Phenylketonuria Diet Promotes Shifts in Firmicutes Populations

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study

AIM

The oral microenvironment contributes to microbial composition and immune equilibrium. It is considered to be influenced by dietary habits. Phenylketonuria (PKU) patients, who follow a lifelong low-protein diet, exhibit higher prevalence of oral diseases such as periodontitis, offering a suitable model to explore the interplay between diet, oral microbiota and oral health.

MATERIALS AND METHODS

We conducted 16S rDNA sequencing on saliva and subgingival plaque from 109 PKU patients (ages 6-68 years) and 114 age-matched controls and correlated oral microbial composition and dental health.

RESULTS

PKU patients exhibited worse dental health, reduced oral microbial diversity and a difference in the abundance of specific taxa, especially Actinobacteriota species, compared to controls. PKU patients with poor periodontal health exhibited higher alpha diversity than the orally healthy ones, marked by high abundance of the genus Tannerella. Notably, the observed taxonomic differences in PKU patients with normal indices of decayed/missing/filled teeth, plaque control record, gingival bleeding index and periodontal screening and recording index generally differed from microbial signatures of periodontitis.

CONCLUSIONS

PKU patients' reduced microbial diversity may be due to their diet's metabolic challenges disrupting microbial and immune balance, thus increasing oral inflammation. Higher alpha diversity in PKU patients with oral inflammation is likely related to expanded microbial niches.

Glycomacropeptide-Based Protein Substitutes for Children with Phenylketonuria in Italy: A Nutritional Comparison

Advancements in food science technology have allowed the development of new products for the therapeutic management of inherited metabolic diseases such as phenylketonuria (PKU). Glycomacropeptide (GMP), a peptide derived from casein, is naturally low in phenylalanine (Phe) and, thus, adequate for protein substitutes (PSs) for the management of PKU in children. This review aims primarily to analyse the differences in the nutritional composition of GMP-based protein substitutes in different formulations (ready to drink, powdered, and bars), and secondarily to assess the quality of these products, comparing their nutritional composition with that of standard amino acid (L-AA) mixtures. Thirty-five GMP-based PSs produced by six different companies were included in this review: twenty-one powdered PSs, eight ready to drink, and six bars. The analysis revealed great heterogeneity not only among the different formulations (powdered, ready to drink, and bars) but also within the same group, in terms of energy content and nutritional composition. GMP-based PSs were shown to have higher contents of sugars and saturated fatty acids compared to L-AA PSs, especially in ready-to-drink formulations and bars. The latter also provided the highest amounts of energy among the GMP-based products. This finding may be related to a higher risk of developing overweight and obesity. The greater palatability of these GMP-based PSs, combined with improved nutritional quality, could not only improve adherence to diet therapy but also reduce the incidence of obesity-related comorbidities in PKU.

Dietary intake in individuals with phenylketonuria: an integrative review

Introduction

Introduction: the dietary intake of individuals with phenylketonuria (PKU) may vary widely according to different cultural eating habits, lifestyle, access to multidisciplinary team, and metabolic formulas available. Thus, knowing the dietary intake of this population makes it possible to tailor nutritional treatment strategies to impact their health. Objective: to analyze the evidence on the dietary intake of individuals with PKU. Methods: an integrative literature review was conducted on the dietary intake of individuals with PKU in the databases PUBMED, BIREME and Science Direct. Original articles that addressed the energy and macronutrient food intake of children, adolescents and/or adults with PKU were included in the study, without time restriction, in any language. A total of 384 articles were found and 27 articles were selected and analyzed. Results: evidence about the nutritional composition of their diet showed that individuals with PKU consume between 1160-2721 kcal of energy -7.2-17.4 % (32.4-76.9 g) of energy as protein, 45.9-69.2 % of energy as carbohydrates, 16.6-39 % of energy as lipids- and between 7.6 and 20 g of fiber. Conclusion: most individuals with PKU have low energy, protein and fiber intake, adequate lipid intake, and high carbohydrate intake. Metabolic control of the disease is still a challenge in all countries. Nutritional strategies to improve dietary nutritional composition and phenylalanine blood levels in individuals with PKU remain an urgent issue.

Body Composition Evaluation and Clinical Markers of Cardiometabolic Risk in Patients with Phenylketonuria

Cardiovascular diseases are the main cause of mortality worldwide. Patients with phenylketonuria (PKU) may be at increased cardiovascular risk. This review provides an overview of clinical and metabolic cardiovascular risk factors, explores the connections between body composition (including fat mass and ectopic fat) and cardiovascular risk, and examines various methods for evaluating body composition. It particularly focuses on nutritional ultrasound, given its emerging availability and practical utility in clinical settings. Possible causes of increased cardiometabolic risk in PKU are also explored, including an increased intake of carbohydrates, chronic exposure to amino acids, and characteristics of microbiota. It is important to evaluate cardiovascular risk factors and body composition in patients with PKU. We suggest systematic monitoring of body composition to develop nutritional management and hydration strategies to optimize performance within the limits of nutritional therapy.

