Microbiome In Health Research Articles

Diet Quality and Liver Health in People Living with HIV in the MASH Cohort: A Multi-Omic Analysis of the Fecal Microbiome and Metabolome.

The gut-liver axis has been recognized as a potential pathway in which dietary factors may contribute to liver disease in people living with HIV (PLWH). The objective of this study was to explore associations between dietary quality, the fecal microbiome, the metabolome, and liver health in PLWH from the Miami Adult Studies on HIV (MASH) cohort. We performed a cross-sectional analysis of 50 PLWH from the MASH cohort and utilized the USDA Healthy Eating Index (HEI)-2015 to measure diet quality. A Fibrosis-4 Index (FIB-4) score < 1.45 was used as a strong indication that advanced liver fibrosis was not present. Stool samples and fasting blood plasma samples were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry. Statistical analyses included biomarker identification using linear discriminant analysis effect size. Compared to participants with FIB-4 ≥ 1.45, participants with FIB-4 < 1.45 had higher intake of dairy (p = 0.006). Fibrosis-4 Index score was inversely correlated with seafood and plant protein HEI component score (r = -0.320, p = 0.022). The relative abundances of butyrate-producing taxa Ruminococcaceae, Roseburia, and Lachnospiraceae were higher in participants with FIB-4 < 1.45. Participants with FIB-4 < 1.45 also had higher levels of caffeine (p = 0.045) and related metabolites such as trigonelline (p = 0.008) and 1-methylurate (p = 0.023). Dietary components appear to be associated with the fecal microbiome and metabolome, and liver health in PLWH. Future studies should investigate whether targeting specific dietary components may reduce liver-related morbidity and mortality in PLWH.

Dietary fibre and health: the story so far.

The present paper reviews progress in research on dietary fibre and human health over the past five decades. There is now convincing evidence from prospective cohort studies that diets low in dietary fibre are associated with increased risk of common non-communicable diseases including CVD, type 2 diabetes and colorectal cancer. These findings provide strong support for hypotheses proposed by Denis Burkitt 50 years ago, based on very limited evidence but with considerable imagination and insight. For the first two to three decades of this period, research on dietary fibre was hampered by the lack of consensus about the definition, and measurement, of this complex and diverse dietary component and by the lack of appropriate tools for investigating the gut microbiome that is central to understanding mechanisms of action. Recent technical and scientific advances in microbiome research (based on fast, low-cost, DNA sequencing) are facilitating investigation of the associations between dietary fibre, the gut microbiome and human health. Current challenges include the need for agreement about the characteristics of a healthy gut microbiome. Although the health benefits attributed to higher dietary fibre intake are likely to be shared with most types of dietary fibre, one should anticipate that different sources of dietary fibre and the other components (resistant starch and non-digestible oligosaccharides) that make up dietary fibre will have characteristically different effects on human physiology and disease risk. In conclusion, population-level intakes of dietary fibre are low and there is a public health priority to develop and implement more effective interventions to increase intake.

Prebiotic mechanisms of resistant starches from dietary beans and pulses on gut microbiome and metabolic health in a humanized murine model of aging.

