence presented in this review provides support for the view that immunity and inflammation serve to amplify the development of SS hypertension and leads to malignant disease accompanied by tissue damage. Interestingly, SS hypertension is modulated by changes in dietary protein intake, which also influences immune mechanisms. Together, the evidence presented in this review from animal and human studies indicates that changes in dietary protein source have profound effects on the gut microbiota, microbiota-derived metabolites, gene expression, immune cell activation, the production of cytokines and other factors, and the development of SS hypertension and kidney damage.

Dietary Patterns, Gut Microbiota Remodeling, and Cardiometabolic Disease

The cardiovascular and metabolic disorders, collectively known as cardiometabolic disease (CMD), are high morbidity and mortality pathologies associated with lower quality of life and increasing health-care costs. The influence of the gut microbiota (GM) in dictating the interpersonal variability in CMD susceptibility, progression and treatment response is beginning to be deciphered, as is the mutualistic relation established between the GM and diet. In particular, dietary factors emerge as pivotal determinants shaping the architecture and function of resident microorganisms in the human gut. In turn, intestinal microbes influence the absorption, metabolism, and storage of ingested nutrients, with potentially profound effects on host physiology. Herein, we present an updated overview on major effects of dietary components on the GM, highlighting the beneficial and detrimental consequences of diet-microbiota crosstalk in the setting of CMD. We also discuss the promises and challenges of integrating microbiome data in dietary planning aimed at restraining CMD onset and progression with a more personalized nutritional approach.

Diets, Gut Microbiota and Metabolites

The gut microbiota refers to the gross collection of microorganisms, estimated trillions of them, which reside within the gut and play crucial roles in the absorption and digestion of dietary nutrients. In the past decades, the new generation 'omics' (metagenomics, transcriptomics, proteomics, and metabolomics) technologies made it possible to precisely identify microbiota and metabolites and describe their variability between individuals, populations and even different time points within the same subjects. With massive efforts made, it is now generally accepted that the gut microbiota is a dynamically changing population, whose composition is influenced by the hosts' health conditions and lifestyles. Diet is one of the major contributors to shaping the gut microbiota. The components in the diets vary in different countries, religions, and populations. Some special diets have been adopted by people for hundreds of years aiming for better health, while the underlying mechanisms remain largely unknown. Recent studies based on volunteers or diet-treated animals demonstrated that diets can greatly and rapidly change the gut microbiota. The unique pattern of the nutrients from the diets and their metabolites produced by the gut microbiota has been linked with the occurrence of diseases, including obesity, diabetes, nonalcoholic fatty liver disease, cardiovascular disease, neural diseases, and more. This review will summarize the recent progress and current understanding of the effects of different dietary patterns on the composition of gut microbiota, bacterial metabolites, and their effects on the host's metabolism.

Colchicine effects on the gut microbiome in adults with metabolic syndrome

Obesity-induced inflammation plays a substantial role in the development of insulin resistance and type 2 diabetes. The altered gut flora in obesity can also contribute to metabolic dysregulation and systemic inflammation. However, it remains unclear how dysregulation of systemic inflammation in obesity affects the gut microbiome. We hypothesized that colchicine's systemic anti-inflammatory effects in obesity would be associated with improvements in gut microbial diversity. We conducted a secondary analysis of a double-blind randomized placebo-controlled trial, in which 40 adults with obesity, high C-reactive protein (CRP) (≥2.0 mg/L), insulin resistance (homeostatic model of insulin resistance: HOMA-IR ≥2.6 mg/L), and metabolic syndrome (MetS) were randomized to three months of colchicine 0.6 mg or placebo tablets twice daily. Serum and stool samples were collected at baseline and final visit. Gut microbiota composition was characterized from stool DNA by dual-index amplification and sequencing of 16S ribosomal RNA. Pre- and post-intervention stool samples were available for 15 colchicine- and 12 placebo-treated subjects. Circulating high sensitivity CRP (hsCRP), interleukin-6, resistin, white blood count, and neutrophils were significantly decreased in the colchicine arm as compared to placebo. However, changes in stool microbiome alpha diversity, as assessed by the Chao1, Shannon, and Pielou indices, were not significant between groups. Amplicon sequence variant counts were unchanged among all examined phyla or families. Oscillibacter was the only genus to demonstrate even a nominally significant change. Among adults with obesity and MetS, colchicine significantly improved systemic inflammation. However, this anti-inflammatory effect was not associated with significant changes in the gut microbiome. Further studies are warranted to investigate this relationship.

Genetically determined gut microbial abundance and 2-year changes in central adiposity and body composition: The POUNDS lost trial

BACKGROUND AND AIM

Growing evidence has linked gut microbiota with regulation of adiposity. We aimed to examine whether the genetically determined relative abundance of gut microbial taxa was associated with long-term changes in adiposity and body composition among individuals who were overweight or obese in weight-loss diet interventions.