Systematic Review and Meta-Analysis of Dietary Interventions and Microbiome in Phenylketonuria

Inborn errors of metabolism (IEMs) comprise a diverse group of monogenic disorders caused by enzyme deficiencies that result either in a toxic accumulation of metabolic intermediates or a shortage of essential end-products. Certain IEMs, like phenylketonuria (PKU), necessitate stringent dietary intervention that could lead to microbiome dysbiosis, thereby exacerbating the clinical phenotype. The objective of this systematic review was to examine the impact of PKU therapies on the intestinal microbiota. This research was conducted following the PRISMA Statement, with data from PubMed, Scopus, ScienceDirect, and Web of Science. A total of 18 articles meeting the inclusion criteria were published from 2011 to 2022. Significant reductions in several taxonomic groups in individuals with PKU when compared to the control group were detected in a quantitative analysis conducted across seven studies. The meta-analysis synthesis indicates a contrast in biodiversity between PKU subjects and the control population. Additionally, the meta-regression results, derived from the Bacillota/Bacteroidota ratio data, suggest a potential influence of diet in adult PKU populations (p = 0.004). It is worth noting that the limited number of studies calls for further research and analysis in this area. Our findings indicate the necessity of enhancing understanding of microbiota variability in reaction to treatments among PKU subjects to design tailored therapeutic and nutritional interventions to prevent complications resulting from microbiota disruption.

Dietary Inflammatory Potential in Pediatric Diseases: A Narrative Review

Inflammatory status is one of the main drivers in the development of non-communicable diseases (NCDs). Specific unhealthy dietary patterns and the growing consumption of ultra-processed foods (UPFs) may influence the inflammation process, which negatively modulates the gut microbiota and increases the risk of NCDs. Moreover, several chronic health conditions require special long-term dietary treatment, characterized by altered ratios of the intake of nutrients or by the consumption of disease-specific foods. In this narrative review, we aimed to collect the latest evidence on the pro-inflammatory potential of dietary patterns, foods, and nutrients in children affected by multifactorial diseases but also on the dietetic approaches used as treatment for specific diseases. Considering multifactorial diet-related diseases, the triggering effect of pro-inflammatory diets has been addressed for metabolic syndrome and inflammatory bowel diseases, and the latter for adults only. Future research is required on multiple sclerosis, type 1 diabetes, and pediatric cancer, in which the role of inflammation is emerging. For diseases requiring special diets, the role of single or multiple foods, possibly associated with inflammation, was assessed, but more studies are needed. The evidence collected highlighted the need for health professionals to consider the entire dietary pattern, providing balanced and healthy diets not only to permit the metabolic control of the disease itself, but also to prevent the development of NCDs in adolescence and adulthood. Personalized nutritional approaches, in close collaboration between the hospital, country, and families, must always be promoted together with the development of new methods for the assessment of pro-inflammatory dietary habits in pediatric age and the implementation of telemedicine.

A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice

The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.

Possible role of tryptophan metabolism along the microbiota-gut-brain axis on cognitive & behavioral aspects in Phenylketonuria

Cognitive and psychiatric disorders are well documented across the lifetime of patients with inborn errors of metabolism (IEMs). Gut microbiota impacts behavior and cognitive functions through the gut-brain axis (GBA). According to recent research, a broad spectrum of GBA disorders may be influenced by a perturbed Tryptophan (Trp) metabolism and are associated with alterations in composition or function of the gut microbiota. Furthermore, early-life diets may influence children's neurodevelopment and cognitive deficits in adulthood. In Phenylketonuria (PKU), since the main therapeutic intervention is based on a life-long restrictive diet, important alterations of gut microbiota have been observed. Studies on PKU highlight the impact of alterations of gut microbiota on the central nervous system (CNS), also investigating the involvement of metabolic pathways, such as Trp and kynurenine (KYN) metabolisms, involved in numerous neurodegenerative disorders. An alteration of Trp metabolism with an imbalance of the KYN pathway towards the production of neurotoxic metabolites implicated in numerous neurodegenerative and inflammatory diseases has been observed in PKU patients supplemented with Phe-free amino acid medical foods (AA-MF). The present review investigates the possible link between gut microbiota and the brain in IEMs, focusing on Trp metabolism in PKU. Considering the evidence collected, cognitive and behavioral well-being should always be monitored in routine IEMs clinical management. Further studies are required to evaluate the possible impact of Trp metabolism, through gut microbiota, on cognitive and behavioral functions in IEMs, to identify innovative dietetic strategies and improve quality of life and mental health of these patients.

Effect of Special Low-Protein Foods Consumption in the Dietary Pattern and Biochemical Profile of Patients with Inborn Errors of Protein Metabolism: Application of a Database of Special Low-Protein Foods

In inborn errors of intermediate protein metabolism (IEM), the effect of special low-protein foods (SLPFs) on dietary intake has been scarcely studied. The aim of this study was to compare the nutritional profile of SLPFs with usual foods and to assess whether their intake determines the dietary pattern and affects the plasma biochemical profile in children with IEMs with different protein restrictions. A database with the nutritional composition of 250 SLPFs was created. A total of 59 children with IEMs were included in this cross-sectional observational study. The greatest significant differences in macronutrient composition were observed between dairy, meat, fish, and egg SLPFs and regular foods. After stratifying subjects by SLPFs, the participants with the highest intake (>32%) had a higher total energy intake and lower intake of natural protein than those in the lowest tertile (<24%) (p < 0.05). However, when stratifying subjects by dairy SLPF intake, children in the highest tertile (>5%) showed a higher intake of sugars, total and saturated fats, and higher plasma levels of total and low-density lipoprotein cholesterol than those in the first tertile (<1%) (p < 0.05). The variability in the nutritional composition of SLPFs highlights the need for up-to-date databases which would greatly assist in optimizing individualized recommendations for children with IEMs and protein restrictions.

