The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample

Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE

Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.

Microbiome-Gut-Mucosal-Immune-Brain Axis and Autism Spectrum Disorder (ASD): A Novel Proposal of the Role of the Gut Microbiome in ASD Aetiology

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterised by deficits in social interaction and communication, as well as restricted and stereotyped interests. Due of the high prevalence of gastrointestinal disorders in individuals with ASD, researchers have investigated the gut microbiota as a potential contributor to its aetiology. The relationship between the microbiome, gut, and brain (microbiome-gut-brain axis) has been acknowledged as a key factor in modulating brain function and social behaviour, but its connection to the aetiology of ASD is not well understood. Recently, there has been increasing attention on the relationship between the immune system, gastrointestinal disorders and neurological issues in ASD, particularly in relation to the loss of specific species or a decrease in microbial diversity. It focuses on how gut microbiota dysbiosis can affect gut permeability, immune function and microbiota metabolites in ASD. However, a very complete study suggests that dysbiosis is a consequence of the disease and that it has practically no effect on autistic manifestations. This is a review of the relationship between the immune system, microbial diversity and the microbiome-gut-brain axis in the development of autistic symptoms severity and a proposal of a novel role of gut microbiome in ASD, where dysbiosis is a consequence of ASD-related behaviour and where dysbiosis in turn accentuates the autistic manifestations of the patients via the microbiome-gut-brain axis in a feedback circuit.

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting

The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use a functional assay to identify and isolate gut bacteria from healthy human volunteers that take up different glycans. The method combines metabolic labeling using fluorescent oligosaccharides with fluorescence-activated cell sorting (FACS), followed by amplicon sequencing or culturomics. Our results demonstrate metabolic labeling in various taxa, such as Prevotella copri, Collinsella aerofaciens and Blautia wexlerae. In vitro validation confirms the ability of most, but not all, labeled species to consume the glycan of interest for growth. In parallel, we show that glycan consumers spanning three major phyla can be isolated from cultures of sorted labeled cells. By linking bacteria to the glycans they consume, this approach increases our basic understanding of glycan metabolism by gut bacteria. Going forward, it could be used to provide insight into the mechanism of prebiotic approaches, where glycans are used to manipulate the gut microbiota composition.

Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota

The gut microbiota contributes to diverse aspects of host physiology, ranging from immunomodulation to drug metabolism. Changes in the gut microbiota composition are associated with various diseases as well as with the response to medications. It is therefore important to understand how different lifestyle and environmental factors shape gut microbiota composition. Beyond the commonly considered factor of diet, small-molecule drugs have recently been identified as major effectors of the microbiota composition. Other xenobiotics, such as environmental or chemical pollutants, can also impact gut bacterial communities. Here, we review the mechanisms of interactions between gut bacteria and antibiotics, host-targeted drugs, natural food compounds, food additives and environmental pollutants. While xenobiotics can impact bacterial growth and metabolism, bacteria in turn can bioaccumulate or chemically modify these compounds. These reciprocal interactions can manifest in complex xenobiotic-microbiota-host relationships. Our Review highlights the need to study mechanisms underlying interactions with pollutants and food additives towards deciphering the dynamics and evolution of the gut microbiota.

Traditional plant use during lactation and postpartum recovery: Infant development and maternal health roles

ETHNOPHARMACOLOGICAL RELEVANCE

Evidence of phytochemical roles in infant development and maternal recovery offers insights into beneficial functions of traditional plant use during lactation and the postpartum period. Ethnopharmacological research has relevance to global priorities on maternal and child health, to understanding origins and determinants of human self-medication, and for reconciling traditional postpartum practices and mainstream healthcare.

AIM OF THE STUDY

Present emerging evidence, within evolutionary and socio-cultural contexts, on the role of maternal consumption on transfer of phytochemicals into breast milk with impacts on maternal and child health, and on infant development. Establish current state of knowledge and an ethnopharmacological research agenda that is attentive to cross-cultural and regional differences in postpartum plant use.

MATERIALS AND METHODS

An extensive literature review using Medline, Scopus, and Web of Science focused on traditional and contemporary use and socio-cultural context, as well as physiological, pharmacological, toxicological, and behavioral activities of plants used medicinally by women during postpartum recovery and lactation.