METHODS

The study included 692 participants with overweight or obese from the POUNDS Lost trial. We created a genetic risk score (GRS) for the relevant abundance of gut microbial taxa using 20 single nucleotide polymorphisms identified from a recent genome-wide association study. Body composition was assessed using dual-energy X-ray absorptiometry.

RESULTS

Higher GRS for the relative abundance of gut microbial taxa was significantly associated with greater reductions in waist circumference, total fat mass (FM), whole-body total percentage of fat mass (FM%), and percentage of trunk fat (TF%) at 2 years (p = 0.022, 0.034, 0.023, 0.023, respectively). In addition, dietary protein significantly modified the association between GRS for gut microbial abundance and changes in total FM, FM%, and TF% (p-interactions = 0.04, 0.013, and 0.006, respectively) at 6-month, when the maximum weight loss was achieved, even though such interactions were attenuated at 2 years. In the average-protein diet group, a higher microbial abundance GRS was associated with greater reductions in total FM (p = 0.007), FM% (p = 0.002), and TF% (p < 0.001) at 6 months, while no associations were found in the high-protein diet group (p > 0.05).

CONCLUSION

Our results suggest that the higher genetically determined relative abundance of gut microbial taxa may be related to long-term improvement of whole-body and central fatness and body composition in response to low-calorie diet interventions.

Dietary protein and the intestinal microbiota: An understudied relationship

Diet has a profound impact on the microbial community in the gastrointestinal tract, the intestinal microbiota, to the benefit or detriment of human health. To understand the influence of diet on the intestinal microbiota, research has focused on individual macronutrients. Some macronutrients (e.g. fiber) have been studied in great detail and have been found to strongly influence the intestinal microbiota. The relationship between dietary protein, a vital macronutrient, and the intestinal microbiota has gone largely unexplored. Emerging evidence suggests that dietary protein strongly impacts intestinal microbiota composition and function and that protein-microbiota interactions can have critical impacts on host health. In this review, we focus on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences. We highlight major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota.

Features of gut microbiota in patients with anorexia nervosa

BACKGROUND

Anorexia nervosa (AN) is a psychological disorder, which is characterized by the misunderstanding of body image, food restriction, and low body weight. An increasing number of studies have reported that the pathophysiological mechanism of AN might be associated with the dysbiosis of gut microbiota. The purpose of our study was to explore the features of gut microbiota in patients with AN, hoping to provide valuable information on its pathogenesis and treatment.

METHODS

In this cross-sectional study, from August 2020 to June 2021, patients with AN who were admitted into Peking University Third Hospital and Peking University Sixth Hospital ( n   =  30) were recruited as the AN group, and healthy controls (HC) were recruited from a middle school and a university in Beijing ( n   =  30). Demographic data, Hamilton Depression Scale (HAMD) scores of the two groups, and length of stay of the AN group were recorded. Microbial diversity analysis of gut microbiota in stool samples from the two groups was analyzed by 16S ribosomal RNA (rRNA) gene sequencing.

RESULTS

The weight (AN vs. HC, [39.31 ± 7.90] kg vs. [56.47 ± 8.88] kg, P  < 0.001) and body mass index (BMI, AN vs. HC, [14.92 ± 2.54] kg/m 2vs. [20.89 ± 2.14] kg/m 2 , P  < 0.001) of patients with AN were statistically significantly lower than those of HC, and HAMD scores in AN group were statistically significantly higher than those of HC. For alpha diversity, there were no statistically significant differences between the two groups; for beta diversity, the two groups differed obviously regarding community composition. Compared to HC, the proportion of Lachnospiraceae in patients with AN was statistically significantly higher (AN vs. HC, 40.50% vs. 31.21%, Z  = -1.981, P  = 0.048), while that of Ruminococcaceae was lower (AN vs. HC, 12.17% vs. 19.15%, Z  = -2.728, P  = 0.007); the proportion of Faecalibacterium (AN vs. HC, 3.97% vs. 9.40%, Z  = -3.638, P  < 0.001) and Subdoligranulum (AN vs. HC, 4.60% vs. 7.02%, Z  = -2.369, P  = 0.018) were statistically significantly lower, while that of Eubacterium_hallii_group was significantly higher (AN vs. HC, 7.63% vs. 3.43%, Z  = -2.115, P  = 0.035). Linear discriminant effect (LEfSe) analysis (LDA score >3.5) showed that o_Lachnospirales, f_Lachnospiraceae, and g_Eubacterium_hallii_group (o, f and g represents order, family and genus respectively) were enriched in patients with AN. Microbial function of nutrient transport and metabolism in AN group were more abundant ( P  > 0.05). In AN group, weight and BMI were significantly negatively correlated with the abundance of Bacteroidota and Bacteroides , while positively correlated with Subdoligranulum . BMI was significantly positively correlated with Firmicutes; HAMD scores were significantly negatively correlated with Faecalibacterium.