Special low protein foods for phenylketonuria in Turkey: An examination of their nutritional composition compared to regular food

Background: Special low protein foods (SLPF) that are phenylalanine (Phe)-free or have a low Phe content are an integral part of PKU diet therapy. Aim: The aim of this study is to determine the nutritional profiles of SLPFs used in Turkey and to compare their contents with equivalent products in the "regular" category, in order to evaluate nutritional and metabolic risks. Methods: Between February and March 2022, the information concerning the nutritional contents of "special low protein products" recommended for PKU and available in Turkey were obtained from the websites of producers/suppliers. Results: A total of 148 SLPFs were identified in Turkey. Compared to regular products, SLPFs were determined to contain less sugar and high carbohydrate content in the Turkish market (p < 0.001). Overall, SLPF products had higher dietary fiber compared to products with regular protein content (p < 0.001). In SLPF subgroups, meat substitutes, rice and pasta, and soup products had significantly less total fat than regular products; low protein bread, sweet snacks, and salted crackers were found to contain less saturated fat (p < 0.05). Moreover, all SLPFs contained significantly more salt than regular products, especially the salt content of subgroups of low protein bread, flour, pasta, and rice was significantly higher than regular products (p < 0.05). Conclusion: Including detailed nutritional information on the Turkish SLPFs' food labels will be effective for patients with PKU to follow themselves on their own.

Altered gut microbiome diversity and function in patients with propionic acidemia

Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.

Effect of β-1,3/1,6-glucan on gut microbiota of yellow-feathered broilers

β-1,3/1,6-glucan as a prebiotic improves immune performance in animals. These functions are closely related to the effect of β-1,3/1,6-glucan on gut microbiota structure. However, the effect of β-1,3/1,6-glucan on the gut microbiota structure of broilers is unclear. The aim of this study was to confirm the effects of β-1,3/1,6-glucan on the cecal microflora structure of yellow-feathered broilers. This study monitored the antimicrobial resistance (AMR) level of Escherichia coli in feces of yellow-feathered broilers by standard broth dilution method and mastered the AMR level of chickens selected. The effects of β-1,3/1,6-glucan on gut microbiota were investigated by 16S rRNA sequencing. The results showed that the number of isolated multidrug-resistant E. coli strains accounted for 98.41%. At 14, 21, and 28 days of age, supplemented of 0.2%, 0.1%, and 0.1% β-1,3/1,6-glucan in yellow-feathered broiler diets significantly altered gut microbial composition, and beneficial bacteria Alistipes, Bacteroides and Faecalibacterium were significantly increased. These findings provide guidance and recommendations for β-1,3/1,6-glucan as a broiler feed additive to improve the growth of broilers.

Special Diets in Infants and Children and Impact on Gut Microbioma

Gut microbiota is a complex system that starts to take shape early in life. Several factors influence the rise of microbial gut colonization, such as term and mode of delivery, exposure to antibiotics, maternal diet, presence of siblings and family members, pets, genetics, local environment, and geographical location. Breastfeeding, complementary feeding, and later dietary patterns during infancy and toddlerhood are major players in the proper development of microbial communities. Nonetheless, if dysbiosis occurs, gut microbiota may remain impaired throughout life, leading to deleterious consequences, such as greater predisposition to non-communicable diseases, more susceptible immune system and altered gut–brain axis. Children with specific diseases (i.e., food allergies, inborn errors of metabolism, celiac disease) need a special formula and later a special diet, excluding certain foods or nutrients. We searched on PubMed/Medline, Scopus and Embase for relevant pediatric studies published over the last twenty years on gut microbiota dietary patterns and excluded case reports or series and letters. The aim of this review is to highlight the changes in the gut microbiota in infants and children fed with special formula or diets for therapeutic requirements and, its potential health implications, with respect to gut microbiota under standard diets.

Protective effect and possible mechanism of arctiin on broilers challenged by Salmonella pullorum

