In sickness and health: Effects of gut microbial metabolites on human physiology

Fecal microbiota transplantation improves growth performance of chickens by increasing the intestinal Lactobacillus and glutamine

Chicken meat is an essential source of high-quality animal protein, mainly derived from slow-growth chicken (SC) and fast-growth chicken (FC) breeds. Skeletal muscle is a highly adaptable tissue that is influenced by breed differences and the gut microbiome. Investigation whether remodeling the gut microbiota by fecal microbiota transplantation (FMT) improves chicken growth is an interesting question. We compared the gut microbial composition of eight breeds of SC (Xinghua chicken, Yangshan chicken, Zhongshan Salan chicken, Qingyuan Partridge chicken, Huiyang Bearded chicken and Huaixiang chicken) and FC (Xiaobai chicken and White rock chicken). Fecal microbiota from donor FC (Xiaobai chickens) with superior growth performance were transferred to SC (Xinghua chickens). The effects of FMT on growth performance, metabolic profile and gut microbiome of recipient chickens were evaluated. We found significant differences in gut microbial composition, with a higher abundance of Bacteroidetes in SC and a higher abundance of Firmicutes in FC. Xiaobai chickens with better growth performance and abundant Lactobacillus, and FMT significantly enhanced growth performance, the expression of mRNA (MYOG, MYF5, MYF6 and IGF1) related to breast and leg muscle development and improved the villus/crypt ratio in the jejunum. FMT altered the microbiota in the duodenum, jejunum, and ileum, increased Lactobacillus abundance, decreased the relative mRNA expression of the intestinal inflammatory factors (IL-1β, IL-6 and TNF-α), increased glutamine levels in the host, including in muscle tissues and intestinal contents, and Spearman correlation analysis indicated that the relative abundance of Lactobacillus was positively correlated with glutamine levels. Additionally, antibiotic treatment reduces glutamine levels in the intestines, blood, and muscle tissues of chickens. Glutamine can increase the expression of cyclinD1, cyclinD2, cyclinB2, MYOG, MYF5, MYF6 and IGF1 mRNA to promote chicken myoblasts proliferation and differentiation. This study found that the SC and FC gut microbes were significantly different, and the FC chicken gut microbes were able to reshape the FC gut microbiota through FMT, i.e., higher Lactobacillus, promoted chicken myoblasts proliferation and differentiation and growth performance by increasing glutamine levels.

The Impact of Mycobacterium avium subsp. paratuberculosis on Intestinal Microbial Community Composition and Diversity in Small-Tail Han Sheep

Paratuberculosis (PTB), primarily caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic infection that affects ruminants and is difficult to prevent, diagnose, and treat. Investigating how MAP infections affect the gut microbiota in sheep can aid in the prevention and treatment of ovine PTB. This study examined fecal samples from eight small-tail Han sheep (STHS) at various stages of infection and from three different field areas. All samples underwent DNA extraction and 16S rRNA sequencing. Among all samples, the phyla p. Firmicutes and p. Bacteroidota exhibited the highest relative abundance. The dominant genera in groups M1-M6 were UCG-005, Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, Akkermansia, UCG-005, and Bacteroides, whereas those in groups A-C were Christensenellaceae_R-7_group, Escherichia-Shigella, and Acinetobacter, respectively. The microbial community structure varied significantly among groups M1-M6. Specifically, 56 microbiota consortia with different taxonomic levels, including the order Clostridiales, were significantly enriched in groups M1-M6, whereas 96 microbiota consortia at different taxonomic levels, including the family Oscillospiraceae, were significantly enriched in groups A-C. To the best of our knowledge, this is the first study to report that MAP infection alters the intestinal microbiota of STHS. Changes in p. Firmicutes abundance can serve as a potential biomarker to distinguish MAP infection and determine the infection stage for its early diagnosis. Our study provides a theoretical basis for the treatment of PTB by regulating the intestinal microbiota, including p. Firmicutes.