RESULTS

The most widely reported postpartum plants show antimicrobial, anti-inflammatory, immunological, and neurophysiological activities, with low toxicity. Phytochemicals transfer from maternal consumption into breast milk in physiological concentrations, while animal studies demonstrate immunomodulation and other actions of medicinal plants during lactation. Reporting on the use and diverse traditional knowledge of women about plants during the postpartum period is obscured by the marginal place of obstetric issues and by gender biases in ethnobotanical research. In many contemporary contexts use is prejudiced by precautionary risk warnings in health literature and practice that confound lactation with pregnancy.

CONCLUSIONS

Although systematic investigation of postpartum plant use is lacking, known pharmacological activities support potential benefits on infant development and maternal health with immediate and long-term consequences in relation to allergic, inflammatory, autoimmune, and other diseases. An ethnopharmacological agenda focused on the perinatal period requires directed methodologies and a regional approach in relation to culturally-specific knowledge and practices, traditional plant use, and local health needs. Testing the hypothesis that phytochemicals transferred from medicinal plants into breast milk impact the human immune system and other aspects of infant development requires extended analysis of phytochemicals in human milk and infant lumen and plasma, as well as effects on gastrointestinal and milk microbiome.

Altered Gut Microbiota in Korean Children with Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and behavioral impairments. Recent studies have suggested that gut microbiota play a critical role in ASD pathogenesis. Herein, we investigated the fecal microflora of Korean ASD children to determine gut microbiota profiles associated with ASD. Specifically, fecal samples were obtained from 54 children with ASD and 38 age-matched children exhibiting typical development. Systematic bioinformatic analysis revealed that the composition of gut microbiota differed between ASD and typically developing children (TDC). Moreover, the total amounts of short-chain fatty acids, metabolites produced by bacteria, were increased in ASD children. At the phylum level, we found a significant decrease in the relative Bacteroidetes abundance of the ASD group, whereas Actinobacteria abundance was significantly increased. Furthermore, we found significantly lower Bacteroides levels and higher Bifidobacterium levels in the ASD group than in the TDC group at the genus level. Functional analysis of the microbiota in ASD children predicted that several pathways, including genetic information processing and amino acid metabolism, can be associated with ASD pathogenesis. Although more research is needed to determine whether the differences between ASD and TDC are actually related to ASD pathogenesis, these results provide further evidence of altered gut microbiota in children with ASD, possibly providing new perspectives on the diagnosis and therapeutic approaches for ASD patients.

A multi-omics approach for understanding the effects of moderate wine consumption on human intestinal health

The human gut is a highly diverse microbial ecosystem. Although showing a well-defined core of dominant taxa, an interindividual variability exists in microbiome arrangement patterns, and the presence and proportion of specific species, determining individual metabolic features-metabotypes-which govern the health effects of dietary interventions (i.e. polyphenol consumption). Starting with a 19-volunteer human intervention study, divided into low, medium, and high wine-polyphenol-metabolizers, we detected interindividual discrepancies on the effect of wine consumption in gut bacterial alpha-diversity, but a significant homogenization of beta-diversity among moderate wine consumers, independently of their metabotype. In addition, the abundance of key health-related taxa such as Akkermansia sp. increased after moderate wine intake in the group of high polyphenol-metabolizers. Regarding the metabolic activity, significant (p < 0.05) positive correlations in the production of SCFAs were observed after wine intake. Finally, we were able to correlate the microbiome and the metabolome of the three metabotypes, and to identify some metabolites-biomarker species, highlighting the genera Phascolarctobacterium, Pelotomaculum and Prevotella, as positively correlated with polyphenol concentration, and Prevotella, Zymophilus and Eubacterium as positively correlated with SCFAs concentration in faeces. Our results contribute to the evidence of the need of including the microbiome variable in personalized nutrition programs, as different metabotyes respond differently to dietary interventions.

Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice

Considered as an essential "metabolic organ", intestinal microbiota plays a key role in human health and the predisposition to diseases. It is an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract. Since the 20th century, researches have showed that intestinal microbiome possesses a variety of metabolic activities that are able to modulate the fate of more than 30 approved drugs and immune checkpoint inhibitors. These drugs are transformed to bioactive, inactive, or toxic metabolites by microbial direct action or host-microbial co-metabolism. These metabolites are responsible for therapeutic effects exerted by these drugs or side effects induced by these drugs, even for death. In view of the significant effect on the drugs metabolism by the gut microbiota, it is pivotal for personalized medicine to explore additional drugs affected by gut microbiota and their involved strains for further making mechanism clear through suitable animal models. This review mainly focus on specific mechanisms involved, with reference to the current literature about drugs metabolism by related bacteria or its enzymes available.