This study was aimed to investigate the effects of dietary arctiin (ARC) supplementation (100, 200, and 400 mg/kg) on the growth performance and immune response of broilers after a Salmonella pullorum (S. pullorum) challenge, and we conducted in vitro antibacterial test to explore the bacteriostatic mechanism of ARC. The in vivo trial was randomly assigned to six groups: noninfected control (NC) group and positive control (PC) group received a basal diet; TET group, received a basal diet supplemented with 100 mg/kg chlortetracycline; ARC100, ARC200, and ARC400 groups received a basal diet containing 100, 200, and 400 mg/kg ARC, respectively. From days 14 to 16, all birds (except the NC group) were infected with 1 mL (1 × 108 CFU per mL) fresh S. pullorum culture by oral gavage per day. In vivo results showed that dietary supplementation of 200 mg/kg ARC significantly increased average daily gain (P < 0.05) and decreased feed-to-gain ratio of broilers vs. the PC group during days 15 to 28 after being challenged with S. pullorum (P < 0.05). The jejunal crypt depth (CD) was decreased by supplementing 100 or 200 mg/kg ARC in diets compared with PC birds at day 19 (P < 0.05). The jejunal villi height (VH) was increased by supplementing 100, 200, or 400 mg/kg ARC in diets compared with PC birds at day 28 (P < 0.05). Besides, dietary supplementation of 200 mg/kg ARC increased the jejunal VH to CD ratio than the PC group both at days 19 and 28 (P < 0.05). Notably, the broilers had lower serum lipopolysaccharide and diamine oxidase levels in the ARC100 and ARC200 groups at day 28 than those in the PC group (P < 0.05). Furthermore, in comparison to PC birds, the birds in ARC groups (100, 200, and 400 mg/kg) had higher serum contents of IgM and IL-10, and the birds in the ARC200 group had higher serum contents of IgA at day 19 (P < 0.05). At day 28, the birds in ARC groups (100, 200, and 400 mg/kg) had lower serum contents of IL-8, and the birds in the ARC200 group had lower serum contents of IFN-γ compared with PC birds (P < 0.05). The in vitro experiment showed that ARC significantly inhibited the biofilm formation and adhesion of S. pullorum (P < 0.05). Metabonomics analysis revealed that ARC can restrain the formation of the biofilm by affecting a variety of metabolic pathways of S. pullorum. Therefore, dietary supplementation of 200 mg/kg ARC might be a potential way to substitute antibiotics to control S. pullorum infection in broilers.

Glycomacropeptide Safety and Its Effect on Gut Microbiota in Patients with Phenylketonuria: A Pilot Study

Glycomacropeptide (GMP) represents a good alternative protein source in Phenylketonuria (PKU). In a mouse model, it has been suggested to exert a prebiotic role on beneficial gut bacteria. In this study, we performed the 16S rRNA sequencing to evaluate the effect of 6 months of GMP supplementation on the gut microbiota of nine PKU patients, comparing their bacterial composition and clinical parameters before and after the intervention. GMP seems to be safe from both the microbiological and the clinical point of view. Indeed, we did not observe dramatic changes in the gut microbiota but a specific prebiotic effect on the butyrate-producer Agathobacter spp. and, to a lesser extent, of Subdoligranulum. Clinically, GMP intake did not show a significant impact on both metabolic control, as phenylalanine values were kept below the age target and nutritional parameters. On the other hand, an amelioration of calcium phosphate homeostasis was observed, with an increase in plasmatic vitamin D and a decrease in alkaline phosphatase. Our results suggest GMP as a safe alternative in the PKU diet and its possible prebiotic role on specific taxa without causing dramatic changes in the commensal microbiota.

Gut-Microbiome Composition in Response to Phenylketonuria Depends on Dietary Phenylalanine in BTBR Pahenu2 Mice

Phenylketonuria (PKU) is a metabolic disorder caused by a hepatic enzyme deficiency causing high blood and brain levels of the amino acid Phenylalanine (Phe), leading to severe cognitive and psychological deficits that can be prevented, but not completely, by dietary treatment. The behavioral outcome of PKU could be affected by the gut-microbiome-brain axis, as diet is one of the major drivers of the gut microbiome composition. Gut-microbiome alterations have been reported in treated patients with PKU, although the question remains whether this is due to PKU, the dietary treatment, or their interaction. We, therefore, examined the effects of dietary Phe restriction on gut-microbiome composition and relationships with behavioral outcome in mice. Male and female BTBR Pah^enu2 mice received either a control diet (normal protein, “high” Phe), liberalized Phe-restricted (33% natural protein restriction), or severe Phe-restricted (75% natural protein restriction) diet with protein substitutes for 10 weeks (n = 14 per group). Their behavioral performance was examined in an open field test, novel and spatial object location tests, and a balance beam. Fecal samples were collected and sequenced for the bacterial 16S ribosomal RNA (rRNA) region. Results indicated that PKU on a high Phe diet reduced Shannon diversity significantly and altered the microbiome composition compared with wild-type animals. Phe-restriction prevented this loss in Shannon diversity but changed community composition even more than the high-Phe diet, depending on the severity of the restriction. Moreover, on a taxonomic level, we observed the highest number of differentially abundant genera in animals that received 75% Phe-restriction. Based on correlation analyses with differentially abundant taxa, the families Entereococacceae, Erysipelotrichaceae, Porphyromonadaceae, and the genus Alloprevotella showed interesting relationships with either plasma Phe levels and/or object memory. According to our results, these bacterial taxa could be good candidates to start examining the microbial metabolic potential and probiotic properties in the context of PKU. We conclude that PKU leads to an altered gut microbiome composition in mice, which is least severe on a liberalized Phe-restricted diet. This may suggest that the current Phe-restricted diet for PKU patients could be optimized by taking dietary effects on the microbiome into account.

Engineering Organoids for in vitro Modeling of Phenylketonuria

Phenylketonuria is a recessive genetic disorder of amino-acid metabolism, where impaired phenylalanine hydroxylase function leads to the accumulation of neurotoxic phenylalanine levels in the brain. Severe cognitive and neuronal impairment are observed in untreated/late-diagnosed patients, and even early treated ones are not safe from life-long sequelae. Despite the wealth of knowledge acquired from available disease models, the chronic effect of Phenylketonuria in the brain is still poorly understood and the consequences to the aging brain remain an open question. Thus, there is the need for better predictive models, able to recapitulate specific mechanisms of this disease. Human induced pluripotent stem cells (hiPSCs), with their ability to differentiate and self-organize in multiple tissues, might provide a new exciting in vitro platform to model specific PKU-derived neuronal impairment. In this review, we gather what is known about the impact of phenylalanine in the brain of patients and highlight where hiPSC-derived organoids could contribute to the understanding of this disease.