CONCLUSIONS

The composition of gut microbiota in patients with AN was different from that of healthy people. Clinical indicators have correlations with the abundance of gut microbiota in patients with AN.

Effects of Lacidophilin Tablets, Yogurt, and Bifid Triple Viable Capsules on the Gut Microbiota of Mice with Antibiotic-Associated Diarrhea

Antibiotic-associated diarrhea (AAD) is a common morbidity caused by antibiotic use and is characterized by the dysbiosis of the gut microbiota. Several clinical trials have shown that probiotics can prevent AAD. This study aimed at investigating the effects of Lacidophilin tablets (LB), yogurt (YG), and bifid triple viable capsules (BT) on the gut microbiota of mice with AAD. Mice with diarrhea were randomly allocated to treatment groups or the control group and were treated with either LB, YG, BT, or vehicle control. The body weight, diarrhea scores, cecum index, and cecal length were determined. Fecal samples of all mice were analyzed using 16S rRNA high-throughput sequencing. The results showed that LB, YG, and BT significantly decreased the diarrhea scores and inhibited increases in the cecum index and cecal length induced by AAD. In addition, they significantly changed the composition and richness of the gut microbiota. Specifically, they increased the abundance of the phylum Firmicutes and decreased the abundance of the phyla Bacteroidetes and the family Bacteroidaceae. Treatment with LB and YG also decreased the abundance of the phylum Proteobacteria and only LB could mediate the reduced levels of Lactobacillaceae in AAD mice. At the genus level, YG and BT treatment decreased the abundance of Bacteroides or Parasutterella. To our surprise, only LB treatment dramatically increased the abundance of Lactobacillus and decreased that of potential pathogens, such as Bacteroides, Parabacteroides, and Parasutterella, to almost normal values. Our findings indicate that LB, YG, and BT ameliorated diarrhea by regulating the composition and structure of the gut microbiota and that LB plays an important role in regulating the gut microbiota.

Effect of Dietary Protein and Processing on Gut Microbiota—A Systematic Review

The effect of diet on the composition of gut microbiota and the consequent impact on disease risk have been of expanding interest. The present review focuses on current insights of changes associated with dietary protein-induced gut microbial populations and examines their potential roles in the metabolism, health, and disease of animals. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol was used, and 29 highly relevant articles were obtained, which included 6 mouse studies, 7 pig studies, 15 rat studies, and 1 in vitro study. Analysis of these studies indicated that several factors, such as protein source, protein content, dietary composition (such as carbohydrate content), glycation of protein, processing factors, and protein oxidation, affect the digestibility and bioavailability of dietary proteins. These factors can influence protein fermentation, absorption, and functional properties in the gut and, consequently, impact the composition of gut microbiota and affect human health. While gut microbiota can release metabolites that can affect host physiology either positively or negatively, the selection of quality of protein and suitable food processing conditions are important to have a positive effect of dietary protein on gut microbiota and human health.

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

Background

Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq.

Results

We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones.

Conclusions

Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00141-0.

Dietary influences on the Dahl SS rat gut microbiota and its effects on salt-sensitive hypertension and renal damage

AIM

Our previous studies have demonstrated the importance of dietary factors in the determination of hypertension in Dahl salt-sensitive (SS) rats. Since the gut microbiota has been implicated in chronic diseases like hypertension, we hypothesized that dietary alterations shift the microbiota to mediate the development of salt-sensitive hypertension and renal disease.

METHODS

This study utilized SS rats from the Medical College of Wisconsin (SS/MCW) maintained on a purified, casein-based diet (0.4% NaCl AIN-76A, Dyets) and from Charles River Laboratories (SS/CRL) fed a whole grain diet (0.75% NaCl 5L79, LabDiet). Faecal 16S rDNA sequencing was used to phenotype the gut microbiota. Directly examining the contribution of the gut microbiota, SS/CRL rats were administered faecal microbiota transfer (FMT) experiments with either SS/MCW stool or vehicle (Vehl) in conjunction with the HS AIN-76A diet.