Bacteriophages: Uncharacterized and Dynamic Regulators of the Immune System

The human gut is an extremely active immunological site interfacing with the densest microbial community known to colonize the human body, the gut microbiota. Despite tremendous advances in our comprehension of how the gut microbiota is involved in human health and interacts with the mammalian immune system, most studies are incomplete as they typically do not consider bacteriophages. These bacterial viruses are estimated to be as numerous as their bacterial hosts, with tremendous and mostly uncharacterized genetic diversity. In addition, bacteriophages are not passive members of the gut microbiota, as highlighted by the recent evidence for their active involvement in human health. Yet, how bacteriophages interact with their bacterial hosts and the immune system in the human gut remains poorly described. Here, we aim to fill this gap by providing an overview of bacteriophage communities in the gut during human development, detailing recent findings for their bacterial-mediated effects on the immune response and summarizing the latest evidence for direct interactions between them and the immune system. The dramatic increase in antibiotic-resistant bacterial pathogens has spurred a renewed interest in using bacteriophages for therapy, despite the many unknowns about bacteriophages in the human body. Going forward, more studies encompassing the communities of bacteria, bacteriophages, and the immune system in diverse health and disease settings will provide invaluable insight into this dynamic trio essential for human health.

Disease-modifying therapies alter gut microbial composition in MS

Objective

To determine the effects of the disease-modifying therapies, glatiramer acetate (GA) and dimethyl fumarate (DMF), on the gut microbiota in patients with MS.

Methods

Participants with relapsing MS who were either treatment-naive or treated with GA or DMF were recruited. Peripheral blood mononuclear cells were immunophenotyped. Bacterial DNA was extracted from stool, and amplicons targeting the V4 region of the bacterial/archaeal 16S rRNA gene were sequenced (Illumina MiSeq). Raw reads were clustered into Operational Taxonomic Units using the GreenGenes database. Differential abundance analysis was performed using linear discriminant analysis effect size. Phylogenetic investigation of communities by reconstruction of unobserved states was used to investigate changes to functional pathways resulting from differential taxon abundance.

Results

One hundred sixty-eight participants were included (treatment-naive n = 75, DMF n = 33, and GA n = 60). Disease-modifying therapies were associated with changes in the fecal microbiota composition. Both therapies were associated with decreased relative abundance of the Lachnospiraceae and Veillonellaceae families. In addition, DMF was associated with decreased relative abundance of the phyla Firmicutes and Fusobacteria and the order Clostridiales and an increase in the phylum Bacteroidetes. Despite the different changes in bacterial taxa, there was an overlap between functional pathways affected by both therapies.

Interpretation

Administration of GA or DMF is associated with differences in gut microbial composition in patients with MS. Because those changes affect critical metabolic pathways, we hypothesize that our findings may highlight mechanisms of pathophysiology and potential therapeutic intervention requiring further investigation.

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron

Preliminary studies conducted on the human gastro-intestinal tract have revealed that enteric viral communities play a preponderant role in microbial homeostatis. However to date, such communities have never been investigated in the fish gut. Herein, we examined the main ecological traits of viruses in the digestive tract of a euryhaline fish, the tilapia Sarotherodon melanotheron. Individuals were collected at 8 different sites in Senegal covering a salinity gradient from 3 to 104‰, and showing large disparities in their organic pollutant concentrations. Results showed that the gut of S. melanotheron is home to a highly abundant viral community (0.2-10.7 × 10⁹ viruses ml^-1), distinct from the surrounding water, and essentially composed of phages of which a substantial proportion is temperate (the fraction of lysogenized cells-FLC ranging from 8.1 to 33.0%). Also, a positive and significant correlation was detected between FLC and the concentrations of polycyclic aromatic hydrocarbon in sediment, while no clear relationships were found between salinity and any of the microbial parameters considered. Finally, our data suggest that virus-bacteria interactions within the fish intestine are likely sensitive to the presence of particular xenobiotics, which may compromise the balance in the gut microbiota, and subsequently affect the health of their host.