The connection between aging, cellular senescence and gut microbiome alterations: A comprehensive review

The intricate interplay between cellular senescence and alterations in the gut microbiome emerges as a pivotal axis in the aging process, increasingly recognized for its contribution to systemic inflammation, physiological decline, and predisposition to age-associated diseases. Cellular senescence, characterized by a cessation of cell division in response to various stressors, induces morphological and functional changes within tissues. The complexity and heterogeneity of senescent cells, alongside the secretion of senescence-associated secretory phenotype, exacerbate the aging process through pro-inflammatory pathways and influence the microenvironment and immune system. Concurrently, aging-associated changes in gut microbiome diversity and composition contribute to dysbiosis, further exacerbating systemic inflammation and undermining the integrity of various bodily functions. This review encapsulates the burgeoning research on the reciprocal relationship between cellular senescence and gut dysbiosis, highlighting their collective impact on age-related musculoskeletal diseases, including osteoporosis, sarcopenia, and osteoarthritis. It also explores the potential of modulating the gut microbiome and targeting cellular senescence as innovative strategies for healthy aging and mitigating the progression of aging-related conditions. By exploring targeted interventions, including the development of senotherapeutic drugs and probiotic therapies, this review aims to shed light on novel therapeutic avenues. These strategies leverage the connection between cellular senescence and gut microbiome alterations to advance aging research and development of interventions aimed at extending health span and improving the quality of life in the older population.

Symbiotic symphony: Understanding host-microbiota dialogues in a spatial context

Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.

The impact of the human gut microbiome on the treatment of autoimmune disease

Autoimmune (or rheumatic) diseases are increasing in prevalence but selecting the best therapy for each patient proceeds in trial-and-error fashion. This strategy can lead to ineffective therapy resulting in irreversible damage and suffering; thus, there is a need to bring the promise of precision medicine to patients with autoimmune disease. While host factors partially determine the therapeutic response to immunosuppressive drugs, these are not routinely used to tailor therapy. Thus, non-host factors likely contribute. Here, we consider the impact of the human gut microbiome in the treatment of autoimmunity. We propose that the gut microbiome can be manipulated to improve therapy and to derive greater benefit from existing therapies. We focus on the mechanisms by which the human gut microbiome impacts treatment response, provide a framework to interrogate these mechanisms, review a case study of a widely-used anti-rheumatic drug, and discuss challenges with studying multiple complex systems: the microbiome, the human immune system, and autoimmune disease. We consider open questions that remain in the field and speculate on the future of drug-microbiome-autoimmune disease interactions. Finally, we present a blue-sky vision for how the microbiome can be used to bring the promise of precision medicine to patients with rheumatic disease.

Lung and Gut Microbiome in COPD

Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. The association between lung and gut microbiomes in the pathogenesis of COPD has been recently uncovered. The goal of this study was to discuss the role of the lung and gut microbiomes in COPD pathophysiology. A systematic search of the PubMed database for relevant articles submitted up to June 2022 was performed. We examined the association between the lung and gut microbiome dysbiosis, reflected in bronchoalveolar lavage (BAL), lung tissue, sputum, and feces samples, and the pathogenesis and progression of COPD. It is evident that the lung and gut microbiomes affect each other and both play a vital role in the pathogenesis of COPD. However, more research needs to be carried out to find the exact associations between microbiome diversity and COPD pathophysiology and exacerbation genesis. Another field that research should focus on is the impact of treatment interventions targeting the human microbiome in preventing COPD genesis and progression.

Human Milk Lipids and Small Metabolites: Maternal and Microbial Origins

Although there has been limited application in the field to date, human milk omics research continues to gain traction. Human milk lipidomics and metabolomics research is particularly important, given the significance of milk lipids and metabolites for infant health. For researchers conducting compositional milk analyses, it is important to consider the origins of these compounds. The current review aims to provide a summary of the existing evidence on the sources of human milk lipids and small metabolites. Here, we describe five major sources of milk lipids and metabolites: de novo synthesis from mammary cells, production by the milk microbiota, dietary consumption, release from non-mammary tissue, and production by the gut microbiota. We synthesize the literature to provide evidence and understanding of these pathways in the context of mammary gland biology. We recommend future research focus areas to elucidate milk lipid and small metabolite synthesis and transport pathways. Better understanding of the origins of human milk lipids and metabolites is important to improve translation of milk omics research, particularly regarding the modulation of these important milk components to improve infant health outcomes.