RESULTS

SS/MCW rats exhibit renal damage and inflammation when fed high salt (HS, 4.0% NaCl AIN-76A), which is significantly attenuated in SS/CRL. Gut microbiota phenotyping revealed distinct profiles that correlate with disease severity. SS/MCW FMT worsened the SS/CRL response to HS, evidenced by increased albuminuria (67.4 ± 6.9 vs 113.7 ± 25.0 mg/day, Vehl vs FMT, P = .007), systolic arterial pressure (158.6 ± 5.8 vs 177.8 ± 8.9 mmHg, Vehl vs FMT, P = .09) and renal T-cell infiltration (1.9-fold). Amplicon sequence variant (ASV)-based analysis of faecal 16S rDNA sequencing data revealed taxa that significantly shifted with FMT: Erysipelotrichaceae_2, Parabacteroides gordonii, Streptococcus alactolyticus, Bacteroidales_1, Desulfovibrionaceae_2, Ruminococcus albus.

CONCLUSIONS

These data demonstrate that dietary modulation of the gut microbiota directly contributes to the development of Dahl SS hypertension and renal injury.

Tryptophan-metabolizing gut microbes regulate adult neurogenesis via the aryl hydrocarbon receptor

While modulatory effects of gut microbes on neurological phenotypes have been reported, the mechanisms remain largely unknown. Here, we demonstrate that indole, a tryptophan metabolite produced by tryptophanase-expressing gut microbes, elicits neurogenic effects in the adult mouse hippocampus. Neurogenesis is reduced in germ-free (GF) mice and in GF mice monocolonized with a single-gene tnaA knockout (KO) mutant Escherichia coli unable to produce indole. External administration of systemic indole increases adult neurogenesis in the dentate gyrus in these mouse models and in specific pathogen-free (SPF) control mice. Indole-treated mice display elevated synaptic markers postsynaptic density protein 95 and synaptophysin, suggesting synaptic maturation effects in vivo. By contrast, neurogenesis is not induced by indole in aryl hydrocarbon receptor KO (AhR-/-) mice or in ex vivo neurospheres derived from them. Neural progenitor cells exposed to indole exit the cell cycle, terminally differentiate, and mature into neurons that display longer and more branched neurites. These effects are not observed with kynurenine, another AhR ligand. The indole-AhR-mediated signaling pathway elevated the expression of β-catenin, Neurog2, and VEGF-α genes, thus identifying a molecular pathway connecting gut microbiota composition and their metabolic function to neurogenesis in the adult hippocampus. Our data have implications for the understanding of mechanisms of brain aging and for potential next-generation therapeutic opportunities.

The Effects of Lifestyle and Diet on Gut Microbiota Composition, Inflammation and Muscle Performance in Our Aging Society

Living longer is associated with an increased risk of chronic diseases, including impairments of the musculoskeletal and immune system as well as metabolic disorders and certain cancers, each of which can negatively affect the relationship between host and microbiota up to the occurrence of dysbiosis. On the other hand, lifestyle factors, including regular physical exercise and a healthy diet, can affect skeletal muscle and immune aging positively at all ages. Accordingly, health benefits could partly depend on the effect of such interventions that influence the biodiversity and functionality of intestinal microbiota. In the present review, we first discuss the physiological effects of aging on the gut microbiota, immune system, and skeletal muscle. Secondly, we describe human epidemiological evidence about the associations between physical activity and fitness and the gut microbiota composition in older adults. The third part highlights the relevance and restorative mechanisms of immune protection through physical activity and specific exercise interventions during aging. Fourth, we present important research findings on the effects of exercise and protein as well as other nutrients on skeletal muscle performance in older adults. Finally, we provide nutritional recommendations to prevent malnutrition and support healthy active aging with a focus on gut microbiota. Key nutrition-related concerns include the need for adequate energy and protein intake for preventing low muscle mass and a higher demand for specific nutrients (e.g., dietary fiber, polyphenols and polyunsaturated fatty acids) that can modify the composition, diversity, and metabolic capacity of the gut microbiota, and may thus provide a practical means of enhancing gut and systemic immune function.

Diet- and sex-related changes of gut microbiota composition and functional profiles after 4 months of weight loss intervention

PURPOSE

Obesity has been related to intestinal dysbiosis and the modification of gut microbiota composition by dietary strategies becomes a promising strategy to help manage obesity. The aim of the current study was to evaluate the effect of two weight-loss diets on the composition and functional profile of gut microbiota.

METHODS

55 men and 124 women with BMI > 25 kg/m² were randomly assigned to moderately high-protein (MHP) or low-fat (LF) diet. Differences in fecal bacteria abundance (based on 16 s rRNA sequencing) between before and after 4 months of calorie restriction was analyzed using EdgeR tool in MicrobiomeAnalyst platform. Bacterial functional profile was predicted using Tax4Fun and metagenomeSeq analysis. Significant KEGG Orthology (KO) terms were selected for the metabolomic study using chromatography.