Preliminary Investigation of Microbiome and Dietary Differences in Patients with Phenylketonuria on Enzyme Substitution Therapy Compared to Traditional Therapies

BACKGROUND

Phenylketonuria (PKU) is an inborn error of metabolism that impairs the function of the enzyme phenylalanine hydroxylase (PAH). Historical treatment includes limiting dietary phenylalanine (Phe) consumption while supplementing with medical food; however, this treatment has been associated with complications, such as nutritional deficiencies and disruptions in the gut microbiota.

OBJECTIVE

The study aim was to compare dietary and gut microbiome differences between adult patients on a traditional PKU diet to those receiving the enzyme substitution therapy Palynziq on a liberalized diet while controlling blood Phe levels to <600 μmol/L.

DESIGN

A cross-sectional study was conducted comparing patients on a traditional Phe-restricted diet with patients receiving Palynziq eating a liberalized diet.

PARTICIPANTS/SETTING

Six patients eating a traditional Phe-restricted diet with medical food and six patients on Palynziq eating a liberalized diet without medical food intake for >3 years were selected from the University of Kentucky Metabolic Clinic August to December 2019.

MAIN OUTCOME MEASURES

Nutrient intake from three-day diet records and fecal microbiome taxonomic abundances were analyzed.

STATISTICAL ANALYSIS

Mann-Whitney U-tests were used for dietary data analysis. Differential abundance analysis for microbiome taxa and pathway data was done using DESeq2 analysis.

RESULTS

Dietary data showed Palynziq patients consumed a lower percent of kilocalories from total protein and lower amounts of most micronutrients but consumed greater amounts of intact protein and cholesterol (P<0.05). Microbiome data revealed a greater abundance of the phylum Verrucomicrobia and genus Lachnobacterium in the Traditional group and a greater abundance of the genus Prevotella in the Palynziq group (P<0.05). Pathway analysis depicted greater enrichment in carotenoid and amino acid metabolism pathways in the Traditional group (P<0.05). Protein (%kcal), dietary fiber (g), fat (%kcal), linolenic acid (%DRI), and age were correlated with the underlying microbial community structure for both groups combined.

CONCLUSIONS

Patients with PKU treated with Palynziq on a liberalized diet manifest significant differences in diet composition compared to those treated with traditional Phe-restricted diets. Several of these dietary differences may affect the microbiome architecture.

Differences in faecal microbiome composition between adult patients with UCD and PKU and healthy control subjects

Urea cycle disorders (UCDs) are a group of rare inherited metabolic diseases causing hyperammonemic encephalopathy. Despite intensive dietary and pharmacological therapy, outcome is poor in a subset of UCD patients. Reducing ammonia production by changing faecal microbiome in UCD is an attractive treatment approach. We compared faecal microbiome composition of 10 UCD patients, 10 healthy control subjects and 10 phenylketonuria (PKU) patients. PKU patients on a low protein diet were included to differentiate between the effect of a low protein diet and the UCD itself on microbial composition. Participants were asked to collect a faecal sample and to fill out a 24 h dietary journal. DNA was extracted from faecal material, taxonomy was assigned and microbiome data was analyzed, with a focus on microbiota involved in ammonia metabolism.In this study we show an altered faecal microbiome in UCD patients, different from both PKU and healthy controls. UCD patients on dietary and pharmacological treatment had a less diverse faecal microbiome, and the faecal microbiome of PKU patients on a protein restricted diet with amino acid supplementation showed reduced richness compared to healthy adults without a specific diet. The differences in the microbiome composition of UCD patients compared to healthy controls were in part related to lactulose use. Other genomic process encodings involved in ammonia metabolism, did not seem to differ. Since manipulation of the microbiome is possible, this could be a potential treatment modality. We propose as a first next step, to study the impact of these faecal microbiome alterations on metabolic stability.

TAKE HOME MESSAGE

The faecal microbiome of UCD patients was less diverse compared to PKU patients and even more compared to healthy controls.

A metagenomic study of the gut microbiome in PTB'S disease

BACKGROUND

There is an abundant link between the gut microbiota and human health and it plays a critical role in the clinic. It is recognized that microbial dysregulation contributes to the pathogenesis of tuberculosis (TB), but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with TB as well as its possible roles in the development of this disease.

METHODS

Fecal samples were collected from 10 TB patients and 20 healthy control samples. DNA extracted from fecal samples was subjected to 16S rDNA gene sequencing analysis on the Illumina MiSeq platform.

RESULTS

Compared with healthy control samples, the gut microbiome of patients with TB was characterized by the decreased Alpha diversity. Perhaps, the decrease of microbial diversity which results in microbial dysregulation is the reason for clinical patients with more symptoms. The PTB group showed the most unique microbiota by higher abundance of Bifidobacteriaceae, Bifidobacteriales, Coriobacteriaceae, Coriobacteriales, Actinobacteria, Caulobacteraceae, Phyllobacteriaceae, Rhizobiales, Burkholderiaceae, Burkholderiaceae. Inflammatory status in PTB patients may be associated with the increased abundance of Clostridia and decreased abundance of Prevotella. We found that the abundance of Solobacterium and Actinobacteria was higher in the patients. There were 4 significant differences (p<0.05) in the two groups which belonged to four metabolic categories, including endocytosis, phosphotransferase system (PTS), toluene degradation, and amoebiasis.