Dietary pulses, being a rich source of fiber and proteins, offer an ideal and inexpensive food choice for older adults to promote gut and metabolic health. However, the prebiotic effects of dietary pulses-derived resistant starches (RS), compared to RS from cereals and tubers, remain relatively underexplored, particularly in context to their gut modulatory potential in old age. We herein investigate the prebiotic effects of pulses-derived RS on the gut microbiome and intestinal health in aged (60-week old) mice colonized with human microbiota. C57B6/J mice were fed for 20 weeks with either a western-style high-fat diet (control; CTL) or CTL diet supplemented (5% w/w) with RS from pinto beans (PTB), black-eyed-peas (BEP), lentils (LEN), chickpeas (CKP), or inulin (INU; reference control). We find that the RS supplementation modulates gut microbiome in a sex-dependent manner. For instance, CKP enriched α-diversity only in females, while β-diversity deviated for both sexes. Further, different RS groups exhibited distinct microbiome differences at bacterial phyla and genera levels. Notably, LEN fostered Firmicutes and depleted Proteobacteria abundance, whereas Bacteroidota was promoted by CKP and INU. Genus Dubosiella increased dominantly in males for all groups except PTB, whilst Faecalibaculum decreased in females by CKP and INU groups. Linear discriminant analysis effect size (LEfSe) and correlational analyzes reveal RS-mediated upregulation of key bacterial genera associated with short-chain fatty acids (butyrate) production and suppression of specific pathobionts. Subsequent machine-learning analysis validate decreased abundance of notorious genera, namely, Enterococcus, Odoribacter, Desulfovibrio, Alistipes and Erysipelatoclostridium among RS groups. CKP and LEN groups partly protected males against post-prandial glycemia. Importantly, RS ameliorated high-fat diet-induced gut hyperpermeability and enhanced expression of tight-junction proteins (claudin-1 and claudin-4), which were more pronounced for LEN. In addition, IL10 upregulation was more prominent for LEN, while TNF-α was downregulated by LEN, CKP, and INU. Together, these findings demonstrate that RS supplementation beneficially modulates the gut microbiome with a reduction in gut leakiness and inflammation, indicating their prebiotic potential for functional food and nutritional applications.

Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study.

To explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets. Ten patients (21.4 ±3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3-v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points. Within 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05). By incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque accumulation as well as the key pathogens S. mutans and F. nucleatum in the early stage of orthodontic treatment.

Berries in Microbiome-Mediated Gastrointestinal, Metabolic, and Immune Health.

Current research has shown that berry-derived polymeric substrates that resist human digestion (dietary fibers and polyphenols) are extensively metabolized in the gastrointestinal tract dominated by microbiota. This review assesses current epidemiological, experimental, and clinical evidence of how berry (strawberry, blueberry, raspberry, blackberry, cranberry, black currant, and grapes) phytochemicals interact with the microbiome and shape health or metabolic risk factor outcomes. There is agrowing evidence that the compositional differences among complex carbohydrate fractions and classes of polyphenols define reversible shifts in microbial populations and human metabolome to promote gastrointestinal health. Interventions to prevent gastrointestinal inflammation and improve metabolic outcomes may be achieved with selection of berries that provide distinct polysaccharide substrates for selective multiplication of beneficial microbiota or oligomeric decoys for binding and elimination of the pathogens, as well as phenolic substrates that hold potential to modulate gastrointestinal mucins, reduce luminal oxygen, and release small phenolic metabolites signatures capable of ameliorating inflammatory and metabolic perturbations. These mechanisms may explain many of the differences in microbiota and host gastrointestinal responses associated with increased consumption of berries, and highlight potential opportunities to intentionally shift gut microbiome profiles or to modulate risk factors associated with better nutrition and health outcomes.

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics-Leveraging Principles of Systems Biology.

The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the "host" are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome "dysbiosis" and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.

Quantification of short-chain fatty acids in human stool samples by LC-MS/MS following derivatization with aniline analogues

The gut microbiome produces a range of short chain fatty acids (SCFA) crucially linked with diet and nutrition, metabolism, gastrointestinal health and homeostasis. SCFA are primarily measured using gas or liquid chromatography-mass spectrometry (LC/MS) after undergoing chemical derivatization. Here we assess the merits of a derivatization protocol using aniline and two aniline analogues (3-phenoxyaniline and 4-(benzyloxy)aniline) for the targeted LC-MS/MS quantification of nine SCFA (acetic, propionic, butyric, valeric, caproic acid, isobutyric, isovaleric, 2-methylbutyric, and 2-ethylbutyric acid). Evaluation of product ion spectra and optimization of MS detection conditions, provided superior detection sensitivity for 3-phenoxyaniline and 4-(benzyloxy)aniline compared to aniline. We developed a facile SCFA derivatization method using 3-phenoxyaniline under mild reaction conditions which allows for the simultaneous quantification of these SCFA in human stool samples in under eleven minutes using multiple reaction monitoring LC-MS/MS. The method was successfully validated and demonstrates intra- and inter-day accuracy (88.5–103% and 86.0–109%) and precision (CV of 0.55–7.00% and 0.33–9.55%) with recoveries (80.1–87.2% for LLOQ, 88.5–93.0% for ULOQ) and carry-over of (2.68–17.9%). Selectivity, stability and matrix effects were also assessed and satisfied validation criteria. Method applicability was demonstrated by analysing SCFA profiles in DNA-stabilized human stool samples from newly diagnosed colorectal cancer patients prior to surgery. The development of this improved method and its compatibility to measure SCFAs from DNA-stabilized stool will facilitate studies investigating the gut microbiome in health and disease.