RESULTS

After the intervention, MHP-men showed a significant decrease in Negativicutes, Selenomonadales, Dielma and Dielma fastidiosa. LF-men showed a significant increase in Bacilli, Lactobacillales, Christensenellaceae, Peptococcaceae, and Streptococcaceae, Peptococcus, Streptococcus and Christensenella, Duncaniella dubosii_CP039396_93.49%, Roseburia sp_AB744234_98.96% and Alistipes inops_KJ572413_99.57%. MHP-women increased Pasteurellales, Phascolarctobacterium succinatutens, Ruthenibacterium lactatiformans_LR215981_99.55% and decreased in Phascolarctobacterium succinatutens_NR112902_99.56%. Finally, LF-women presented a significant decrease in Bacteroides clarus and Erysipelothrix inopinata_CP060715_84.4%. Surprisingly, no matching bacterial changes were found between these four groups. A total of 42 KO, 10 metabolic pathways and 107 related metabolites related were found implicated in these bacterial changes. Seven metabolites were confirmed in plasma.

CONCLUSION

Weight-loss-related-changes in gut microbiome composition and the functional profile occur in a sex- and diet-related manner, showing that women and men could differentially benefit from the consumption of MHP and LF diets.

TRIAL REGISTRATION

NCT02737267, 10th March 2016 retrospectively registered.

Modulation of gut microbiota in healthy rats after exposure to nutritional supplements

INTRODUCTION

Rats are experimental animals, frequently used as model organisms in the biomedical studies, and increasingly used to study the gut microbiota. Specifically, the aim of latter studies is either the elucidation of relationship between intestinal dysbiosis and diseases or the determination of nutrients or pharmaceutical agents which can cause the modulation in the presence or abundance of gut microbiota.

AIM

Herein, the research studies conducted on the gut microbiota of healthy rats are presented in a summarized and concise overview. The focus is on studies aimed to reveal the shifts in microbial composition and functional changes after exposure to various types of nutritional supplements.

METHODS

We performed the search of PubMed database using the term "rat gut microbiome microbiota" and examined studies aimed to assess the composition of gut microbiota in physiological homeostasis as well as the effect of various nutritional supplements on the gut microbiota of healthy rats.

Changes in intestinal barrier functions and gut microbiota in rats exposed to zearalenone

Zearalenone (ZEN) is a mycotoxin that causes serious health problems in humans and animals. However, few studies have focused on the destruction of the intestinal barrier caused by ZEN. In this study, rats were exposed to different dosages of ZEN (0, 0.2, 1.0 and 5.0 mg/kg bw) by gavage for 4 weeks. The results showed that 1.0 and 5.0 mg/kg ZEN impaired gut morphology, induced the inflammatory response, reduced mucin expression, increased intestinal permeability, decreased the expression of TJ proteins and activated the RhoA/ROCK pathway. However, 0.2 mg/kg ZEN had no significant effect on intestinal barrier except for reducing the expression of some TJ proteins and mucins. Moreover, exposure to ZEN led to slight imbalance in microbiota. In conclusion, ZEN exposure resulted in intestinal barrier dysfunction by inducing intestinal microbiota dysbiosis, decreasing the expression of TJ proteins, activating the RhoA/ROCK pathway, and inducing the inflammatory response.

Human gut-derived commensal suppresses generation of T-cell response to gliadin in humanized mice by modulating gut microbiota

The human intestinal tract is colonized by a large number of diverse microorganisms that play various important physiologic functions. In inflammatory gut diseases including celiac disease (CeD), a dysbiotic state of microbiome has been observed. Interestingly, this perturbed microbiome is normalized towards eubiosis in patients showing recovery after treatment. The treatment has been observed to increase the abundance of beneficial microbes in comparison to non-treated patients. In this study, we investigated the effect of Prevotella histicola or Prevotella melaninogenica, isolated from the duodenum of a treated CeD patient, on the induction and maintenance of oral tolerance to gliadin, a CeD associated subgroup of gluten proteins, in NOD.DQ8.ABo transgenic mice. Conventionally raised mice on a gluten free diet were orally gavaged with bacteria before and after injection with pepsin trypsin digested gliadin (PTD-gliadin). P. histicola suppressed the cellular response to gliadin, whereas P. melaninogenica failed to suppress an immune response against gliadin. Interestingly, tolerance to gliadin in NOD.DQ8.ABo mice may be associated with gut microbiota as mice gavaged with P melaninogenica harbored a different microbial diversity as compared to P. histicola treated mice. This study provides experimental evidence that gut microbes like P. histicola from treated patients can suppress the immune response against gliadin epitopes.