Gut microbiota-bile acid-skeletal muscle axis

The gut microbiota represents a 'metabolic organ' that can regulate human metabolism. Intact gut microbiota contributes to host homeostasis, whereas compositional perturbations, termed dysbiosis, are associated with a wide range of diseases. Recent evidence demonstrates that dysbiosis, and the accompanying loss of microbiota-derived metabolites, results in a substantial alteration of skeletal muscle metabolism. As an example, bile acids, produced in the liver and further metabolized by intestinal microbiota, are of considerable interest since they regulate several host metabolic pathways by activating nuclear receptors, including the farnesoid X receptor (FXR). Indeed, alteration of gut microbiota may lead to skeletal muscle atrophy via a bile acid-FXR pathway. This Review aims to suggest a new pathway that connects different mechanisms, involving the gut-muscle axis, that are often seen as unrelated, and, starting from preclinical studies, we hypothesize new strategies aimed at optimizing skeletal muscle functionality.

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes

Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.

Gut metabolite trimethylamine N-oxide induces aging-associated phenotype of midbrain organoids for the induced pluripotent stem cell-based modeling of late-onset disease

Brain organoids are valuable research models for human development and disease since they mimic the various cell compositions and structures of the human brain; however, they have challenges in presenting aging phenotypes for degenerative diseases. This study analyzed the association between aging and the gut metabolite trimethylamine N-oxide (TMAO), which is highly found in the midbrain of elderly and Parkinson’s disease (PD) patients. TMAO treatment in midbrain organoid induced aging-associated molecular changes, including increased senescence marker expression (P21, P16), p53 accumulation, and epigenetic alterations. In addition, TMAO-treated midbrain organoids have shown parts of neurodegeneration phenotypes, including impaired brain-derived neurotrophic factor (BDNF) signaling, loss of dopaminergic neurons, astrocyte activation, and neuromelanin accumulation. Moreover, we found TMAO treatment-induced pathophysiological phosphorylation of α-synuclein protein at Ser-129 residues and Tau protein at Ser202/Thr205. These results suggest a role of TMAO in the aging and pathogenesis of the midbrain and provide insight into how intestinal dysfunction increases the risk of PD. Furthermore, this system can be utilized as a novel aging model for induced pluripotent stem cell (iPSC)-based modeling of late-onset diseases.

Ecological modelling approaches for predicting emergent properties in microbial communities

Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties-patterns or functions that cannot be deduced linearly from the properties of the constituent parts-underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that emergent properties are a consequence of interactions within the community, their non-linear nature makes mathematical modelling imperative for establishing the quantitative link between community structure and function. As the need for conservation and rational modulation of microbial ecosystems is increasingly apparent, so is the consideration of the benefits and limitations of the approaches to model emergent properties. Here we review ecosystem modelling approaches from the viewpoint of emergent properties. We consider the scope, advantages and limitations of Lotka-Volterra, consumer-resource, trait-based, individual-based and genome-scale metabolic models. Future efforts in this research area would benefit from capitalizing on the complementarity between these approaches towards enabling rational modulation of complex microbial ecosystems.

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes

Gut microbiota metabolism of dietary compounds generates a vast array of microbiome-dependent metabolites (MDMs), which are highly variable between individuals. The uremic MDMs (uMDMs) phenylacetylglutamine (PAG), p-cresol sulfate (PCS), and indoxyl sulfate (IS) accumulate during renal failure and are associated with poor outcomes. Targeted dietary interventions may reduce toxic MDM generation; however, it is unclear if inter-individual differences in diet or gut microbiome dominantly contribute to MDM variance. Here, we use a 7-day homogeneous average American diet to standardize dietary precursor availability in 21 healthy individuals. During dietary homogeneity, the coefficient of variation in PAG, PCS, and IS (primary outcome) did not decrease, nor did inter-individual variation in most identified metabolites; other microbiome metrics showed no or modest responses to the intervention. Host identity and age are dominant contributors to variability in MDMs. These results highlight the potential need to pair dietary modification with microbial therapies to control MDM profiles.

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Species belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. This study is aimed to address this research gap. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in their genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.