CONCLUSION

We applied the approach of metagenomic sequencing to characterize the features of gut microbiota in PTB patients. The present study provided a detailed analysis of the characterization of the gut microbiota in patients based on the clinic. According to the metagenome analysis, our results indicated that the gut microbiota in PTB patients was significantly different from healthy control samples as characterized by the bacteria and metabolic pathway. The richness of the gut microbiota in patients was revealed. It was hypothesized that the above-mentioned changes of the gut microbiota could exert an impact on the development of PTB through the downstream regulation of the immune status of the host by way of the gut-lung axis.

Effects of Dietary Glucose Oxidase Supplementation on the Performance, Apparent Ileal Amino Acids Digestibility, and Ileal Microbiota of Broiler Chickens

Simple Summary

Glucose oxidase was used as a potential additive to improve intestinal health in livestock and poultry industry. This study aimed to investigate the effects of glucose oxidase supplementation on performance, ileal microbiota, ileal short-chain fatty acids profile, and apparent ileal digestibility in grower broilers. Our findings will provide a valuable insight into the possibility of glucose oxidase as an alternative of antibiotic growth promoters in broiler diets.

Abstract

This study aimed to investigate the effects of glucose oxidase (GOD) supplementation on growth performance, apparent ileal digestibility (AID) of nutrients, intestinal morphology, and short-chain fatty acids (SCFAs) and microbiota in the ileum of broilers. Six hundred 1-day-old male broilers were randomly allotted to four groups of 10 replicates each with 15 birds per replicate cage. The four treatments included the basal diet without antibiotics (Control) and the basal diet supplemented with 250, 500, or 1000 U GOD/kg diet (E250, E500 or E1000). The samples of different intestinal segments, ileal mucosa, and ileal digesta were collected on d 42. Dietary GOD supplementation did not affect daily bodyweight gain (DBWG) and the ratio of feed consumption and bodyweight gain (FCR) during d 1-21 (p > 0.05); however, the E250 treatment increased DBWG (p = 0.03) during d 22–42 as compared to control. Dietary GOD supplementation increased the AIDs of arginine, isoleucine, lysine, methionine, threonine, cysteine, serine, and tyrosine (p < 0.05), while no significant difference was observed among the GOD added groups. The E250 treatment increased the villus height of the jejunum and ileum. The concentrations of secreted immunoglobulin A (sIgA) in ileal mucosa and the contents of acetic acid and butyric acid in ileal digesta were higher in the E250 group than in the control (p < 0.05), whereas no significant differences among E500, E1000, and control groups. The E250 treatment increased the richness of ileal microbiota, but E500 and E100 treatment did not significantly affect it. Dietary E250 treatment increased the relative abundance of Firmicutes phylum and Lactobacillus genus, while it decreased the relative abundance of genus Escherichina-Shigella (p < 0.05). Phylum Fusobacteria only colonized in the ileal digesta of E500 treated broilers and E500 and E1000 did not affect the relative abundance of Firmicutes phylum and Lactobacillus and Escherichina-Shigella genera as compared to control. These results suggested that dietary supplementation of 250 U GOD/kg diet improves the growth performance of broilers during d 22–42, which might be associated with the alteration of the intestinal morphology, SCFAs composition, and ileal microbiota composition.

A low abundance of genus Bacteroides in gut microbiota is negatively correlated with blood phenylalanine levels in Uygur patients with phenylketonuria

BACKGROUND

A low-phenylalanine (Phe) diet affects the metabolism and diversity of gut microbial communities in children with phenylketonuria (PKU). Our study examined gut microbiota characteristics and metabolic pathways, and their correlations with clinical phenotypes in a high-incidence population.

METHODS

We assessed clinical phenotypes and gut microbiota by 16S ribosomal RNA (rRNA) sequencing, and performed a correlation analysis between phenotype and gut microbiota in a PKU group (n=11) and a healthy group (n=11).

RESULTS

The PKU group had significantly lower microbiota diversity than the healthy group (P_shannon=0.014). Phylum-level composition differed significantly between the PKU and healthy groups (Firmicutes: 44.3% vs. 43.1%; Actinobacteria: 25.9% vs. 3.3%; Bacteroidetes: 16.6% vs. 53.2%; and Proteobacteria: 10.9% vs. 0.12%, respectively). Further, a significantly decreased level of genus Bacteroidetes (P<0.0001) in the PKU group was negatively correlated with blood Phe level (P=0.014). The microbial function prediction of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways exhibited a decreased ability of glycan degradation and glutamate metabolism in the PKU group.

CONCLUSIONS

Our findings revealed that genus Bacteroide was not only in extremely low abundance in the PKU group, but was also negatively correlated with blood Phe level. The remarkable capability of genus Bacteroides to use complex recalcitrant glycans may be the main reason for the decreased ability of glycan degradation in the PKU group.