The Controversial Role of Human Gut Lachnospiraceae

The complex polymicrobial composition of human gut microbiota plays a key role in health and disease. Lachnospiraceae belong to the core of gut microbiota, colonizing the intestinal lumen from birth and increasing, in terms of species richness and their relative abundances during the host's life. Although, members of Lachnospiraceae are among the main producers of short-chain fatty acids, different taxa of Lachnospiraceae are also associated with different intra- and extraintestinal diseases. Their impact on the host physiology is often inconsistent across different studies. Here, we discuss changes in Lachnospiraceae abundances according to health and disease. With the aim of harnessing Lachnospiraceae to promote human health, we also analyze how nutrients from the host diet can influence their growth and how their metabolites can, in turn, influence host physiology.

Dietary Protein: Mechanisms Influencing Hypertension and Renal Disease

PURPOSE OF REVIEW

This review will provide an in-depth coverage of the epidemiological and pre-clinical literature surrounding the role of dietary protein in hypertension, with a special emphasis on the history of our work on the Dahl salt-sensitive rat.

RECENT FINDINGS

Our studies have dedicated much effort into understanding the relationship between dietary protein and its effect on the development of salt-sensitive hypertension and renal injury. Our evidence over the last 15 years have demonstrated that both the source and amount of dietary protein can influence the severity of disease, where we have determined mechanisms related to immunity, the maternal environment during pregnancy, and more recently the gut microbiota, which significantly contribute to these diet-induced effects. Deeper understanding of these dietary protein-related mechanisms may provide insight on the plausibility of dietary modifications as future therapeutic avenues for hypertension and renal disease.

Influence of Gut Microbiota on Progression to Tuberculosis Generated by High Fat Diet-Induced Obesity in C3HeB/FeJ Mice

The administration of a high fat content diet is an accelerating factor for metabolic syndrome, impaired glucose tolerance, and early type 2 diabetes. The present study aims to assess the impact of a high fat diet on tuberculosis progression and microbiota composition in an experimental animal model using a C3HeB/FeJ mouse strain submitted to single or multiple consecutive aerosol infections. These models allowed us to study the protection induced by Bacillus Calmette-Guérin vaccination as well as by the natural immunity induced by chemotherapy after a low dose Mycobacterium tuberculosis infection. Our results show that a high fat diet is able to trigger a pro-inflammatory response, which results in a faster progression toward active tuberculosis and an impaired protective effect of BCG vaccination, which is not the case for natural immunity. This may be related to dysbiosis and a reduction in the Firmicutes/Bacteroidetes ratio in the gut microbiota caused by a decrease in the abundance of the Porphyromonadaceae family and, in particular, the Barnesiella genus. It should also be noted that a high fat diet is also related to an increase in the genera Alistipes, Parasuterella, Mucispirillum, and Akkermansia, which have previously been related to dysbiotic processes. As diabetes mellitus type 2 is a risk factor for developing tuberculosis, these findings may prove useful in the search for new prophylactic strategies for this population subset.

Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota

In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into two groups fed either a standard-protein (SP) or a low-protein (LP) diet. In the last month (165-195 days), all pigs received a LP diet, either carotene-enriched (CE) or not (NC). Significant differences were observed between T1 and T2 at Amplicon Sequences Variants (ASVs), phylum and genus levels. In T1 group, Prevotella, Faecalibacterium and Treponema were the genera most influenced by dietary protein, together with predicted functions related with the degradation of protein. In contrast, the CE diet did not impact the microbiome diversity, although 160 ASVs were differentially abundant between CE and NC groups at T2. Weak stability of enterotype clusters across time-points was observed as consequence of medium-term dietary interventions. Our results suggest that during the last month of fattening, dietary protein have a stronger effect than carotenes on the modulation of the compositional and functional structure of the pig microbiota.

Ameliorative effect of Atractylodes macrocephala essential oil combined with Panax ginseng total saponins on 5-fluorouracil induced diarrhea is associated with gut microbial modulation

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese medicine (TCM) holds that deficiency of spleen-Qi is the major pathogenesis of chemotherapy-induced diarrhea (CID). Herb pair of Atractylodes macrocephala Koidz. (AM) and Panax ginseng C. A. Mey. (PG) has good effects of supplementing Qi and strengthening spleen.

AIM OF THE STUDY

To investigate therapeutic effects and mechanism of Atractylodes macrocephala essential oil (AMO) and Panax ginseng total saponins (PGS) alone and in combination (AP) on 5-fluorouracil (5-FU) chemotherapy induced diarrhea in mice.