The appendix‐mucosal immunity and tolerance in the gut: consequences for the syndromes of appendicitis and its epidemiology

The cause of appendicitis is unknown. A review is presented across diverse sources relating to the biology of the appendix and its perturbations. A mechanistic model of the function of the appendix is presented, and its application to the syndromes and consequences of appendicitis is described.

Impact of purple sweet potato (Ipomoea batatas L.) polysaccharides on the fecal metabolome in a murine colitis model

Purple sweet potato polysaccharides (PSPP) play an important role in regulating the gut microbiota, modulating intestinal immunity and ameliorating colonic inflammation. In this study, the impact of two PSPPs (PSWP-I and PSAP-I) on the metabolomic profiling of feces from dextran sulfate sodium (DSS)-induced colitis mice was evaluated by ultra-high performance liquid chromatography coupled with triple time-of-flight tandem mass spectrometry (UPLC-Triple-TOF-MS/MS). Results indicated that there were twenty-five metabolites with significant changes and four remarkable metabolic pathways, i.e., cutin, suberine and wax biosynthesis, biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, and steroid hormone biosynthesis. Two key biomarkers of oleic acid and 17-hydroxyprogesterone were screened that responded to PSPPs in colitis mice. The identified metabolites were correlated with the amelioration of intestinal immune function and the modulation of the gut microbiota. Nine pro-inflammatory and eight anti-inflammatory compounds responded to PSPPs, which were related to Bacteroides, norank_f__Clostridiales_vadinBB60_group, unclassified_o__Bacteroidales, Rikenella and Lachnospiraceae_UCG-001. Moreover, PSWP-I and PSAP-I had different regulating effects on intestinal metabolites. Our results revealed a possible metabolomic mechanism of PSPPs to regulate intestinal inflammation function.

Purple sweet potato polysaccharides (PSPP) play an important role in regulating the gut microbiota, modulating intestinal immunity and ameliorating colonic inflammation.

Microbial Flavonoid Metabolism: A Cardiometabolic Disease Perspective

Cardiometabolic disease (CMD) is a leading cause of death worldwide and encompasses the inflammatory metabolic disorders of obesity, type 2 diabetes mellitus, nonalcoholic fatty liver disease, and cardiovascular disease. Flavonoids are polyphenolic plant metabolites that are abundantly present in fruits and vegetables and have biologically relevant protective effects in a number of cardiometabolic disorders. Several epidemiological studies underscored a negative association between dietary flavonoid consumption and the propensity to develop CMD. Recent studies elucidated the contribution of the gut microbiota in metabolizing dietary intake as it relates to CMD. Importantly, the biological efficacy of flavonoids in humans and animal models alike is linked to the gut microbial community. Herein, we discuss the opportunities and challenges of leveraging flavonoid intake as a potential strategy to prevent and treat CMD in a gut microbe-dependent manner, with special emphasis on flavonoid-derived microbial metabolites.

Gut Microbiota as a Potential Player in Mn-Induced Neurotoxicity

Manganese (Mn) is an essential metal, which at high exposures causes neurotoxic effects and neurodegeneration. The neurotoxic effects of Mn are mediated by neuroinflammation, oxidative and endoplasmic reticulum stress, mitochondrial dysfunction, and other mechanisms. Recent findings have demonstrated the potential impact of Mn overexposure on gut microbiota dysbiosis, which is known to contribute to neurodegeneration via secretion of neuroactive and proinflammatory metabolites. Therefore, in this review, we discuss the existing data on the impact of Mn exposure on gut microbiota biodiversity, bacterial metabolite production, and gut wall permeability regulating systemic levels. Recent data have demonstrated that Mn exposure may affect gut microbiota biodiversity by altering the abundance of Shiegella, Ruminococcus, Dorea, Fusicatenibacter, Roseburia, Parabacteroides, Bacteroidetes, Firmicutes, Ruminococcaceae, Streptococcaceae, and other bacterial phyla. A Mn-induced increase in Bacteroidetes abundance and a reduced Firmicutes/Bacteroidetes ratio may increase lipopolysaccharide levels. Moreover, in addition to increased systemic lipopolysaccharide (LPS) levels, Mn is capable of potentiating LPS neurotoxicity. Due to the high metabolic activity of intestinal microflora, Mn-induced perturbations in gut microbiota result in a significant alteration in the gut metabolome that has the potential to at least partially mediate the biological effects of Mn overexposure. At the same time, a recent study demonstrated that healthy microbiome transplantation alleviates Mn-induced neurotoxicity, which is indicative of the significant role of gut microflora in the cascade of Mn-mediated neurotoxicity. High doses of Mn may cause enterocyte toxicity and affect gut wall integrity through disruption of tight junctions. The resulting increase in gut wall permeability further promotes increased translocation of LPS and neuroactive bacterial metabolites to the systemic blood flow, ultimately gaining access to the brain and leading to neuroinflammation and neurotransmitter imbalance. Therefore, the existing data lead us to hypothesize that gut microbiota should be considered as a potential target of Mn toxicity, although more detailed studies are required to characterize the interplay between Mn exposure and the gut, as well as its role in the pathogenesis of neurodegeneration and other diseases.