The Vaginal Microbiome in Health and Disease—What Role Do Common Intimate Hygiene Practices Play?

The vaginal microbiome is a dynamic, sensitive microenvironment. The hallmark of a 'healthy' vaginal microbiome is currently believed to be one dominated by Lactobacillus spp., which acidifies the vaginal environment and help to protect against invading pathogens. However, a 'normal' microbiome is often difficult, if not impossible, to characterise given that it varies in response to numerous variables, including pregnancy, the menstrual cycle, contraceptive use, diet, ethnicity, and stress. A Lactobacillus-depleted microbiome has been linked to a variety of adverse vaginal health outcomes, including preterm birth (PTB), bacterial vaginosis (BV), and increased risk of sexually transmitted infections. The latter two of these have also been associated with feminine intimate hygiene practices, many of which are practised without any evidence of health benefits. The most extensively studied practice is vaginal douching, which is known to cause vaginal dysbiosis, predisposing women to BV, pelvic inflammatory disease, and PTB. However, little is known of the impact that intimate hygiene practices and associated products have on the vaginal microbiome. This review aims to outline the major factors influencing the vaginal microbiome and common vaginal infections, as well as to summarise current research surrounding the impact of hygiene products and practices on the vaginal microbiome.

A Limited Effect of Chronic Renal Insufficiency on the Colon Microbiome.

A Limited Effect of Chronic Renal Insufficiency on the Colon Microbiome.

All fibers are not created equal: The microbiome, postbiotics, and pet health

The gastrointestinal microbiome comprises trillions of bacteria, and is a vitally important organ with wide ranging effects on pet health Food impacts the composition and metabolism of the microbiome, as well as the production of postbiotics, which are bioactive end products of microbial consumption of prebiotics. Postbiotics include metabolites of nutrients like fatty acids, amino acids, vitamins and polysaccharides. Also gut bacteria can produce postbiotics from plant antioxidants like polyphenols. A growing body of evidence has shown that influencing postbiotic production may have beneficial effects on pet health. Soluble and insoluble fibers are commonly used sources of prebiotics in the pet food industry, some of these fibers have polyphenols bound to them. Understanding the impact of each fiber type on the microbiome composition, metabolism and postbiotic production provides insights into formulating foods that are optimal for pet health.

Oral Microbiome and Systemic Diseases

As one of the most diverse microbial communities within the human body, the oral microbiome is an important component that contributes to the maintenance of human health. The microbial composition of different sites in the oral cavity varies significantly and a dynamic equilibrium is maintained through communications with the environment and oral and distal organs of the host. It has been reported that there is significant correlation between dysbiotic oral microbiome and the occurrence or progression of a variety of systemic diseases. In this review, we summarized recent advances in research on the relationship between oral microbiome and systemic health, focusing on the interaction and pathological mechanisms between oral microbiome and systemic health and hoping to provide new avenues for the early prevention and clinical diagnosis and treatment of systemic diseases.

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy.

Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.

Does Fibre-fix provided to people with irritable bowel syndrome who are consuming a low FODMAP diet improve their gut health, gut microbiome, sleep and mental health?

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The gut microbiome in children with mood, anxiety, and neurodevelopmental disorders: An umbrella review.