MATERIALS AND METHODS

The mice were administered with AMO, PGS and AP respectively for 11 days, and intraperitoneally injected with 5-FU for 6 days since the 3rd day of the experiment. During the experiment, the body weights and diarrhea scores of mice were recorded daily. Thymus and spleen indexes were calculated after sacrifice of the mice. Pathological changes in ileum and colonic tissues were examined by hematoxylin-eosin (HE) staining. And the content levels of intestinal inflammatory cytokines were measured by enzyme-linked immmunosorbent assays (ELISA). 16S rDNA Amplicon Sequencing was used to analyze and interpret the gut microbiota of fecal samples.

RESULTS

AP significantly inhibited body weights loss, diarrhea, reductions of thymus and spleen indexes, and pathological changes of ileums and colons induced by 5-FU. Neither AMO nor PGS alone significantly improved above-mentioned abnormalities. Besides, AP could significantly suppressed the 5-FU-mediated increases of the intestinal inflammatory cytokines (TNF-α, IFN-γ, IL-6, IL-1β and IL-17), while AMO or PGS only inhibited some of them after 5-FU chemotherapy. Gut microbiota analysis indicated that 5-FU induced overall structural changes of gut microbiota were reversed after AP treatment. Additionally, AP significantly modulated the abundances of different phyla similar to normal values, and restored the ratios of Firmicutes/Bacteroidetes (F/B). At genus level, AP treatment dramatically decreased potential pathogens like Bacteroides, Ruminococcus, Anaerotruncus and Desulfovibrio. AP also antagonized the abnormal effects of AMO and PGS alone on certain genera like Blautia, Parabacteroides and Lactobacillus. Neither AMO nor PGS alone inhibited changes of gut microbial structure caused by 5-FU.

CONCLUSIONS

AP, combination of AMO and PGS, not AMO or PGS alone, significantly ameliorated diarrhea, inhibited intestinal pathology, and modulated gut microbial structure in 5-FU induced mice. AP also antagonized abnormal effects of AMO or PGS on certain genera. The results illustrated that gut microbiota was involved in the combined effects of AP on 5-FU induced diarrhea.

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations

Background

The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.

Results

We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.

Conclusions

Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We’ve proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2623-x) contains supplementary material, which is available to authorized users.

Many Canadian dog and cat foods fail to comply with the guaranteed analyses reported on packages

We compared analyzed nutrient contents of Canadian-specific dry dog and cat foods to the guaranteed analyses on packages and to the Association of American Feed Control Officials (AAFCO) 2018 nutrient targets to assess compliance with the Consumer Packaging and Labelling Act. We also explored differences in macronutrient content between species (dog and cat) and life stage for adult pet foods (all life stages and senior). Extruded dog (n = 16) or cat (n = 11) foods advertised as all life stage or senior, sold only in Canada, and carrying an AAFCO nutritional adequacy statement were selected. Proximate analyses and amino acid analyses were completed on all diets. Of the 27 foods, 25 met or exceeded the AAFCO nutrient recommendations. Only 9 foods met all nutrient content claims listed in their guaranteed analyses. Nutrient content between species or life stages was not different (P > 0.10).

Papio spp. Colon microbiome and its link to obesity in pregnancy

INTRODUCTION

Gut microbial communities are critical players in the pathogenesis of obesity. Pregnancy is associated with increased bacterial load and changes in gut bacterial diversity. Sparse data exist regarding composition of gut microbial communities in obesity combined with pregnancy.

MATERIAL AND METHODS

Banked tissues were collected under sterile conditions during necropsy, from three non-obese (nOb) and four obese (Ob) near-term pregnant baboons. Sequences were assigned taxonomy using the Ribosomal Database Project classifier. Microbiome abundance and its difference between distinct groups were assessed by a nonparametric test.

RESULTS

Three families predominated in both the nOb and Ob colonic microbiome: Prevotellaceae (25.98% and 32.71% respectively), Ruminococcaceae (12.96% and 7.48%), and Lachnospiraceae (8.78% and 11.74%). Seven families of the colon microbiome displayed differences between Ob and nOb groups.

CONCLUSION

Changes in gut microbiome in pregnant obese animals open the venue for dietary manipulation in pregnancy.

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut

Undigestible food ingredients are converted by the microbiota into a large range of metabolites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and functionality in mice were analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology were complemented with metatranscriptome and SCFA analyses to obtain insight in in situ expression of protein fermentation pathways and the phylogenetic groups involved. High protein diets led to increased luminal concentrations of branched-SCFA, in accordance with protein fermentation in the gut. Bacteria dominantly participating in protein catabolism belonged to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae families in both normal- and high- protein diet regimes. This study identifies the microbial groups involved in protein catabolism in the intestine and underpins the value of in situ metatranscriptome analyses as an approach to decipher locally active metabolic networks and pathways as a function of the dietary regime, as well as the phylogeny of the microorganisms executing them.