Dysbiosis, Host Metabolism, and Non-communicable Diseases: Trialogue in the Inborn Errors of Metabolism

Inborn errors of metabolism (IEMs) represent a complex system model, in need of a shift of approach exploring the main factors mediating the regulation of the system, internal or external and overcoming the traditional concept of biochemical and genetic defects. In this context, among the established factors influencing the metabolic flux, i.e., diet, lifestyle, antibiotics, xenobiotics, infectious agents, also the individual gut microbiota should be considered. A healthy gut microbiota contributes in maintaining human health by providing unique metabolic functions to the human host. Many patients with IEMs are on special diets, the main treatment for these diseases. Hence, IEMs represent a good model to evaluate how specific dietary patterns, in terms of macronutrients composition and quality of nutrients, can be related to a characteristic microbiota associated with a specific clinical phenotype (“enterophenotype”). In the present review, we aim at reporting the possible links existing between dysbiosis, a condition reported in IEMs patients, and a pro-inflammatory status, through an altered “gut-liver” cross-talk network and a major oxidative stress, with a repercussion on the health status of the patient, increasing the risk of non-communicable diseases (NCDs). On this basis, more attention should be paid to the nutritional status assessment and the clinical and biochemical signs of possible onset of comorbidities, with the goal of improving the long-term wellbeing in IEMs. A balanced intestinal ecosystem has been shown to positively contribute to patient health and its perturbation may influence the clinical spectrum of individuals with IEMs. For this, reaching eubiosis through the improvement of the quality of dietary products and mixtures, the use of pre-, pro- and postbiotics, could represent both a preventive and therapeutic strategy in these complex diseases.

Insights into the Role of the Microbiota and of Short-Chain Fatty Acids in Rubinstein-Taybi Syndrome

The short-chain fatty acid butyrate, produced by the gut microbiota, acts as a potent histone deacetylase (HDAC) inhibitor. We assessed possible ameliorative effects of butyrate, relative to other HDAC inhibitors, in in vitro and in vivo models of Rubinstein–Taybi syndrome (RSTS), a severe neurodevelopmental disorder caused by variants in the genes encoding the histone acetyltransferases CBP and p300. In RSTS cell lines, butyrate led to the patient-specific rescue of acetylation defects at subtoxic concentrations. Remarkably, we observed that the commensal gut microbiota composition in a cohort of RSTS patients is significantly depleted in butyrate-producing bacteria compared to healthy siblings. We demonstrate that the effects of butyrate and the differences in microbiota composition are conserved in a Drosophila melanogaster mutant for CBP, enabling future dissection of the gut–host interactions in an in vivo RSTS model. This study sheds light on microbiota composition in a chromatinopathy, paving the way for novel therapeutic interventions.

Changes in Gut Microbiota after a Four-Week Intervention with Vegan vs. Meat-Rich Diets in Healthy Participants: A Randomized Controlled Trial

An essential role of the gut microbiota in health and disease is strongly suggested by recent research. The composition of the gut microbiota is modified by multiple internal and external factors, such as diet. A vegan diet is known to show beneficial health effects, yet the role of the gut microbiota is unclear. Within a 4-week, monocentric, randomized, controlled trial with a parallel group design (vegan (VD) vs. meat-rich (MD)) with 53 healthy, omnivore, normal-weight participants (62% female, mean 31 years of age), fecal samples were collected at the beginning and at the end of the trial and were analyzed using 16S rRNA gene amplicon sequencing (Clinical Trial register: DRKS00011963). Alpha diversity as well as beta diversity did not differ significantly between MD and VD. Plotting of baseline and end samples emphasized a highly intra-individual microbial composition. Overall, the gut microbiota was not remarkably altered between VD and MD after the trial. Coprococcus was found to be increased in VD while being decreased in MD. Roseburia and Faecalibacterium were increased in MD while being decreased in VD. Importantly, changes in genera Coprococcus, Roseburia and Faecalibacterium should be subjected to intense investigation as markers for physical and mental health.

Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mouse models, depending on sex and metabolic status in well controlled experimental setting. Our study aimed to examine metformin-induced alterations in gut microbiome diversity, composition, and functional implications of high-fat diet-induced type 2 diabetes mouse model, using, for the first time in mice study, the shotgun metagenomic sequencing that allows estimation of microorganisms at species level. We also employed a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups to systematically evaluate the effect of sex and metabolic status on metformin interaction with microbiome. We used DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species relative abundances increased. In contrast, no significant changes were observed in control diet-fed mice. Functional analysis targeted to carbohydrate, lipid, and amino acid metabolism pathways revealed 14 significantly altered hierarchies. We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while in females the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. The same pattern manifested regarding the functional analysis, where we discovered 5 significantly affected hierarchies in female groups but not in males. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.

The Adult Phenylketonuria (PKU) Gut Microbiome

Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 region of the 16S rRNA gene from stool samples collected from adults with PKU (n = 11) and non-PKU controls (n = 21). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria. Gut community diversity was lower in PKU individuals, though this effect was only statistically suggestive. A total of 65 genera across 5 phyla were statistically differentially abundant between PKU and control samples (p < 0.001). Additionally, we identified six metabolic pathways that differed between groups (p < 0.05), with four enriched in PKU samples and two in controls. While the child PKU gut microbiome has been previously investigated, this is the first study to explore the gut microbiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKU adults and highlights the need for further studies to understand the effects of dietary restrictions.