Research on the gut microbiome and mental health among children and adolescents is growing. This umbrella review provides a high-level overview of current evidence syntheses to amalgamate current research and inform future directions. Searches were conducted across seven databases for peer-reviewed pediatric (<18years) review literature. Studies reporting gut microbiome composition and/or biotic supplementation on depression, bipolar disorder, anxiety, attention deficit hyperactivity disorder, autism spectrum disorder (ASD), or obsessive-compulsive disorder (OCD) were included. Deduplication and screening took place in Covidence. A sensitivity analysis was conducted to assess the degree of primary study overlap. Among the 39 included review studies, 23 (59%) were observational and 16 (41%) were interventional. Most reviews (92%) focused on ASD. Over half (56%) of the observational and interventional reviews scored low or critically low for methodological quality. A higher abundance of Clostridium clusters and a lower abundance of Bifidobacterium were consistently observed in ASD studies. Biotic supplementation was associated with ASD symptom improvement. Gut microbiome-mental health evidence syntheses in child and youth depression, anxiety, bipolar disorder, and OCD are lacking. Preliminary evidence suggests an association between specific microbiota and ASD symptoms, with some evidence supporting a role for probiotic supplementation ASD therapy.

The effects of dairy on the gut microbiome and gastrointestinal health in gastrointestinal disease cohorts: a systematic review

The effects of dairy on the gut microbiome and gastrointestinal health in gastrointestinal disease cohorts: a systematic review

Integrating seed microbiome knowledge into restoration and ex situ conservation of native Australian plants

Context Seeds harbour a diversity of microbes, which in some plants aid with germination and establishment. Seeds form a critical part in the lifecycle of plants and a role in many conservation and restoration activities. Aims Because this is an emerging field in seed biology, we aim to highlight the key research gaps of interest to seed on the basis of restoration and ex situ conservation. Methods We identify knowledge gaps associated with the seed endophytic microbiome of native Australian plants through undertaking a literature review. Additionally, culturing methods were used to identify the fungal seed endophytes of five native Australian species. Key results We identified a diversity of taxa within the native seed and show three taxa that are common to all study hosts. Sampling seed from additional hosts at a site and additional sites of a host species showed new fungal diversity. Our literature review showed that little information is available on native seed microbiomes and we identified four key areas where research gaps exist, linking with seed-based restoration practices. Conclusions We provide evidence that there is a complex and diverse seed microbiome within some Australian native plants and suggest ways that it could be integrated into restoration and conservation practices. Implications We propose that by taking into consideration the presence of a seed microbiome and its potential impacts on plant health, seed microbiomes could be used as one method to restore microbial diversity into an ecosystem and to contribute to the seedling microbiome and plant health at restored sites.

Analyzing the Prebiotic Potential of Glucosamine for Targeting the Gut Microbiome Health

Recognizing the composition and modulation of the microbiome, a viable therapeutic tool for multi-targeted therapy is a new strategy that has recently been explored. Glucosamine (GS) is being studied for its prebiotic potential in addition to being the most abundant and naturally occurring amino monosaccharide. The current study focuses on glucosamine’s prebiotic potential by assessing the stability of various GS concentrations (1% - 5%) in the gastrointestinal tract (GIT) and its ability to be fermented by the gut microbiota. The results showed that GS stimulated the most growth in L. acidophilus even after a longer incubation time than B. bifidum and L. acidophilus growth was concentration-dependent, with maximum growth at 3% with a simultaneous decrease in pH (5.6 - 1.7). The decrease in GS concentration with time also represented the growth of bacterial species, demonstrating the species’ utilization of GS. Furthermore, at 3%, GS also represented the prebiotic index of 1.9. In addition, the concentration of GS in various simulated GIT fluids was estimated in both fast and fed conditions to examine GS stability at various levels in the gut. The results showed that GS remained unaffected and non-digestible in all of the simulated GIT fluids (salivary, gastric, intestinal, and colonic), but there was a slight decrease in GS concentration (2.8%) in the fasted state of gastric fluid due to low pH levels (1.6). As a result, the findings are conclusive and suggest that GS possesses prebiotic properties.