Low Crude Protein Diet Affects the Intestinal Microbiome and Metabolome Differently in Barrows and Gilts

Low protein diets are commonly used in the growing-finishing pig stage of swine production; however, the effects of low dietary protein on the intestinal microbiota and their metabolites, and their association with pig sex, remain unclear. The present study aimed to assess the impact of a low crude protein (CP) diet on the gut microbiome and metabolome, and to reveal any relationship with sex. Barrows and gilts (both n = 24; initial body = 68.33 ± 0.881 kg) were allocated into two treatments according to sex. The four groups comprised two pairs of gilts and barrows fed with a high protein diet (CP 17% at stage I; CP 13% at stage II) and a low protein diet (CP 15% at stage I; CP 11% at stage II), respectively, for 51 d. Eight pigs in each group were slaughtered and their colon contents were collected. Intestinal microbiota and their metabolites were assessed using 16S rRNA sequencing and tandem mass spectrometry, respectively. The low protein diet increased intestinal microbiota species and richness indices (P < 0.05) in both sexes compared with the high protein diet. The sample Shannon index was different (P < 0.01) between barrows and gilts. At the genus level, unidentified Clostridiales (P < 0.05), Neisseria (P < 0.05), unidentified Prevotellaceae (P < 0.01) and Gracilibacteria (P < 0.05) were affected by dietary protein levels. The relative abundance of unidentified Prevotellaceae was different (P < 0.01) between barrows and gilts. The influence of dietary protein levels on Neisseria (P < 0.05), unidentified Prevotellaceae (P < 0.01) and Gracilibacteria (P < 0.05) were associated with sex. Metabolomic profiling indicated that dietary protein levels mainly affected intestinal metabolites in gilts rather than barrows. A total of 434 differentially abundant metabolites were identified in gilts fed the two protein diets. Correlation analysis identified that six differentially abundant microbiota communities were closely associated with twelve metabolites that were enriched for amino acids, inflammation, immune, and disease-related metabolic pathways. These results suggested that decreasing dietary protein contents changed the intestinal microbiota in growing-finishing pigs, which selectively affected the intestinal metabolite profiles in gilts.

Gut Microbiota and Urine Metabonomics Alterations in Constitution after Chinese Medicine and Lifestyle Intervention

Traditional Chinese Medicine Constitution (TCMC) divides human beings into balanced (ping-he) constitution (PH) and unbalanced constitution. Yang-deficiency (yang-xu) constitution (YAX) is one of the most common unbalanced constitutions in Chinese general population, and it causes susceptibility to particular diseases. However, unbalanced constitutions can be regulated by Chinese medicine and lifestyle intervention in clinical practice. Gui-fu-di-huang-wan (GFDHW) is a well-known Chinese medicine with yang-invigorating activity and is regarded as improving YAX. In this study, 60 healthy YAX students selected from a prospective population of 5185 were enrolled in a randomized clinical trial and completed the study. We compared the gut microbiota and urinary metabolome between individuals with PH and those with YAX before and after one-month-intervention. Compared with the control group, the health status of the intervention group improved significantly, the YAX symptom score was reduced, and the efficacy remained high at the one-year follow-up. The gut microbiota of the healthy PH exhibited greater diversity, and significantly higher species were identified. Compared to PH group, YAX individuals showed increased abundance of Bacteroidetes and Bacteroides, also had higher levels of gut microbial-derived urinary metabolites. After one-month-intervention, both GFDHW treatment and lifestyle intervention enriched the diversity and modulated the structure in YAX. The intervention group also partially restored the microbiome and metabolome to healthy PH-like levels. Further, a microbiota co-occurrence network analysis showed that the metabolites enriched in YAX were correlated with microbial community structure. Taken together, our results suggest that Chinese medicine combined with lifestyle intervention benefits YAX individuals. Gut microbiota/metabolite crosstalk might be involved in the Chinese medicine-mediated effects.