The influence of diet and environment on the gut microbial community of field crickets

The extent to which diet and environment influence gut community membership (presence or absence of taxa) and structure (individual taxon abundance) is the subject of growing interest in microbiome research. Here, we examined the gut bacterial communities of three cricket groups: (1) wild caught field crickets, (2) laboratory-reared crickets fed cat chow, and (3) laboratory-reared crickets fed chemically defined diets. We found that both environment and diet greatly altered the structure of the gut bacterial community. Wild crickets had greater gut microbial diversity and higher Firmicutes to Bacteroidetes ratios, in contrast to laboratory-reared crickets. Predictive metagenomes revealed that laboratory-reared crickets were significantly enriched in amino acid degradation pathways, while wild crickets had a higher relative abundance of peptidases that would aid in amino acid release. Although wild and laboratory animals differ greatly in their bacterial communities, we show that the community proportional membership remains stable from Phylum to Family taxonomic levels regardless of differences in environment and diet, suggesting that endogenous factors, such as host genetics, have greater control in shaping gut community membership.

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review

Imbalances in the gut microbiota, the bacteria that inhabit the intestines, are central to the pathogenesis of obesity. This systematic review assesses the association between the gut microbiota and weight loss in overweight/obese adults and its potential manipulation as a target for treating obesity. This review identified 43 studies using the keywords 'overweight' or 'obesity' and 'microbiota' and related terms; among these studies, 17 used dietary interventions, 11 used bariatric surgery and 15 used microbiota manipulation. The studies differed in their methodologies as well as their intervention lengths. Restrictive diets decreased the microbiota abundance, correlated with nutrient deficiency rather than weight loss and generally reduced the butyrate producers Firmicutes, Lactobacillus sp. and Bifidobacterium sp. The impact of surgical intervention depended on the given technique and showed a similar effect on butyrate producers, in addition to increasing the presence of the Proteobacteria phylum, which is related to changes in the intestinal absorptive surface, pH and digestion time. Probiotics differed in strain and duration with diverse effects on the microbiota, and they tended to reduce body fat. Prebiotics had a bifidogenic effect and increased butyrate producers, likely due to cross-feeding interactions, contributing to the gut barrier and improving metabolic outcomes. All of the interventions under consideration had impacts on the gut microbiota, although they did not always correlate with weight loss. These results show that restrictive diets and bariatric surgery reduce microbial abundance and promote changes in microbial composition that could have long-term detrimental effects on the colon. In contrast, prebiotics might restore a healthy microbiome and reduce body fat.

Effect of Sweetened Dried Cranberry Consumption on Urinary Proteome and Fecal Microbiome in Healthy Human Subjects

The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state. The subjects then consumed one serving (42 g) of SDC daily with lunch for 2 weeks. Urine and fecal samples were collected again the day after 2 weeks of SDC consumption. Orbitrap Q-Exactive mass spectrometry of urinary proteins showed that consumption of SDC resulted in changes to 22 urinary proteins. Multiplex sequencing of 16S ribosomal RNA genes in fecal samples indicated changes in relative abundance of several bacterial taxonomic units after consumption of SDC. There was a shift in the Firmicutes:Bacteroidetes ratio, increases in commensal bacteria, and decreases or the absence of bacteria associated with negative health effects. A decrease in uromodulin in all subjects and an increase in Akkermansia bacteria in most subjects were observed and warrant further investigation. Future larger clinical studies with multiomics and multitissue sampling designs are required to determine the effects of SDC consumption on nutrition and health.

Fecal Microbiota and Diet of Children with Chronic Constipation

Many factors explain dysbiosis in chronic constipation (CC), such as a low-fiber diet. The objective of this study was to compare the fecal microbiota of constipated and nonconstipated children and their intake frequencies of food. Methods. This observational study included 79 children (M/F 43/36) aged six to 36 months divided into two groups: cases (39 constipated children) and controls (40 nonconstipated children). We used a structured form to collect demographic variables, conducted anthropometric assessment, and collected food intake frequency data. The fecal microbiota of the stool samples was analyzed by real-time polymerase chain reaction (PCR) using the fluorophore SYBR® Green. Results. Constipated children had a smaller concentration of Lactobacillus per milligram of stool (p = 0.015) than nonconstipated children, but the concentration of Bifidobacterium per milligram of stool (p = 0.323) and the intake of fruits, vegetables (p = 0.563), and junk food (p = 0.093) of the two groups did not differ. Constipated children consumed more dairy products (0.45 ± 0.8; p > 0.001), were more frequently delivered via caesarean section (69.2%), were weaned earlier (median: 120; 60Q₁–240Q₃), and had a family history of constipation (71.8%). Conclusions. Children with CC have a smaller concentration of Lactobacillus in their stools and consume more dairy products.