Nutrition, Microbiota and Role of Gut-Brain Axis in Subjects with Phenylketonuria (PKU): A Review

The composition and functioning of the gut microbiota, the complex population of microorganisms residing in the intestine, is strongly affected by endogenous and exogenous factors, among which diet is key. Important perturbations of the microbiota have been observed to contribute to disease risk, as in the case of neurological disorders, inflammatory bowel disease, obesity, diabetes, cardiovascular disease, among others. Although mechanisms are not fully clarified, nutrients interacting with the microbiota are thought to affect host metabolism, immune response or disrupt the protective functions of the intestinal barrier. Similarly, key intermediaries, whose presence may be strongly influenced by dietary habits, sustain the communication along the gut-brain-axis, influencing brain functions in the same way as the brain influences gut activity. Due to the role of diet in the modulation of the microbiota, its composition is of high interest in inherited errors of metabolism (IEMs) and may reveal an appealing therapeutic target. In IEMs, for example in phenylketonuria (PKU), since part of the therapeutic intervention is based on chronic or life-long tailored dietetic regimens, important variations of the microbial diversity or relative abundance have been observed. A holistic approach, including a healthy composition of the microbiota, is recommended to modulate host metabolism and affected neurological functions.

Proteobacteria Overgrowth and Butyrate-Producing Taxa Depletion in the Gut Microbiota of Glycogen Storage Disease Type 1 Patients

A life-long dietary intervention can affect the substrates’ availability for gut fermentation in metabolic diseases such as the glycogen-storage diseases (GSD). Besides drug consumption, the main treatment of types GSD-Ia and Ib to prevent metabolic complications is a specific diet with definite nutrient intakes. In order to evaluate how deeply this dietary treatment affects gut bacteria, we compared the gut microbiota of nine GSD-I subjects and 12 healthy controls (HC) through 16S rRNA gene sequencing; we assessed their dietary intake and nutrients, their microbial short chain fatty acids (SCFAs) via gas chromatography and their hematic values. Both alpha-diversity and phylogenetic analysis revealed a significant biodiversity reduction in the GSD group compared to the HC group, and highlighted profound differences of their gut microbiota. GSD subjects were characterized by an increase in the relative abundance of Enterobacteriaceae and Veillonellaceae families, while the beneficial genera Faecalibacterium and Oscillospira were significantly reduced. SCFA quantification revealed a significant increase of fecal acetate and propionate in GSD subjects, but with a beneficial role probably reduced due to unbalanced bacterial interactions; nutritional values correlated to bacterial genera were significantly different between experimental groups, with nearly opposite cohort trends.

Culturable gut bacteria lack Escherichia coli in children with phenylketonuria

Phenylketonuria (PKU) is an inherited metabolic disorder that affects phenylalanine metabolism. If left untreated, phenylalanine builds up to harmful levels in the body and may cause intellectual disability and other serious health problems. The aim of this study was to compare the culturable predominant bacteria in the gut of PKU versus non-PKU children in Jordan to measure the effect of a PKU low-protein diet on the normal flora. Escherichia coli is a bacterium of the normal gut flora in humans and vitally benefits the hosts in producing vitamin B₂ (riboflavin) and vitamin K₂ (menaquinone) involved in human cellular and bone metabolism, respectively. For a small-scale observational study, stool samples were collected from 25 children divided into 20 subjects without PKU as controls and five PKU subjects. Only predominant culturable bacteria were isolated from the stool on CLED (cysteine-lactose-electrolyte-deficient) agar, which was a limitation of this study. Samples were incubated at 35 ± 2°C, observed after 24-48 h, and transported to an automated microbial analyser. Data analysis was obtained using the independent sample t-test to determine any statistically significant difference in the microbial gut community between the associated population means. It was statistically significant (p < 0.01) that E. coli was present in all control subjects, while it was absent from the gut flora of all PKU subjects. Additional studies on a larger scale are needed to confirm these results and also any association with blood serum levels of phenylalanine and vitamins B₂ and K₂.

Differential Effects of Typical Korean Versus American-Style Diets on Gut Microbial Composition and Metabolic Profile in Healthy Overweight Koreans: A Randomized Crossover Trial

The Westernized diet has been associated with the pathogenesis of metabolic diseases, whereas a Korean diet has been reported to exert beneficial effects on health in several studies. However, the effects of Western and Korean diets on the gut microbiome and host metabolome are unclear. To examine the diet-specific effects on microbiome and metabolome, we conducted a randomized crossover clinical trial of typical Korean diet (TKD), typical American diet (TAD), and recommended American diet (RAD). The trial involved a 4-week consumption of an experimental diet followed by a 2-week interval before diet crossover. 16S rRNA sequencing analysis identified 16, 10, and 14 differential bacteria genera specific to TKD, RAD, and TAD, respectively. The Firmucutes-Bacteroidetes ratio was increased by TKD. Nuclear magnetic resonance metabolome profiling revealed that TKD enriched branched chain amino acid metabolism, whereas ketone body metabolism was evident in RAD and TAD. Microbiome and metabolome responses to the experimental diets varied with individual enterotypes. These findings provide evidence that the gut microbiome and host metabolome rapidly respond to different cultural diets. The findings will inform clarification of the diet-related communication networks of the gut microbiome and host metabolome in humans.