Metabolic profile of the masked mycotoxin T-2 toxin-3-glucoside in rats (in vitro and in vivo) and humans (in vitro)

The metabolic profile of T-2 toxin-3-glucoside (T2-Glc) in humans and rats was investigated using ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF). When rat and human liver microsomes were incubated with T2-Glc, a total of five metabolites were detected. T2-Glc exposed a higher metabolic stability in rats and human than T-2 toxin (T-2). The metabolism of T2-Glc by the intestinal microbiota of human and rats was also investigated, and three metabolites were observed. T2-Glc was reconverted to T-2 during incubation with fresh faeces. Furthermore, in vivo metabolism of T2-Glc in rats after oral administration was carried out, and three metabolites were detected in rat urine and faeces (T-2, HT-2 toxin and 3'-OH-T2-Glc). In vivo metabolism results indicated that T2-Glc was mainly metabolised in the gastro-intestinal tract with a low absorption level in rats. The results demonstrated that hydroxylation (C-3' and C-4'), hydrolysis (C-4 and C-8) and deconjugation are the main metabolic pathways of T2-Glc in mammals.

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals

Therapeutically active glycosylated phytochemicals are ubiquitous in the human diet. The human gut microbiota (HGM) modulates the bioactivities of these compounds, which consequently affect host physiology and microbiota composition. Despite a significant impact on human health, the key players and the underpinning mechanisms of this interplay remain uncharacterized. Here, we demonstrate the growth of Lactobacillus acidophilus on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones. Transcriptional analysis revealed the upregulation of host interaction genes and identified two loci that encode phosphotransferase system (PTS) transporters and phospho-β-glucosidases, which mediate the uptake and deglucosylation of these compounds, respectively. Inactivating these transport and hydrolysis genes abolished or severely reduced growth on PG, establishing the specificity of the loci to distinct groups of PGs. Following intracellular deglucosylation, the aglycones of PGs are externalized, rendering them available for absorption by the host or for further modification by other microbiota taxa. The PG utilization loci are conserved in L. acidophilus and closely related lactobacilli, in correlation with versatile growth on these compounds. Growth on the tested PG appeared more common among human gut lactobacilli than among counterparts from other ecologic niches. The PGs that supported the growth of L. acidophilus were utilized poorly or not at all by other common HGM strains, underscoring the metabolic specialization of L. acidophilus. These findings highlight the role of human gut L. acidophilus and select lactobacilli in the bioconversion of glycoconjugated phytochemicals, which is likely to have an important impact on the HGM and human host.

Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by Lactobacillus acidophilus and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota.

Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a serious neurodevelopmental disorder that affects one in 45 children in the United States, with a similarly striking prevalence in countries around the world. However, mechanisms underlying its etiology and manifestations remain poorly understood. Although ASD is diagnosed based on the presence and severity of impaired social communication and repetitive behavior, immune dysregulation and gastrointestinal issues are common comorbidities. The microbiome is an integral part of human physiology; recent studies show that changes in the gut microbiota can modulate gastrointestinal physiology, immune function, and even behavior. Links between particular bacteria from the indigenous gut microbiota and phenotypes relevant to ASD raise the important question of whether microbial dysbiosis plays a role in the development or presentation of ASD symptoms. Here we review reports of microbial dysbiosis in ASD. We further discuss potential effects of the microbiota on ASD-associated symptoms, drawing on signaling mechanisms for reciprocal interactions among the microbiota, immunity, gut function, and behavior. In addition, we discuss recent findings supporting a role for the microbiome as an interface between environmental and genetic risk factors that are associated with ASD. These studies highlight the integration of pathways across multiple body systems that together can impact brain and behavior and suggest that changes in the microbiome may contribute to symptoms of neurodevelopmental disease.