A surgical method for continuous intraportal infusion of gut microbial metabolites in mice

Gut microbe-derived metabolites influence human physiology and disease. However, establishing mechanistic links between gut microbial metabolites and disease pathogenesis in animal models remains challenging. The major route of absorption for microbe-derived small molecules is venous drainage via the portal vein to the liver. In the event of presystemic hepatic metabolism, the route of metabolite administration becomes critical. To our knowledge, we describe here a novel portal vein cannulation technique using a s.c. implanted osmotic pump to achieve continuous portal vein infusion in mice. We first administered the microbial metabolite trimethylamine (TMA) over 4 weeks, during which increased peripheral plasma levels of TMA and its host liver-derived cometabolite, trimethylamine-N-oxide, were observed when compared with a vehicle control. Next, 4-hydroxyphenylacetic acid (4-HPAA), a microbial metabolite that undergoes extensive presystemic hepatic metabolism, was administered intraportally to examine effects on hepatic gene expression. As expected, hepatic levels of 4-HPAA were elevated when compared with the control group while peripheral plasma 4-HPAA levels remained the same. Moreover, significant changes in the hepatic transcriptome were revealed by an unbiased RNA-Seq approach. Collectively, to our knowledge this work describes a novel method for administering gut microbe-derived metabolites via the portal vein, mimicking their physiologic delivery in vivo.

Sex differences in gut microbiota modulation of aversive conditioning, open field activity, and basolateral amygdala dendritic spine density

Gut microbiota influence numerous aspects of host biology, including brain structure and function. Growing evidence implicates gut microbiota in aversive conditioning and anxiety-related behaviors, but research has focused almost exclusively on males. To investigate whether effects of gut dysbiosis on aversive learning and memory differ by sex, adult female and male C57BL/6N mice were orally administered a moderate dose of nonabsorbable antimicrobial medications (ATMs: neomycin, bacitracin, and pimaricin) or a control over 10 days. Changes in gut microbiome composition were analyzed by 16S rRNA sequencing. Open field behavior, cued aversive learning, context recall, and cued recall were assessed. Following behavioral testing, the morphology of basolateral amygdala (BLA) principal neuron dendrites and spines was characterized. Results revealed that ATMs induced gut dysbiosis in both sexes, with stronger effects in females. ATMs also exerted sex-specific effects on behavior and neuroanatomy. Males were more susceptible than females to microbial modulation of locomotor activity and anxiety-like behavior. Females were more susceptible than males to ATM-induced impairments in aversive learning and cued recall. Context recall remained intact, as did dendritic structure of BLA principal neurons. However, ATMs exerted a sex-specific effect on spine density. A second experiment was conducted to isolate the effects of gut perturbation to cued recall. Extinction was also examined. Results revealed no effect of ATMs on cued recall or extinction, suggesting that gut dysbiosis preferentially impacts aversive learning. These data shed new light on how gut microbiota interact with sex to influence aversive conditioning, open field behavior, and BLA dendritic spine architecture.