The concept of "metabolic jet lag" in the pathophysiology of bipolar disorder: implications for research and clinical care.

Bipolar disorder (BD) is a potentially chronic mental disorder marked by recurrent depressive and manic episodes, circadian rhythm disruption, and changes in energetic metabolism. "Metabolic jet lag" refers to a state of shift in circadian patterns of energy homeostasis, affecting neuroendocrine, immune, and adipose tissue function, expressed through behavioral changes such as irregularities in sleep and appetite. Risk factors include genetic variation, mitochondrial dysfunction, lifestyle factors, poor gut microbiome health and abnormalities in hunger, satiety, and hedonistic function. Evidence suggests metabolic jet lag is a core component of BD pathophysiology, as individuals with BD frequently exhibit irregular eating rhythms and circadian desynchronization of their energetic metabolism, which is associated with unfavorable clinical outcomes. Although current diagnostic criteria lack any assessment of eating rhythms, technological advancements including mobile phone applications and ecological momentary assessment allow for the reliable tracking of biological rhythms. Overall, methodological refinement of metabolic jet lag assessment will increase knowledge in this field and stimulate the development of interventions targeting metabolic rhythms, such as time-restricted eating.

The gut microbiome and child mental health: A population-based study

The link between the gut microbiome and the brain has gained increasing scientific and public interest for its potential to explain psychiatric risk. While differences in gut microbiome composition have been associated with several mental health problems, evidence to date has been largely based on animal models and human studies with modest sample sizes. In this cross-sectional study in 1,784 ten-year-old children from the multi-ethnic, population-based Generation R Study, we aimed to characterize associations of the gut microbiome with child mental health problems. Gut microbiome was assessed from stool samples using 16S rRNA sequencing. We focused on overall psychiatric symptoms as well as with specific domains of emotional and behavioral problems, assessed via the maternally rated Child Behavior Checklist. While we observed lower gut microbiome diversity in relation to higher overall and specific mental health problems, associations were not significant. Likewise, we did not identify any taxonomic feature associated with mental health problems after multiple testing correction, although suggestive findings indicated depletion of genera previously associated with psychiatric disorders, including Hungatella, Anaerotruncus and Oscillospiraceae. The identified compositional abundance differences were found to be similar across all mental health problems. Finally, we did not find significant enrichment for specific microbial functions in relation to mental health problems. In conclusion, based on the largest sample examined to date, we do not find clear evidence of associations between gut microbiome diversity, taxonomies or functions and mental health problems in the general pediatric population. In future, the use of longitudinal designs with repeated measurements of microbiome and psychiatric outcomes will be critical to identify whether and when associations between the gut microbiome and mental health emerge across development and into adulthood.

The Gut Microbiome and Alzheimer’s Disease: Can the Gut be Used to Prevent or Treat Dementia?

Alzheimer’s disease (AD) is a neurodegenerative disease and the most common cause of dementia1. There are currently no effective therapies for AD and its etiology remains poorly understood. Recent research has suggested that the gut microbiome may modulate risk for AD, as well as the disease process itself. This paper reviews the current knowledge surrounding AD and the gut microbiome, and aims to explore how this relationship may be used to advance our clinical understanding of the disease; including whether the gut microbiome could be a novel drug target or even serve as a potential biomarker for AD. Although this relationship between AD and the microbiome has not yet been fully elucidated, the gut microbiome is known to dynamically respond to lifestyle factors including sleep, exercise, and nutrition, all of which impact AD-risk. This body of evidence suggests that there may be a relationship between microbiome health and AD. Early studies are investigating whether the microbiome is changed in individuals with AD, and whether any metabolites or bacterial signatures unique in AD populations could be used as a biomarker for early detection of the disease. This review will discuss these points and reflect on how the clinical landscape for AD may be improved by assaying the microbiome and implementing lifestyle factors that both improve microbiome health and reduce AD risk. &#x0D;