An Integrated View of the Effects of Wine Polyphenols and Their Relevant Metabolites on Gut and Host Health

Over the last few decades, polyphenols, and flavonoids in particular, have attracted the interest of researchers, as they have been associated with the health-promoting effects derived from diets rich in vegetables and fruits, including moderate wine consumption. Recent scientific evidence suggests that wine polyphenols exert their effects through interactions with the gut microbiota, as they seem to modulate microbiota and, at the same time, are metabolized by intestinal bacteria into specific bioavailable metabolites. Microbial metabolites are better absorbed than their precursors and may be responsible for positive health activities in the digestive system (local effects) and, after being absorbed, in tissues and organs (systemic effects). Differences in gut microbiota composition and functionality among individuals can affect polyphenol activity and, therefore, their health effects. The aim of this review is to integrate the understanding of the metabolism and mechanisms of action of wine polyphenols at both local and systemic levels, underlining their impact on the gut microbiome and the inter-individual variability associated with polyphenols' metabolism and further physiological effects. The advent of promising dietary approaches linked to wine polyphenols beyond the gut microbiota community and metabolism are also discussed.

The influence of gut-decontamination prophylactic antibiotics on acute graft-versus-host disease and survival following allogeneic hematopoietic stem cell transplantation

The intestinal microbiota plays a key role in the pathogenesis of acute graft-versus-host disease (aGVHD). High-dose conditioning regimens given prior to allogeneic hematopoietic stem cell transplantation (aHSCT) modulate the composition of gut microbiota and damage the gut epithelial barrier, resulting in increased systemic inflammation. We assessed whether gut decontamination with antibiotics (ATB) prior to aHSCT influenced the frequency of aGVHD and mortality in 500 patients from two Canadian centers between 2005 and 2012. The rate of grade II-IV aGVHD was higher in the ATB arm compared with the arm without ATB (42% vs 28%; p < 0.001). This difference was mainly driven by a 2-fold higher rate of grade II-IV gastrointestinal aGVHD (GI-GVHD) in the ATB arm compared with the arm without ATB (20.7% vs 10.8%; p = 0.003). Multivariate analyses adjusted for known aGVHD risk factors revealed that more patients in the ATB group developed clinically significant GI-GVHD and liver aGVHD; adjusted odds ratio (aOR) = 1.83; p = 0.023 and aOR = 3.56; p = 0.047, respectively. Importantly, median overall survival (OS) was significantly lower in the group receiving ATB and the OS at 10 y remained decreased in the ATB group; adjusted hazard ratio (aHR) = 1.61 (p < 0.001). Without undermining the role of ATB prophylaxis to prevent infection in aHSCT, we have shown that the use of ATB that targets intestinal bacteria is associated with a more severe aGVHD that involves the GI organs and impacts OS. Prospective studies that evaluate the contribution of bacterial decontamination to aGVHD are warranted.

Probiotics in Human Immunodeficiency Virus Infection: A Systematic Review and Evidence Synthesis of Benefits and Risks

The risk of sepsis is low. The best probiotic to optimize outcomes has not yet been identified. Potential benefit for CD4 count, recurrence or management of bacterial vaginosis and diarrhea. Uncertain effect on translocation, BV treatment.

People living with human immunodeficiency virus frequently use dietary supplements, including probiotics, but concern exists about ingesting live organisms. We performed a systematic review of the benefits of probiotics and a meta-analysis of sepsis risk. We undertook a protocol-driven, comprehensive review to identify all relevant studies, assess their quality, and summarize the evidence. Of 2068 references, 27 were analyzed. The data suggest possible benefits for CD4 count, recurrence or management of bacterial vaginosis, and diarrhea management. We examined randomized, controlled studies explicitly assessing sepsis in any patient population, and we found zero cases of supplement-associated bacteremia or fungemia in 39 randomized controlled trials comprising 9402 subjects. The estimated number needed to harm is 7369 in Bayesian approach (95% credible interval: 1689, ∞), which should reassure clinicians. No or mild adverse effects were reported. Longer duration studies investigating different individual and mixed strains for plausible indications are needed to establish best practices.

The Bugs Within Our Body: The Human Microbiota

The human microbiota is the ecological community of microorganisms that live within our bodies. Emerging evidence has revealed that dysregulation of the host-microbe symbiotic relationship contributes to the pathogenesis of a vast number of human diseases and impacts the efficacy and toxicity of therapeutic drugs. Therefore, a deeper understanding of the human microbiota is crucial to the development of therapeutic interventions that target the microbiota and also provides fundamental insights towards understanding intersubject variability in therapeutic outcomes.