Colonization of the Caenorhabditis elegans gut with human enteric bacterial pathogens leads to proteostasis disruption that is rescued by butyrate

Protein conformational diseases are characterized by misfolding and toxic aggregation of metastable proteins, often culminating in neurodegeneration. Enteric bacteria influence the pathogenesis of neurodegenerative diseases; however, the complexity of the human microbiome hinders our understanding of how individual microbes influence these diseases. Disruption of host protein homeostasis, or proteostasis, affects the onset and progression of these diseases. To investigate the effect of bacteria on host proteostasis, we used Caenorhabditis elegans expressing tissue-specific polyglutamine reporters that detect changes in the protein folding environment. We found that colonization of the C. elegans gut with enteric bacterial pathogens disrupted proteostasis in the intestine, muscle, neurons, and the gonad, while the presence of bacteria that conditionally synthesize butyrate, a molecule previously shown to be beneficial in neurodegenerative disease models, suppressed aggregation and the associated proteotoxicity. Co-colonization with this butyrogenic strain suppressed bacteria-induced protein aggregation, emphasizing the importance of microbial interaction and its impact on host proteostasis. Further experiments demonstrated that the beneficial effect of butyrate depended on the bacteria that colonized the gut and that this protective effect required SKN-1/Nrf2 and DAF-16/FOXO transcription factors. We also found that bacteria-derived protein aggregates contribute to the observed disruption of host proteostasis. Together, these results reveal the significance of enteric infection and gut dysbiosis on the pathogenesis of protein conformational diseases and demonstrate the potential of using butyrate-producing microbes as a preventative and treatment strategy for neurodegenerative disease.

Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids

A mounting body of evidence indicates that dietary fiber (DF) metabolites produced by commensal bacteria play essential roles in balancing the immune system. DF, considered nonessential nutrients in the past, is now considered to be necessary to maintain adequate levels of immunity and suppress inflammatory and allergic responses. Short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate, are the major DF metabolites and mostly produced by specialized commensal bacteria that are capable of breaking down DF into simpler saccharides and further metabolizing the saccharides into SCFAs. SCFAs act on many cell types to regulate a number of important biological processes, including host metabolism, intestinal functions, and immunity system. This review specifically highlights the regulatory functions of DF and SCFAs in the immune system with a focus on major innate and adaptive lymphocytes. Current information regarding how SCFAs regulate innate lymphoid cells, T helper cells, cytotoxic T cells, and B cells and how these functions impact immunity, inflammation, and allergic responses are discussed.

Reducing versus Embracing Variation as Strategies for Reproducibility: The Microbiome of Laboratory Mice

Irreproducibility is a well-recognized problem in biomedical animal experimentation. Phenotypic variation in animal models is one of the many challenging causes of irreproducibility. How to deal with phenotypic variation in experimental designs is a topic of debate. Both reducing and embracing variation are highlighted as strategies for reproducibility. In this theoretical review, we use variation in mouse microbiome composition as an example to analyze this ongoing discussion, drawing on both animal research and philosophy of science. We provide a conceptual explanation of reproducibility and analyze how the microbiome affects mouse phenotypes to demonstrate that the role of the microbiome in irreproducibility can be understood in two ways: (i) the microbiome can act as a confounding factor, and (ii) the result may not be generalizable to mice harboring a different microbiome composition. We elucidate that reducing variation minimizes confounding, whereas embracing variation ensures generalizability. These contrasting strategies make dealing with variation in experimental designs extremely complex. Here, we conclude that the most effective strategy depends on the specific research aim and question. The field of biomedical animal experimentation is too broad to identify a single optimal strategy. Thus, dealing with variation should be considered on a case-by-case basis, and awareness amongst researchers is essential.

Communal living: glycan utilization by the human gut microbiota

Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate-active enzymes (CAZymes), carbohydrate-binding proteins, and transporters. The glycan utilization profile of individual taxa, whether 'specialist' or 'generalist', is dictated by the number and functional diversity of these glycan utilization systems. Furthermore, taxa in the HGM may either compete or cooperate in glycan deconstruction, thereby creating a complex ecological web spanning diverse nutrient niches. As a result, our diet plays a central role in shaping the composition of the HGM. This review presents an overview of our current understanding of glycan utilization by the HGM on three levels: (i) molecular mechanisms of individual glycan deconstruction and uptake by key bacteria, (ii) glycan-mediated microbial interactions, and (iii) community-scale effects of dietary changes. Despite significant recent advancements, there remains much to be discovered regarding complex glycan metabolism in the HGM and its potential to affect positive health outcomes.